From marcel at physik.tu-berlin.de  Wed Oct  1 12:36:23 2008
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Wed, 1 Oct 2008 12:36:23 +0200 (CEST)
Subject: [Pw_forum] Two binaries for serial and parallel use needed
In-Reply-To: <Pine.LNX.4.64.0809291017090.25291@localhost.localdomain>
References: <138754.30673.qm@web59811.mail.ac4.yahoo.com>
	<DBECD80D-06E1-429D-872C-BEBB32F79787@sissa.it>
	<alpine.BSF.1.10.0809291017330.51302@rosa.physik-pool.tu-berlin.de>
	<Pine.LNX.4.64.0809291017090.25291@localhost.localdomain>
Message-ID: <alpine.BSF.1.10.0810011219520.94594@rosa.physik-pool.tu-berlin.de>

> MM> Dear linux experts
> MM>
> MM> I have newly set up our computer cluster with new mpich2 (1.07)
> MM> and ifort.
> MM> In the last cluster the binary pw.x (compiled with mpich2 1.04) could be
> MM> executed directly or with mpiexec for serial or parallel use,
> MM> respectively.
> MM> Now, this is not possible anymore, I always have to start an smpd
> MM> and run pw.x with mpiexec, even for serial usage.
> MM> It is a bit uncomfortable, so if anyone knows a switch for the compiler,
> MM> or could comment I would greatly appreciate it.

It was a bug in mpich2-1.0.7, with pre release 1.1... it works both ways.

>
> this has to be a "feature" of MPICH, or the way
> you compiled it.
>
> i'm using OpenMPI and don't have that problem.
> if you are after convenience, you should seriously
> consider switching to OpenMPI. particularly on PBS/Torque
> managed clusters, it is _extremely_ convenient
> (job launch through torque, flexible choice of node
> assignment, high efficiency, independence of the
> executable from the underlying communication layer
> (i can compile executable on my desktop with no network
> and run them on myrinet, or infiniband machines directly)).

we are using SGE, but it was a bit tricky to get parallel environments 
working.
On the next cluster I will give it a try.

Cheers
Marcel


>
> cheers,
>   axel.
>
>
> -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================

From vegalew at hotmail.com  Thu Oct  2 08:28:59 2008
From: vegalew at hotmail.com (vega)
Date: Thu, 2 Oct 2008 14:28:59 +0800
Subject: [Pw_forum] Compiling with intel fortran,
	MKL and MKL FFT wrappers
In-Reply-To: <48E26D7B.2050809@anl.gov>
References: <48E26D7B.2050809@anl.gov>
Message-ID: <BAY124-DS5E0A9CC8F5CD907977605A43D0@phx.gbl>


=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China

--------------------------------------------------
From: "Serge Nakhmanson" <nakhmanson at anl.gov>
Sent: Wednesday, October 01, 2008 2:18 AM
To: "PWSCF Forum" <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] Compiling with intel fortran,MKL and MKL FFT 
wrappers

> Lorenzo, Axel,
>
> Thank you for your comments. I expected the serial lib
> to be "it" but decided to check in with the forum just
> to be sure. I have not tested the new "MKL FTT" binary
> extensively yet but I will. As I understand, I should not
> expect a tremendous performance improvement over plain
> vanilla fftw2 lib, however, if I see something interesting
> I will drop a line here.
>
>
> What is given below is a comment to answer Vega's questions.
> It could be skipped unless one's interested in the nitty-gritty
> details and/or wants to find and expose flaws in my operating
> procedures.
>
> > could you tell me which dir should be added to the LD_LIBRARY_PATH, or 
> > which
> > flags should be added after the QE configure command?
>
> Vega,
>
> Here's what you can do, if, against Axel's advice, you
> just gotta have an MKL FFT binary in your {espresso}/bin.
>
> I usually do not use configure. Instead I edit make.sys
> directly, which seems to be much more convenient. If you
> take a look at the end of my original message you will
> see how I set all the important flags (including include
> and lib paths) to compile everything without problems.
> The only thing you have to do is put in your own paths
> to MKL instead of my paths.
>
> Regarding the FFT_LIBS flag, by default, my sysadmin placed
> all the compiled MKL FFT libs into {mkl}/{number}/lib/64
> but you can place them anywhere as long as you provide a
> correct path to them in make.sys.
>
> Regarding the LD_LIBRARY_PATH, I usually set it inside my
> PBS job script, e.g.,
>
> #
> # Set up some compiler-dependent things:
> #
> if [ $COMPILER = intel ]; then
>
>   # Set up some things to run an Intel-compiler binary:
>   MPIRUN=/usr/local/bin/mpiexec
>   MPIFLAGS='-verbose -kill'
>   export
> LD_LIBRARY_PATH=/usr/local/intel/mkl/10.0.4.023/lib/em64t/:$LD_LIBRARY_PATH
>
> elif [ $COMPILER = pgi64 ]; then
>
>   {do something else here}
>
> else
>
>   echo "Compiler $COMPILER unsupported for parallel execution"
>   exit 1
>
> fi
>
> You can then check if all the appropriate libs are found correctly
> by doing "ldd your_binary.x" (in the same PBS script, of course)
> before you run it:
>
> # Run the job in /<local scratch>/<run>:
>
> DATE=`date`
> echo ""
> echo "Time at the start of the job is: $DATE"
> echo ""
>
> cd $SCRATCH/$RUNDIR
>
> echo ""
> echo "ldd pw.x:"
> ldd $SCRATCH/$RUNDIR/pw.$ARCH.x
> echo ""
>
> echo ""
> echo "Running the job:"
> echo "$MPIRUN $MPIFLAGS $SCRATCH/$RUNDIR/pw.$ARCH.x $NPOOL <
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.inp > 
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.out"
> echo ""
> $MPIRUN $MPIFLAGS $SCRATCH/$RUNDIR/pw.$ARCH.x $NPOOL <
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.inp > 
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.out
>
> DATE=`date`
> echo ""
> echo "Time at the end of the job is: $DATE"
> echo "Doing some housekeeping duties..."
> echo ""
>
>
> Here's a sample output from this part of the script that I get on my 
> cluster,
> which shows that at least the MKL libraries from BLAS_LIBS and LAPACK_LIBS
> are found correctly:
>
> > Time at the start of the job is: Mon Sep 29 17:37:18 CDT 2008
> >
> >
> > ldd pw.x:
> >         libmkl_intel_lp64.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so 
> (0x0000002a95557000)
> >         libmkl_sequential.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_sequential.so 
> (0x0000002a9586d000)
> >         libmkl_core.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_core.so 
> (0x0000002a95a1a000)
> >         libpthread.so.0 => /lib64/tls/libpthread.so.0 
> > (0x000000375f300000)
> >         librt.so.1 => /lib64/tls/librt.so.1 (0x000000375e900000)
> >         libm.so.6 => /lib64/tls/libm.so.6 (0x000000375e300000)
> >         libc.so.6 => /lib64/tls/libc.so.6 (0x000000375de00000)
> >         libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x000000375eb00000)
> >         libdl.so.2 => /lib64/libdl.so.2 (0x000000375e100000)
> >         /lib64/ld-linux-x86-64.so.2 (0x000000375dc00000)
> >
> >
> > Running the job:
> > /usr/local/bin/mpiexec -verbose -kill 
> > /scratch/nakhmanson/PWtest3/pw.test.x
> -npool 2 < /scratch/nakhmanson/PWtest3/C1c.relaxed.pw.inp > 
> /scratch/nakhmanson/PWt
> > est3/C1c.relaxed.pw.out
> >
> > mpiexec: resolve_exe: using absolute path
> "/scratch/nakhmanson/PWtest3/pw.test.x".
> > mpiexec: process_start_event: evt 2 task 0 on node09.cluster.
> > mpiexec: read_p4_master_port: waiting for port from master.
> > mpiexec: read_p4_master_port: got port 33007.
> > mpiexec: process_start_event: evt 4 task 1 on node09.cluster.
> > mpiexec: All 2 tasks (spawn 0) started.
> > mpiexec: wait_tasks: waiting for node09.cluster node09.cluster.
> > mpiexec: process_obit_event: evt 3 task 0 on node09.cluster stat 0.
> > mpiexec: process_obit_event: evt 5 task 1 on node09.cluster stat 0.
> >
> > Time at the end of the job is: Mon Sep 29 17:41:03 CDT 2008
> > Doing some housekeeping duties...
>
> Hope this helps,
>
> Serge
>
> -- 
> *********************************************************
>  Serge M. Nakhmanson               phone: (630) 252-5205
>  Assistant Scientist                 fax: (630) 252-4798
>  MSD-212, Rm. C-224
>  Argonne National Laboratory
>  9700 S. Cass Ave.
>  Argonne, IL 60439
> *********************************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

From vegalew at hotmail.com  Thu Oct  2 08:29:16 2008
From: vegalew at hotmail.com (vega)
Date: Thu, 2 Oct 2008 14:29:16 +0800
Subject: [Pw_forum] Compiling with intel fortran,
	MKL and MKL FFT wrappers
In-Reply-To: <48E26D7B.2050809@anl.gov>
References: <48E26D7B.2050809@anl.gov>
Message-ID: <BAY124-DS574285818F53569623858A43D0@phx.gbl>

Thank you Serge

vega
=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China

--------------------------------------------------
From: "Serge Nakhmanson" <nakhmanson at anl.gov>
Sent: Wednesday, October 01, 2008 2:18 AM
To: "PWSCF Forum" <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] Compiling with intel fortran,MKL and MKL FFT 
wrappers

> Lorenzo, Axel,
>
> Thank you for your comments. I expected the serial lib
> to be "it" but decided to check in with the forum just
> to be sure. I have not tested the new "MKL FTT" binary
> extensively yet but I will. As I understand, I should not
> expect a tremendous performance improvement over plain
> vanilla fftw2 lib, however, if I see something interesting
> I will drop a line here.
>
>
> What is given below is a comment to answer Vega's questions.
> It could be skipped unless one's interested in the nitty-gritty
> details and/or wants to find and expose flaws in my operating
> procedures.
>
> > could you tell me which dir should be added to the LD_LIBRARY_PATH, or 
> > which
> > flags should be added after the QE configure command?
>
> Vega,
>
> Here's what you can do, if, against Axel's advice, you
> just gotta have an MKL FFT binary in your {espresso}/bin.
>
> I usually do not use configure. Instead I edit make.sys
> directly, which seems to be much more convenient. If you
> take a look at the end of my original message you will
> see how I set all the important flags (including include
> and lib paths) to compile everything without problems.
> The only thing you have to do is put in your own paths
> to MKL instead of my paths.
>
> Regarding the FFT_LIBS flag, by default, my sysadmin placed
> all the compiled MKL FFT libs into {mkl}/{number}/lib/64
> but you can place them anywhere as long as you provide a
> correct path to them in make.sys.
>
> Regarding the LD_LIBRARY_PATH, I usually set it inside my
> PBS job script, e.g.,
>
> #
> # Set up some compiler-dependent things:
> #
> if [ $COMPILER = intel ]; then
>
>   # Set up some things to run an Intel-compiler binary:
>   MPIRUN=/usr/local/bin/mpiexec
>   MPIFLAGS='-verbose -kill'
>   export
> LD_LIBRARY_PATH=/usr/local/intel/mkl/10.0.4.023/lib/em64t/:$LD_LIBRARY_PATH
>
> elif [ $COMPILER = pgi64 ]; then
>
>   {do something else here}
>
> else
>
>   echo "Compiler $COMPILER unsupported for parallel execution"
>   exit 1
>
> fi
>
> You can then check if all the appropriate libs are found correctly
> by doing "ldd your_binary.x" (in the same PBS script, of course)
> before you run it:
>
> # Run the job in /<local scratch>/<run>:
>
> DATE=`date`
> echo ""
> echo "Time at the start of the job is: $DATE"
> echo ""
>
> cd $SCRATCH/$RUNDIR
>
> echo ""
> echo "ldd pw.x:"
> ldd $SCRATCH/$RUNDIR/pw.$ARCH.x
> echo ""
>
> echo ""
> echo "Running the job:"
> echo "$MPIRUN $MPIFLAGS $SCRATCH/$RUNDIR/pw.$ARCH.x $NPOOL <
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.inp > 
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.out"
> echo ""
> $MPIRUN $MPIFLAGS $SCRATCH/$RUNDIR/pw.$ARCH.x $NPOOL <
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.inp > 
> $SCRATCH/$RUNDIR/$NAME.$PREFIX.pw.out
>
> DATE=`date`
> echo ""
> echo "Time at the end of the job is: $DATE"
> echo "Doing some housekeeping duties..."
> echo ""
>
>
> Here's a sample output from this part of the script that I get on my 
> cluster,
> which shows that at least the MKL libraries from BLAS_LIBS and LAPACK_LIBS
> are found correctly:
>
> > Time at the start of the job is: Mon Sep 29 17:37:18 CDT 2008
> >
> >
> > ldd pw.x:
> >         libmkl_intel_lp64.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so 
> (0x0000002a95557000)
> >         libmkl_sequential.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_sequential.so 
> (0x0000002a9586d000)
> >         libmkl_core.so =>
> /usr/local/intel/mkl/10.0.4.023/lib/em64t/libmkl_core.so 
> (0x0000002a95a1a000)
> >         libpthread.so.0 => /lib64/tls/libpthread.so.0 
> > (0x000000375f300000)
> >         librt.so.1 => /lib64/tls/librt.so.1 (0x000000375e900000)
> >         libm.so.6 => /lib64/tls/libm.so.6 (0x000000375e300000)
> >         libc.so.6 => /lib64/tls/libc.so.6 (0x000000375de00000)
> >         libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x000000375eb00000)
> >         libdl.so.2 => /lib64/libdl.so.2 (0x000000375e100000)
> >         /lib64/ld-linux-x86-64.so.2 (0x000000375dc00000)
> >
> >
> > Running the job:
> > /usr/local/bin/mpiexec -verbose -kill 
> > /scratch/nakhmanson/PWtest3/pw.test.x
> -npool 2 < /scratch/nakhmanson/PWtest3/C1c.relaxed.pw.inp > 
> /scratch/nakhmanson/PWt
> > est3/C1c.relaxed.pw.out
> >
> > mpiexec: resolve_exe: using absolute path
> "/scratch/nakhmanson/PWtest3/pw.test.x".
> > mpiexec: process_start_event: evt 2 task 0 on node09.cluster.
> > mpiexec: read_p4_master_port: waiting for port from master.
> > mpiexec: read_p4_master_port: got port 33007.
> > mpiexec: process_start_event: evt 4 task 1 on node09.cluster.
> > mpiexec: All 2 tasks (spawn 0) started.
> > mpiexec: wait_tasks: waiting for node09.cluster node09.cluster.
> > mpiexec: process_obit_event: evt 3 task 0 on node09.cluster stat 0.
> > mpiexec: process_obit_event: evt 5 task 1 on node09.cluster stat 0.
> >
> > Time at the end of the job is: Mon Sep 29 17:41:03 CDT 2008
> > Doing some housekeeping duties...
>
> Hope this helps,
>
> Serge
>
> -- 
> *********************************************************
>  Serge M. Nakhmanson               phone: (630) 252-5205
>  Assistant Scientist                 fax: (630) 252-4798
>  MSD-212, Rm. C-224
>  Argonne National Laboratory
>  9700 S. Cass Ave.
>  Argonne, IL 60439
> *********************************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

From chenhanghuipwscf at gmail.com  Thu Oct  2 17:48:40 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Thu, 2 Oct 2008 11:48:40 -0400
Subject: [Pw_forum] charge-density file
Message-ID: <22ae3ca40810020848i77878cbbx2d667b0fa645108@mail.gmail.com>

Dear PWSCF users,
      I have encountered this problem a couple of times.  When I compile
PWSCF on different machines, I find that on some machines, the charge
density file has the suffix .xml (like charge-density.xml). On other
machines, the file has the suffix .dat (like charge-density.dat). Does that
have anything to do with my compilations? Since in my old calculation they
are all .xml format, I do want the new version of PWSCF to generate
charge-density.xml rather than charge-density.dat. How can I control that?
      Thank you.

Hanghui
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From willykohn at gmail.com  Thu Oct  2 17:52:44 2008
From: willykohn at gmail.com (willy kohn)
Date: Thu, 2 Oct 2008 11:52:44 -0400
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
Message-ID: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>

Dear PWSCF users:

I have a quick question about using
Hartwigsen-Goedeker-Hutter<http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade>pseudopotential
with PWSCF. Is there any converter to transfer the HGH pp
format to UPF used in PWSCF?

Best,

Wei

Georgia Tech
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From akohlmey at cmm.chem.upenn.edu  Thu Oct  2 17:54:53 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 2 Oct 2008 11:54:53 -0400 (EDT)
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
 pseudopotential
In-Reply-To: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>

On Thu, 2 Oct 2008, willy kohn wrote:

WK> Dear PWSCF users:
WK> 
WK> I have a quick question about using
WK> Hartwigsen-Goedeker-Hutter<http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade>pseudopotential
WK> with PWSCF. Is there any converter to transfer the HGH pp
WK> format to UPF used in PWSCF?

none that i am aware of.

the GTH pseudopotentials are analytical in real and reciprocal
space and to incorporate them properly, one would have to do a 
lot of programming. in the CPMD code (from http://www.cpmd.org)
they are treated as a special case, similar to ultra-soft psps.

is there any particularly reason you'd need any of those?

cheers,
   axel.


WK> 
WK> Best,
WK> 
WK> Wei
WK> 
WK> Georgia Tech
WK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From willykohn at gmail.com  Thu Oct  2 18:20:43 2008
From: willykohn at gmail.com (willy kohn)
Date: Thu, 2 Oct 2008 12:20:43 -0400
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
In-Reply-To: <Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>
	<Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>
Message-ID: <8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>

Hi, Axel:

Thanks a lot for your quick answer. I need to do some calculations on some
compound semiconductors of Ge. But the PP (Ge.pz-bhs.UPF) provided in the
PWSCF website yeided some results that I don't understand. So I would like
to use some other PP's to check if I did the calculation correctly. Any
suggestions?

Best,

Wei

On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu
> wrote:

> On Thu, 2 Oct 2008, willy kohn wrote:
>
> WK> Dear PWSCF users:
> WK>
> WK> I have a quick question about using
> WK> Hartwigsen-Goedeker-Hutter<
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> >pseudopotential
> WK> with PWSCF. Is there any converter to transfer the HGH pp
> WK> format to UPF used in PWSCF?
>
> none that i am aware of.
>
> the GTH pseudopotentials are analytical in real and reciprocal
> space and to incorporate them properly, one would have to do a
> lot of programming. in the CPMD code (from http://www.cpmd.org)
> they are treated as a special case, similar to ultra-soft psps.
>
> is there any particularly reason you'd need any of those?
>
> cheers,
>   axel.
>
>
> WK>
> WK> Best,
> WK>
> WK> Wei
> WK>
> WK> Georgia Tech
> WK>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
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From giannozz at democritos.it  Thu Oct  2 19:39:58 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 2 Oct 2008 19:39:58 +0200
Subject: [Pw_forum] charge-density file
In-Reply-To: <22ae3ca40810020848i77878cbbx2d667b0fa645108@mail.gmail.com>
References: <22ae3ca40810020848i77878cbbx2d667b0fa645108@mail.gmail.com>
Message-ID: <7A89BCA3-F631-426A-883E-D60217A67E5C@democritos.it>


On Oct 2, 2008, at 17:48 , alan chen wrote:

>  When I compile PWSCF on different machines, I find that on some  
> machines, the charge density file has the suffix .xml (like charge- 
> density.xml). On other machines, the file has the suffix .dat (like  
> charge-density.dat). Does that have anything to do with my  
> compilations?

no, but it has to do with the version you are compiling. The suffix  
change was
made some time ago in order to have a more uniform naming convention

> Since in my old calculation they are all .xml format, I do want the  
> new version of PWSCF to generate charge-density.xml rather than  
> charge-density.dat. How can I control that?

you have to change the code, if you really want to

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From akohlmey at cmm.chem.upenn.edu  Thu Oct  2 20:12:47 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 2 Oct 2008 14:12:47 -0400 (EDT)
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
 pseudopotential
In-Reply-To: <8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com> 
	<Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>
	<8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810021401580.18122@localhost.localdomain>

On Thu, 2 Oct 2008, willy kohn wrote:

WK> Hi, Axel:
WK> 
WK> Thanks a lot for your quick answer. I need to do some calculations on some
WK> compound semiconductors of Ge. But the PP (Ge.pz-bhs.UPF) provided in the
WK> PWSCF website yeided some results that I don't understand. So I would like

perhaps it would be useful to explain in more detail what 
is confusing you and what calculation you did with what input.
perhaps some people here can comment on it. it is always easy
to blame the pseudopotential (sometimes rightfully so), but 
more often than not, the real cause is in not doing a calculation
correctly, or not using a pseudopotential correct.

WK> to use some other PP's to check if I did the calculation correctly. Any
WK> suggestions?

i have a set of Ge pseudopotentials generated from parameters 
for a norm-conserving troullier-martins potential that is in
the extended CPMD psp library. they have seen only very minimal 
transferability testing (using an atomic code in bessel basis),
but so far seem to be ok, except for the OLYP one which has a 
ghost in the s-channel.

i can send them to you in a private mail, if you are interested.
no guarantees etc...

cheers,
   axel.

WK> 
WK> Best,
WK> 
WK> Wei
WK> 
WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu
WK> > wrote:
WK> 
WK> > On Thu, 2 Oct 2008, willy kohn wrote:
WK> >
WK> > WK> Dear PWSCF users:
WK> > WK>
WK> > WK> I have a quick question about using
WK> > WK> Hartwigsen-Goedeker-Hutter<
WK> > http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
WK> > >pseudopotential
WK> > WK> with PWSCF. Is there any converter to transfer the HGH pp
WK> > WK> format to UPF used in PWSCF?
WK> >
WK> > none that i am aware of.
WK> >
WK> > the GTH pseudopotentials are analytical in real and reciprocal
WK> > space and to incorporate them properly, one would have to do a
WK> > lot of programming. in the CPMD code (from http://www.cpmd.org)
WK> > they are treated as a special case, similar to ultra-soft psps.
WK> >
WK> > is there any particularly reason you'd need any of those?
WK> >
WK> > cheers,
WK> >   axel.
WK> >
WK> >
WK> > WK>
WK> > WK> Best,
WK> > WK>
WK> > WK> Wei
WK> > WK>
WK> > WK> Georgia Tech
WK> > WK>
WK> >
WK> > --
WK> > =======================================================================
WK> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
WK> >   Center for Molecular Modeling   --   University of Pennsylvania
WK> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
WK> > =======================================================================
WK> > If you make something idiot-proof, the universe creates a better idiot.
WK> >
WK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From willykohn at gmail.com  Thu Oct  2 22:54:43 2008
From: willykohn at gmail.com (willy kohn)
Date: Thu, 2 Oct 2008 16:54:43 -0400
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
In-Reply-To: <Pine.LNX.4.64.0810021401580.18122@localhost.localdomain>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>
	<Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>
	<8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>
	<Pine.LNX.4.64.0810021401580.18122@localhost.localdomain>
Message-ID: <8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>

Hi, Axel:

Well, I didn't blame the PP, and I didn't mean to. My question is quite
simple. I was told that with a LDA PP, Ge has a vanishing or negative band
gap at Gamma point. But with this PP, it has a gap of 0.50 eV (using
experimental lattice) or 0.80 eV (after relaxation). I'm not sure what I
knew is correct, and that is the reason I wanted another PP to verify.

Best,

Wei



On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
<akohlmey at cmm.chem.upenn.edu>wrote:

> On Thu, 2 Oct 2008, willy kohn wrote:
>
> WK> Hi, Axel:
> WK>
> WK> Thanks a lot for your quick answer. I need to do some calculations on
> some
> WK> compound semiconductors of Ge. But the PP (Ge.pz-bhs.UPF) provided in
> the
> WK> PWSCF website yeided some results that I don't understand. So I would
> like
>
> perhaps it would be useful to explain in more detail what
> is confusing you and what calculation you did with what input.
> perhaps some people here can comment on it. it is always easy
> to blame the pseudopotential (sometimes rightfully so), but
> more often than not, the real cause is in not doing a calculation
> correctly, or not using a pseudopotential correct.
>
> WK> to use some other PP's to check if I did the calculation correctly. Any
> WK> suggestions?
>
> i have a set of Ge pseudopotentials generated from parameters
> for a norm-conserving troullier-martins potential that is in
> the extended CPMD psp library. they have seen only very minimal
> transferability testing (using an atomic code in bessel basis),
> but so far seem to be ok, except for the OLYP one which has a
> ghost in the s-channel.
>
> i can send them to you in a private mail, if you are interested.
> no guarantees etc...
>
> cheers,
>   axel.
>
> WK>
> WK> Best,
> WK>
> WK> Wei
> WK>
> WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer <
> akohlmey at cmm.chem.upenn.edu
> WK> > wrote:
> WK>
> WK> > On Thu, 2 Oct 2008, willy kohn wrote:
> WK> >
> WK> > WK> Dear PWSCF users:
> WK> > WK>
> WK> > WK> I have a quick question about using
> WK> > WK> Hartwigsen-Goedeker-Hutter<
> WK> >
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> WK> > >pseudopotential
> WK> > WK> with PWSCF. Is there any converter to transfer the HGH pp
> WK> > WK> format to UPF used in PWSCF?
> WK> >
> WK> > none that i am aware of.
> WK> >
> WK> > the GTH pseudopotentials are analytical in real and reciprocal
> WK> > space and to incorporate them properly, one would have to do a
> WK> > lot of programming. in the CPMD code (from http://www.cpmd.org)
> WK> > they are treated as a special case, similar to ultra-soft psps.
> WK> >
> WK> > is there any particularly reason you'd need any of those?
> WK> >
> WK> > cheers,
> WK> >   axel.
> WK> >
> WK> >
> WK> > WK>
> WK> > WK> Best,
> WK> > WK>
> WK> > WK> Wei
> WK> > WK>
> WK> > WK> Georgia Tech
> WK> > WK>
> WK> >
> WK> > --
> WK> >
> =======================================================================
> WK> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> WK> >   Center for Molecular Modeling   --   University of Pennsylvania
> WK> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
> 1-215-898-5425
> WK> >
> =======================================================================
> WK> > If you make something idiot-proof, the universe creates a better
> idiot.
> WK> >
> WK>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
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From eyvaz_isaev at yahoo.com  Fri Oct  3 01:10:53 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 2 Oct 2008 16:10:53 -0700 (PDT)
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
In-Reply-To: <8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>
Message-ID: <958267.94779.qm@web65715.mail.ac4.yahoo.com>

Dear Willy,

--- On Fri, 10/3/08, willy kohn <willykohn at gmail.com> wrote:

> I was told that with a LDA PP, Ge has a vanishing
> or negative band gap at Gamma point. But with this PP, > it has a gap of 0.50eV (using experimental lattice) or 
> 0.80 eV (after relaxation).

Please recall that we use the Density Functional Theory, that is the theory of the ground state, and it is not obliged to give correct excitation energies in semiconductors. Besides, we apply the Local Density Approximation which underestimates the band gap, even gives negative band gap in Ge. This is well known fact. The source of this fault is the use of single-particle Shrodinger equation, but the use of the quasiparticle equation with the self-energy operator is more correct. There are few recipes how to deal with this equation. The so called GW method is among them. 

Another point is proper account of exchange-correlation interactions. It is well known that the use of the functionals like PBE0, B3LYP gives improved results for insulating systems concerning their electronic structure. For the reference please have a look at /examples-EXX (for Si).  

So, if the HGH pseudopotentials are used in the framework of the DFT-LDA, unlikely they can give correct band gap due to the fault of the underlying method.  
Even all-electron methods within the LDA fail to predict the band gap (as example see PHYSICAL REVIEW B 67, 155208 2003).

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com






> I'm not sure what I
> knew is correct, and that is the reason I wanted another PP
> to verify.
> 
> Best,
> 
> Wei
> 
> 
> 
> On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
> <akohlmey at cmm.chem.upenn.edu>wrote:
> 
> > On Thu, 2 Oct 2008, willy kohn wrote:
> >
> > WK> Hi, Axel:
> > WK>
> > WK> Thanks a lot for your quick answer. I need to
> do some calculations on
> > some
> > WK> compound semiconductors of Ge. But the PP
> (Ge.pz-bhs.UPF) provided in
> > the
> > WK> PWSCF website yeided some results that I
> don't understand. So I would
> > like
> >
> > perhaps it would be useful to explain in more detail
> what
> > is confusing you and what calculation you did with
> what input.
> > perhaps some people here can comment on it. it is
> always easy
> > to blame the pseudopotential (sometimes rightfully
> so), but
> > more often than not, the real cause is in not doing a
> calculation
> > correctly, or not using a pseudopotential correct.
> >
> > WK> to use some other PP's to check if I did
> the calculation correctly. Any
> > WK> suggestions?
> >
> > i have a set of Ge pseudopotentials generated from
> parameters
> > for a norm-conserving troullier-martins potential that
> is in
> > the extended CPMD psp library. they have seen only
> very minimal
> > transferability testing (using an atomic code in
> bessel basis),
> > but so far seem to be ok, except for the OLYP one
> which has a
> > ghost in the s-channel.
> >
> > i can send them to you in a private mail, if you are
> interested.
> > no guarantees etc...
> >
> > cheers,
> >   axel.
> >
> > WK>
> > WK> Best,
> > WK>
> > WK> Wei
> > WK>
> > WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer
> <
> > akohlmey at cmm.chem.upenn.edu
> > WK> > wrote:
> > WK>
> > WK> > On Thu, 2 Oct 2008, willy kohn wrote:
> > WK> >
> > WK> > WK> Dear PWSCF users:
> > WK> > WK>
> > WK> > WK> I have a quick question about using
> > WK> > WK> Hartwigsen-Goedeker-Hutter<
> > WK> >
> >
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> > WK> > >pseudopotential
> > WK> > WK> with PWSCF. Is there any converter
> to transfer the HGH pp
> > WK> > WK> format to UPF used in PWSCF?
> > WK> >
> > WK> > none that i am aware of.
> > WK> >
> > WK> > the GTH pseudopotentials are analytical in
> real and reciprocal
> > WK> > space and to incorporate them properly,
> one would have to do a
> > WK> > lot of programming. in the CPMD code (from
> http://www.cpmd.org)
> > WK> > they are treated as a special case,
> similar to ultra-soft psps.
> > WK> >
> > WK> > is there any particularly reason you'd
> need any of those?
> > WK> >
> > WK> > cheers,
> > WK> >   axel.
> > WK> >
> > WK> >
> > WK> > WK>
> > WK> > WK> Best,
> > WK> > WK>
> > WK> > WK> Wei
> > WK> > WK>
> > WK> > WK> Georgia Tech
> > WK> > WK>
> > WK> >
> > WK> > --
> > WK> >
> >
> =======================================================================
> > WK> > Axel Kohlmeyer  
> akohlmey at cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > WK> >   Center for Molecular Modeling   --  
> University of Pennsylvania
> > WK> > Department of Chemistry, 231 S.34th
> Street, Philadelphia, PA
> > 19104-6323
> > WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,
>  office-tel:
> > 1-215-898-5425
> > WK> >
> >
> =======================================================================
> > WK> > If you make something idiot-proof, the
> universe creates a better
> > idiot.
> > WK> >
> > WK>
> >
> > --
> >
> =======================================================================
> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu  
> http://www.cmm.upenn.edu
> >   Center for Molecular Modeling   --   University of
> Pennsylvania
> > Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582,  fax: 1-215-573-6233, 
> office-tel: 1-215-898-5425
> >
> =======================================================================
> > If you make something idiot-proof, the universe
> creates a better idiot.
> >
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From babderre at physics.auth.gr  Fri Oct  3 01:44:49 2008
From: babderre at physics.auth.gr (babderre at physics.auth.gr)
Date: Fri,  3 Oct 2008 02:44:49 +0300
Subject: [Pw_forum] about projwfc.x
Message-ID: <1222991089.48e55cf10b729@mail.physics.auth.gr>


 Dear all users,

 I work with QE 4.0.1 in cluster

 the pw.x work fine ,for projwfc.x  I have use :
 [mpirun -np 4 projwfc.x -npool 4 < input ] , I have also try -npool 1 with
(wf_collect=.true.) to save wavefunctions into a single directory)
I got the following error:

----------------------------------------------------------------
 Program POST-PROC v.4.0.1  starts ...
     Today is  2Oct2008 at 16:41:51

     Parallel version (MPI)

     Number of processors in use:       4
     K-points division:     npool     =    4
MPI Application rank 0 killed before MPI_Finalize() with signal 11
----------------------------------------------------------------------

hope to have some help.

Belabbes.
http://parsem.physics.auth.gr/belabbes.htm



From degironc at sissa.it  Fri Oct  3 09:00:55 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 03 Oct 2008 09:00:55 +0200
Subject: [Pw_forum] Quick question on
	Hartwigsen-Goedeker-Hutter	pseudopotential
In-Reply-To: <8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>	<Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>	<8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>	<Pine.LNX.4.64.0810021401580.18122@localhost.localdomain>
	<8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>
Message-ID: <48E5C327.6060200@sissa.it>


I don't know the details of the generation of  this particular PP but in 
the old good times there has been a very detailed comparison of LDA band 
structure calculation of Ge and GaAs between the PP method and LMTO [GB 
Bachelet and NE Christensen, Phys.Rev.B 31, 879 (1985) ].
The main result is that in order to get the correct (bad) gap in Ge and 
GaAs  1) scalar relativistic, 2) spin-orbit coupling, 3) 3d-state relaxation
are important... not to mention convergence w.r.t. to cutoff ...

Hope  this helps,

 Stefano de Gironcoli - SISSA and DEMOCRITOS

willy kohn wrote:
> Hi, Axel:
>
> Well, I didn't blame the PP, and I didn't mean to. My question is 
> quite simple. I was told that with a LDA PP, Ge has a vanishing or 
> negative band gap at Gamma point. But with this PP, it has a gap of 
> 0.50 eV (using experimental lattice) or 0.80 eV (after relaxation). 
> I'm not sure what I knew is correct, and that is the reason I wanted 
> another PP to verify.
>
> Best,
>
> Wei
>
> On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer 
> <akohlmey at cmm.chem.upenn.edu <mailto:akohlmey at cmm.chem.upenn.edu>> wrote:
>
>     On Thu, 2 Oct 2008, willy kohn wrote:
>
>     WK> Hi, Axel:
>     WK>
>     WK> Thanks a lot for your quick answer. I need to do some
>     calculations on some
>     WK> compound semiconductors of Ge. But the PP (Ge.pz-bhs.UPF)
>     provided in the
>     WK> PWSCF website yeided some results that I don't understand. So
>     I would like
>
>     perhaps it would be useful to explain in more detail what
>     is confusing you and what calculation you did with what input.
>     perhaps some people here can comment on it. it is always easy
>     to blame the pseudopotential (sometimes rightfully so), but
>     more often than not, the real cause is in not doing a calculation
>     correctly, or not using a pseudopotential correct.
>
>     WK> to use some other PP's to check if I did the calculation
>     correctly. Any
>     WK> suggestions?
>
>     i have a set of Ge pseudopotentials generated from parameters
>     for a norm-conserving troullier-martins potential that is in
>     the extended CPMD psp library. they have seen only very minimal
>     transferability testing (using an atomic code in bessel basis),
>     but so far seem to be ok, except for the OLYP one which has a
>     ghost in the s-channel.
>
>     i can send them to you in a private mail, if you are interested.
>     no guarantees etc...
>
>     cheers,
>       axel.
>
>     WK>
>     WK> Best,
>     WK>
>     WK> Wei
>     WK>
>     WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer
>     <akohlmey at cmm.chem.upenn.edu <mailto:akohlmey at cmm.chem.upenn.edu>
>     WK> > wrote:
>     WK>
>     WK> > On Thu, 2 Oct 2008, willy kohn wrote:
>     WK> >
>     WK> > WK> Dear PWSCF users:
>     WK> > WK>
>     WK> > WK> I have a quick question about using
>     WK> > WK> Hartwigsen-Goedeker-Hutter<
>     WK> >
>     http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
>     WK> > >pseudopotential
>     WK> > WK> with PWSCF. Is there any converter to transfer the HGH pp
>     WK> > WK> format to UPF used in PWSCF?
>     WK> >
>     WK> > none that i am aware of.
>     WK> >
>     WK> > the GTH pseudopotentials are analytical in real and reciprocal
>     WK> > space and to incorporate them properly, one would have to do a
>     WK> > lot of programming. in the CPMD code (from http://www.cpmd.org)
>     WK> > they are treated as a special case, similar to ultra-soft psps.
>     WK> >
>     WK> > is there any particularly reason you'd need any of those?
>     WK> >
>     WK> > cheers,
>     WK> >   axel.
>     WK> >
>     WK> >
>     WK> > WK>
>     WK> > WK> Best,
>     WK> > WK>
>     WK> > WK> Wei
>     WK> > WK>
>     WK> > WK> Georgia Tech
>     WK> > WK>
>     WK> >
>     WK> > --
>     WK> >
>     =======================================================================
>     WK> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
>     <mailto:akohlmey at cmm.chem.upenn.edu>   http://www.cmm.upenn.edu
>     WK> >   Center for Molecular Modeling   --   University of
>     Pennsylvania
>     WK> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>     19104-6323
>     WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
>     1-215-898-5425
>     WK> >
>     =======================================================================
>     WK> > If you make something idiot-proof, the universe creates a
>     better idiot.
>     WK> >
>     WK>
>
>     --
>     =======================================================================
>     Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
>     <mailto:akohlmey at cmm.chem.upenn.edu>   http://www.cmm.upenn.edu
>       Center for Molecular Modeling   --   University of Pennsylvania
>     Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>     19104-6323
>     tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
>     =======================================================================
>     If you make something idiot-proof, the universe creates a better
>     idiot.
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From arunmanna at jncasr.ac.in  Fri Oct  3 11:24:38 2008
From: arunmanna at jncasr.ac.in (Arun Kumar Manna)
Date: Fri, 3 Oct 2008 13:24:38 +0400 (RET)
Subject: [Pw_forum] Problem with phonon calculation
In-Reply-To: <mailman.1.1223015597.15872.pw_forum@pwscf.org>
References: <mailman.1.1223015597.15872.pw_forum@pwscf.org>
Message-ID: <47589.172.16.1.1.1223025878.squirrel@172.16.1.1>

 Dear All,
 I am facing problem during phonon calculation with PWscf.
 It creates a lot of files of total size about 65GB and on successfully
 completion of scf step, it starts to calculate phonon step but after some
 time it was killed.  Herein, I have attached my input file.
 Could anybody please help me regarding this?.

 Thanks,
 Arun




 Send Pw_forum mailing list submissions to
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> Today's Topics:
>
>    1. Re: Quick question on Hartwigsen-Goedeker-Hutter
>       pseudopotential (Eyvaz Isaev)
>    2. about projwfc.x (babderre at physics.auth.gr)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 2 Oct 2008 16:10:53 -0700 (PDT)
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: Re: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
> 	pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <958267.94779.qm at web65715.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Willy,
>
> --- On Fri, 10/3/08, willy kohn <willykohn at gmail.com> wrote:
>
>> I was told that with a LDA PP, Ge has a vanishing
>> or negative band gap at Gamma point. But with this PP, > it has a gap of
>> 0.50eV (using experimental lattice) or
>> 0.80 eV (after relaxation).
>
> Please recall that we use the Density Functional Theory, that is the
> theory of the ground state, and it is not obliged to give correct
> excitation energies in semiconductors. Besides, we apply the Local Density
> Approximation which underestimates the band gap, even gives negative band
> gap in Ge. This is well known fact. The source of this fault is the use of
> single-particle Shrodinger equation, but the use of the quasiparticle
> equation with the self-energy operator is more correct. There are few
> recipes how to deal with this equation. The so called GW method is among
> them.
>
> Another point is proper account of exchange-correlation interactions. It
> is well known that the use of the functionals like PBE0, B3LYP gives
> improved results for insulating systems concerning their electronic
> structure. For the reference please have a look at /examples-EXX (for Si).
>
> So, if the HGH pseudopotentials are used in the framework of the DFT-LDA,
> unlikely they can give correct band gap due to the fault of the underlying
> method.
> Even all-electron methods within the LDA fail to predict the band gap (as
> example see PHYSICAL REVIEW B 67, 155208 2003).
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>
>
>
>
>> I'm not sure what I
>> knew is correct, and that is the reason I wanted another PP
>> to verify.
>>
>> Best,
>>
>> Wei
>>
>>
>>
>> On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
>> <akohlmey at cmm.chem.upenn.edu>wrote:
>>
>> > On Thu, 2 Oct 2008, willy kohn wrote:
>> >
>> > WK> Hi, Axel:
>> > WK>
>> > WK> Thanks a lot for your quick answer. I need to
>> do some calculations on
>> > some
>> > WK> compound semiconductors of Ge. But the PP
>> (Ge.pz-bhs.UPF) provided in
>> > the
>> > WK> PWSCF website yeided some results that I
>> don't understand. So I would
>> > like
>> >
>> > perhaps it would be useful to explain in more detail
>> what
>> > is confusing you and what calculation you did with
>> what input.
>> > perhaps some people here can comment on it. it is
>> always easy
>> > to blame the pseudopotential (sometimes rightfully
>> so), but
>> > more often than not, the real cause is in not doing a
>> calculation
>> > correctly, or not using a pseudopotential correct.
>> >
>> > WK> to use some other PP's to check if I did
>> the calculation correctly. Any
>> > WK> suggestions?
>> >
>> > i have a set of Ge pseudopotentials generated from
>> parameters
>> > for a norm-conserving troullier-martins potential that
>> is in
>> > the extended CPMD psp library. they have seen only
>> very minimal
>> > transferability testing (using an atomic code in
>> bessel basis),
>> > but so far seem to be ok, except for the OLYP one
>> which has a
>> > ghost in the s-channel.
>> >
>> > i can send them to you in a private mail, if you are
>> interested.
>> > no guarantees etc...
>> >
>> > cheers,
>> >   axel.
>> >
>> > WK>
>> > WK> Best,
>> > WK>
>> > WK> Wei
>> > WK>
>> > WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer
>> <
>> > akohlmey at cmm.chem.upenn.edu
>> > WK> > wrote:
>> > WK>
>> > WK> > On Thu, 2 Oct 2008, willy kohn wrote:
>> > WK> >
>> > WK> > WK> Dear PWSCF users:
>> > WK> > WK>
>> > WK> > WK> I have a quick question about using
>> > WK> > WK> Hartwigsen-Goedeker-Hutter<
>> > WK> >
>> >
>> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
>> > WK> > >pseudopotential
>> > WK> > WK> with PWSCF. Is there any converter
>> to transfer the HGH pp
>> > WK> > WK> format to UPF used in PWSCF?
>> > WK> >
>> > WK> > none that i am aware of.
>> > WK> >
>> > WK> > the GTH pseudopotentials are analytical in
>> real and reciprocal
>> > WK> > space and to incorporate them properly,
>> one would have to do a
>> > WK> > lot of programming. in the CPMD code (from
>> http://www.cpmd.org)
>> > WK> > they are treated as a special case,
>> similar to ultra-soft psps.
>> > WK> >
>> > WK> > is there any particularly reason you'd
>> need any of those?
>> > WK> >
>> > WK> > cheers,
>> > WK> >   axel.
>> > WK> >
>> > WK> >
>> > WK> > WK>
>> > WK> > WK> Best,
>> > WK> > WK>
>> > WK> > WK> Wei
>> > WK> > WK>
>> > WK> > WK> Georgia Tech
>> > WK> > WK>
>> > WK> >
>> > WK> > --
>> > WK> >
>> >
>> =======================================================================
>> > WK> > Axel Kohlmeyer
>> akohlmey at cmm.chem.upenn.edu
>> > http://www.cmm.upenn.edu
>> > WK> >   Center for Molecular Modeling   --
>> University of Pennsylvania
>> > WK> > Department of Chemistry, 231 S.34th
>> Street, Philadelphia, PA
>> > 19104-6323
>> > WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,
>>  office-tel:
>> > 1-215-898-5425
>> > WK> >
>> >
>> =======================================================================
>> > WK> > If you make something idiot-proof, the
>> universe creates a better
>> > idiot.
>> > WK> >
>> > WK>
>> >
>> > --
>> >
>> =======================================================================
>> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
>> http://www.cmm.upenn.edu
>> >   Center for Molecular Modeling   --   University of
>> Pennsylvania
>> > Department of Chemistry, 231 S.34th Street,
>> Philadelphia, PA 19104-6323
>> > tel: 1-215-898-1582,  fax: 1-215-573-6233,
>> office-tel: 1-215-898-5425
>> >
>> =======================================================================
>> > If you make something idiot-proof, the universe
>> creates a better idiot.
>> >
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri,  3 Oct 2008 02:44:49 +0300
> From: babderre at physics.auth.gr
> Subject: [Pw_forum] about projwfc.x
> To: pw_forum at pwscf.org
> Message-ID: <1222991089.48e55cf10b729 at mail.physics.auth.gr>
> Content-Type: text/plain; charset=ISO-8859-1
>
>
>  Dear all users,
>
>  I work with QE 4.0.1 in cluster
>
>  the pw.x work fine ,for projwfc.x  I have use :
>  [mpirun -np 4 projwfc.x -npool 4 < input ] , I have also try -npool 1
> with
> (wf_collect=.true.) to save wavefunctions into a single directory)
> I got the following error:
>
> ----------------------------------------------------------------
>  Program POST-PROC v.4.0.1  starts ...
>      Today is  2Oct2008 at 16:41:51
>
>      Parallel version (MPI)
>
>      Number of processors in use:       4
>      K-points division:     npool     =    4
> MPI Application rank 0 killed before MPI_Finalize() with signal 11
> ----------------------------------------------------------------------
>
> hope to have some help.
>
> Belabbes.
> http://parsem.physics.auth.gr/belabbes.htm
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 16, Issue 4
> ***************************************
>


-- 
PhD Student
JNCASR, Bangalore-560064
India
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From giannozz at democritos.it  Fri Oct  3 12:19:11 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 03 Oct 2008 12:19:11 +0200
Subject: [Pw_forum] about projwfc.x
In-Reply-To: <1222991089.48e55cf10b729@mail.physics.auth.gr>
References: <1222991089.48e55cf10b729@mail.physics.auth.gr>
Message-ID: <48E5F19F.5080006@democritos.it>

babderre at physics.auth.gr wrote:

> MPI Application rank 0 killed before MPI_Finalize() with signal 11
> ----------------------------------------------------------------------
> 
> hope to have some help.

hopeless unless you provide a test job that can be reproduced
(in a reasonable time).

 > http://parsem.physics.auth.gr/belabbes.htm

good substitute for affiliation, but:
"The network link was interrupted while negotiating a connection.
Please try again."

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Fri Oct  3 12:25:00 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 03 Oct 2008 12:25:00 +0200
Subject: [Pw_forum] Problem with phonon calculation
In-Reply-To: <47589.172.16.1.1.1223025878.squirrel@172.16.1.1>
References: <mailman.1.1223015597.15872.pw_forum@pwscf.org>
	<47589.172.16.1.1.1223025878.squirrel@172.16.1.1>
Message-ID: <48E5F2FC.9070805@democritos.it>

Arun Kumar Manna wrote:

>  I am facing problem during phonon calculation with PWscf.
>  It creates a lot of files of total size about 65GB and on 
>  successfully completion of scf step, it starts to calculate 
>  phonon step but after some time it was killed.

out of memory? if pw.x writes 65Gb (!) the system you have is
big, maybe too big for a phonon calculation. Also note that
for a full phonon calculation you need 3*Natoms linear-response
calculations, each of which takes at least as much CPU time as
the single SCF calcultion.

Please do not send messages with a long useless quote
(this is valid for everybody!)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From anamikasingh85 at yahoo.co.in  Fri Oct  3 19:07:06 2008
From: anamikasingh85 at yahoo.co.in (anamika singh)
Date: Fri, 3 Oct 2008 22:37:06 +0530 (IST)
Subject: [Pw_forum] fftw-int.h and fftw scope errors
Message-ID: <514330.92549.qm@web8706.mail.in.yahoo.com>

Hi,

When i compile teh test test_main.c in teh tests folder of FFTW I get an error saying 

adatta at imaa-caribou /usr/src/fftw-2.1.5/tests
$ g++ test_main.c
test_main.c:25:22: fftw-int.h: No such file or directory
In file included from test_main.c:33:
test_main.h:87: warning: `compute_error_complex' initialized and declared `exter
n'
test_main.h:87: error: `fftw_complex' was not declared in this scope
test_main.h:87: error: `A' was not declared in this scope
test_main.h:87: error: expected primary-expression before "int"
test_main.h:88: error: `fftw_complex' was not declared in this scope
test_main.h:88: error: `B' was not declared in this scope
test_main.h:88: error: expected primary-expression before "int"
test_main.h:88: error: expected primary-expression before "int"
test_main.h:88: error: initializer expression list treated as compound expressio
n
test_main.h:90: error: `fftw_direction' does not name a type
test_main.h:94: error: `fftw_direction' has not been declared
test_main.h:94: error: ISO C++ forbids declaration of `dir' with no type
test_main.h:95: error: `fftw_direction' has not been declared
test_main.h:96: error: ISO C++ forbids declaration of `dir' with no type
test_main.h:98: error: `fftw_direction' has not been declared
test_main.h:99: error: ISO C++ forbids declaration of `dir' with no type
test_main.c: In function `size parse_size(char*)':
test_main.c:74: error: `fftw_die' undeclared (first use this function)
test_main.c:74: error: (Each undeclared identifier is reported only once for eac
h function it appears in.)
test_main.c: At global scope:
test_main.c:103: error: `FFTW_ESTIMATE' was not declared in this scope
test_main.c:104: error: `FFTW_MEASURE' was not declared in this scope
test_main.c: In function `void test_speed(int)':
test_main.c:226: error: `FFTW_FORWARD' undeclared (first use this function)
test_main.c:231: error: `FFTW_IN_PLACE' undeclared (first use this function)
test_main.c:236: error: `FFTW_BACKWARD' undeclared (first use this function)
test_main.c: In function `void test_speed_nd(size)':
test_main.c:269: error: `FFTW_FORWARD' undeclared (first use this function)
test_main.c:270: error: `FFTW_IN_PLACE' undeclared (first use this function)
test_main.c:276: error: `FFTW_BACKWARD' undeclared (first use this function)
test_main.c: At global scope:
test_main.c:293: error: redefinition of `double compute_error_complex'
test_main.h:87: error: `double compute_error_complex' previously defined here
test_main.c:293: error: `fftw_complex' was not declared in this scope
test_main.c:293: error: `A' was not declared in this scope
test_main.c:293: error: expected primary-expression before "int"
test_main.c:294: error: `fftw_complex' was not declared in this scope
test_main.c:294: error: `B' was not declared in this scope
test_main.c:294: error: expected primary-expression before "int"
test_main.c:294: error: expected primary-expression before "int"
test_main.c:295: error: expected `,' or `;' before '{' token
test_main.c: In function `void test_all()':
test_main.c:329: error: `FFTW_USE_WISDOM' undeclared (first use this function)
test_main.c:330: error: `fftw_check_memory_leaks' undeclared (first use this fun
ction)
test_main.c: In function `void testnd_correctness_both(size, int, int, int)':
test_main.c:408: error: `FFTW_FORWARD' undeclared (first use this function)
test_main.c:409: error: `FFTW_BACKWARD' undeclared (first use this function)
test_main.c: At global scope:
test_main.c:489: error: `fftw_direction' does not name a type
test_main.c: In function `void test_timer_paranoid()':
test_main.c:517: error: `fftw_time' undeclared (first use this function)
test_main.c:517: error: expected `;' before "start_t"
test_main.c:521: error: `start_t' undeclared (first use this function)
test_main.c:521: error: `fftw_get_time' undeclared (first use this function)
test_main.c:527: error: `end_t' undeclared (first use this function)
test_main.c:528: error: `fftw_time_diff' undeclared (first use this function)
test_main.c:528: error: `fftw_time_to_sec' undeclared (first use this function)
test_main.c: In function `void test_timer()':
test_main.c:552: error: `fftw_time' undeclared (first use this function)
test_main.c:552: error: expected `;' before "begin"
test_main.c:559: error: `start' undeclared (first use this function)
test_main.c:559: error: `fftw_get_time' undeclared (first use this function)
test_main.c:566: error: `FFTW_TIME_REPEAT' undeclared (first use this function)
test_main.c:567: error: `begin' undeclared (first use this function)
test_main.c:571: error: `end' undeclared (first use this function)
test_main.c:573: error: `fftw_time_diff' undeclared (first use this function)
test_main.c:573: error: `fftw_time_to_sec' undeclared (first use this function)
test_main.c:581: error: `FFTW_TIME_LIMIT' undeclared (first use this function)
test_main.c:637: error: `FFTW_TIME_MIN' undeclared (first use this function)
test_main.c: In function `void handle_option(char, char*)':
test_main.c:748: error: `fftw_die' undeclared (first use this function)
test_main.c:753: error: `FFTW_MEASURE' undeclared (first use this function)
test_main.c:757: error: `FFTW_ESTIMATE' undeclared (first use this function)
test_main.c:761: error: `FFTW_NO_VECTOR_RECURSE' undeclared (first use this func
tion)
test_main.c:765: error: `FFTW_USE_WISDOM' undeclared (first use this function)
test_main.c:772: error: `FFTW_SUCCESS' undeclared (first use this function)
test_main.c:772: error: `fftw_import_wisdom_from_file' undeclared (first use thi
s function)
test_main.c:787: error: `fftw_version' undeclared (first use this function)
test_main.c:790: error: `fftw_real' undeclared (first use this function)
test_main.c:820: error: `fftw_check_memory_leaks' undeclared (first use this fun
ction)
test_main.c: In function `int main(int, char**)':
test_main.c:990: error: `FFTW_USE_WISDOM' undeclared (first use this function)
test_main.c:994: error: `fftw_export_wisdom_to_string' undeclared (first use thi
s function)
test_main.c:995: error: `fftw_die' undeclared (first use this function)
test_main.c:997: error: `fftw_forget_wisdom' undeclared (first use this function
)
test_main.c:998: error: `FFTW_SUCCESS' undeclared (first use this function)
test_main.c:998: error: `fftw_import_wisdom_from_string' undeclared (first use t
his function)
test_main.c:1000: error: `fftw_free' undeclared (first use this function)
test_main.c:1005: error: `fftw_export_wisdom_to_file' undeclared (first use this
?function)
test_main.c:1012: error: `fftw_check_memory_leaks' undeclared (first use this fu
nction)
test_main.c:1014: error: `fftw_print_max_memory_usage' undeclared (first use thi
s function)
fftw-int.h is unedr fftw folder. I am not sure what is wrong.

Can anyone please take a look and help?

Regards
Ana



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From giannozz at democritos.it  Fri Oct  3 19:17:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 3 Oct 2008 19:17:35 +0200
Subject: [Pw_forum] fftw-int.h and fftw scope errors
In-Reply-To: <514330.92549.qm@web8706.mail.in.yahoo.com>
References: <514330.92549.qm@web8706.mail.in.yahoo.com>
Message-ID: <E387DF09-884E-4C8D-B25B-B32124737991@democritos.it>


On Oct 3, 2008, at 19:07 , anamika singh wrote:

> When i compile teh test test_main.c in teh tests folder of FFTW I  
> get an error saying
>
> adatta at imaa-caribou /usr/src/fftw-2.1.5/tests
> $ g++ test_main.c
> test_main.c:25:22: fftw-int.h: No such file or directory
> [...]
> fftw-int.h is under fftw folder. I am not sure what is wrong.

I am not sure you are in the right forum

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From chenhanghuipwscf at gmail.com  Sat Oct  4 02:10:46 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Fri, 3 Oct 2008 20:10:46 -0400
Subject: [Pw_forum] forces in the 'sawtooth' method
Message-ID: <22ae3ca40810031710i7e5b2557q6ccc60c4cc05eb06@mail.gmail.com>

Dear PWSCF users,
   In order to check whether the forces in the 'sawtooth' method are
calculated correctly in the latest version-4.0.2(no offense intended), we
carry out the following test. We calculate an isolated symmetric 5-layer STO
slab (input file is attached below). In the absence of electric field, there
are no forces on the middle TiO2 layer due to symmetry. Then we turn on a
weak electric field (0.0001 a.u.) and obtain the forces on Ti and on O are
0.00046 and -0.00013 Ry/au, respectively (in the middle TiO2 layer).
Therefore the Born effective charges of Ti and O are approximately

e*(Ti)=0.00046/0.0001/2= 2.3
e*(O)=-0.00013/0.0001/2= -0.65

The factor '2' is due to the units. However from both phonon frequency
calculation and literature, the Born effective charges of Ti and O are:

e*(Ti)= 7.25
e*(O)= -2.06

I am just wondering whether my method is correct. If it is correct, does
that imply there might be something wrong with the forces in the 'sawtooth'
method.
Thank you very much.

Hanghui Chen
Department of Physics, Yale University

&CONTROL
  calculation='scf'
  wf_collect=.true.
  pseudo_dir = './psp'
  outdir='.'
  wfcdir='/scratch'
  prefix='STO-5.5uc-EF0.0001-scf'
  tprnfor = .true.
  tstress = .true.
  disk_io='low'
  verbosity='high'
  dt=80.D0
  tefield=.true.
/
&SYSTEM
  ibrav=  6
  celldm(1) = 7.27
  celldm(3) = 10.0
  nat=  27
  ntyp= 3
  ecutwfc = 30.0
  ecutrho = 180.0
  occupations='smearing'
  smearing=gauss
  degauss=0.005
  edir=3
  emaxpos=0.8
  eopreg=0.1
  eamp=0.0001
/
&ELECTRONS
  diagonalization='david'
  mixing_beta = 0.7D0
  diago_david_ndim = 4
  startingwfc='atomic'
  startingpot='file'
  conv_thr = 1.0d-8
/
&IONS
  ion_dynamics = 'damp'
  phase_space = 'full'
  pot_extrapolation = 'second_order'
  wfc_extrapolation = 'second_order'
/
&CELL
  cell_dynamics = 'damp-w'
/
ATOMIC_SPECIES
 Sr  87.62   038-Sr-ca-sp-vgrp.uspp.format.UPF
 Ti  47.90   022-Ti-ca-sp-vgrp.uspp.format.UPF
 O   16.00   008-O-ca--vgrp.uspp.format.UPF
ATOMIC_POSITIONS alat
 Sr 0.00 0.00 0.00
 O  0.50 0.50 0.00
 Ti 0.50 0.50 0.50
 O  0.00 0.50 0.50
 O  0.50 0.00 0.50
 Sr 0.00 0.00 1.00
 O  0.50 0.50 1.00
 Ti 0.50 0.50 1.50
 O  0.00 0.50 1.50
 O  0.50 0.00 1.50
 Sr 0.00 0.00 2.00
 O  0.50 0.50 2.00
 Ti 0.50 0.50 2.50
 O  0.00 0.50 2.50
 O  0.50 0.00 2.50
 Sr 0.00 0.00 3.00
 O  0.50 0.50 3.00
 Ti 0.50 0.50 3.50
 O  0.00 0.50 3.50
 O  0.50 0.00 3.50
 Sr 0.00 0.00 4.00
 O  0.50 0.50 4.00
 Ti 0.50 0.50 4.50
 O  0.00 0.50 4.50
 O  0.50 0.00 4.50
 Sr 0.00 0.00 5.00
 O  0.50 0.50 5.00
K_POINTS {automatic}
8 8 1 0 0 0
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From sagarambavale at yahoo.co.in  Sat Oct  4 06:46:27 2008
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Sat, 4 Oct 2008 10:16:27 +0530 (IST)
Subject: [Pw_forum] some querries about pwcond
Message-ID: <354987.95024.qm@web94608.mail.in2.yahoo.com>

Dear all,
I have some queries about pwcond input file.

1.how k-perpendicular points are defined. (can you give any example except 'number of k-perpendicular points = 1' used in example 12) 
2. How weight is defined here for k-points? maximum weight?
3.how ecut2D (2-D cut off) it effects the calculation.

Thanks.

Best regards
Sagar Ambavale
Research student
The M.S. University of Baroda





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From baroni at sissa.it  Sat Oct  4 09:24:12 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 4 Oct 2008 09:24:12 +0200
Subject: [Pw_forum] forces in the 'sawtooth' method
In-Reply-To: <22ae3ca40810031710i7e5b2557q6ccc60c4cc05eb06@mail.gmail.com>
References: <22ae3ca40810031710i7e5b2557q6ccc60c4cc05eb06@mail.gmail.com>
Message-ID: <CDB8BFD8-9DC6-4C79-ABA5-7AC1E862F155@sissa.it>

Dear Chen: just two remarks that may or may not be relevant.
1) The "measured" forces seem to me rather small in magnitude. There  
may be accuracy issues. I would try to increase the value of the  
electric field and check that estimated effective charges are  
numerically stable in the range of the linear regime (this check  
should always be done when estimating derivatives numerically).
2) I am out of town at this time, without any textbook handy, so I  
cannot check the correct definitions and current nomenclature.  
However, in the literature one defines two different "effective  
charges" which differ by a factor equal to the dielectric constant  
(basically, one is the force generated by an unit *applied* field, the  
other is the one generated by a unit *internal* field. You may want to  
check the consistency of what you calculate with what the phonon code  
provides.
Cheers - SB

On Oct 4, 2008, at 2:10 AM, alan chen wrote:

> Dear PWSCF users,
>    In order to check whether the forces in the 'sawtooth' method are  
> calculated correctly in the latest version-4.0.2(no offense  
> intended), we carry out the following test. We calculate an isolated  
> symmetric 5-layer STO slab (input file is attached below). In the  
> absence of electric field, there are no forces on the middle TiO2  
> layer due to symmetry. Then we turn on a weak electric field (0.0001  
> a.u.) and obtain the forces on Ti and on O are 0.00046 and -0.00013  
> Ry/au, respectively (in the middle TiO2 layer). Therefore the Born  
> effective charges of Ti and O are approximately
>
> e*(Ti)=0.00046/0.0001/2= 2.3
> e*(O)=-0.00013/0.0001/2= -0.65
>
> The factor '2' is due to the units. However from both phonon  
> frequency calculation and literature, the Born effective charges of  
> Ti and O are:
>
> e*(Ti)= 7.25
> e*(O)= -2.06
>
> I am just wondering whether my method is correct. If it is correct,  
> does that imply there might be something wrong with the forces in  
> the 'sawtooth' method.
>
> Thank you very much.
>
> Hanghui Chen
> Department of Physics, Yale University
>
> &CONTROL
>   calculation='scf'
>   wf_collect=.true.
>   pseudo_dir = './psp'
>   outdir='.'
>   wfcdir='/scratch'
>   prefix='STO-5.5uc-EF0.0001-scf'
>   tprnfor = .true.
>   tstress = .true.
>   disk_io='low'
>   verbosity='high'
>   dt=80.D0
>   tefield=.true.
> /
> &SYSTEM
>   ibrav=  6
>   celldm(1) = 7.27
>   celldm(3) = 10.0
>   nat=  27
>   ntyp= 3
>   ecutwfc = 30.0
>   ecutrho = 180.0
>   occupations='smearing'
>   smearing=gauss
>   degauss=0.005
>   edir=3
>   emaxpos=0.8
>   eopreg=0.1
>   eamp=0.0001
> /
> &ELECTRONS
>   diagonalization='david'
>   mixing_beta = 0.7D0
>   diago_david_ndim = 4
>   startingwfc='atomic'
>   startingpot='file'
>   conv_thr = 1.0d-8
> /
> &IONS
>   ion_dynamics = 'damp'
>   phase_space = 'full'
>   pot_extrapolation = 'second_order'
>   wfc_extrapolation = 'second_order'
> /
> &CELL
>   cell_dynamics = 'damp-w'
> /
> ATOMIC_SPECIES
>  Sr  87.62   038-Sr-ca-sp-vgrp.uspp.format.UPF
>  Ti  47.90   022-Ti-ca-sp-vgrp.uspp.format.UPF
>  O   16.00   008-O-ca--vgrp.uspp.format.UPF
> ATOMIC_POSITIONS alat
>  Sr 0.00 0.00 0.00
>  O  0.50 0.50 0.00
>  Ti 0.50 0.50 0.50
>  O  0.00 0.50 0.50
>  O  0.50 0.00 0.50
>  Sr 0.00 0.00 1.00
>  O  0.50 0.50 1.00
>  Ti 0.50 0.50 1.50
>  O  0.00 0.50 1.50
>  O  0.50 0.00 1.50
>  Sr 0.00 0.00 2.00
>  O  0.50 0.50 2.00
>  Ti 0.50 0.50 2.50
>  O  0.00 0.50 2.50
>  O  0.50 0.00 2.50
>  Sr 0.00 0.00 3.00
>  O  0.50 0.50 3.00
>  Ti 0.50 0.50 3.50
>  O  0.00 0.50 3.50
>  O  0.50 0.00 3.50
>  Sr 0.00 0.00 4.00
>  O  0.50 0.50 4.00
>  Ti 0.50 0.50 4.50
>  O  0.00 0.50 4.50
>  O  0.50 0.00 4.50
>  Sr 0.00 0.00 5.00
>  O  0.50 0.50 5.00
> K_POINTS {automatic}
> 8 8 1 0 0 0
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html






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From vegalew at hotmail.com  Sat Oct  4 14:12:23 2008
From: vegalew at hotmail.com (vega)
Date: Sat, 4 Oct 2008 20:12:23 +0800
Subject: [Pw_forum] about projwfc.x
In-Reply-To: <1222991089.48e55cf10b729@mail.physics.auth.gr>
	<48E5F19F.5080006@democritos.it>
References: <1222991089.48e55cf10b729@mail.physics.auth.gr>
	<48E5F19F.5080006@democritos.it>
Message-ID: <BAY124-DS4635BFFFC071F8959047BA43F0@phx.gbl>


> > http://parsem.physics.auth.gr/belabbes.htm
>
> good substitute for affiliation, but:
> "The network link was interrupted while negotiating a connection.
> Please try again."

I could connect the website. but it's quite slow. Greece~ a wonderful place.

=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China

--------------------------------------------------
From: "Paolo Giannozzi" <giannozz at democritos.it>
Sent: Friday, October 03, 2008 6:19 PM
To: "PWSCF Forum" <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] about projwfc.x

> babderre at physics.auth.gr wrote:
>
>> MPI Application rank 0 killed before MPI_Finalize() with signal 11
>> ----------------------------------------------------------------------
>>
>> hope to have some help.
>
> hopeless unless you provide a test job that can be reproduced
> (in a reasonable time).
>

>
> Paolo
> -- 
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

From lyu7 at ncsu.edu  Sat Oct  4 14:36:14 2008
From: lyu7 at ncsu.edu (Liping Yu)
Date: Sat, 4 Oct 2008 08:36:14 -0400 (EDT)
Subject: [Pw_forum] forces in the 'sawtooth' method
In-Reply-To: <22ae3ca40810031710i7e5b2557q6ccc60c4cc05eb06@mail.gmail.com>
References: <22ae3ca40810031710i7e5b2557q6ccc60c4cc05eb06@mail.gmail.com>
Message-ID: <4519.65.87.183.47.1223123774.squirrel@webmail.ncsu.edu>

Just one comment on this:

The Born effective charge should be defined as Force/macroscopic internal
field. The applied field in the slab by sawtooth method actually is the
electric displacement D not the field in the slab. So your obtained
effective charge maybe differ from the one from bulk phonon calculation by
 a factor of the dielectric constant of the slab. On the other hand,
please note that for such a thin slab, the calculated dielectric constant
may depend on how you average the field or polarization of the slab, and
may differ a lot from bulk dielectric constant.

Best

Liping YU
Department of Physics,
North Carolina State University

> Dear PWSCF users,
>    In order to check whether the forces in the 'sawtooth' method are
> calculated correctly in the latest version-4.0.2(no offense intended), we
> carry out the following test. We calculate an isolated symmetric 5-layer
> STO
> slab (input file is attached below). In the absence of electric field,
> there
> are no forces on the middle TiO2 layer due to symmetry. Then we turn on a
> weak electric field (0.0001 a.u.) and obtain the forces on Ti and on O are
> 0.00046 and -0.00013 Ry/au, respectively (in the middle TiO2 layer).
> Therefore the Born effective charges of Ti and O are approximately
>
> e*(Ti)=0.00046/0.0001/2= 2.3
> e*(O)=-0.00013/0.0001/2= -0.65
>
> The factor '2' is due to the units. However from both phonon frequency
> calculation and literature, the Born effective charges of Ti and O are:
>
> e*(Ti)= 7.25
> e*(O)= -2.06
>
> I am just wondering whether my method is correct. If it is correct, does
> that imply there might be something wrong with the forces in the
> 'sawtooth'
> method.
> Thank you very much.
>
> Hanghui Chen
> Department of Physics, Yale University
>
> &CONTROL
>   calculation='scf'
>   wf_collect=.true.
>   pseudo_dir = './psp'
>   outdir='.'
>   wfcdir='/scratch'
>   prefix='STO-5.5uc-EF0.0001-scf'
>   tprnfor = .true.
>   tstress = .true.
>   disk_io='low'
>   verbosity='high'
>   dt=80.D0
>   tefield=.true.
> /
> &SYSTEM
>   ibrav=  6
>   celldm(1) = 7.27
>   celldm(3) = 10.0
>   nat=  27
>   ntyp= 3
>   ecutwfc = 30.0
>   ecutrho = 180.0
>   occupations='smearing'
>   smearing=gauss
>   degauss=0.005
>   edir=3
>   emaxpos=0.8
>   eopreg=0.1
>   eamp=0.0001
> /
> &ELECTRONS
>   diagonalization='david'
>   mixing_beta = 0.7D0
>   diago_david_ndim = 4
>   startingwfc='atomic'
>   startingpot='file'
>   conv_thr = 1.0d-8
> /
> &IONS
>   ion_dynamics = 'damp'
>   phase_space = 'full'
>   pot_extrapolation = 'second_order'
>   wfc_extrapolation = 'second_order'
> /
> &CELL
>   cell_dynamics = 'damp-w'
> /
> ATOMIC_SPECIES
>  Sr  87.62   038-Sr-ca-sp-vgrp.uspp.format.UPF
>  Ti  47.90   022-Ti-ca-sp-vgrp.uspp.format.UPF
>  O   16.00   008-O-ca--vgrp.uspp.format.UPF
> ATOMIC_POSITIONS alat
>  Sr 0.00 0.00 0.00
>  O  0.50 0.50 0.00
>  Ti 0.50 0.50 0.50
>  O  0.00 0.50 0.50
>  O  0.50 0.00 0.50
>  Sr 0.00 0.00 1.00
>  O  0.50 0.50 1.00
>  Ti 0.50 0.50 1.50
>  O  0.00 0.50 1.50
>  O  0.50 0.00 1.50
>  Sr 0.00 0.00 2.00
>  O  0.50 0.50 2.00
>  Ti 0.50 0.50 2.50
>  O  0.00 0.50 2.50
>  O  0.50 0.00 2.50
>  Sr 0.00 0.00 3.00
>  O  0.50 0.50 3.00
>  Ti 0.50 0.50 3.50
>  O  0.00 0.50 3.50
>  O  0.50 0.00 3.50
>  Sr 0.00 0.00 4.00
>  O  0.50 0.50 4.00
>  Ti 0.50 0.50 4.50
>  O  0.00 0.50 4.50
>  O  0.50 0.00 4.50
>  Sr 0.00 0.00 5.00
>  O  0.50 0.50 5.00
> K_POINTS {automatic}
> 8 8 1 0 0 0
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From zdw2000 at gmail.com  Sat Oct  4 15:22:18 2008
From: zdw2000 at gmail.com (Wei Zhou)
Date: Sat, 4 Oct 2008 21:22:18 +0800
Subject: [Pw_forum] about the number of Projectors in uspp
Message-ID: <3e36a8fc0810040622l1c336130hf1c734f949af246d@mail.gmail.com>

dear all users
              I feel puzzled about the number of Projectors in uspp , how
this value is determine.
any help will be appreciated.


-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From paulatto at sissa.it  Sat Oct  4 17:15:50 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 4 Oct 2008 17:15:50 +0200 (CEST)
Subject: [Pw_forum] about the number of Projectors in uspp
In-Reply-To: <3e36a8fc0810040622l1c336130hf1c734f949af246d@mail.gmail.com>
References: <3e36a8fc0810040622l1c336130hf1c734f949af246d@mail.gmail.com>
Message-ID: <19596.82.50.174.28.1223133350.squirrel@webmail.sissa.it>

Wei Zhou ha scritto:
> dear all users
>               I feel puzzled about the number of Projectors in uspp ,
how this value is determine.

Dear Wei Zhou,
the number of projectors is chosen arbitrarily by the psudopotential
author in order to trade off accuracy and efficiency. Usually you take two
projectors per each ultrasoft wavefunction and only one for
norm-conserving ones (they can coexist in the same pseudo).

More projectors are added only in some specific cases, as far as I know
for reproducing more accurately high-energy (normally empty) bands.

regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/




----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From manoj at phys.ufl.edu  Sat Oct  4 19:08:24 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Sat, 4 Oct 2008 13:08:24 -0400 (EDT)
Subject: [Pw_forum] some querries about pwcond
In-Reply-To: <354987.95024.qm@web94608.mail.in2.yahoo.com>
Message-ID: <Pine.GSO.4.21.0810041250370.22000-100000@neptune.phys.ufl.edu>

Dear Sagar, 
 i am attempting to answer one of the questions raised by you. I am not
entirely sure about the answer, I am just telling you what i have
understood and i am hoping somebody in the forum could correct me, if I am
wrong. 

On Sat, 4 Oct 2008, ambavale sagar wrote:

> Dear all,
> I have some queries about pwcond input file.
> 
> 1.how k-perpendicular points are defined. (can you give any example except 'number of k-perpendicular points = 1' used in example 12) 
> 2. How weight is defined here for k-points? maximum weight?
  
 If the number of K point is one. You can choose any weight you like, it
normalizes to one. if you look at the file do_cond.f90 under PWCOND, you
would get the idea. I have never done any calculation with more than 1
k point, so i have not thought about that yet. 
 > 3.how ecut2D (2-D cut off) it effects the calculation. >
 
  ecut2D determines how many 2D reciprocal space vectors (G) (ngper)you
will be using in the calculation,|G+k|^2<ecut2d. So, yourc alcultion would
depend on the cutoff, but once a you have chosen high enough cutoff for
energy, so that you have enough Gper, choosing higher cutoff should not
change calculation much. Have a look at init_gper.f90 file for more
details.
 
Regards, 
Manoj Srivastava 
Ph.D. Student 
Department of Physics
University of Florida 
Gainesville, FL 
USA

> Best regards
> Sagar Ambavale
> Research student
> The M.S. University of Baroda
> 
> 
> 


      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/


From jgrz2010 at yahoo.com.mx  Sun Oct  5 03:00:59 2008
From: jgrz2010 at yahoo.com.mx (JAIME GUSTAVO RODRIGUEZ ZAVALA)
Date: Sat, 4 Oct 2008 18:00:59 -0700 (PDT)
Subject: [Pw_forum] pseudopotential for Gd
Message-ID: <280254.67509.qm@web34208.mail.mud.yahoo.com>

Hello every one, 

I?m trying to do some tests of fullerenes containing an encapsulated Gd atom. 
Does anybody has a pseudopotential for Gd?

Thank you very much for all the help you can provide!

Best regards.

 


      ?Todo sobre Amor y Sexo!
La gu?a completa para tu vida en Mujer de Hoy.                       
http://mx.mujer.yahoo.com/

From zdw2000 at gmail.com  Sun Oct  5 03:16:58 2008
From: zdw2000 at gmail.com (Wei Zhou)
Date: Sun, 5 Oct 2008 09:16:58 +0800
Subject: [Pw_forum] about the number of Projectors in uspp
In-Reply-To: <19596.82.50.174.28.1223133350.squirrel@webmail.sissa.it>
References: <3e36a8fc0810040622l1c336130hf1c734f949af246d@mail.gmail.com>
	<19596.82.50.174.28.1223133350.squirrel@webmail.sissa.it>
Message-ID: <3e36a8fc0810041816i7e48a10enea84aa508fe27749@mail.gmail.com>

thank  your for you reply in detais , best wishes

2008/10/4 Lorenzo Paulatto <paulatto at sissa.it>

> Wei Zhou ha scritto:
> > dear all users
> >               I feel puzzled about the number of Projectors in uspp ,
> how this value is determine.
>
> Dear Wei Zhou,
> the number of projectors is chosen arbitrarily by the psudopotential
> author in order to trade off accuracy and efficiency. Usually you take two
> projectors per each ultrasoft wavefunction and only one for
> norm-conserving ones (they can coexist in the same pseudo).
>
> More projectors are added only in some specific cases, as far as I know
> for reproducing more accurately high-energy (normally empty) bands.
>
> regards
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>
>
>
> ----------------------------------------------------------------
>  SISSA Webmail https://webmail.sissa.it/
>  Powered by SquirrelMail http://www.squirrelmail.org/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From willykohn at gmail.com  Sun Oct  5 03:24:43 2008
From: willykohn at gmail.com (willy kohn)
Date: Sat, 4 Oct 2008 21:24:43 -0400
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
In-Reply-To: <48E5C327.6060200@sissa.it>
References: <8a1b6d820810020852k1b96aea1q4d713da43e0ceb66@mail.gmail.com>
	<Pine.LNX.4.64.0810021148450.18122@localhost.localdomain>
	<8a1b6d820810020920h132e2a68i655fb941091be0af@mail.gmail.com>
	<Pine.LNX.4.64.0810021401580.18122@localhost.localdomain>
	<8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>
	<48E5C327.6060200@sissa.it>
Message-ID: <8a1b6d820810041824y534a2aa7lcf0e4691a47c0448@mail.gmail.com>

Hi, Stefano:
Many thanks for the literature you brought up. That's what I'm looking for.

Best,

Wei


On Fri, Oct 3, 2008 at 3:00 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>
> I don't know the details of the generation of  this particular PP but in
> the old good times there has been a very detailed comparison of LDA band
> structure calculation of Ge and GaAs between the PP method and LMTO [GB
> Bachelet and NE Christensen, Phys.Rev.B 31, 879 (1985) ].
> The main result is that in order to get the correct (bad) gap in Ge and
> GaAs  1) scalar relativistic, 2) spin-orbit coupling, 3) 3d-state
> relaxation
> are important... not to mention convergence w.r.t. to cutoff ...
>
> Hope  this helps,
>
>  Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> willy kohn wrote:
> > Hi, Axel:
> >
> > Well, I didn't blame the PP, and I didn't mean to. My question is
> > quite simple. I was told that with a LDA PP, Ge has a vanishing or
> > negative band gap at Gamma point. But with this PP, it has a gap of
> > 0.50 eV (using experimental lattice) or 0.80 eV (after relaxation).
> > I'm not sure what I knew is correct, and that is the reason I wanted
> > another PP to verify.
> >
> > Best,
> >
> > Wei
> >
> > On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
> > <akohlmey at cmm.chem.upenn.edu <mailto:akohlmey at cmm.chem.upenn.edu>>
> wrote:
> >
> >     On Thu, 2 Oct 2008, willy kohn wrote:
> >
> >     WK> Hi, Axel:
> >     WK>
> >     WK> Thanks a lot for your quick answer. I need to do some
> >     calculations on some
> >     WK> compound semiconductors of Ge. But the PP (Ge.pz-bhs.UPF)
> >     provided in the
> >     WK> PWSCF website yeided some results that I don't understand. So
> >     I would like
> >
> >     perhaps it would be useful to explain in more detail what
> >     is confusing you and what calculation you did with what input.
> >     perhaps some people here can comment on it. it is always easy
> >     to blame the pseudopotential (sometimes rightfully so), but
> >     more often than not, the real cause is in not doing a calculation
> >     correctly, or not using a pseudopotential correct.
> >
> >     WK> to use some other PP's to check if I did the calculation
> >     correctly. Any
> >     WK> suggestions?
> >
> >     i have a set of Ge pseudopotentials generated from parameters
> >     for a norm-conserving troullier-martins potential that is in
> >     the extended CPMD psp library. they have seen only very minimal
> >     transferability testing (using an atomic code in bessel basis),
> >     but so far seem to be ok, except for the OLYP one which has a
> >     ghost in the s-channel.
> >
> >     i can send them to you in a private mail, if you are interested.
> >     no guarantees etc...
> >
> >     cheers,
> >       axel.
> >
> >     WK>
> >     WK> Best,
> >     WK>
> >     WK> Wei
> >     WK>
> >     WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer
> >     <akohlmey at cmm.chem.upenn.edu <mailto:akohlmey at cmm.chem.upenn.edu>
> >     WK> > wrote:
> >     WK>
> >     WK> > On Thu, 2 Oct 2008, willy kohn wrote:
> >     WK> >
> >     WK> > WK> Dear PWSCF users:
> >     WK> > WK>
> >     WK> > WK> I have a quick question about using
> >     WK> > WK> Hartwigsen-Goedeker-Hutter<
> >     WK> >
> >
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> >     WK> > >pseudopotential
> >     WK> > WK> with PWSCF. Is there any converter to transfer the HGH pp
> >     WK> > WK> format to UPF used in PWSCF?
> >     WK> >
> >     WK> > none that i am aware of.
> >     WK> >
> >     WK> > the GTH pseudopotentials are analytical in real and reciprocal
> >     WK> > space and to incorporate them properly, one would have to do a
> >     WK> > lot of programming. in the CPMD code (from http://www.cpmd.org
> )
> >     WK> > they are treated as a special case, similar to ultra-soft psps.
> >     WK> >
> >     WK> > is there any particularly reason you'd need any of those?
> >     WK> >
> >     WK> > cheers,
> >     WK> >   axel.
> >     WK> >
> >     WK> >
> >     WK> > WK>
> >     WK> > WK> Best,
> >     WK> > WK>
> >     WK> > WK> Wei
> >     WK> > WK>
> >     WK> > WK> Georgia Tech
> >     WK> > WK>
> >     WK> >
> >     WK> > --
> >     WK> >
> >
> =======================================================================
> >     WK> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
> >     <mailto:akohlmey at cmm.chem.upenn.edu>   http://www.cmm.upenn.edu
> >     WK> >   Center for Molecular Modeling   --   University of
> >     Pennsylvania
> >     WK> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> >     19104-6323
> >     WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
> >     1-215-898-5425
> >     WK> >
> >
> =======================================================================
> >     WK> > If you make something idiot-proof, the universe creates a
> >     better idiot.
> >     WK> >
> >     WK>
> >
> >     --
> >
> =======================================================================
> >     Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
> >     <mailto:akohlmey at cmm.chem.upenn.edu>   http://www.cmm.upenn.edu
> >       Center for Molecular Modeling   --   University of Pennsylvania
> >     Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> >     19104-6323
> >     tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
> 1-215-898-5425
> >
> =======================================================================
> >     If you make something idiot-proof, the universe creates a better
> >     idiot.
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From willykohn at gmail.com  Sun Oct  5 03:33:41 2008
From: willykohn at gmail.com (willy kohn)
Date: Sat, 4 Oct 2008 21:33:41 -0400
Subject: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
	pseudopotential
In-Reply-To: <958267.94779.qm@web65715.mail.ac4.yahoo.com>
References: <8a1b6d820810021354h5778d99av2babfadf6971c9d0@mail.gmail.com>
	<958267.94779.qm@web65715.mail.ac4.yahoo.com>
Message-ID: <8a1b6d820810041833p50edf4f9tbe47f1d58c518bc0@mail.gmail.com>

Dear Eyvaz:
Thank you for your long reply. What you mentioned was correct. I didn't
expect LDA PP's can gave me a good prediction to the band gap and in fact
the band gap given by the PP is closer to the experimental data than other
PP's. What I would like to know is what value for Ge is 'typical' or
'normal' for a LDA PP.

Best,

Wei

On Thu, Oct 2, 2008 at 7:10 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Dear Willy,
>
> --- On Fri, 10/3/08, willy kohn <willykohn at gmail.com> wrote:
>
> > I was told that with a LDA PP, Ge has a vanishing
> > or negative band gap at Gamma point. But with this PP, > it has a gap of
> 0.50eV (using experimental lattice) or
> > 0.80 eV (after relaxation).
>
> Please recall that we use the Density Functional Theory, that is the theory
> of the ground state, and it is not obliged to give correct excitation
> energies in semiconductors. Besides, we apply the Local Density
> Approximation which underestimates the band gap, even gives negative band
> gap in Ge. This is well known fact. The source of this fault is the use of
> single-particle Shrodinger equation, but the use of the quasiparticle
> equation with the self-energy operator is more correct. There are few
> recipes how to deal with this equation. The so called GW method is among
> them.
>
> Another point is proper account of exchange-correlation interactions. It is
> well known that the use of the functionals like PBE0, B3LYP gives improved
> results for insulating systems concerning their electronic structure. For
> the reference please have a look at /examples-EXX (for Si).
>
> So, if the HGH pseudopotentials are used in the framework of the DFT-LDA,
> unlikely they can give correct band gap due to the fault of the underlying
> method.
> Even all-electron methods within the LDA fail to predict the band gap (as
> example see PHYSICAL REVIEW B 67, 155208 2003).
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>
>
>
>
> > I'm not sure what I
> > knew is correct, and that is the reason I wanted another PP
> > to verify.
> >
> > Best,
> >
> > Wei
> >
> >
> >
> > On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
> > <akohlmey at cmm.chem.upenn.edu>wrote:
> >
> > > On Thu, 2 Oct 2008, willy kohn wrote:
> > >
> > > WK> Hi, Axel:
> > > WK>
> > > WK> Thanks a lot for your quick answer. I need to
> > do some calculations on
> > > some
> > > WK> compound semiconductors of Ge. But the PP
> > (Ge.pz-bhs.UPF) provided in
> > > the
> > > WK> PWSCF website yeided some results that I
> > don't understand. So I would
> > > like
> > >
> > > perhaps it would be useful to explain in more detail
> > what
> > > is confusing you and what calculation you did with
> > what input.
> > > perhaps some people here can comment on it. it is
> > always easy
> > > to blame the pseudopotential (sometimes rightfully
> > so), but
> > > more often than not, the real cause is in not doing a
> > calculation
> > > correctly, or not using a pseudopotential correct.
> > >
> > > WK> to use some other PP's to check if I did
> > the calculation correctly. Any
> > > WK> suggestions?
> > >
> > > i have a set of Ge pseudopotentials generated from
> > parameters
> > > for a norm-conserving troullier-martins potential that
> > is in
> > > the extended CPMD psp library. they have seen only
> > very minimal
> > > transferability testing (using an atomic code in
> > bessel basis),
> > > but so far seem to be ok, except for the OLYP one
> > which has a
> > > ghost in the s-channel.
> > >
> > > i can send them to you in a private mail, if you are
> > interested.
> > > no guarantees etc...
> > >
> > > cheers,
> > >   axel.
> > >
> > > WK>
> > > WK> Best,
> > > WK>
> > > WK> Wei
> > > WK>
> > > WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel Kohlmeyer
> > <
> > > akohlmey at cmm.chem.upenn.edu
> > > WK> > wrote:
> > > WK>
> > > WK> > On Thu, 2 Oct 2008, willy kohn wrote:
> > > WK> >
> > > WK> > WK> Dear PWSCF users:
> > > WK> > WK>
> > > WK> > WK> I have a quick question about using
> > > WK> > WK> Hartwigsen-Goedeker-Hutter<
> > > WK> >
> > >
> >
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> > > WK> > >pseudopotential
> > > WK> > WK> with PWSCF. Is there any converter
> > to transfer the HGH pp
> > > WK> > WK> format to UPF used in PWSCF?
> > > WK> >
> > > WK> > none that i am aware of.
> > > WK> >
> > > WK> > the GTH pseudopotentials are analytical in
> > real and reciprocal
> > > WK> > space and to incorporate them properly,
> > one would have to do a
> > > WK> > lot of programming. in the CPMD code (from
> > http://www.cpmd.org)
> > > WK> > they are treated as a special case,
> > similar to ultra-soft psps.
> > > WK> >
> > > WK> > is there any particularly reason you'd
> > need any of those?
> > > WK> >
> > > WK> > cheers,
> > > WK> >   axel.
> > > WK> >
> > > WK> >
> > > WK> > WK>
> > > WK> > WK> Best,
> > > WK> > WK>
> > > WK> > WK> Wei
> > > WK> > WK>
> > > WK> > WK> Georgia Tech
> > > WK> > WK>
> > > WK> >
> > > WK> > --
> > > WK> >
> > >
> > =======================================================================
> > > WK> > Axel Kohlmeyer
> > akohlmey at cmm.chem.upenn.edu
> > > http://www.cmm.upenn.edu
> > > WK> >   Center for Molecular Modeling   --
> > University of Pennsylvania
> > > WK> > Department of Chemistry, 231 S.34th
> > Street, Philadelphia, PA
> > > 19104-6323
> > > WK> > tel: 1-215-898-1582,  fax: 1-215-573-6233,
> >  office-tel:
> > > 1-215-898-5425
> > > WK> >
> > >
> > =======================================================================
> > > WK> > If you make something idiot-proof, the
> > universe creates a better
> > > idiot.
> > > WK> >
> > > WK>
> > >
> > > --
> > >
> > =======================================================================
> > > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > >   Center for Molecular Modeling   --   University of
> > Pennsylvania
> > > Department of Chemistry, 231 S.34th Street,
> > Philadelphia, PA 19104-6323
> > > tel: 1-215-898-1582,  fax: 1-215-573-6233,
> > office-tel: 1-215-898-5425
> > >
> > =======================================================================
> > > If you make something idiot-proof, the universe
> > creates a better idiot.
> > >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From mansourehp at gmail.com  Sun Oct  5 08:37:45 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Sun, 5 Oct 2008 10:07:45 +0330
Subject: [Pw_forum] file.xml
Message-ID: <cbe1626b0810042337v3c227508x8e954e479a6554ee@mail.gmail.com>

Dear all
How can I plot a file with xml format?
good luck
Mansoureh
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From eyvaz_isaev at yahoo.com  Sun Oct  5 13:46:05 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 5 Oct 2008 04:46:05 -0700 (PDT)
Subject: [Pw_forum]  k-points mismatch
In-Reply-To: <8a1b6d820810041833p50edf4f9tbe47f1d58c518bc0@mail.gmail.com>
Message-ID: <829678.87709.qm@web65715.mail.ac4.yahoo.com>

Dear developers,

I have observed a mismatch between k-points generated 
by means of kpoints.x and phonons program, ph.x.

The problem is that first I did phonon calculations for a base centered orthorhombic cell (ibrav=9) using 4x2x2 mesh (10 q-points) and got an error message from q2r.x "q not allowed".
Well, something is wrong with the q-points. 
Then I tried to generate q-points using kpoints.x which stated that 4x2x2 mesh "has not the correct symmetry" and gave only 6 q-points.
OK, I used 4x3x3 to generate q-points and got 10 q-points without any message from kpoints.x.
But when I started phonons with 4x3x3 q-mesh, the ph.x program generated 14 q-points.

Can someone explain such kind discrepancy between two programs generating q-points? I used c/a=1.720447
and b/a=1.857204.

Bests,
Eyvaz. 
  

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Sun, 10/5/08, willy kohn <willykohn at gmail.com> wrote:

> From: willy kohn <willykohn at gmail.com>
> Subject: Re: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter pseudopotential
> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Sunday, October 5, 2008, 5:33 AM
> Dear Eyvaz:
> Thank you for your long reply. What you mentioned was
> correct. I didn't
> expect LDA PP's can gave me a good prediction to the
> band gap and in fact
> the band gap given by the PP is closer to the experimental
> data than other
> PP's. What I would like to know is what value for Ge is
> 'typical' or
> 'normal' for a LDA PP.
> 
> Best,
> 
> Wei
> 
> On Thu, Oct 2, 2008 at 7:10 PM, Eyvaz Isaev
> <eyvaz_isaev at yahoo.com> wrote:
> 
> > Dear Willy,
> >
> > --- On Fri, 10/3/08, willy kohn
> <willykohn at gmail.com> wrote:
> >
> > > I was told that with a LDA PP, Ge has a vanishing
> > > or negative band gap at Gamma point. But with
> this PP, > it has a gap of
> > 0.50eV (using experimental lattice) or
> > > 0.80 eV (after relaxation).
> >
> > Please recall that we use the Density Functional
> Theory, that is the theory
> > of the ground state, and it is not obliged to give
> correct excitation
> > energies in semiconductors. Besides, we apply the
> Local Density
> > Approximation which underestimates the band gap, even
> gives negative band
> > gap in Ge. This is well known fact. The source of this
> fault is the use of
> > single-particle Shrodinger equation, but the use of
> the quasiparticle
> > equation with the self-energy operator is more
> correct. There are few
> > recipes how to deal with this equation. The so called
> GW method is among
> > them.
> >
> > Another point is proper account of
> exchange-correlation interactions. It is
> > well known that the use of the functionals like PBE0,
> B3LYP gives improved
> > results for insulating systems concerning their
> electronic structure. For
> > the reference please have a look at /examples-EXX (for
> Si).
> >
> > So, if the HGH pseudopotentials are used in the
> framework of the DFT-LDA,
> > unlikely they can give correct band gap due to the
> fault of the underlying
> > method.
> > Even all-electron methods within the LDA fail to
> predict the band gap (as
> > example see PHYSICAL REVIEW B 67, 155208 2003).
> >
> > Bests,
> > Eyvaz.
> >
> >
> -------------------------------------------------------------------
> > Prof. Eyvaz Isaev,
> > Theoretical Physics Department, Moscow State Institute
> of Steel & Alloys,
> > Russia,
> > Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University,
> > Sweden
> > Condensed Matter Theory Group, Uppsala University,
> Sweden
> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com
> >
> >
> >
> >
> >
> >
> > > I'm not sure what I
> > > knew is correct, and that is the reason I wanted
> another PP
> > > to verify.
> > >
> > > Best,
> > >
> > > Wei
> > >
> > >
> > >
> > > On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
> > > <akohlmey at cmm.chem.upenn.edu>wrote:
> > >
> > > > On Thu, 2 Oct 2008, willy kohn wrote:
> > > >
> > > > WK> Hi, Axel:
> > > > WK>
> > > > WK> Thanks a lot for your quick answer. I
> need to
> > > do some calculations on
> > > > some
> > > > WK> compound semiconductors of Ge. But
> the PP
> > > (Ge.pz-bhs.UPF) provided in
> > > > the
> > > > WK> PWSCF website yeided some results
> that I
> > > don't understand. So I would
> > > > like
> > > >
> > > > perhaps it would be useful to explain in
> more detail
> > > what
> > > > is confusing you and what calculation you
> did with
> > > what input.
> > > > perhaps some people here can comment on it.
> it is
> > > always easy
> > > > to blame the pseudopotential (sometimes
> rightfully
> > > so), but
> > > > more often than not, the real cause is in
> not doing a
> > > calculation
> > > > correctly, or not using a pseudopotential
> correct.
> > > >
> > > > WK> to use some other PP's to check
> if I did
> > > the calculation correctly. Any
> > > > WK> suggestions?
> > > >
> > > > i have a set of Ge pseudopotentials
> generated from
> > > parameters
> > > > for a norm-conserving troullier-martins
> potential that
> > > is in
> > > > the extended CPMD psp library. they have
> seen only
> > > very minimal
> > > > transferability testing (using an atomic
> code in
> > > bessel basis),
> > > > but so far seem to be ok, except for the
> OLYP one
> > > which has a
> > > > ghost in the s-channel.
> > > >
> > > > i can send them to you in a private mail, if
> you are
> > > interested.
> > > > no guarantees etc...
> > > >
> > > > cheers,
> > > >   axel.
> > > >
> > > > WK>
> > > > WK> Best,
> > > > WK>
> > > > WK> Wei
> > > > WK>
> > > > WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel
> Kohlmeyer
> > > <
> > > > akohlmey at cmm.chem.upenn.edu
> > > > WK> > wrote:
> > > > WK>
> > > > WK> > On Thu, 2 Oct 2008, willy kohn
> wrote:
> > > > WK> >
> > > > WK> > WK> Dear PWSCF users:
> > > > WK> > WK>
> > > > WK> > WK> I have a quick question
> about using
> > > > WK> > WK>
> Hartwigsen-Goedeker-Hutter<
> > > > WK> >
> > > >
> > >
> >
> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
> > > > WK> > >pseudopotential
> > > > WK> > WK> with PWSCF. Is there any
> converter
> > > to transfer the HGH pp
> > > > WK> > WK> format to UPF used in
> PWSCF?
> > > > WK> >
> > > > WK> > none that i am aware of.
> > > > WK> >
> > > > WK> > the GTH pseudopotentials are
> analytical in
> > > real and reciprocal
> > > > WK> > space and to incorporate them
> properly,
> > > one would have to do a
> > > > WK> > lot of programming. in the CPMD
> code (from
> > > http://www.cpmd.org)
> > > > WK> > they are treated as a special
> case,
> > > similar to ultra-soft psps.
> > > > WK> >
> > > > WK> > is there any particularly reason
> you'd
> > > need any of those?
> > > > WK> >
> > > > WK> > cheers,
> > > > WK> >   axel.
> > > > WK> >
> > > > WK> >
> > > > WK> > WK>
> > > > WK> > WK> Best,
> > > > WK> > WK>
> > > > WK> > WK> Wei
> > > > WK> > WK>
> > > > WK> > WK> Georgia Tech
> > > > WK> > WK>
> > > > WK> >
> > > > WK> > --
> > > > WK> >
> > > >
> > >
> =======================================================================
> > > > WK> > Axel Kohlmeyer
> > > akohlmey at cmm.chem.upenn.edu
> > > > http://www.cmm.upenn.edu
> > > > WK> >   Center for Molecular Modeling 
>  --
> > > University of Pennsylvania
> > > > WK> > Department of Chemistry, 231
> S.34th
> > > Street, Philadelphia, PA
> > > > 19104-6323
> > > > WK> > tel: 1-215-898-1582,  fax:
> 1-215-573-6233,
> > >  office-tel:
> > > > 1-215-898-5425
> > > > WK> >
> > > >
> > >
> =======================================================================
> > > > WK> > If you make something
> idiot-proof, the
> > > universe creates a better
> > > > idiot.
> > > > WK> >
> > > > WK>
> > > >
> > > > --
> > > >
> > >
> =======================================================================
> > > > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
> > > http://www.cmm.upenn.edu
> > > >   Center for Molecular Modeling   --  
> University of
> > > Pennsylvania
> > > > Department of Chemistry, 231 S.34th Street,
> > > Philadelphia, PA 19104-6323
> > > > tel: 1-215-898-1582,  fax: 1-215-573-6233,
> > > office-tel: 1-215-898-5425
> > > >
> > >
> =======================================================================
> > > > If you make something idiot-proof, the
> universe
> > > creates a better idiot.
> > > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > >
> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From eyvaz_isaev at yahoo.com  Sun Oct  5 13:49:04 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 5 Oct 2008 04:49:04 -0700 (PDT)
Subject: [Pw_forum] Sorry
Message-ID: <34891.93876.qm@web65706.mail.ac4.yahoo.com>

Sorry, I was not so careful, I did not clean the previous message at the end of my mail.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


      

From paulatto at sissa.it  Mon Oct  6 00:45:14 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 6 Oct 2008 00:45:14 +0200 (CEST)
Subject: [Pw_forum] file.xml
In-Reply-To: <cbe1626b0810042337v3c227508x8e954e479a6554ee@mail.gmail.com>
References: <cbe1626b0810042337v3c227508x8e954e479a6554ee@mail.gmail.com>
Message-ID: <21803.82.50.174.28.1223246714.squirrel@webmail.sissa.it>


On Dom, Ottobre 5, 2008 08:37, Mansoureh Pashangpour wrote:
>  Dear all
>  How can I plot a file with xml format?

Dear Mansoureh,
you cannot plot them, they internal files in unsuitable format. Please
read pp.x documentation instead, you'll find it in the Doc directory.
There are also a few examples covering various kinds of plot.

regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From giannozz at democritos.it  Mon Oct  6 08:40:43 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 06 Oct 2008 08:40:43 +0200
Subject: [Pw_forum] pseudopotential for Gd
In-Reply-To: <280254.67509.qm@web34208.mail.mud.yahoo.com>
References: <280254.67509.qm@web34208.mail.mud.yahoo.com>
Message-ID: <48E9B2EB.6070204@democritos.it>

JAIME GUSTAVO RODRIGUEZ ZAVALA wrote:

> I?m trying to do some tests of fullerenes containing an encapsulated 
> Gd atom. Does anybody has a pseudopotential for Gd?

excerpt from a message I sent some time ago:
---
as I already mentioned several times in this forum: the problem with
such elements [rare earths] is not only the pseudopotential (which IS
anyway a problem: generating ultrasoft PP's for those elements is a
full-time job) but the reliability of the current DFT approximations.
---

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From sagarambavale at yahoo.co.in  Mon Oct  6 08:45:39 2008
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Mon, 6 Oct 2008 12:15:39 +0530 (IST)
Subject: [Pw_forum] some querries about pwcond
In-Reply-To: <Pine.GSO.4.21.0810041250370.22000-100000@neptune.phys.ufl.edu>
Message-ID: <939192.22386.qm@web94613.mail.in2.yahoo.com>

Dear Manoj,
Thank you very much. I will try to understand both f90 files. And contact you as any query arise again..
Best regards
Sagar Ambavale
Research student
The M.S. University of Baroda
India


--- On Sat, 4/10/08, Manoj Srivastava <manoj at phys.ufl.edu> wrote:
From: Manoj Srivastava <manoj at phys.querries about pwcond
To: "ambavale sagar" <sagarambavaleufl.edu>
Subject: Re: [Pw_forum] some @yahoo.co.in>
Cc: "pwforum que-ans" <pw_forum at pwscf.org>
Date: Saturday, 4 October, 2008, 10:38 PM

Dear Sagar, 
 i am attempting to answer one of the questions raised by you. I am not
entirely sure about the answer, I am just telling you what i have
understood and i am hoping somebody in the forum could correct me, if I am
wrong. 

On Sat, 4 Oct 2008, ambavale sagar wrote:

> Dear all,
> I have some queries about pwcond input file.
> 
> 1.how k-perpendicular points are defined. (can you give any example except
'number of k-perpendicular points = 1' used in example 12) 
> 2. How weight is defined here for k-points? maximum weight?
  
 If the number of K point is one. You can choose any weight you like, it
normalizes to one. if you look at the file do_cond.f90 under PWCOND, you
would get the idea. I have never done any calculation with more than 1
k point, so i have not thought about that yet. 
 > 3.how ecut2D (2-D cut off) it effects the calculation. >
 
  ecut2D determines how many 2D reciprocal space vectors (G) (ngper)you
will be using in the calculation,|G+k|^2<ecut2d. So, yourc alcultion would
depend on the cutoff, but once a you have chosen high enough cutoff for
energy, so that you have enough Gper, choosing higher cutoff should not
change calculation much. Have a look at init_gper.f90 file for more
details.
 
Regards, 
Manoj Srivastava 
Ph.D. Student 
Department of Physics
University of Florida 
Gainesville, FL 
USA

> Best regards
> Sagar Ambavale
> Research student
> The M.S. University of Baroda
> 
> 
> 


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From arunmanna at jncasr.ac.in  Mon Oct  6 10:54:22 2008
From: arunmanna at jncasr.ac.in (Arun Kumar Manna)
Date: Mon, 6 Oct 2008 12:54:22 +0400 (RET)
Subject: [Pw_forum] problem with ram.x
In-Reply-To: <mailman.1.1223274770.18059.pw_forum@pwscf.org>
References: <mailman.1.1223274770.18059.pw_forum@pwscf.org>
Message-ID: <52391.172.16.1.1.1223283262.squirrel@172.16.1.1>


 Dear All,
 Could anyone please help me regarding how to use ram.x executable to
 calculate raman tensors?.
 Actually, in the example15, it is given but I didn't find the ram.x
 executable after successful installation of the package.

 Thanks,
 Arun




> Send Pw_forum mailing list submissions to
> 	pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
> 	pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
> 	pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. file.xml (Mansoureh Pashangpour)
>    2.  k-points mismatch (Eyvaz Isaev)
>    3. Sorry (Eyvaz Isaev)
>    4. Re: file.xml (Lorenzo Paulatto)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 5 Oct 2008 10:07:45 +0330
> From: "Mansoureh Pashangpour" <mansourehp at gmail.com>
> Subject: [Pw_forum] file.xml
> To: Pw_forum at pwscf.org
> Message-ID:
> 	<cbe1626b0810042337v3c227508x8e954e479a6554ee at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all
> How can I plot a file with xml format?
> good luck
> Mansoureh
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.democritos.it/pipermail/pw_forum/attachments/20081005/0be70685/attachment.html
>
> ------------------------------
>
> Message: 2
> Date: Sun, 5 Oct 2008 04:46:05 -0700 (PDT)
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: [Pw_forum]  k-points mismatch
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <829678.87709.qm at web65715.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear developers,
>
> I have observed a mismatch between k-points generated
> by means of kpoints.x and phonons program, ph.x.
>
> The problem is that first I did phonon calculations for a base centered
> orthorhombic cell (ibrav=9) using 4x2x2 mesh (10 q-points) and got an
> error message from q2r.x "q not allowed".
> Well, something is wrong with the q-points.
> Then I tried to generate q-points using kpoints.x which stated that 4x2x2
> mesh "has not the correct symmetry" and gave only 6 q-points.
> OK, I used 4x3x3 to generate q-points and got 10 q-points without any
> message from kpoints.x.
> But when I started phonons with 4x3x3 q-mesh, the ph.x program generated
> 14 q-points.
>
> Can someone explain such kind discrepancy between two programs generating
> q-points? I used c/a=1.720447
> and b/a=1.857204.
>
> Bests,
> Eyvaz.
>
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Sun, 10/5/08, willy kohn <willykohn at gmail.com> wrote:
>
>> From: willy kohn <willykohn at gmail.com>
>> Subject: Re: [Pw_forum] Quick question on Hartwigsen-Goedeker-Hutter
>> pseudopotential
>> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
>> Date: Sunday, October 5, 2008, 5:33 AM
>> Dear Eyvaz:
>> Thank you for your long reply. What you mentioned was
>> correct. I didn't
>> expect LDA PP's can gave me a good prediction to the
>> band gap and in fact
>> the band gap given by the PP is closer to the experimental
>> data than other
>> PP's. What I would like to know is what value for Ge is
>> 'typical' or
>> 'normal' for a LDA PP.
>>
>> Best,
>>
>> Wei
>>
>> On Thu, Oct 2, 2008 at 7:10 PM, Eyvaz Isaev
>> <eyvaz_isaev at yahoo.com> wrote:
>>
>> > Dear Willy,
>> >
>> > --- On Fri, 10/3/08, willy kohn
>> <willykohn at gmail.com> wrote:
>> >
>> > > I was told that with a LDA PP, Ge has a vanishing
>> > > or negative band gap at Gamma point. But with
>> this PP, > it has a gap of
>> > 0.50eV (using experimental lattice) or
>> > > 0.80 eV (after relaxation).
>> >
>> > Please recall that we use the Density Functional
>> Theory, that is the theory
>> > of the ground state, and it is not obliged to give
>> correct excitation
>> > energies in semiconductors. Besides, we apply the
>> Local Density
>> > Approximation which underestimates the band gap, even
>> gives negative band
>> > gap in Ge. This is well known fact. The source of this
>> fault is the use of
>> > single-particle Shrodinger equation, but the use of
>> the quasiparticle
>> > equation with the self-energy operator is more
>> correct. There are few
>> > recipes how to deal with this equation. The so called
>> GW method is among
>> > them.
>> >
>> > Another point is proper account of
>> exchange-correlation interactions. It is
>> > well known that the use of the functionals like PBE0,
>> B3LYP gives improved
>> > results for insulating systems concerning their
>> electronic structure. For
>> > the reference please have a look at /examples-EXX (for
>> Si).
>> >
>> > So, if the HGH pseudopotentials are used in the
>> framework of the DFT-LDA,
>> > unlikely they can give correct band gap due to the
>> fault of the underlying
>> > method.
>> > Even all-electron methods within the LDA fail to
>> predict the band gap (as
>> > example see PHYSICAL REVIEW B 67, 155208 2003).
>> >
>> > Bests,
>> > Eyvaz.
>> >
>> >
>> -------------------------------------------------------------------
>> > Prof. Eyvaz Isaev,
>> > Theoretical Physics Department, Moscow State Institute
>> of Steel & Alloys,
>> > Russia,
>> > Department of Physics, Chemistry, and Biology (IFM),
>> Linkoping University,
>> > Sweden
>> > Condensed Matter Theory Group, Uppsala University,
>> Sweden
>> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
>> eyvaz_isaev at yahoo.com
>> >
>> >
>> >
>> >
>> >
>> >
>> > > I'm not sure what I
>> > > knew is correct, and that is the reason I wanted
>> another PP
>> > > to verify.
>> > >
>> > > Best,
>> > >
>> > > Wei
>> > >
>> > >
>> > >
>> > > On Thu, Oct 2, 2008 at 2:12 PM, Axel Kohlmeyer
>> > > <akohlmey at cmm.chem.upenn.edu>wrote:
>> > >
>> > > > On Thu, 2 Oct 2008, willy kohn wrote:
>> > > >
>> > > > WK> Hi, Axel:
>> > > > WK>
>> > > > WK> Thanks a lot for your quick answer. I
>> need to
>> > > do some calculations on
>> > > > some
>> > > > WK> compound semiconductors of Ge. But
>> the PP
>> > > (Ge.pz-bhs.UPF) provided in
>> > > > the
>> > > > WK> PWSCF website yeided some results
>> that I
>> > > don't understand. So I would
>> > > > like
>> > > >
>> > > > perhaps it would be useful to explain in
>> more detail
>> > > what
>> > > > is confusing you and what calculation you
>> did with
>> > > what input.
>> > > > perhaps some people here can comment on it.
>> it is
>> > > always easy
>> > > > to blame the pseudopotential (sometimes
>> rightfully
>> > > so), but
>> > > > more often than not, the real cause is in
>> not doing a
>> > > calculation
>> > > > correctly, or not using a pseudopotential
>> correct.
>> > > >
>> > > > WK> to use some other PP's to check
>> if I did
>> > > the calculation correctly. Any
>> > > > WK> suggestions?
>> > > >
>> > > > i have a set of Ge pseudopotentials
>> generated from
>> > > parameters
>> > > > for a norm-conserving troullier-martins
>> potential that
>> > > is in
>> > > > the extended CPMD psp library. they have
>> seen only
>> > > very minimal
>> > > > transferability testing (using an atomic
>> code in
>> > > bessel basis),
>> > > > but so far seem to be ok, except for the
>> OLYP one
>> > > which has a
>> > > > ghost in the s-channel.
>> > > >
>> > > > i can send them to you in a private mail, if
>> you are
>> > > interested.
>> > > > no guarantees etc...
>> > > >
>> > > > cheers,
>> > > >   axel.
>> > > >
>> > > > WK>
>> > > > WK> Best,
>> > > > WK>
>> > > > WK> Wei
>> > > > WK>
>> > > > WK> On Thu, Oct 2, 2008 at 11:54 AM, Axel
>> Kohlmeyer
>> > > <
>> > > > akohlmey at cmm.chem.upenn.edu
>> > > > WK> > wrote:
>> > > > WK>
>> > > > WK> > On Thu, 2 Oct 2008, willy kohn
>> wrote:
>> > > > WK> >
>> > > > WK> > WK> Dear PWSCF users:
>> > > > WK> > WK>
>> > > > WK> > WK> I have a quick question
>> about using
>> > > > WK> > WK>
>> Hartwigsen-Goedeker-Hutter<
>> > > > WK> >
>> > > >
>> > >
>> >
>> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/potentials/Goedecker/abinit/pade
>> > > > WK> > >pseudopotential
>> > > > WK> > WK> with PWSCF. Is there any
>> converter
>> > > to transfer the HGH pp
>> > > > WK> > WK> format to UPF used in
>> PWSCF?
>> > > > WK> >
>> > > > WK> > none that i am aware of.
>> > > > WK> >
>> > > > WK> > the GTH pseudopotentials are
>> analytical in
>> > > real and reciprocal
>> > > > WK> > space and to incorporate them
>> properly,
>> > > one would have to do a
>> > > > WK> > lot of programming. in the CPMD
>> code (from
>> > > http://www.cpmd.org)
>> > > > WK> > they are treated as a special
>> case,
>> > > similar to ultra-soft psps.
>> > > > WK> >
>> > > > WK> > is there any particularly reason
>> you'd
>> > > need any of those?
>> > > > WK> >
>> > > > WK> > cheers,
>> > > > WK> >   axel.
>> > > > WK> >
>> > > > WK> >
>> > > > WK> > WK>
>> > > > WK> > WK> Best,
>> > > > WK> > WK>
>> > > > WK> > WK> Wei
>> > > > WK> > WK>
>> > > > WK> > WK> Georgia Tech
>> > > > WK> > WK>
>> > > > WK> >
>> > > > WK> > --
>> > > > WK> >
>> > > >
>> > >
>> =======================================================================
>> > > > WK> > Axel Kohlmeyer
>> > > akohlmey at cmm.chem.upenn.edu
>> > > > http://www.cmm.upenn.edu
>> > > > WK> >   Center for Molecular Modeling
>>  --
>> > > University of Pennsylvania
>> > > > WK> > Department of Chemistry, 231
>> S.34th
>> > > Street, Philadelphia, PA
>> > > > 19104-6323
>> > > > WK> > tel: 1-215-898-1582,  fax:
>> 1-215-573-6233,
>> > >  office-tel:
>> > > > 1-215-898-5425
>> > > > WK> >
>> > > >
>> > >
>> =======================================================================
>> > > > WK> > If you make something
>> idiot-proof, the
>> > > universe creates a better
>> > > > idiot.
>> > > > WK> >
>> > > > WK>
>> > > >
>> > > > --
>> > > >
>> > >
>> =======================================================================
>> > > > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
>> > > http://www.cmm.upenn.edu
>> > > >   Center for Molecular Modeling   --
>> University of
>> > > Pennsylvania
>> > > > Department of Chemistry, 231 S.34th Street,
>> > > Philadelphia, PA 19104-6323
>> > > > tel: 1-215-898-1582,  fax: 1-215-573-6233,
>> > > office-tel: 1-215-898-5425
>> > > >
>> > >
>> =======================================================================
>> > > > If you make something idiot-proof, the
>> universe
>> > > creates a better idiot.
>> > > >
>> > > _______________________________________________
>> > > Pw_forum mailing list
>> > > Pw_forum at pwscf.org
>> > >
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 5 Oct 2008 04:49:04 -0700 (PDT)
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: [Pw_forum] Sorry
> To: pw_forum at pwscf.org
> Message-ID: <34891.93876.qm at web65706.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Sorry, I was not so careful, I did not clean the previous message at the
> end of my mail.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 6 Oct 2008 00:45:14 +0200 (CEST)
> From: "Lorenzo Paulatto" <paulatto at sissa.it>
> Subject: Re: [Pw_forum] file.xml
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <21803.82.50.174.28.1223246714.squirrel at webmail.sissa.it>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> On Dom, Ottobre 5, 2008 08:37, Mansoureh Pashangpour wrote:
>>  Dear all
>>  How can I plot a file with xml format?
>
> Dear Mansoureh,
> you cannot plot them, they internal files in unsuitable format. Please
> read pp.x documentation instead, you'll find it in the Doc directory.
> There are also a few examples covering various kinds of plot.
>
> regards
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by SquirrelMail http://www.squirrelmail.org/
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 16, Issue 9
> ***************************************
>


-- 
PhD Student
JNCASR, Bangalore-560064
India

From giannozz at democritos.it  Mon Oct  6 11:07:32 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 06 Oct 2008 11:07:32 +0200
Subject: [Pw_forum] problem with ram.x
In-Reply-To: <52391.172.16.1.1.1223283262.squirrel@172.16.1.1>
References: <mailman.1.1223274770.18059.pw_forum@pwscf.org>
	<52391.172.16.1.1.1223283262.squirrel@172.16.1.1>
Message-ID: <48E9D554.3060300@democritos.it>

Arun Kumar Manna wrote:

>  Could anyone please help me regarding how to use ram.x executable to
>  calculate raman tensors?. Actually, in the example15, it is given 

no it isn't. The ram.x executable doesn't exists any longer since years.
Its functionality was merged into the ph.x executable.

Your messages consisted of approx. 10 lines of contents and 450 lines
of quotes. Signal-to-noise ratio: less than 2%
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From yuminqian at gmail.com  Mon Oct  6 11:30:23 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 6 Oct 2008 17:30:23 +0800
Subject: [Pw_forum] phonon calculation
Message-ID: <aa128b2c0810060230n59fde599s2110d56fbdfe64a8@mail.gmail.com>

     I did a phonon calculation with the  A-spin type CaCrO3 system , the
system is Pbnm structure , in the unit cell there are 20 atoms and the  Cr
atoms are spin parallel in a-b plane and anti-parallel along c axis .
After a scf calculation by pw.x whit a k-point mesh of 6?6?4  I choose a q
point mesh of 4?4?4 but the  thresh cann't be reached and  ddv_scf|^2
dangling around 1.0E-7  ,I use the alpha_mix =  0.700 , how to make it
converge for such large system?

-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From prasenjit.jnc at gmail.com  Mon Oct  6 11:54:43 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Mon, 6 Oct 2008 11:54:43 +0200
Subject: [Pw_forum] phonon calculation
In-Reply-To: <aa128b2c0810060230n59fde599s2110d56fbdfe64a8@mail.gmail.com>
References: <aa128b2c0810060230n59fde599s2110d56fbdfe64a8@mail.gmail.com>
Message-ID: <627e0ffa0810060254k51d4df29xa858053d3f76a445@mail.gmail.com>

Dear Y. M. Qian,
you may try to reduce alpha_mix to 0.3/0.4 and restart your calculation,
because if you use a very high value of alpha_mix and you are near the
minima, it may be possible that that the new potential overshoot the
minimum.

Prasenjit.

2008/10/6 yumin qian <yuminqian at gmail.com>

>      I did a phonon calculation with the  A-spin type CaCrO3 system , the
> system is Pbnm structure , in the unit cell there are 20 atoms and the  Cr
> atoms are spin parallel in a-b plane and anti-parallel along c axis .
> After a scf calculation by pw.x whit a k-point mesh of 6?6?4  I choose a q
> point mesh of 4?4?4 but the  thresh cann't be reached and  ddv_scf|^2
> dangling around 1.0E-7  ,I use the alpha_mix =  0.700 , how to make it
> converge for such large system?
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel:  + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603   Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From iori at theory.polytechnique.fr  Mon Oct  6 15:09:04 2008
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Mon, 06 Oct 2008 15:09:04 +0200
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
Message-ID: <48EA0DF0.7010504@theory.polytechnique.fr>

Dear all.

I was compiling my Pwscf on this machine (PLATINE the common name)
* Marque : BULL
* Modele : 3045
* Systeme d'exploitation : Bull Advanced Server 4 version 5
* Nom : platine
* Itanium2 1.6 GHz|
in  the CCRT computing centre when i found this problem during the  make 
pp  step.

""""""""""""""""""""""""""""""""""""""""""""""""""""""
mpif90 -i-static -openmp  -o average.x \
    average.o addusdens1d.o add_shift_cc.o add_shift_lc.o add_shift_us.o 
atomic_wfc_nc_proj.o cft.o cgracsc.o compute_ppsi.o compute_sigma_avg.o 
cube.o cubicspinsym.o dosg.o do_initial_state.o do_shift_ew.o 
d_matrix_nc.o d_matrix_so.o elf.o ggen1d.o hexspinsym.o local_dos.o 
local_dos_mag.o local_dos1d.o openfil_pp.o plot_io.o plot_whole_cell.o 
punch_plot.o smallgk.o start_postproc.o stm.o stop_pp.o sym_band.o 
work_function.o write_p_avg.o xsf.o  ../Modules/atom.o 
../Modules/basic_algebra_routines.o ../Modules/cell_base.o 
../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o 
../Modules/constraints_module.o ../Modules/control_flags.o 
../Modules/descriptors.o ../Modules/dspev_drv.o 
../Modules/electrons_base.o ../Modules/error_handler.o 
../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o 
../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o 
../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o 
../Modules/input_parameters.o ../Modules/kind.o ../Modules/mp_global.o 
../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o 
../Modules/metagga.o ../Modules/parallel_include.o 
../Modules/parameters.o ../Modules/parser.o ../Modules/paw_variables.o 
../Modules/printout_base.o ../Modules/pseudo_types.o 
../Modules/ptoolkit.o ../Modules/random_numbers.o 
../Modules/radial_grids.o ../Modules/read_ncpp.o 
../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/read_uspp.o 
../Modules/recvec.o ../Modules/shmem_include.o ../Modules/stick_base.o 
../Modules/splinelib.o ../Modules/task_groups.o ../Modules/timestep.o 
../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o 
../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o 
../Modules/wavefunctions.o ../Modules/wannier.o 
../Modules/write_upf_v2.o ../Modules/xml_io_base.o 
../Modules/zhpev_drv.o ../PW/libpw.a ../flib/ptools.a ../flib/flib.a 
../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack  
-L/applications/intel/ict/3.0/cmkl/9.0/lib/64 -lmkl_ipf   
-L/applications/intel/ict/3.0/cmkl/9.0/lib/64 -lmkl_ipf      
backend signals

*fortcom: Severe: **Internal compiler error: internal abort** Please 
report this error along with the circumstances in which it occurred in a 
Software Problem Report.  Note: File and line given may not be explicit 
cause of this error.

ifort: error: problem during multi-file optimization compilation (code 3)
make[1]: *** [average.x] Error 3
make[1]: Leaving directory 
`/home/cont003/feffe/CODES/PLATINE/espresso-4.0.2/PP'
make: *** [pp] Error 2
*
"""""""""""""""""""""""""""""""""""""""

doing the ./configure everything seems to work perfectly.
Then the make pw step works perfectly.
But in the end i cant compile the pp or pwall stuff.

What do you suggest me to do? Should I bother you or directly the 
technicians in the CCRT centre??
Thanks so much in advance!
federico iori


-- 
Dr. Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
email: federico.iori @ polytechnique.edu 


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From paulatto at sissa.it  Mon Oct  6 15:52:24 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 06 Oct 2008 15:52:24 +0200
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <48EA0DF0.7010504@theory.polytechnique.fr>
References: <48EA0DF0.7010504@theory.polytechnique.fr>
Message-ID: <48EA1818.9090509@sissa.it>

Dear Federico,
> I was compiling my Pwscf on this machine (PLATINE the common name)
> [cut]
You've omitted the only important information: the compiler version.

> What do you suggest me to do? Should I bother you or directly the
> technicians in the CCRT centre??
You should bother them, but it may be enough to follow the error message
suggestion: disable inter-file optimization. The switch should be
-no-ipo, but you've better check in the documentation.

> Thanks so much in advance!
you're welcome, bye

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From akohlmey at cmm.chem.upenn.edu  Mon Oct  6 16:15:40 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 6 Oct 2008 10:15:40 -0400 (EDT)
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <48EA0DF0.7010504@theory.polytechnique.fr>
References: <48EA0DF0.7010504@theory.polytechnique.fr>
Message-ID: <Pine.LNX.4.64.0810061010040.18122@localhost.localdomain>

On Mon, 6 Oct 2008, Federico Iori wrote:

FI> Dear all.

dear federico!
 
FI> I was compiling my Pwscf on this machine (PLATINE the common name)

[...]

FI> *fortcom: Severe: **Internal compiler error: internal abort** Please report
FI> this error along with the circumstances in which it occurred in a Software
FI> Problem Report.  Note: File and line given may not be explicit cause of this
FI> error.
FI> 
FI> ifort: error: problem during multi-file optimization compilation (code 3)

[...]

FI> doing the ./configure everything seems to work perfectly.
FI> Then the make pw step works perfectly.
FI> But in the end i cant compile the pp or pwall stuff.
FI> 
FI> What do you suggest me to do? Should I bother you or directly the
FI> technicians in the CCRT centre??

as stated here many times before: an internal compiler error
is a bug in the _compiler_, not the application. given the 
hardware configuration that you describe, it is very likely that 
you have a broken intel compiler and you need to update it to 
the latest patchlevel. this is a quite common problem. 

i also strongly advise to run tests with the compiled executables,
as there are very high chances that those are miscompiled. these
days, a successful compilation does not mean, that you have a
correctly working executables. the itanium architecture is quite
notorious there, since the compiler has to do more work compared
to other architectures.

cheers,
   axel.



FI> Thanks so much in advance!
FI> federico iori
FI> 
FI> 
FI> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From iori at theory.polytechnique.fr  Mon Oct  6 16:30:28 2008
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Mon, 06 Oct 2008 16:30:28 +0200
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <Pine.LNX.4.64.0810061010040.18122@localhost.localdomain>
References: <48EA0DF0.7010504@theory.polytechnique.fr>
	<Pine.LNX.4.64.0810061010040.18122@localhost.localdomain>
Message-ID: <48EA2104.40605@theory.polytechnique.fr>

oookey!

thanks so much for the advice.
Btw, as Lorenzo pointed out i didn't  specified the compiler. I'm gonna 
do now:

FC intel 9.1.045
CC intel 9.1.049

but i have also to add that:

espresso_4.0 doesnt give any problems, nor with make pw nor with make pp

while the espresso_4.0.1 and the next one espresso_4.0.2 give the same 
problem i described before.

well...let me try now with the option -no-ipo suggested before.
i will tell you. and also i will communicate this error to the CCRT guys.

thanks to everybody!



Axel Kohlmeyer wrote:
> On Mon, 6 Oct 2008, Federico Iori wrote:
>
> FI> Dear all.
>
> dear federico!
>  
> FI> I was compiling my Pwscf on this machine (PLATINE the common name)
>
> [...]
>
> FI> *fortcom: Severe: **Internal compiler error: internal abort** Please report
> FI> this error along with the circumstances in which it occurred in a Software
> FI> Problem Report.  Note: File and line given may not be explicit cause of this
> FI> error.
> FI> 
> FI> ifort: error: problem during multi-file optimization compilation (code 3)
>
> [...]
>
> FI> doing the ./configure everything seems to work perfectly.
> FI> Then the make pw step works perfectly.
> FI> But in the end i cant compile the pp or pwall stuff.
> FI> 
> FI> What do you suggest me to do? Should I bother you or directly the
> FI> technicians in the CCRT centre??
>
> as stated here many times before: an internal compiler error
> is a bug in the _compiler_, not the application. given the 
> hardware configuration that you describe, it is very likely that 
> you have a broken intel compiler and you need to update it to 
> the latest patchlevel. this is a quite common problem. 
>
> i also strongly advise to run tests with the compiled executables,
> as there are very high chances that those are miscompiled. these
> days, a successful compilation does not mean, that you have a
> correctly working executables. the itanium architecture is quite
> notorious there, since the compiler has to do more work compared
> to other architectures.
>
> cheers,
>    axel.
>
>
>
> FI> Thanks so much in advance!
> FI> federico iori
> FI> 
> FI> 
> FI> 
>
>   


-- 
Dr. Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
emails: federico.iori @ polytechnique.edu 
        iori.federico @ unimore.it
http://www.dsmodena.it/home.html
http://www.comune.mo.it



From giannozz at democritos.it  Mon Oct  6 17:42:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 06 Oct 2008 17:42:16 +0200
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <48EA2104.40605@theory.polytechnique.fr>
References: <48EA0DF0.7010504@theory.polytechnique.fr>	<Pine.LNX.4.64.0810061010040.18122@localhost.localdomain>
	<48EA2104.40605@theory.polytechnique.fr>
Message-ID: <48EA31D8.2000309@democritos.it>

Federico Iori wrote:

> espresso_4.0 doesnt give any problems, nor with make pw nor with make pp
> while the espresso_4.0.1 and the next one espresso_4.0.2 give the same 
> problem i described before.

compiler bugs may be triggered or suppressed by minimal code changes,
like those between the 4.0 and 4.0.1 versions

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From szs_naghavi at yahoo.com  Mon Oct  6 22:23:23 2008
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Mon, 6 Oct 2008 13:23:23 -0700 (PDT)
Subject: [Pw_forum] negative freqency
Message-ID: <754677.78400.qm@web63002.mail.re1.yahoo.com>

Dear pwscf users!
I run ph.x for a grid of qs and there is not any negative freqency but as?I run matdyn.x they emerg what should I do ??


      
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From eyvaz_isaev at yahoo.com  Mon Oct  6 23:10:42 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 6 Oct 2008 14:10:42 -0700 (PDT)
Subject: [Pw_forum] negative freqency
In-Reply-To: <754677.78400.qm@web63002.mail.re1.yahoo.com>
Message-ID: <611261.28427.qm@web65707.mail.ac4.yahoo.com>

Dear Zahra,

--- On Tue, 10/7/08, zahra sadat naghavi <szs_naghavi at yahoo.com> wrote:

> I run ph.x for a grid of qs and there is not any > negative freqency but as I run matdyn.x they emerg what > should I do? 

Can you submit the picture? 
In my experience this might happen due to insufficient number of dynamical matrices.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com



 


      

From nakhmanson at anl.gov  Mon Oct  6 23:14:22 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Mon, 06 Oct 2008 16:14:22 -0500
Subject: [Pw_forum] Is the "cell_dofree" functionality fully implemented in
 Espresso 4.0.x?
Message-ID: <48EA7FAE.7090708@anl.gov>

Dear All,

Is "cell_dofree" feature in &CELL completely implemented
in Espresso 4.0.x? I have checked out the previous forum
postings but I think that the question I have below has
not been brought up before.

When I had to do my own modifications to achieve a similar
goal in Espresso 3.x, I ended up changing vcsmd.f90 (to pin
certain lattice consts) and in stress.f90 (to zero out some
stress tensor components).

In the current version everything seems to be conveniently
controlled through the use if "iforceh" parameter set in
input.f90. However, when I trace how it is used, I can see
something similar to what I did in vcsmd.f90 and nothing in
stress.f90 or any other place that deals with stresses.

So what happens, as it seems to me, is that this algorithm
works (i.e., keeps certain lattice consts fixed during a
vc-relax run) but never finishes, even when the appropriate
stress tensor components get relaxed (e.g., to zero). Since
the unneeded stress tensor components (as it seems) do not
get zeroed out, the

   ( ABS( sigma(i,j) ) * uakbar < epsp )

condition in vcsmd.f90 is never reached. Or am I missing
something?

Would appreciate any sage comments on this.

THX,

Serge

-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From w2agz at pacbell.net  Tue Oct  7 00:26:17 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 6 Oct 2008 15:26:17 -0700
Subject: [Pw_forum] Making Changes in pw.x
Message-ID: <00d201c92802$8db42990$a91c7cb0$@net>

I know I've done this before, but can't remember how.  Suppose I want to
make a small change in one of the routines used by pw.x, let's say
electrons.f90.  What do I do after making and saving the changes?  Do a
fortran compile and then make all?

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/> 
 
 


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From prasenjit.jnc at gmail.com  Tue Oct  7 00:36:26 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Tue, 7 Oct 2008 00:36:26 +0200
Subject: [Pw_forum] Making Changes in pw.x
In-Reply-To: <00d201c92802$8db42990$a91c7cb0$@net>
References: <00d201c92802$8db42990$a91c7cb0$@net>
Message-ID: <627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>

if you have the make.sys file, then make all or make pw will be sufficient.
The subroutines which have been changed will be recompiled, linked and the
pw.x will be created.

Prasenjit

2008/10/7 Paul M. Grant <w2agz at pacbell.net>

>  I know I've done this before, but can't remember how.  Suppose I want to
> make a small change in one of the routines used by pw.x, let's say
> electrons.f90.  What do I do after making and saving the changes?  Do a
> fortran compile and then make all?
>
> *******Paul M. Grant, PhD*
>
> *******Principal, W2AGZ Technologies*
>
> *******Visiting Scholar, Applied Physics, Stanford (2005-2008)*
>
> *******EPRI Science Fellow (Retired)*
>
> *******IBM Research Staff Member Emeritus*
>
> *******w2agz at pacbell.net* <w2agz at pacbell.net>
>
> *******http://www.w2agz.com* <http://www.w2agz.com/>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From w2agz at pacbell.net  Tue Oct  7 03:44:43 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 6 Oct 2008 18:44:43 -0700
Subject: [Pw_forum] Making Changes in pw.x
In-Reply-To: <627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>
References: <00d201c92802$8db42990$a91c7cb0$@net>
	<627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>
Message-ID: <010301c9281e$45d051a0$d170f4e0$@net>

Thanks, Prasenjit.

 

I do have the make.sys file.but how does make "know" what's been changed.is
there a database of original electron.f90 creation dates somewhere?  I
confess I'm not exactly an expert on the linker process in linux.for OS/360
I once was!  Is there an online manual on fortran and linking resultant .o
and the (mysterious to me) .mod files?

 

Thanks again.

 

-Paul

 

Paul M. Grant, PhD

Principal, W2AGZ Technologies

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

 <mailto:w2agz at pacbell.net> w2agz at pacbell.net

 <http://www.w2agz.com/> http://www.w2agz.com

 

 

 

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Prasenjit Ghosh
Sent: Monday, October 06, 2008 3:36 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Making Changes in pw.x

 

if you have the make.sys file, then make all or make pw will be sufficient.
The subroutines which have been changed will be recompiled, linked and the
pw.x will be created.

Prasenjit

2008/10/7 Paul M. Grant <w2agz at pacbell.net>

I know I've done this before, but can't remember how.  Suppose I want to
make a small change in one of the routines used by pw.x, let's say
electrons.f90.  What do I do after making and saving the changes?  Do a
fortran compile and then make all?

Paul M. Grant, PhD

Principal, W2AGZ Technologies

Visiting Scholar, Applied Physics, Stanford (2005-2008)

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

 <mailto:w2agz at pacbell.net> w2agz at pacbell.net

 <http://www.w2agz.com/> http://www.w2agz.com

 

 


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum




-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)

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From yuminqian at gmail.com  Tue Oct  7 04:30:27 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 7 Oct 2008 10:30:27 +0800
Subject: [Pw_forum] xml file format control
Message-ID: <aa128b2c0810061930t6ff573c3ud5e4dae85eeaba56@mail.gmail.com>

> I meet with a problem , I use the newest version of PWSCF code. the output
> file of charge density is suffix.dat , it's a binary file . and the wave
> function file is suffix.wfcx  is also a binary file. but the

   file contains the system info is data-file.xml , my question is how to
set input parameter to make the out put files of  wavefuntion and charge
density in xml format.


-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From sauluck at iitk.ac.in  Tue Oct  7 04:34:00 2008
From: sauluck at iitk.ac.in (Sushil Auluck)
Date: Tue, 7 Oct 2008 08:04:00 +0530 (IST)
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <48EA0DF0.7010504@theory.polytechnique.fr>
References: <48EA0DF0.7010504@theory.polytechnique.fr>
Message-ID: <35348.122.162.199.111.1223346840.squirrel@newwebmail.iitk.ac.in>

hi,
just a wild guess....try make clean first and then make or make all.
s.auluck

> Dear all.
>
> I was compiling my Pwscf on this machine (PLATINE the common name)
> * Marque : BULL
> * Modele : 3045
> * Systeme d'exploitation : Bull Advanced Server 4 version 5
> * Nom : platine
> * Itanium2 1.6 GHz|
> in  the CCRT computing centre when i found this problem during the  make
> pp  step.
>
> """"""""""""""""""""""""""""""""""""""""""""""""""""""
> mpif90 -i-static -openmp  -o average.x \
>     average.o addusdens1d.o add_shift_cc.o add_shift_lc.o add_shift_us.o
> atomic_wfc_nc_proj.o cft.o cgracsc.o compute_ppsi.o compute_sigma_avg.o
> cube.o cubicspinsym.o dosg.o do_initial_state.o do_shift_ew.o
> d_matrix_nc.o d_matrix_so.o elf.o ggen1d.o hexspinsym.o local_dos.o
> local_dos_mag.o local_dos1d.o openfil_pp.o plot_io.o plot_whole_cell.o
> punch_plot.o smallgk.o start_postproc.o stm.o stop_pp.o sym_band.o
> work_function.o write_p_avg.o xsf.o  ../Modules/atom.o
> ../Modules/basic_algebra_routines.o ../Modules/cell_base.o
> ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o
> ../Modules/constraints_module.o ../Modules/control_flags.o
> ../Modules/descriptors.o ../Modules/dspev_drv.o
> ../Modules/electrons_base.o ../Modules/error_handler.o
> ../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o
> ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o
> ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o
> ../Modules/input_parameters.o ../Modules/kind.o ../Modules/mp_global.o
> ../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o
> ../Modules/metagga.o ../Modules/parallel_include.o
> ../Modules/parameters.o ../Modules/parser.o ../Modules/paw_variables.o
> ../Modules/printout_base.o ../Modules/pseudo_types.o
> ../Modules/ptoolkit.o ../Modules/random_numbers.o
> ../Modules/radial_grids.o ../Modules/read_ncpp.o
> ../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/read_uspp.o
> ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/stick_base.o
> ../Modules/splinelib.o ../Modules/task_groups.o ../Modules/timestep.o
> ../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o
> ../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o
> ../Modules/wavefunctions.o ../Modules/wannier.o
> ../Modules/write_upf_v2.o ../Modules/xml_io_base.o
> ../Modules/zhpev_drv.o ../PW/libpw.a ../flib/ptools.a ../flib/flib.a
> ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack
> -L/applications/intel/ict/3.0/cmkl/9.0/lib/64 -lmkl_ipf
> -L/applications/intel/ict/3.0/cmkl/9.0/lib/64 -lmkl_ipf
> backend signals
>
> *fortcom: Severe: **Internal compiler error: internal abort** Please
> report this error along with the circumstances in which it occurred in a
> Software Problem Report.  Note: File and line given may not be explicit
> cause of this error.
>
> ifort: error: problem during multi-file optimization compilation (code 3)
> make[1]: *** [average.x] Error 3
> make[1]: Leaving directory
> `/home/cont003/feffe/CODES/PLATINE/espresso-4.0.2/PP'
> make: *** [pp] Error 2
> *
> """""""""""""""""""""""""""""""""""""""
>
> doing the ./configure everything seems to work perfectly.
> Then the make pw step works perfectly.
> But in the end i cant compile the pp or pwall stuff.
>
> What do you suggest me to do? Should I bother you or directly the
> technicians in the CCRT centre??
> Thanks so much in advance!
> federico iori
>
>
> --
> Dr. Dr. Federico Iori, PhD!
>
> Laboratoire des Solides Irradi?s,
> Ecole Polytechnique - CEA/DSM, CNRS
> 91128 Palaiseau, France
>
> www.etsf.polytechnique.fr
>
> phone: +33 (0) 1 69 33 44 85
> email: federico.iori @ polytechnique.edu
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


.......................................................................
Prof. Sushil Auluck                      Phone:+91-512-6797092/6148
Department of Physics                          +91-512-6798177(Home)
Indian Institute of Technology           Cell :+91-9305548667
Kanpur 208016 (UP)                       Fax  :+91-512-6790914
India                                    E-mail:sauluck at iitk.ac.in        
     ...............................................:sauluck at gmail.com
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
.......................................................................
~

From yuminqian at gmail.com  Tue Oct  7 04:51:00 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 7 Oct 2008 10:51:00 +0800
Subject: [Pw_forum] data structure of wave function and charge density
Message-ID: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>

    I need to write a small program to do some  post -process calcualtion ,
and I need to read in the wave function and charge density , But I
don't know the data structure of the wave function evc(npwx,nbnd)  or
evc(npwx*npol,nbnd) in noncolinear case ,In LSDA case what about the
spin part of wavefunction ?and what is the mean of npol (
number of coordinates of wfc) ?
  thank you




-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From matteo at umn.edu  Tue Oct  7 06:08:39 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 06 Oct 2008 23:08:39 -0500
Subject: [Pw_forum] Making Changes in pw.x
In-Reply-To: <010301c9281e$45d051a0$d170f4e0$@net>
References: <00d201c92802$8db42990$a91c7cb0$@net>	<627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>
	<010301c9281e$45d051a0$d170f4e0$@net>
Message-ID: <48EAE0C7.1010900@umn.edu>


Hi Paul,

as far as I know what make does is checking the dates when routine.f90 
and routine.o were generated. if routine.f90 is younger than routine.o 
(because it's been changed) then it will be recompiled, re-linked etc.
In any case don't worry it will do the right thing.

Regards,

Matteo




Paul M. Grant wrote:
>
> Thanks, Prasenjit.
>
> I do have the make.sys file?but how does make ?know? what?s been 
> changed?is there a database of original electron.f90 creation dates 
> somewhere? I confess I?m not exactly an expert on the linker process 
> in linux?for OS/360 I once was! Is there an online manual on fortran 
> and linking resultant .o and the (mysterious to me) .mod files?
>
> Thanks again.
>
> -Paul
>
> */Paul M. Grant, PhD/*
>
> *Principal, W2AGZ Technologies*
>
> *Visiting Scholar, Applied Physics, Stanford (2005-2008)*
>
> *EPRI Science Fellow (Retired)*
>
> *IBM Research Staff Member Emeritus*
>
> *w2agz at pacbell.net* <mailto:w2agz at pacbell.net>
>
> *http://www.w2agz.com* <http://www.w2agz.com/>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On Behalf Of *Prasenjit Ghosh
> *Sent:* Monday, October 06, 2008 3:36 PM
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] Making Changes in pw.x
>
> if you have the make.sys file, then make all or make pw will be 
> sufficient. The subroutines which have been changed will be 
> recompiled, linked and the pw.x will be created.
>
> Prasenjit
>
> 2008/10/7 Paul M. Grant <w2agz at pacbell.net <mailto:w2agz at pacbell.net>>
>
> I know I've done this before, but can't remember how. Suppose I want 
> to make a small change in one of the routines used by pw.x, let's say 
> electrons.f90. What do I do after making and saving the changes? Do a 
> fortran compile and then make all?
>
> */Paul M. Grant, PhD/*
>
> *Principal, W2AGZ Technologies*
>
> *Visiting Scholar, Applied Physics, Stanford (2005-2008)*
>
> *EPRI Science Fellow (Retired)*
>
> *IBM Research Staff Member Emeritus*
>
> *w2agz at pacbell.net* <mailto:w2agz at pacbell.net>
>
> *http://www.w2agz.com* <http://www.w2agz.com/>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
> +39 3807528672 (M)
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From w2agz at pacbell.net  Tue Oct  7 07:17:07 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 6 Oct 2008 22:17:07 -0700
Subject: [Pw_forum] Making Changes in pw.x
In-Reply-To: <48EAE0C7.1010900@umn.edu>
References: <00d201c92802$8db42990$a91c7cb0$@net>	<627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>	<010301c9281e$45d051a0$d170f4e0$@net>
	<48EAE0C7.1010900@umn.edu>
Message-ID: <012d01c9283b$f1cf83a0$d56e8ae0$@net>

Mateo, right on. Got it.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Matteo Cococcioni
Sent: Monday, October 06, 2008 9:09 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Making Changes in pw.x


Hi Paul,

as far as I know what make does is checking the dates when routine.f90 
and routine.o were generated. if routine.f90 is younger than routine.o 
(because it's been changed) then it will be recompiled, re-linked etc.
In any case don't worry it will do the right thing.

Regards,

Matteo




Paul M. Grant wrote:
>
> Thanks, Prasenjit.
>
> I do have the make.sys file
but how does make ?know? what?s been 
> changed
is there a database of original electron.f90 creation dates 
> somewhere? I confess I?m not exactly an expert on the linker process 
> in linux
for OS/360 I once was! Is there an online manual on fortran 
> and linking resultant .o and the (mysterious to me) .mod files?
>
> Thanks again.
>
> -Paul
>
> */Paul M. Grant, PhD/*
>
> *Principal, W2AGZ Technologies*
>
> *Visiting Scholar, Applied Physics, Stanford (2005-2008)*
>
> *EPRI Science Fellow (Retired)*
>
> *IBM Research Staff Member Emeritus*
>
> *w2agz at pacbell.net* <mailto:w2agz at pacbell.net>
>
> *http://www.w2agz.com* <http://www.w2agz.com/>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On Behalf Of *Prasenjit Ghosh
> *Sent:* Monday, October 06, 2008 3:36 PM
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] Making Changes in pw.x
>
> if you have the make.sys file, then make all or make pw will be 
> sufficient. The subroutines which have been changed will be 
> recompiled, linked and the pw.x will be created.
>
> Prasenjit
>
> 2008/10/7 Paul M. Grant <w2agz at pacbell.net <mailto:w2agz at pacbell.net>>
>
> I know I've done this before, but can't remember how. Suppose I want 
> to make a small change in one of the routines used by pw.x, let's say 
> electrons.f90. What do I do after making and saving the changes? Do a 
> fortran compile and then make all?
>
> */Paul M. Grant, PhD/*
>
> *Principal, W2AGZ Technologies*
>
> *Visiting Scholar, Applied Physics, Stanford (2005-2008)*
>
> *EPRI Science Fellow (Retired)*
>
> *IBM Research Staff Member Emeritus*
>
> *w2agz at pacbell.net* <mailto:w2agz at pacbell.net>
>
> *http://www.w2agz.com* <http://www.w2agz.com/>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
> +39 3807528672 (M)
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From giannozz at democritos.it  Tue Oct  7 08:21:21 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 07 Oct 2008 08:21:21 +0200
Subject: [Pw_forum] Making Changes in pw.x
In-Reply-To: <48EAE0C7.1010900@umn.edu>
References: <00d201c92802$8db42990$a91c7cb0$@net>	<627e0ffa0810061536y3773a47bg44777557c70b276@mail.gmail.com>	<010301c9281e$45d051a0$d170f4e0$@net>
	<48EAE0C7.1010900@umn.edu>
Message-ID: <48EAFFE1.2080006@democritos.it>

Matteo Cococcioni wrote:

> as far as I know what make does is checking the dates when routine.f90 
> and routine.o were generated. 

it actually checks the date of all "dependencies" of a "target".
Files Makefile, make.sys, make.depend contain list of dependencies,
either implied (some-file.o depends on some-file.o) or explicit
(some-file.o depends on some-module.o, or some-include-file.h).
For small changes, executing "make pw" is just fine. For more
extensive changes that modify the dependencies, one should also
run the script "./makedeps.sh".

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Oct  7 08:24:37 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 07 Oct 2008 08:24:37 +0200
Subject: [Pw_forum] xml file format control
In-Reply-To: <aa128b2c0810061930t6ff573c3ud5e4dae85eeaba56@mail.gmail.com>
References: <aa128b2c0810061930t6ff573c3ud5e4dae85eeaba56@mail.gmail.com>
Message-ID: <48EB00A5.4040607@democritos.it>

yumin qian wrote:

>  the output file of charge density is suffix.dat , it's a binary file .
>  and the wave function file is suffix.wfcx  is also a binary file.
>  but the file contains the system info is data-file.xml , my question 
>  is how to set input parameter to make the out put files of wavefuntion
>  and charge density in xml format. 

formatted xml? you can't: you have to modify the code where it
reads and writes the data files. It is not a great idea, though:
binary files are much smaller than formatted files

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From paulatto at sissa.it  Tue Oct  7 11:22:51 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 07 Oct 2008 11:22:51 +0200
Subject: [Pw_forum] Is the "cell_dofree" functionality fully implemented
 in Espresso 4.0.x?
In-Reply-To: <48EA7FAE.7090708@anl.gov>
References: <48EA7FAE.7090708@anl.gov>
Message-ID: <48EB2A6B.4070005@sissa.it>

Serge Nakhmanson ha scritto:
> Dear All,
>
> Is "cell_dofree" feature in &CELL completely implemented
> in Espresso 4.0.x?
Dear Serge,
I can't give you a definitive answer, as I haven't really used this
feature. What I can say is that it is not implemented with bfgs
algorithm and even with damp I'm not really sure it is working. I tried
to find a quick fix some time ago, but had to give up due to other work.

> condition in vcsmd.f90 is never reached. Or am I missing
> something?
>   
I think you are right, but it is easy to fix, change
  ABS( sigma(i,j) ) * uakbar
to
  ABS( sigma(i,j) ) * iforceh(i,j) * uakbar
in both places (be careful with the indexes), and it *should* work.

I say "should" because I have done a few tries, but couldn't make it
converge; it is probably due to my inexperience with damped dynamics.

> Would appreciate any sage comments on this.
>   
I''m not really a sage, I hope it helped

bye

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From prasenjit.jnc at gmail.com  Tue Oct  7 11:24:00 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Tue, 7 Oct 2008 11:24:00 +0200
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
Message-ID: <627e0ffa0810070224p6d8d1f5ahb91e7b00f3d9fdec@mail.gmail.com>

You can find the necessary details in the following links:
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#How_is_the_charge_density_.28the_potential.2C_etc..29_stored.3F_What_position_in_real_space_corresponds_to_an_array_value.3F
http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#File_Formats

Prasenjit.

2008/10/7 yumin qian <yuminqian at gmail.com>

>     I need to write a small program to do some  post -process calcualtion ,
> and I need to read in the wave function and charge density , But I
> don't know the data structure of the wave function evc(npwx,nbnd)  or
> evc(npwx*npol,nbnd) in noncolinear case ,In LSDA case what about the
> spin part of wavefunction ?and what is the mean of npol (
> number of coordinates of wfc) ?
>   thank you
>
>
>
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel:  + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603   Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From giannozz at democritos.it  Tue Oct  7 11:36:03 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 07 Oct 2008 11:36:03 +0200
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
Message-ID: <48EB2D83.8070905@democritos.it>

yumin qian wrote:

>     I need to write a small program to do some  post-process 
> calculation , and I need to read in the wave function and 
> charge density

modify one of the many codes in PP/ that read from the data file

> But I don't know the data structure of the wave 
> function evc(npwx,nbnd)  or evc(npwx*npol,nbnd) in noncolinear case

evc(i,ibnd): ibnd is the band index, i is the index of plane waves
for the noncolinear case:
   i=1,npw  are plane waves with up spin (polarization 1)
   i=npwx+1,npwx+npw are PW with down spin (polarization 2)
npw depends on the k-point, npwx is the maximum npw

> In LSDA case what about the spin part of wavefunction

in LSDA you have only spin-up or spin-down components. The
number of k-points is doubled and the first set contains
spin-up states, the second set spin-down states. The different
approach between LSDA and noncolinear approaches is somewhat
confusing. LSDA was implemented this way because it was easy
(causing minimal disruption to the codes, originally written
for unpolarized systems) and efficient

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From babderre at physics.auth.gr  Tue Oct  7 13:13:42 2008
From: babderre at physics.auth.gr (babderre at physics.auth.gr)
Date: Tue,  7 Oct 2008 14:13:42 +0300
Subject: [Pw_forum] Phonon partial density of state
Message-ID: <1223378022.48eb4466bed76@mail.physics.auth.gr>



 Dear pwscf users,

 I want to calculate phonon partial density of state.
 Could you please tell me how to calculate them?

thanks in advance!
belabbes.
http://parsem.physics.auth.gr/belabbes.htm


From yuminqian at gmail.com  Tue Oct  7 14:10:53 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 7 Oct 2008 20:10:53 +0800
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <48EB2D83.8070905@democritos.it>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
	<48EB2D83.8070905@democritos.it>
Message-ID: <aa128b2c0810070510v7fdcd28bwcc46938a4175f2b1@mail.gmail.com>

>
> Thanks for your replay ,but there may be an error
>
>>
>>
>>
>> evc(i,ibnd): ibnd is the band index, i is the index of plane waves
>> for the noncolinear case:
>>   i=1,npw  are plane waves with up spin (polarization 1)
>>   i=npwx+1,npwx+npw are PW with down spin (polarization 2)
>> npw depends on the k-point, npwx is the maximum npw
>
> i=npw+1 ,npw+npw are the PW with down spin polorization
> because the file leading dimension of evc is npwx , is this the correct
> understanding?
>
>
>
>  **
>
>



-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From yuminqian at gmail.com  Tue Oct  7 14:11:16 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 7 Oct 2008 20:11:16 +0800
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <627e0ffa0810070224p6d8d1f5ahb91e7b00f3d9fdec@mail.gmail.com>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
	<627e0ffa0810070224p6d8d1f5ahb91e7b00f3d9fdec@mail.gmail.com>
Message-ID: <aa128b2c0810070511w8046699lb4012ff309297060@mail.gmail.com>

thanks for your replay

2008/10/7 Prasenjit Ghosh <prasenjit.jnc at gmail.com>

> You can find the necessary details in the following links:
>
> http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#How_is_the_charge_density_.28the_potential.2C_etc..29_stored.3F_What_position_in_real_space_corresponds_to_an_array_value.3F
>
> http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#File_Formats
>
> Prasenjit.
>
> 2008/10/7 yumin qian <yuminqian at gmail.com>
>
>>       I need to write a small program to do some  post
>> -process calcualtion , and I need to read in the wave function and charge
>> density , But I don't know the data structure of the wave function
>> evc(npwx,nbnd)  or evc(npwx*npol,nbnd) in noncolinear case ,In
>> LSDA case what about the spin part of wavefunction ?and what is the mean of
>> npol (number of coordinates of wfc) ?
>>   thank you
>>
>>
>>
>>
>> --
>> Sincerely Y. M. Qian
>> Lab.of Condensed Matter Theory and Materials Computation
>> Institute of Physics
>> Chinese Academy of Sciences
>> Tel:  + 8610 8264 9147
>> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
>> P.O.Box 603   Beijing 100190
>> China
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
>              +39 3807528672 (M)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From eyvaz_isaev at yahoo.com  Tue Oct  7 14:26:54 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 7 Oct 2008 05:26:54 -0700 (PDT)
Subject: [Pw_forum] Phonon partial density of state
In-Reply-To: <1223378022.48eb4466bed76@mail.physics.auth.gr>
Message-ID: <226112.10531.qm@web65715.mail.ac4.yahoo.com>

Hi,

I will send you the code.       

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Tue, 10/7/08, babderre at physics.auth.gr <babderre at physics.auth.gr> wrote:

> From: babderre at physics.auth.gr <babderre at physics.auth.gr>
> Subject: [Pw_forum] Phonon partial density of state
> To: pw_forum at pwscf.org
> Date: Tuesday, October 7, 2008, 3:13 PM
> Dear pwscf users,
> 
>  I want to calculate phonon partial density of state.
>  Could you please tell me how to calculate them?
> 
> thanks in advance!
> belabbes.
> http://parsem.physics.auth.gr/belabbes.htm
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From andrea.ferretti at unimore.it  Tue Oct  7 14:38:12 2008
From: andrea.ferretti at unimore.it (Andrea Ferretti)
Date: Tue, 7 Oct 2008 14:38:12 +0200 (CEST)
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <627e0ffa0810070224p6d8d1f5ahb91e7b00f3d9fdec@mail.gmail.com>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>
	<627e0ffa0810070224p6d8d1f5ahb91e7b00f3d9fdec@mail.gmail.com>
Message-ID: <alpine.DEB.0.99.0810071434570.26315@bamboo.fisica.unimo.it>


Dear all,

as a further possibility, the pieces of code needed to read wfcs and 
charge density are also distributed with espresso as a general purpose 
library

~espresso/PP/qexml.f90

where "general purpose" means that there is no reference to any specific 
module in espresso except the iotk library (needed to parse xml).

hope it helps
andrea


> You can find the necessary details in the following links:
> http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#How_is_the_charge_density_.28the_potential.2C_etc..29_stored.3F_What_position_in_real_space_corresponds_to_an_array_value.3F
> http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#File_Formats
>
> Prasenjit.
>
> 2008/10/7 yumin qian <yuminqian at gmail.com>
>
>>     I need to write a small program to do some  post -process calcualtion ,
>> and I need to read in the wave function and charge density , But I
>> don't know the data structure of the wave function evc(npwx,nbnd)  or
>> evc(npwx*npol,nbnd) in noncolinear case ,In LSDA case what about the
>> spin part of wavefunction ?and what is the mean of npol (
>> number of coordinates of wfc) ?
>>   thank you
>>
>>

-- 
Andrea Ferretti
National Research Center S3, CNR-INFM  ( http://s3.infm.it )
Dip. Fisica, Univ. di Modena e Reggio E. (Italy)
Tel: +39 059 2055301;  Fax: +39 059 374794;  Skype: andrea_ferretti
URL: http://www.nanoscience.unimo.it

Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html

From giannozz at democritos.it  Tue Oct  7 18:05:11 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 07 Oct 2008 18:05:11 +0200
Subject: [Pw_forum] data structure of wave function and charge density
In-Reply-To: <aa128b2c0810070510v7fdcd28bwcc46938a4175f2b1@mail.gmail.com>
References: <aa128b2c0810061951q293a548boc802bc43c96af656@mail.gmail.com>	<48EB2D83.8070905@democritos.it>
	<aa128b2c0810070510v7fdcd28bwcc46938a4175f2b1@mail.gmail.com>
Message-ID: <48EB88B7.2070002@democritos.it>

yumin qian wrote:

>         evc(i,ibnd): ibnd is the band index, i is the index of plane waves
>         for the noncolinear case:
>           i=1,npw  are plane waves with up spin (polarization 1)
>           i=npwx+1,npwx+npw are PW with down spin (polarization 2)
>         npw depends on the k-point, npwx is the maximum npw
> 
>     i=npw+1 ,npw+npw are the PW with down spin polorization
>     because the file leading dimension of evc is npwx , is this the
>     correct understanding? 

no it isn't
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From nakhmanson at anl.gov  Tue Oct  7 21:22:47 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 07 Oct 2008 14:22:47 -0500
Subject: [Pw_forum] Is the "cell_dofree" functionality fully implemented
 in Espresso 4.0.x?
In-Reply-To: <48EB2A6B.4070005@sissa.it>
References: <48EA7FAE.7090708@anl.gov> <48EB2A6B.4070005@sissa.it>
Message-ID: <48EBB707.6040400@anl.gov>

Hi Lorenzo,

thank you very much for your comment, I do appreciate it and it does help!

Fixing this is not a problem. I already did it VASP-style, which requires
compiling a separate binary for every particular cell-relaxation constraint.
Granted, this is much less elegant than using the "cell_dofree" switch
but it gets the job done.

BTW, I have a tiny and very conservative example that I used to study the
"cell_dofree" functionality, which converges in around 20 damped-dynamics
steps (and then sits around doing nothing until the limit of ionic steps
is reached). I can send it to you privately if you are interested and willing
to play with it.

Cheers,

Serge

Lorenzo Paulatto wrote:
> Serge Nakhmanson ha scritto:
>> Dear All,
>>
>> Is "cell_dofree" feature in &CELL completely implemented
>> in Espresso 4.0.x?
> Dear Serge,
> I can't give you a definitive answer, as I haven't really used this
> feature. What I can say is that it is not implemented with bfgs
> algorithm and even with damp I'm not really sure it is working. I tried
> to find a quick fix some time ago, but had to give up due to other work.
> 
>> condition in vcsmd.f90 is never reached. Or am I missing
>> something?
>>   
> I think you are right, but it is easy to fix, change
>   ABS( sigma(i,j) ) * uakbar
> to
>   ABS( sigma(i,j) ) * iforceh(i,j) * uakbar
> in both places (be careful with the indexes), and it *should* work.
> 
> I say "should" because I have done a few tries, but couldn't make it
> converge; it is probably due to my inexperience with damped dynamics.
> 
>> Would appreciate any sage comments on this.
>>   
> I''m not really a sage, I hope it helped
> 
> bye
> 


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From nakhmanson at anl.gov  Tue Oct  7 23:45:09 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 07 Oct 2008 16:45:09 -0500
Subject: [Pw_forum] Should I scrap the nonanalytic part of DM in electroded
	thin films?
Message-ID: <48EBD865.8020701@anl.gov>

Dear All,

A small question to those of you with expertise in
phonon calculations of ionic crystals.

I understand that in bulk calculations the dynamical
matrices at small q are split into analytic and
nonanalytic parts, with the latter accounting for the
effects of macroscopic electric field. However, if
we want to study phonons in a model representing an
electroded thin film instead of a bulk crystal (i.e.,
the electrodes are not explicitly included in such a
calculation), we should assume that such an electric
field will be screened out by the free charges and
its influence onto ionic vibrations should not be
considered.

I am under an impression that to achieve this in pwscf
I need to block the calls to nonanal(...) subroutine
in dynmat and matdyn, while leaving everything else
intact. Would this work out or could it possibly be not
as trivial as I imagine it?

Would appreciate your comments,

Serge

-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From marzari at MIT.EDU  Wed Oct  8 00:31:54 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 08 Oct 2008 01:31:54 +0300
Subject: [Pw_forum] Should I scrap the nonanalytic part of DM in
 electroded thin films?
In-Reply-To: <48EBD865.8020701@anl.gov>
References: <48EBD865.8020701@anl.gov>
Message-ID: <48EBE35A.1080609@mit.edu>



Dear Serge,


fascinating question. Not sure about the answer - I'll
ramble a bit here.

Let's see - if we go from the bulk to a thin film (let's
forget the shortcircuiting for a moment) what should happen
is that the 2 TO phonons that were degenerate should now split
in TOpara and TOperp, depending if the modes are perpendicular
or parallel to the thin film.

Would the LO and the TOpara be degenerate ? I think not, for
a suspended thin film, since in the limit of q going to 0 (q of
course now lives in 2d, not in 3d), for a LO mode, you would
still create a dipole per unit cell, i.e. an additional energy
density.

Would contacting this with a metal change what's happening ?
Well, I guess it there were  screening, probably, with the
LO mode dropping down - in case of perfect screening,
becoming degenerate with TOpara. In that case, I presume dropping
the nonalaytic term would do the trick, as you suggest.

Still, I cannot see perfect screening happening, in general -
it will depend on the metal/insulator contact, the thickness, etc...
So you might actually try some calculations in which you keep 
everything, and do a sandwich of real metal and real ionic material ?

I'd be curious to know what people think about Serge's question.

				nicola



Serge Nakhmanson wrote:
> Dear All,
> 
> A small question to those of you with expertise in
> phonon calculations of ionic crystals.
> 
> I understand that in bulk calculations the dynamical
> matrices at small q are split into analytic and
> nonanalytic parts, with the latter accounting for the
> effects of macroscopic electric field. However, if
> we want to study phonons in a model representing an
> electroded thin film instead of a bulk crystal (i.e.,
> the electrodes are not explicitly included in such a
> calculation), we should assume that such an electric
> field will be screened out by the free charges and
> its influence onto ionic vibrations should not be
> considered.
> 
> I am under an impression that to achieve this in pwscf
> I need to block the calls to nonanal(...) subroutine
> in dynmat and matdyn, while leaving everything else
> intact. Would this work out or could it possibly be not
> as trivial as I imagine it?
> 
> Would appreciate your comments,
> 
> Serge
> 


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From iphyboy at hotmail.com  Wed Oct  8 03:19:57 2008
From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=)
Date: Wed, 8 Oct 2008 09:19:57 +0800
Subject: [Pw_forum] code calculating the linear thermal expansion
Message-ID: <COL110-W343DE41DE2433063BDCBD2B33B0@phx.gbl>


Dear all :
 
   I want to investigate the temperature effect on lattice constant.Does anyone have 
the code calculating following qualities.
--Gruneisen parameter
--the linear thermal expansion
--correction bulk modulus
 
please send me a copy of the code
 
Thanks very much .

 
Best wishes
 
Ming Wenmei
 
================================================
Condensed matter physics,Institute of Physics
Chinese Academy of Sciences
P.O.Box 603 Beijing
China
================================================
 
 
_________________________________________________________________
??????????????????????????
http://im.live.cn/Share/18.htm
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From hahoney at gmail.com  Wed Oct  8 07:03:04 2008
From: hahoney at gmail.com (hahoney at gmail.com)
Date: Tue, 7 Oct 2008 21:03:04 -0800
Subject: [Pw_forum] code calculating the linear thermal expansion
Message-ID: <48ec30c5.1e038e0a.3852.ffffe56c@mx.google.com>


If you have any package capable of calculating the phonon properties (dispersion, DOS), there is nothing you can't do.

--Gruneisen parameter: 1. change volume of the primitive cell, 2. fit the frequency variation of a specific mode. 3. calculate the "mode" Gruneisen parameter by definition. 

-- the linear thermal expansion: Try quasi-harmonic approximation. 
 
--correction bulk modulus:  what's this? 

Yi 


Dear all :

   I want to investigate the temperature effect on lattice constant.Does anyone have 
the code calculating following qualities.
--Gruneisen parameter
--the linear thermal expansion
--correction bulk modulus

please send me a copy of the code

Thanks very much .

Best wishes

Ming Wenmei

================================================
Condensed matter physics,Institute of Physics
Chinese Academy of Sciences
P.O.Box 603 Beijing
China
================================================





?????MSN?????????? ????? 
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From baroni at sissa.it  Wed Oct  8 08:03:36 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 8 Oct 2008 08:03:36 +0200
Subject: [Pw_forum] Should I scrap the nonanalytic part of DM in
	electroded thin films?
In-Reply-To: <48EBD865.8020701@anl.gov>
References: <48EBD865.8020701@anl.gov>
Message-ID: <1D8CFCA6-C407-46DC-AA84-65FDE2AD3E4E@sissa.it>

Dear Serge:

>
> I understand that in bulk calculations the dynamical
> matrices at small q are split into analytic and
> nonanalytic parts, with the latter accounting for the
> effects of macroscopic electric field. However, if
> we want to study phonons in a model representing an
> electroded thin film instead of a bulk crystal (i.e.,
> the electrodes are not explicitly included in such a
> calculation), we should assume that such an electric
> field will be screened out by the free charges and
> its influence onto ionic vibrations should not be
> considered.
>
> I am under an impression that to achieve this in pwscf
> I need to block the calls to nonanal(...) subroutine
> in dynmat and matdyn, while leaving everything else
> intact. Would this work out or could it possibly be not
> as trivial as I imagine it?

I am afraid it is indeed not as trivial as you imagine it ... I am no  
longer familiar with the guts of the code, but the only thing the code  
can possibly do is to make the phonons calculated at q=0 equal to the  
values that the phonon branches would have in the long-wavelength  
limit (and those depend in a non trivial way on the combination of  
wavevector/polarization, because of the long range character of the  
Coulomb interaction). I think that, in the presence of free carriers,  
the results of the code are in principle correct whenever the phonon  
wavelength is smaller that the screening length. At q=0 just setting  
the effective charges equal to zero (which is what you would  
presumably get by commenting out some appropriate routine calls)  
should do the job, but you would then get frequencies that are  
inconsistent with those calculated at finite q. To get fully  
consistent results, I think that screening from free carriers should  
be explicitly accounted for in the calculation of the dynamical  
matrix. Possible, but "not as trivial as one could imagine".

Cheers - stefano

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html






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From dmitry at korotin.name  Wed Oct  8 09:59:36 2008
From: dmitry at korotin.name (Dmitry Korotin)
Date: Wed, 8 Oct 2008 13:59:36 +0600
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
Message-ID: <166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>

Dear QE developers,

Does some rigid list of changes in QE between versions 3.2 and 4.0 or
4.0.1 and 4.0.2 exists? I prefer one created by a human, not a
computer. Does the cv2html.pl script the only possibility to get such
kind of information?

--
Best regards,
Dmitry Korotin

Ph. D. Student,
Institute of Metal Physics
S. Kovalevskaya, 18
620041 Ekaterinburg GSP-170
Russia

From paulatto at sissa.it  Wed Oct  8 09:24:32 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 08 Oct 2008 09:24:32 +0200
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
Message-ID: <48EC6030.4030907@sissa.it>

Dmitry Korotin ha scritto:
> Does some rigid list of changes in QE between versions 3.2 and 4.0 or
> 4.0.1 and 4.0.2 exists? I prefer one created by a human, not a
> computer. Does the cv2html.pl script the only possibility to get such
> kind of information?
>   
Dear Dmitry,
yes and no, it is indeed the only rigid list, but there are other ways
to see what has happened to the code:
1. you can see how the BUGS file has been changed to check which serious
bugs have been fixed
<http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/Doc/BUGS>
2. you can check which wanted features have been added by monitoring the
changes in the TODO file:
<http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/TODO>

regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From marzari at MIT.EDU  Wed Oct  8 10:49:21 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 08 Oct 2008 11:49:21 +0300
Subject: [Pw_forum] compiling HELPDOC
Message-ID: <48EC7411.8050307@mit.edu>



Dear All,

I have a problem in compiling HELPDOC (this is the new way
in which INPUT_XX are created, from .def files).

I have tcl and tcllib installed under fedora core 8, but when
I "make" it, it complains that "can't find package tclu 0.9" .

Note that I also have libxslt - the only thing missing is
xsltproc (yum xsltproc, as suggested in the README, complains
that no package with that name exists).

Thanks,

			nicola

-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From meghdad_saeedian at yahoo.com  Wed Oct  8 10:44:00 2008
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Wed, 8 Oct 2008 01:44:00 -0700 (PDT)
Subject: [Pw_forum] about relaxation
Message-ID: <719081.81629.qm@web31403.mail.mud.yahoo.com>

Hi everyone
trying to relax my case(a large one with 24 atoms per cell) i get the famous error? message:
"not orthogonal oporation"
i do? use the symmetry-conserving Wentzecovic algorithm.
so what's the point?
Thanks for any comment.





      
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From djaithania at hotmail.com  Wed Oct  8 11:07:56 2008
From: djaithania at hotmail.com (hania djani-ait aissa)
Date: Wed, 8 Oct 2008 09:07:56 +0000
Subject: [Pw_forum] problems in phonons calculations
Message-ID: <BLU115-W16E889A0875557E7A20C40D23B0@phx.gbl>


Dear all,
I am trying to calculate phonon at Gamma for insulator material with 38 atoms /cell. I have got this error message:
Program PHONON    v.3.2.3  starts ...     Today is  7Oct2008 at 19: 3:42      Ultrasoft (Vanderbilt) Pseudopotentials %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%     from phq_readin : error #         1     reading inputph namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%     stopping ...
I tried to figure out by checking several times, but it seems i am missing something...
thanks a lot for any help.
 Hania Djani-Ait Aissa
Centre for Development of Advanced Technologies,
Algiers, Algeria
 
here my input file:
# self-consistent calculationcat > bto.scf.in << EOF &control    calculation  = 'scf'    restart_mode = 'from_scratch'    pseudo_dir   = '$PSEUDO_DIR/'    outdir       = '$TMP_DIR/' / &system    ibrav=7    celldm(1)=7.294,    celldm(3)=8.557,    nat=19    ntyp=3    nbnd=84    ecutwfc=25.0    ecutrho=180.0,     / &electrons    conv_thr = 1e-6,    mixing_beta=0.2, /ATOMIC_SPECIES  
  Bi    208.98    083-Bi-ca-d-vgrp_ji.uspp.UPF  Ti    47.867    Ti.pz-sp-van.UPF  O     15.9994   O.pz-van_ak.UPF ATOMIC_POSITIONS Bi 0.00000000 0.00000000 0.561 Bi 0.00000000 0.00000000 7.994 Bi 0.00000000 0.00000000 1.812 Bi 0.00000000 0.00000000 6.744 Ti 0.00000000 0.00000000 3.208 Ti 0.00000000 0.00000000 5.347 Ti 0.00000000 0.00000000 4.2785 O  0.50000000 0.00000000 0.0000 O  0.00000000 0.50000000 0.0000 O  0.50000000 0.00000000 2.138 O  0.50000000 0.00000000 6.417 O  0.00000000 0.00000000 3.774 O  0.00000000 0.00000000 4.782 O  0.00000000 0.00000000 2.745 O  0.00000000 0.00000000 5.811 O  0.50000000 0.00000000 0.968 O  0.50000000 0.00000000 7.587 O  0.00000000 0.50000000 0.968 O  0.00000000 0.50000000 7.587 K_POINTS {automatic}  5 5 5 1 1 1EOF$ECHO "  running self-consistent calculation in BTO...\c"$PW_COMMAND < bto.scf.in > bto.scf.out$ECHO " done"# phonon calculation at Gammacat > bto.phG.in << EOF&inputphtr2_ph=1.0d-14,prefix='bto',epsil=.true.,amass(1)=208.98,amass(2)=47.86,amass(3)=15.99,outdir='$TMP_DIR/',fildyn='bto.dynG',/0.0 0.0 0.0EOF$ECHO "  running the phonon calculation at Gamma...\c"$PH_COMMAND < bto.phG.in > bto.phG.out$ECHO " done"
  
 
_________________________________________________________________
Appelez vos amis de PC ? PC -- C'EST GRATUIT
http://get.live.com/messenger/overview
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From paulatto at sissa.it  Wed Oct  8 11:29:01 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 08 Oct 2008 11:29:01 +0200
Subject: [Pw_forum] compiling HELPDOC
In-Reply-To: <48EC7411.8050307@mit.edu>
References: <48EC7411.8050307@mit.edu>
Message-ID: <48EC7D5D.8050109@sissa.it>

Nicola Marzari ha scritto:
> I have tcl and tcllib installed under fedora core 8, but when
> I "make" it, it complains that "can't find package tclu 0.9" .
>   
Hi Nicola,
tclu is part of QE-GUI, if you have downloaded it from cvs you have to
do an "update -dP" to get the GUI files.

I hope it is enough

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From paulatto at sissa.it  Wed Oct  8 11:51:27 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 08 Oct 2008 11:51:27 +0200
Subject: [Pw_forum] problems in phonons calculations
In-Reply-To: <BLU115-W16E889A0875557E7A20C40D23B0@phx.gbl>
References: <BLU115-W16E889A0875557E7A20C40D23B0@phx.gbl>
Message-ID: <48EC829F.4090009@sissa.it>

hania djani-ait aissa ha scritto:
Dear Hania,
I don't know why this is happening, but if you leave an empty line
before &inputph it should not happen anymore:

cat > bto.phG.in << EOF

&inputph
tr2_ph=1.0d-14,
prefix='bto',
epsil=.true.,
amass(1)=208.98,
amass(2)=47.86,
amass(3)=15.99,
outdir='$TMP_DIR/',
fildyn='bto.dynG',
/
0.0 0.0 0.0
EOF


bye

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From baroni at sissa.it  Wed Oct  8 13:15:57 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 8 Oct 2008 13:15:57 +0200
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
Message-ID: <F35316C9-9A4E-485A-B11D-A85E4C2B84C5@sissa.it>

Dear Dmitry:

>
> Does some rigid list of changes in QE between versions 3.2 and 4.0 or
> 4.0.1 and 4.0.2 exists?

what is a "rigid" list? one written steel? ;-)

> I prefer one created by a human, not a
> computer.

computers are there to do what is presumably too boring for a human to  
do

> Does the cv2html.pl script the only possibility to get such
> kind of information?

if you tell us what kind of info you need, and for what purpose, it  
would probably be easier for somebody willing to help to do so

cheers - Stefano

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html






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From giannozz at democritos.it  Wed Oct  8 15:20:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 08 Oct 2008 15:20:52 +0200
Subject: [Pw_forum] problems in phonons calculations
In-Reply-To: <48EC829F.4090009@sissa.it>
References: <BLU115-W16E889A0875557E7A20C40D23B0@phx.gbl>
	<48EC829F.4090009@sissa.it>
Message-ID: <48ECB3B4.8010105@democritos.it>

Lorenzo Paulatto wrote:

> I don't know why this is happening, but if you leave an empty line
> before &inputph it should not happen anymore:

the title of the job is read from the first line of the input file.
This is documented.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Wed Oct  8 15:27:03 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 08 Oct 2008 15:27:03 +0200
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
Message-ID: <48ECB527.6030806@democritos.it>

Dmitry Korotin wrote:

> Does some rigid list of changes in QE between versions 3.2 
> and 4.0 or 4.0.1 and 4.0.2 exists? I prefer one created by
> a human, not a computer.  Does the cv2html.pl script the only
> possibility to get such kind of information?

the list is created by the computer, but the information that
is listed is written by humans (and it shows). If you are looking
for a less verbose list of changes, the message announcing the
new release contained this list (admittedly not very verbose):

- Better scalability on massively parallel machines: more arrays are
   distributed and processed in parallel, thus removing CPU and memory
   bottlenecks - CP has been demonstrated to run on up to 4000 processors

- Projector Augmented Wave (PAW) is implemented

- Calculation of NMR chemical shifts using GIPAW (Gauge-Independent PAW)

- Inclusion of the Wannier90 code (http://www.wannier.org/) for
   calculation of maximally localized Wannier functions

- Many other minor improvements: cleanup, porting to new architectures,
   many bugs fixed (and new bug opportunities added: please help
   debugging!)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From manoj at phys.ufl.edu  Wed Oct  8 17:42:54 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Wed, 8 Oct 2008 11:42:54 -0400 (EDT)
Subject: [Pw_forum] possible bug in scatter_forw.f90
Message-ID: <Pine.GSO.4.21.0810081112500.13663-100000@neptune.phys.ufl.edu>


Dear All, 
 Is any body familiar with the scatter_forw.f90 subroutine of PWCOND? I
think there is a bug in this subroutine at the place where you calculate
intw2, which is z integration of nonlocal wavefunction with beta function.
I have looked up the necessary formulae in the Choi & Ihm's paper (PRB 59,
2267, Jan 1999). In the paper, nonlocal wavefunction has 3 terms, one of
which contains beta function, say W. The other two parts dont have any W
in them, rather they are just plane wave solution. (Please have a look at
equation 24 and 26 of the paper ). So, when we are doing z integration of
nonlocal wavefunction with beta function W, we should have three terms,
one of which should contain two W, but rest should just have one W. On the
other hand in the code all three terms contain two beta functions!!
(please have a look at line 228 of scatter_forw.f90). I am wondering if my
understanding is right? 
I have one more question in the later part of the same subroutine. What
does the lapack subroutine 
ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
do? 
I tried to look it up and i got the idea that it is trying to solve 
amat*x=xmat, with amat and xmat known and x unknown, and at the end of
calculation it stores x in xmat. 
so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it changes
the structure of xmat from what is defined in 'constructs matrices'
part. Is it correct? 
Also, afterwards in this code where  it 'rotates integrals' is not very
clear to me. 
Could somebody please tell me in little detail, what is going on
here? Also, is this subroutine written just on the basis of Choi and Ihm
paper, or are there more reference to it? If yes, would someone mind
mentioning them? 

Regards, 
Manoj Srivastava 
Physics Graduate Student 
University of Florida, 
Gainesville,FL, USA


From niuli1978 at yahoo.com.cn  Thu Oct  9 03:35:47 2008
From: niuli1978 at yahoo.com.cn (li niu)
Date: Thu, 9 Oct 2008 09:35:47 +0800 (CST)
Subject: [Pw_forum] about the calculation of partial Raman
Message-ID: <167194.97762.qm@web15004.mail.cnb.yahoo.com>

Hello pwscf users,
I am doing Raman calculation on boron doped diamond by second-order response method, as described in example 15. I used the dynmat.x code
to obtain Raman cross sections. Now I want to perform a Raman projected 
  on specific atoms (partial Raman), but don't know how to do?  Any suggestions would be appreciated!
   
   thanks
   
  Li Niu
Harbin Institue of Technology                     
China


       
---------------------------------
 ????????????
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From dmitry at korotin.name  Thu Oct  9 06:45:31 2008
From: dmitry at korotin.name (Dmitry Korotin)
Date: Thu, 9 Oct 2008 10:45:31 +0600
Subject: [Pw_forum] Changelogs
In-Reply-To: <48ECB527.6030806@democritos.it>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
	<48ECB527.6030806@democritos.it>
Message-ID: <166cd7c60810082145r2ac4980y146f0b40803d8a27@mail.gmail.com>

Dear Paolo,
It would be nice if I see something intermediate between data produced
by cv2html.pl and data posted by you:

> - Better scalability on massively parallel machines: more arrays are
>   distributed and processed in parallel, thus removing CPU and memory
>   bottlenecks - CP has been demonstrated to run on up to 4000 processors ...

Anyway, I have seen this changelog for the first time in you e-mail.
May be I should subscribe for some special mailing-list to receive it?

Dear Stefano,
> if you tell us what kind of info you need, and for what purpose, it would probably be easier for somebody willing to help to do so
Some time ago I modified ESPRESSO-3.0 to implement construction of
atomic-like Wannier-functions and generation of LDA Hamiltonian on
Wannier basis set. My code was far from perfect but it works nice. Now
I am trying to understand a need to rewrite my code for ESPRESSO-4.0.2
and to realize the amount of changes that I should make for this
purpose. I want to know how deep ESPRESSO source have changed.

Dear Lorenzo,
thank you for your information (and thank you for a brilliant
pseudopotential-presentation that I have found on your homepage).


Best regards,
Dmitry Korotin

Ph. D. Student,
Institute of Metal Physics
S. Kovalevskaya, 18
620041 Ekaterinburg GSP-170
Russia

From arunmanna at jncasr.ac.in  Thu Oct  9 07:57:51 2008
From: arunmanna at jncasr.ac.in (Arun Kumar Manna)
Date: Thu, 9 Oct 2008 09:57:51 +0400 (RET)
Subject: [Pw_forum] Problem regarding raman calculation
In-Reply-To: <mailman.677.1223464571.1801.pw_forum@pwscf.org>
References: <mailman.677.1223464571.1801.pw_forum@pwscf.org>
Message-ID: <42405.172.16.1.1.1223531871.squirrel@172.16.1.1>


  Dear Users,
           Is it possible to get raman tensors at k-points other that
  gamma point?. If possibe, could you please tell me how to modify $inputph
  file for ph.x?.

  Thanks
   Arun










> Send Pw_forum mailing list submissions to
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. Changelogs (Dmitry Korotin)
>    2. Re: Changelogs (Lorenzo Paulatto)
>    3. compiling HELPDOC (Nicola Marzari)
>    4. about relaxation (meghdad saeedian)
>    5. problems in phonons calculations (hania djani-ait aissa)
>    6. Re: compiling HELPDOC (Lorenzo Paulatto)
>    7. Re: problems in phonons calculations (Lorenzo Paulatto)
>    8. Re: Changelogs (Stefano Baroni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 8 Oct 2008 13:59:36 +0600
> From: "Dmitry Korotin" <dmitry at korotin.name>
> Subject: [Pw_forum] Changelogs
> To: "PWSCF Forum" <Pw_forum at pwscf.org>
> Message-ID:
> 	<166cd7c60810080059w77ff4824mf7e83ab770515dd7 at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear QE developers,
>
> Does some rigid list of changes in QE between versions 3.2 and 4.0 or
> 4.0.1 and 4.0.2 exists? I prefer one created by a human, not a
> computer. Does the cv2html.pl script the only possibility to get such
> kind of information?
>
> --
> Best regards,
> Dmitry Korotin
>
> Ph. D. Student,
> Institute of Metal Physics
> S. Kovalevskaya, 18
> 620041 Ekaterinburg GSP-170
> Russia
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 08 Oct 2008 09:24:32 +0200
> From: Lorenzo Paulatto <paulatto at sissa.it>
> Subject: Re: [Pw_forum] Changelogs
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <48EC6030.4030907 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-15
>
> Dmitry Korotin ha scritto:
>> Does some rigid list of changes in QE between versions 3.2 and 4.0 or
>> 4.0.1 and 4.0.2 exists? I prefer one created by a human, not a
>> computer. Does the cv2html.pl script the only possibility to get such
>> kind of information?
>>
> Dear Dmitry,
> yes and no, it is indeed the only rigid list, but there are other ways
> to see what has happened to the code:
> 1. you can see how the BUGS file has been changed to check which serious
> bugs have been fixed
> <http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/Doc/BUGS>
> 2. you can check which wanted features have been added by monitoring the
> changes in the TODO file:
> <http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/TODO>
>
> regards
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 08 Oct 2008 11:49:21 +0300
> From: Nicola Marzari <marzari at MIT.EDU>
> Subject: [Pw_forum] compiling HELPDOC
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <48EC7411.8050307 at mit.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Dear All,
>
> I have a problem in compiling HELPDOC (this is the new way
> in which INPUT_XX are created, from .def files).
>
> I have tcl and tcllib installed under fedora core 8, but when
> I "make" it, it complains that "can't find package tclu 0.9" .
>
> Note that I also have libxslt - the only thing missing is
> xsltproc (yum xsltproc, as suggested in the README, complains
> that no package with that name exists).
>
> Thanks,
>
> 			nicola
>
> --
> ---------------------------------------------------------------------
> Prof Nicola Marzari   Department of Materials Science and Engineering
> 13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
> tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 8 Oct 2008 01:44:00 -0700 (PDT)
> From: meghdad saeedian <meghdad_saeedian at yahoo.com>
> Subject: [Pw_forum] about relaxation
> To: pw_forum at pwscf.org
> Message-ID: <719081.81629.qm at web31403.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone
> trying to relax my case(a large one with 24 atoms per cell) i get the
> famous error? message:
> "not orthogonal oporation"
> i do? use the symmetry-conserving Wentzecovic algorithm.
> so what's the point?
> Thanks for any comment.
>
>
>
>
>
>
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>
> ------------------------------
>
> Message: 5
> Date: Wed, 8 Oct 2008 09:07:56 +0000
> From: hania djani-ait aissa <djaithania at hotmail.com>
> Subject: [Pw_forum] problems in phonons calculations
> To: <pw_forum at pwscf.org>
> Message-ID: <BLU115-W16E889A0875557E7A20C40D23B0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear all,
> I am trying to calculate phonon at Gamma for insulator material with 38
> atoms /cell. I have got this error message:
> Program PHONON    v.3.2.3  starts ...     Today is  7Oct2008 at 19: 3:42
>    Ultrasoft (Vanderbilt) Pseudopotentials
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from phq_readin : error #         1     reading inputph namelist
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     stopping ...
> I tried to figure out by checking several times, but it seems i am missing
> something...
> thanks a lot for any help.
>  Hania Djani-Ait Aissa
> Centre for Development of Advanced Technologies,
> Algiers, Algeria
>
> here my input file:
> # self-consistent calculationcat > bto.scf.in << EOF &control
> calculation  = 'scf'    restart_mode = 'from_scratch'    pseudo_dir   =
> '$PSEUDO_DIR/'    outdir       = '$TMP_DIR/' / &system    ibrav=7
> celldm(1)=7.294,    celldm(3)=8.557,    nat=19    ntyp=3    nbnd=84
> ecutwfc=25.0    ecutrho=180.0,     / &electrons    conv_thr = 1e-6,
> mixing_beta=0.2, /ATOMIC_SPECIES
>   Bi    208.98    083-Bi-ca-d-vgrp_ji.uspp.UPF  Ti    47.867
> Ti.pz-sp-van.UPF  O     15.9994   O.pz-van_ak.UPF ATOMIC_POSITIONS Bi
> 0.00000000 0.00000000 0.561 Bi 0.00000000 0.00000000 7.994 Bi 0.00000000
> 0.00000000 1.812 Bi 0.00000000 0.00000000 6.744 Ti 0.00000000 0.00000000
> 3.208 Ti 0.00000000 0.00000000 5.347 Ti 0.00000000 0.00000000 4.2785 O
> 0.50000000 0.00000000 0.0000 O  0.00000000 0.50000000 0.0000 O
> 0.50000000 0.00000000 2.138 O  0.50000000 0.00000000 6.417 O  0.00000000
> 0.00000000 3.774 O  0.00000000 0.00000000 4.782 O  0.00000000 0.00000000
> 2.745 O  0.00000000 0.00000000 5.811 O  0.50000000 0.00000000 0.968 O
> 0.50000000 0.00000000 7.587 O  0.00000000 0.50000000 0.968 O  0.00000000
> 0.50000000 7.587 K_POINTS {automatic}  5 5 5 1 1 1EOF$ECHO "  running
> self-consistent calculation in BTO...\c"$PW_COMMAND < bto.scf.in >
> bto.scf.out$ECHO " done"# phonon calculation at Gammacat > bto.phG.in <<
> EOF&inputphtr2_ph=1.0d-14,prefix='bto',epsil=.true.,amass(1)=208.98,amass(2)=47.86,amass(3)=15.99,outdir='$TMP_DIR/',fildyn='bto.dynG',/0.0
> 0.0 0.0EOF$ECHO "  running the phonon calculation at
> Gamma...\c"$PH_COMMAND < bto.phG.in > bto.phG.out$ECHO " done"
>
>
> _________________________________________________________________
> Appelez vos amis de PC ? PC -- C'EST GRATUIT
> http://get.live.com/messenger/overview
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>
> ------------------------------
>
> Message: 6
> Date: Wed, 08 Oct 2008 11:29:01 +0200
> From: Lorenzo Paulatto <paulatto at sissa.it>
> Subject: Re: [Pw_forum] compiling HELPDOC
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <48EC7D5D.8050109 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-15
>
> Nicola Marzari ha scritto:
>> I have tcl and tcllib installed under fedora core 8, but when
>> I "make" it, it complains that "can't find package tclu 0.9" .
>>
> Hi Nicola,
> tclu is part of QE-GUI, if you have downloaded it from cvs you have to
> do an "update -dP" to get the GUI files.
>
> I hope it is enough
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 08 Oct 2008 11:51:27 +0200
> From: Lorenzo Paulatto <paulatto at sissa.it>
> Subject: Re: [Pw_forum] problems in phonons calculations
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <48EC829F.4090009 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-15
>
> hania djani-ait aissa ha scritto:
> Dear Hania,
> I don't know why this is happening, but if you leave an empty line
> before &inputph it should not happen anymore:
>
> cat > bto.phG.in << EOF
>
> &inputph
> tr2_ph=1.0d-14,
> prefix='bto',
> epsil=.true.,
> amass(1)=208.98,
> amass(2)=47.86,
> amass(3)=15.99,
> outdir='$TMP_DIR/',
> fildyn='bto.dynG',
> /
> 0.0 0.0 0.0
> EOF
>
>
> bye
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 8 Oct 2008 13:15:57 +0200
> From: Stefano Baroni <baroni at sissa.it>
> Subject: Re: [Pw_forum] Changelogs
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <F35316C9-9A4E-485A-B11D-A85E4C2B84C5 at sissa.it>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dmitry:
>
>>
>> Does some rigid list of changes in QE between versions 3.2 and 4.0 or
>> 4.0.1 and 4.0.2 exists?
>
> what is a "rigid" list? one written steel? ;-)
>
>> I prefer one created by a human, not a
>> computer.
>
> computers are there to do what is presumably too boring for a human to
> do
>
>> Does the cv2html.pl script the only possibility to get such
>> kind of information?
>
> if you tell us what kind of info you need, and for what purpose, it
> would probably be easier for somebody willing to help to do so
>
> cheers - Stefano
>
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -
> Trieste
> http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale
> de la pens?e - Jean Piaget
>
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 16, Issue 16
> ****************************************
>


-- 
PhD Student
JNCASR, Bangalore-560064
India

From baroni at sissa.it  Thu Oct  9 08:39:33 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 9 Oct 2008 08:39:33 +0200
Subject: [Pw_forum] Problem regarding raman calculation
In-Reply-To: <42405.172.16.1.1.1223531871.squirrel@172.16.1.1>
References: <mailman.677.1223464571.1801.pw_forum@pwscf.org>
	<42405.172.16.1.1.1223531871.squirrel@172.16.1.1>
Message-ID: <39D5F4B5-D737-40FA-8589-3A2287312EAF@sissa.it>

phonon modes are only Raman active at q=0 (more exactly, at very small  
q)
Exercise: WHY?
SB

PS: your e-mail contained several kbytes of (undeleted) garbage:  
please, take the time to remove them the next time you post


On Oct 9, 2008, at 7:57 AM, Arun Kumar Manna wrote:

>
>  Dear Users,
>           Is it possible to get raman tensors at k-points other that
>  gamma point?. If possibe, could you please tell me how to modify  
> $inputph
>  file for ph.x?.
>
>  Thanks
>   Arun


---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html






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From giannozz at democritos.it  Thu Oct  9 09:12:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 09 Oct 2008 09:12:33 +0200
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810082145r2ac4980y146f0b40803d8a27@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>	<48ECB527.6030806@democritos.it>
	<166cd7c60810082145r2ac4980y146f0b40803d8a27@mail.gmail.com>
Message-ID: <48EDAEE1.5040606@democritos.it>

Dmitry Korotin wrote:

> It would be nice if I see something intermediate between data
> produced by cv2html.pl and data posted by you:

sure it would be nice, but it would also take a lot of time

> Anyway, I have seen this changelog for the first time in you e-mail.
> May be I should subscribe for some special mailing-list to receive it?

a not-so-special mailing list: pw_users at pwscf.org, containing
(sparse) announcements about quantum-espresso:
    http://www.democritos.it/pipermail/pw_users/
Mailing lists will move to a new server, by the way, so there
might be some "reshuffling" of mailing lists soon

> Some time ago I modified ESPRESSO-3.0 to implement construction of
> atomic-like Wannier-functions and generation of LDA Hamiltonian on
> Wannier basis set. My code was far from perfect but it works nice.
> Now I am trying to understand a need to rewrite my code for ESPRESSO-4.0.2
> and to realize the amount of changes that I should make for this
> purpose. I want to know how deep ESPRESSO source have changed.

The core of quantum-espresso doesn't change much and not often,
but v3.0 was released 3 years ago, so it is very likely that you
need to change something. It also depends a lot on how you wrote
your code and how tightly bound it is to the q-e code. Also note
that there is quite a lot of Wannier-related stuff in q-e now.

We hope to have soon in place a server where add-ons and
contributions to q-e are posted and developed. This should
solve problems like yours.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Thu Oct  9 09:15:01 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 09 Oct 2008 09:15:01 +0200
Subject: [Pw_forum] about the calculation of partial Raman
In-Reply-To: <167194.97762.qm@web15004.mail.cnb.yahoo.com>
References: <167194.97762.qm@web15004.mail.cnb.yahoo.com>
Message-ID: <48EDAF75.6090006@democritos.it>

li niu wrote:

> I am doing Raman calculation on boron doped diamond by second-order 
> response method, as described in example 15. I used the dynmat.x code
> to obtain Raman cross sections. Now I want to perform a Raman projected
> on specific atoms (partial Raman), but don't know how to do?  

you have Raman coefficients for each single atom: what do you mean by
"Raman projected on specific atoms (partial Raman)"?

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From wangqj1 at 126.com  Thu Oct  9 09:34:28 2008
From: wangqj1 at 126.com (wangqj1)
Date: Thu, 9 Oct 2008 15:34:28 +0800 (CST)
Subject: [Pw_forum] About LDA+U
Message-ID: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>

 
 Dear Mansoureh

      I have not got U for this system ,So I want to caculate it .Can you give some advice and examples ? Thank you !
 
 
 
 
 
 
 Dear Wang
have you got U for this system?or do you want to calculate it?
Mansoureh

>
>  Dear pwscf users
>
>     I want to do some LDA+U caculations of Mn adoped ZnO, but I don't know
> how to set
>
> the parameter of Hubbard_U(I) , *Does anyone know the Hubbard U parameter
> of ZnO and Mn ?*
> *   *
>  *Any help will be greatly appreciated.*
> **
>
> Sincerely.
>
> Wang
> **
>
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From giannozz at democritos.it  Thu Oct  9 10:07:31 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 09 Oct 2008 10:07:31 +0200
Subject: [Pw_forum] About LDA+U
In-Reply-To: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
Message-ID: <48EDBBC3.2000908@democritos.it>

wangqj1 wrote:

> Does anyone know the Hubbard U parameter of ZnO and Mn ?

for what is worth: for Mn a "typical" U parameter is in
the order of 4eV

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From chen_shao_hua197 at yahoo.com.tw  Thu Oct  9 10:18:38 2008
From: chen_shao_hua197 at yahoo.com.tw (=?big5?B?s68gpNa12A==?=)
Date: Thu, 9 Oct 2008 16:18:38 +0800 (CST)
Subject: [Pw_forum] Phonon partial density of state
In-Reply-To: <226112.10531.qm@web65715.mail.ac4.yahoo.com>
Message-ID: <234538.12981.qm@web73004.mail.tp2.yahoo.com>

Dear Prof. Eyvaz Isaev,

I also want to calculate phonon partial DOS.
Could I have one ?
Thank you very much.

Max

Candidate of Doctor
Physics department, National Taiwan University, Taipei, Taiwan



--- 08/10/7 (???)?Eyvaz Isaev <eyvaz_isaev at yahoo.com> ???

> ???: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> ??: Re: [Pw_forum] Phonon partial density of state
> ???: "PWSCF Forum" <pw_forum at pwscf.org>
> ??: 2008 10 7 ??? ?? 8:26
> Hi,
> 
> I will send you the code.       
> 
> Bests,
> Eyvaz.
> 
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev, 
> Theoretical Physics Department, Moscow State Institute of
> Steel & Alloys, Russia, 
> Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University, Sweden 
> Condensed Matter Theory Group, Uppsala University, Sweden 
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com
> 
> 
> --- On Tue, 10/7/08, babderre at physics.auth.gr
> <babderre at physics.auth.gr> wrote:
> 
> > From: babderre at physics.auth.gr
> <babderre at physics.auth.gr>
> > Subject: [Pw_forum] Phonon partial density of state
> > To: pw_forum at pwscf.org
> > Date: Tuesday, October 7, 2008, 3:13 PM
> > Dear pwscf users,
> > 
> >  I want to calculate phonon partial density of state.
> >  Could you please tell me how to calculate them?
> > 
> > thanks in advance!
> > belabbes.
> > http://parsem.physics.auth.gr/belabbes.htm
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
>       
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      ______________________________________________________________________________________________________
?????????Yahoo!??????2.0????????????? http://tw.mg0.mail.yahoo.com/dc/landing


From sauluck at iitk.ac.in  Thu Oct  9 11:16:04 2008
From: sauluck at iitk.ac.in (Sushil Auluck)
Date: Thu, 9 Oct 2008 14:46:04 +0530 (IST)
Subject: [Pw_forum] About LDA+U
In-Reply-To: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
Message-ID: <46280.122.162.199.64.1223543764.squirrel@newwebmail.iitk.ac.in>

hi,
in a recent paper on LiMnO2 (doi:10.10.1016/j.jallcom.2008.06.123)
the authors claim that U for Mn is between 4-5 eV. in their own work
they varied it from 3-6 eV and finally settled for 4.5 e.V
U is calculated using a supercell approach......
s.auluck

>
>  Dear Mansoureh
>
>       I have not got U for this system ,So I want to caculate it .Can you
> give some advice and examples ? Thank you !
>
>
>
>
>
>
>  Dear Wang
> have you got U for this system?or do you want to calculate it?
> Mansoureh
>
>>
>>  Dear pwscf users
>>
>>     I want to do some LDA+U caculations of Mn adoped ZnO, but I don't
>> know
>> how to set
>>
>> the parameter of Hubbard_U(I) , *Does anyone know the Hubbard U
>> parameter
>> of ZnO and Mn ?*
>> *   *
>>  *Any help will be greatly appreciated.*
>> **
>>
>> Sincerely.
>>
>> Wang
>> **
>>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


.......................................................................
Prof. Sushil Auluck                      Phone:+91-512-6797092/6148
Department of Physics                          +91-512-6798177(Home)
Indian Institute of Technology           Cell :+91-9305548667
Kanpur 208016 (UP)                       Fax  :+91-512-6790914
India                                    E-mail:sauluck at iitk.ac.in        
     ...............................................:sauluck at gmail.com
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
.......................................................................
~

From marzari at MIT.EDU  Thu Oct  9 11:24:04 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 09 Oct 2008 12:24:04 +0300
Subject: [Pw_forum] About LDA+U
In-Reply-To: <48EDBBC3.2000908@democritos.it>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
	<48EDBBC3.2000908@democritos.it>
Message-ID: <48EDCDB4.3030904@mit.edu>

Paolo Giannozzi wrote:
> wangqj1 wrote:
> 
>> Does anyone know the Hubbard U parameter of ZnO and Mn ?
> 
> for what is worth: for Mn a "typical" U parameter is in
> the order of 4eV
> 
> Paolo

Dear Wangqj1,

as a side note to Paolo's comments:

1) the value of U is fairly sensitive to the oxidation state of
the pseudopotential - so the same element, generated with different
reference atomic configurations (e.g. neutral, +1, +2.5, etc...)
would give fairly different U, as calculated according to the
procedure of Cococcioni and de Gironcoli, PRB 2005. We have an
example in the appendix of Kulik and Marzari JCP 129 134314 (2008).

2) the U implemented in PWSCF is more like a U-J, so you might
want even more care in comparing this with other published results.

My own comment is that the numerical value of U shouldn't be
given too much importance. What is important is stating what is the
the analytic shape of the Hubbard term (e.g. PWSCf adopts the C&dG PRB
2005 rotationally-invariant functional), and agreeing that, for
a given structure, for a given electronic-structure configuration,
and for a given pseudopotential, the linear-response procedure
gives us a well-defined, first-principles U to use.

Last - extra-care should be paid to the fact that some of the 
pseudopotentials in the PWSCF database have non-normalized atomic 
wavefunctions - I've lost track of what is the latest status on
this (Matteo, Heather - can you comment ?) but I believe
norm-atomic would fix that automatically.

Best,

			nicola

---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu


From giannozz at democritos.it  Thu Oct  9 11:59:29 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 09 Oct 2008 11:59:29 +0200
Subject: [Pw_forum] About LDA+U
In-Reply-To: <48EDCDB4.3030904@mit.edu>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>	<48EDBBC3.2000908@democritos.it>
	<48EDCDB4.3030904@mit.edu>
Message-ID: <48EDD601.9050601@democritos.it>

Nicola Marzari wrote:s:

> Last - extra-care should be paid to the fact that some of the 
> pseudopotentials in the PWSCF database have non-normalized 
> atomic  wavefunctions 

fixed in the CVS version (at least based on the annoying
messages that are issued when non-normalized atomic
wavefunctions are found)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From greencomp86 at yahoo.com  Thu Oct  9 13:38:58 2008
From: greencomp86 at yahoo.com (ha salem)
Date: Thu, 9 Oct 2008 04:38:58 -0700 (PDT)
Subject: [Pw_forum] mkl
Message-ID: <913014.19858.qm@web45812.mail.sp1.yahoo.com>

dear users
I have problem with intel mkl
I want some help for mkl installation
I get this error undefine refrence
thank you



      


From lanhaiping at gmail.com  Thu Oct  9 16:05:54 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 9 Oct 2008 22:05:54 +0800
Subject: [Pw_forum] mkl
In-Reply-To: <913014.19858.qm@web45812.mail.sp1.yahoo.com>
References: <913014.19858.qm@web45812.mail.sp1.yahoo.com>
Message-ID: <c92002fa0810090705i67b06aafge687a065af5d050e@mail.gmail.com>

i think you can find related docs at intel's website
just using google to reach this site

On Thu, Oct 9, 2008 at 7:38 PM, ha salem <greencomp86 at yahoo.com> wrote:

> dear users
> I have problem with intel mkl
> I want some help for mkl installation
> I get this error undefine refrence
> thank you
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From akohlmey at cmm.chem.upenn.edu  Thu Oct  9 16:13:04 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 9 Oct 2008 10:13:04 -0400 (EDT)
Subject: [Pw_forum] Changelogs
In-Reply-To: <166cd7c60810082145r2ac4980y146f0b40803d8a27@mail.gmail.com>
References: <166cd7c60810070128i4e3c1604m80dd1bec0add13e@mail.gmail.com>
	<166cd7c60810080059w77ff4824mf7e83ab770515dd7@mail.gmail.com>
	<48ECB527.6030806@democritos.it>
	<166cd7c60810082145r2ac4980y146f0b40803d8a27@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810091005520.15555@localhost.localdomain>

On Thu, 9 Oct 2008, Dmitry Korotin wrote:

dear dmitry,

DK> > if you tell us what kind of info you need, and for what purpose, it would probably be easier for somebody willing to help to do so
DK> Some time ago I modified ESPRESSO-3.0 to implement construction of
DK> atomic-like Wannier-functions and generation of LDA Hamiltonian on
DK> Wannier basis set. My code was far from perfect but it works nice. Now
DK> I am trying to understand a need to rewrite my code for ESPRESSO-4.0.2
DK> and to realize the amount of changes that I should make for this
DK> purpose. I want to know how deep ESPRESSO source have changed.

_no_ form of changelog will _ever_ be able to tell you that.
in fact, what you'd need to know would be even more detailed.
however, with a publically accessable cvs you can do it yourself.
rather than looking at the changelogs for the whole package,
i would suggest to have a look of the individual changelogs 
for the files that you had to modify and the modules that you
import. after identifying the "interesting" commits you can
then create diff files (prefereably with context, i.e. diff -u
or diff -c) to see what was changed in particular and how this
would affect your code.

an interesting tool that can be helpful in this regard is
a program called "cvsps" that will combine detailed changelog
and diffs into patchsets and one can generate diffs for patch
sets that correlate to groups of commits.

cheers,
   axel.

DK> 
DK> Best regards,
DK> Dmitry Korotin
DK> 
DK> Ph. D. Student,
DK> Institute of Metal Physics
DK> S. Kovalevskaya, 18
DK> 620041 Ekaterinburg GSP-170
DK> Russia
DK> _______________________________________________
DK> Pw_forum mailing list
DK> Pw_forum at pwscf.org
DK> http://www.democritos.it/mailman/listinfo/pw_forum
DK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From guido.roma at cea.fr  Thu Oct  9 16:02:31 2008
From: guido.roma at cea.fr (Guido Roma)
Date: Thu, 09 Oct 2008 16:02:31 +0200
Subject: [Pw_forum] Compiling problem on itanium2 bull cluster
In-Reply-To: <48EA2104.40605@theory.polytechnique.fr>
References: <48EA0DF0.7010504@theory.polytechnique.fr>	<Pine.LNX.4.64.0810061010040.18122@localhost.localdomain>
	<48EA2104.40605@theory.polytechnique.fr>
Message-ID: <48EE0EF7.10508@cea.fr>

Dear Federico,

maybe you already solved the problem in the meanwhile, anyway:
I just compiled the 4.0.2 version (pw and pp) with the compiler versions 
10.1.011.
You can switch to them on platine by:
module switch intel/cc/9.1.049 intel/cc/10.1.011
module switch intel/fc/9.1.045 intel/fc/10.1.011
However I had compiled (and used) the 4.0.1 with the previous compiler 
versions that you mention without any problem.

Guido


Federico Iori wrote:
> oookey!
>
> thanks so much for the advice.
> Btw, as Lorenzo pointed out i didn't  specified the compiler. I'm gonna 
> do now:
>
> FC intel 9.1.045
> CC intel 9.1.049
>
> but i have also to add that:
>
> espresso_4.0 doesnt give any problems, nor with make pw nor with make pp
>
> while the espresso_4.0.1 and the next one espresso_4.0.2 give the same 
> problem i described before.
>
> well...let me try now with the option -no-ipo suggested before.
> i will tell you. and also i will communicate this error to the CCRT guys.
>
> thanks to everybody!
>
>
>
> Axel Kohlmeyer wrote:
>   
>> On Mon, 6 Oct 2008, Federico Iori wrote:
>>
>> FI> Dear all.
>>
>> dear federico!
>>  
>> FI> I was compiling my Pwscf on this machine (PLATINE the common name)
>>
>> [...]
>>
>> FI> *fortcom: Severe: **Internal compiler error: internal abort** Please report
>> FI> this error along with the circumstances in which it occurred in a Software
>> FI> Problem Report.  Note: File and line given may not be explicit cause of this
>> FI> error.
>> FI> 
>> FI> ifort: error: problem during multi-file optimization compilation (code 3)
>>
>> [...]
>>
>> FI> doing the ./configure everything seems to work perfectly.
>> FI> Then the make pw step works perfectly.
>> FI> But in the end i cant compile the pp or pwall stuff.
>> FI> 
>> FI> What do you suggest me to do? Should I bother you or directly the
>> FI> technicians in the CCRT centre??
>>
>> as stated here many times before: an internal compiler error
>> is a bug in the _compiler_, not the application. given the 
>> hardware configuration that you describe, it is very likely that 
>> you have a broken intel compiler and you need to update it to 
>> the latest patchlevel. this is a quite common problem. 
>>
>> i also strongly advise to run tests with the compiled executables,
>> as there are very high chances that those are miscompiled. these
>> days, a successful compilation does not mean, that you have a
>> correctly working executables. the itanium architecture is quite
>> notorious there, since the compiler has to do more work compared
>> to other architectures.
>>
>> cheers,
>>    axel.
>>
>>
>>
>> FI> Thanks so much in advance!
>> FI> federico iori
>> FI> 
>> FI> 
>> FI> 
>>
>>   
>>     
>
>
>   

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From matteo at umn.edu  Thu Oct  9 16:35:45 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 09 Oct 2008 09:35:45 -0500
Subject: [Pw_forum] About LDA+U
In-Reply-To: <48EDD601.9050601@democritos.it>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>	<48EDBBC3.2000908@democritos.it>	<48EDCDB4.3030904@mit.edu>
	<48EDD601.9050601@democritos.it>
Message-ID: <48EE16C1.5040002@umn.edu>


I just confirm that the bug was fixed by Stefano de Gironcoli few months 
ago. so in the cvs version (maybe also in the latest releases)
norm-atomic should not be needed anymore. As far as I remember the code 
also prints at the beginning of the output few lines saying
that it's normalizing the atomic wavefunctions of the pseudo.

Matteo


Paolo Giannozzi wrote:
> Nicola Marzari wrote:s:
>
>> Last - extra-care should be paid to the fact that some of the 
>> pseudopotentials in the PWSCF database have non-normalized atomic 
>> wavefunctions 
>
> fixed in the CVS version (at least based on the annoying
> messages that are issued when non-normalized atomic
> wavefunctions are found)
>
> Paolo
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From ski2 at mail.uh.edu  Thu Oct  9 22:26:05 2008
From: ski2 at mail.uh.edu (ski2 at mail.uh.edu)
Date: Thu, 09 Oct 2008 15:26:05 -0500
Subject: [Pw_forum] elf calculation with USPP
Message-ID: <f5dcee411c0a1.48ee228d@mail.uh.edu>

Dear all,

When I did ELF calculation, I got the message in the out file as the following:

???? Calling punch_plot, plot_num =?? 8
???? Message from routine do_elf:
???? elf + US not fully implemented
???? Writing data to file? elf

Does this mean the elf data were incompletely calculated? 

Please let me know.

Best Wishes,
Sang-Hwan (postdoc)



Department of Chemistry
University of Houston
136 Fleming Building
Houston, TX 77204-5003
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From akohlmey at cmm.chem.upenn.edu  Thu Oct  9 23:23:43 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 9 Oct 2008 17:23:43 -0400 (EDT)
Subject: [Pw_forum] elf calculation with USPP
In-Reply-To: <f5dcee411c0a1.48ee228d@mail.uh.edu>
References: <f5dcee411c0a1.48ee228d@mail.uh.edu>
Message-ID: <Pine.LNX.4.64.0810091722270.15555@localhost.localdomain>

On Thu, 9 Oct 2008, ski2 at mail.uh.edu wrote:

SH> Dear all,
SH> 
SH> When I did ELF calculation, I got the message in the out file as the following:
SH> 
SH> ???? Calling punch_plot, plot_num =?? 8
SH> ???? Message from routine do_elf:
SH> ???? elf + US not fully implemented
SH> ???? Writing data to file? elf
SH> 
SH> Does this mean the elf data were incompletely calculated? 

yes! 

what else? the message is pretty obvious, isn't it?

please see the mailing list archives for previous responses
to the same question that give more details.

cheers,
   axel.

SH> 
SH> Please let me know.
SH> 
SH> Best Wishes,
SH> Sang-Hwan (postdoc)
SH> 
SH> 
SH> 
SH> Department of Chemistry
SH> University of Houston
SH> 136 Fleming Building
SH> Houston, TX 77204-5003
SH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From szs_naghavi at yahoo.com  Fri Oct 10 01:05:25 2008
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Thu, 9 Oct 2008 16:05:25 -0700 (PDT)
Subject: [Pw_forum] phonon error
Message-ID: <493480.10906.qm@web63007.mail.re1.yahoo.com>

Dear everybody
I checked both approches : doing nscf run and puttin option lnscf=.true. in ph.in
but I have ?
?from phq_readin : error #???????? 9
???? k-points are odd
for lnscf=true
and  from phq_init : error #???????? 1?
? ?? wrong order of k points
when I run nscf file 
in a point other than gamma.
I dont know what should I?do !


      
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From chenhanghuipwscf at gmail.com  Fri Oct 10 02:55:12 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Thu, 9 Oct 2008 20:55:12 -0400
Subject: [Pw_forum] unit of the polarization
Message-ID: <22ae3ca40810091755y30c8fa78h1cca8893d4f0e1a6@mail.gmail.com>

Dear PWSCF users,
     I have a question about the polarization unit which has confused me for
a long time.
     The atomic unit of electric field is: e/a0^2 where 'e' is the electron
charge and a0 is the Bohr radius. The unit of polarization (i.e. dipole per
unit volume) should have the same unit as electric field. However from the
source code c_phase_field.f90(version4.0.2), the output of dipole per cell
has a factor sqrt(2) which is the electron in the Ry units. So 'e' becomes
sqrt(2).
    Then if I want to calculate P/E which is dimensionless, shall I convert
the output of P into P/sqrt(2). Note when we input the electric field E, E
is in the atomic unit, i.e. 'e' is not converted into sqrt(2).
    I am just confused that since you use atomic unit, why you explicitly
convert 'e' into sqrt(2) rather than implicitly retain it in the unit?

Hanghui Chen
Department of Physics,
Yale University
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From yuminqian at gmail.com  Fri Oct 10 03:58:24 2008
From: yuminqian at gmail.com (yumin qian)
Date: Fri, 10 Oct 2008 09:58:24 +0800
Subject: [Pw_forum] Perturbation in electronic field
Message-ID: <aa128b2c0810091858j61ec12c3wc5b324473e70daa6@mail.gmail.com>

>
> There is one problem I am not clear about DFPT in external electronmagnetic
> field. How to switch on the external field since the field will distroy the
> translational symmetry(periodic boundary condition ).



> There a two way right now : one is add a dipole layer in vaccum layers ,
> this method can only be used in slab calculation



> the other is to add a periodic field and at the end make the periodic to
> infinite (long wave appriximation). Vanderbilt also made a proposal using
> the Berry phase approach,


 My question is in PWSCF how the electronic field is added , and whether the
method can be used in metal system ? thank you

-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From njuxuyuehua at gmail.com  Fri Oct 10 04:44:38 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 10:44:38 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
Message-ID: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>

hi everyone here:
i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux system
.and *when I ran   xcrysden, the
** graphic interface can appear, but could open any file ,when i open some
file ,the error message is below "error couldn't change working directory to
"Y/xc_23632": no such file or directory"*
*AND  i found out the Y  directory is generated automatically  in the
directory  where the software is running . i have specified the
XCRYSDEN_SCRATCH  ,it seems the right place to store such files as
xc_23632.but it do not work. *
**
-- 
Xu Yuehua
physics Department of Nanjing university
China
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From manoj at phys.ufl.edu  Fri Oct 10 05:20:12 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Thu, 9 Oct 2008 23:20:12 -0400 (EDT)
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <Pine.GSO.4.21.0810081112500.13663-100000@neptune.phys.ufl.edu>
Message-ID: <Pine.GSO.4.21.0810092319250.25585-100000@neptune.phys.ufl.edu>


Any follow ups on the message below? Alexander? 

Regards, 
Manoj
On Wed, 8 Oct 2008, Manoj Srivastava wrote:

> 
> Dear All, 
>  Is any body familiar with the scatter_forw.f90 subroutine of PWCOND? I
> think there is a bug in this subroutine at the place where you calculate
> intw2, which is z integration of nonlocal wavefunction with beta function.
> I have looked up the necessary formulae in the Choi & Ihm's paper (PRB 59,
> 2267, Jan 1999). In the paper, nonlocal wavefunction has 3 terms, one of
> which contains beta function, say W. The other two parts dont have any W
> in them, rather they are just plane wave solution. (Please have a look at
> equation 24 and 26 of the paper ). So, when we are doing z integration of
> nonlocal wavefunction with beta function W, we should have three terms,
> one of which should contain two W, but rest should just have one W. On the
> other hand in the code all three terms contain two beta functions!!
> (please have a look at line 228 of scatter_forw.f90). I am wondering if my
> understanding is right? 
> I have one more question in the later part of the same subroutine. What
> does the lapack subroutine 
> ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> do? 
> I tried to look it up and i got the idea that it is trying to solve 
> amat*x=xmat, with amat and xmat known and x unknown, and at the end of
> calculation it stores x in xmat. 
> so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it changes
> the structure of xmat from what is defined in 'constructs matrices'
> part. Is it correct? 
> Also, afterwards in this code where  it 'rotates integrals' is not very
> clear to me. 
> Could somebody please tell me in little detail, what is going on
> here? Also, is this subroutine written just on the basis of Choi and Ihm
> paper, or are there more reference to it? If yes, would someone mind
> mentioning them? 
> 
> Regards, 
> Manoj Srivastava 
> Physics Graduate Student 
> University of Florida, 
> Gainesville,FL, USA
> 
> 


From giannozz at democritos.it  Fri Oct 10 08:06:05 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 08:06:05 +0200
Subject: [Pw_forum] phonon error
In-Reply-To: <493480.10906.qm@web63007.mail.re1.yahoo.com>
References: <493480.10906.qm@web63007.mail.re1.yahoo.com>
Message-ID: <48EEF0CD.8080707@democritos.it>

zahra sadat naghavi wrote:

>  from phq_readin : error #         9
>      k-points are odd
> /for lnscf=true/
> and from phq_init : error #         1 
>      wrong order of k points
> /when I run nscf file /
> /in a point other than gamma./
> /I dont know what should I do !/

you should read more carefully the documentation
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From roccad at gmail.com  Fri Oct 10 08:41:24 2008
From: roccad at gmail.com (dario rocca)
Date: Thu, 9 Oct 2008 23:41:24 -0700
Subject: [Pw_forum] k point convergence of dielectric properties
Message-ID: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>

Dear Users
I have an issue related to the convergence of the static dielectric  matrix
using the PH code. I have performed calculations
on bulk silicon using different k point meshes and I have obtained the
following results:

k grid              diagonal component of      number of k points in
                         the dielectric tensor           the irreducible
Brillouin zone

4*4*4                   23.668350065                        8
 6 *6*6                16.297485614                       16
8 *8*8                  14.044830694                       29
10 *10*10             13.288531964                     47
12*12*12              13.029602882                     72
16 *16*16             12.908820645                    145
20 *20*20             12.894538380                    256

k grid+ 1 1 1 shift              diagonal component of      number of k
points in
                                            the dielectric tensor
the irreducible Brillouin zone

4*4*4                                      13.840844632
                          10
6*6*6
12.997009732                           28
8*8*8
12.903849607                           60
10*10*10                               12.893711596
110
12*12*12                               12.892685597
182
16*16*16                               12.892482798
408
20*20*20                               12.892537346
770

I was surprised of the improvement in the convergence due to the shift of
the grid. I don't think this is related to the number of k points
in the IBZ (at least not exclusively).
I have observed a similar behavior in diamond.
The ground state energy convergence also benefits from the shift, but the
improvement is not so striking.
Does someone has any hint on why the shift of the grid improves the
calculation of the dielectric properties of silicon?
Thanks a lot
Dario Rocca, dept. of chemistry, UC Davis
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From baroni at sissa.it  Fri Oct 10 08:43:22 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 10 Oct 2008 08:43:22 +0200
Subject: [Pw_forum] Perturbation in electronic field
In-Reply-To: <aa128b2c0810091858j61ec12c3wc5b324473e70daa6@mail.gmail.com>
References: <aa128b2c0810091858j61ec12c3wc5b324473e70daa6@mail.gmail.com>
Message-ID: <084A79E6-AEFC-4160-984A-DEC38B5D1983@sissa.it>


On Oct 10, 2008, at 3:58 AM, yumin qian wrote:

> There is one problem I am not clear about DFPT in external  
> electronmagnetic field. How to switch on the external field since  
> the field will distroy the translational symmetry(periodic boundary  
> condition ).

please, take the time to have a glance at:
S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Phonons  
and related crystal properties from density-functional perturbation  
theory, Rev. Mod. Phys. 73, 515 (2001).


>
> There a two way right now : one is add a dipole layer in vaccum  
> layers , this method can only be used in slab calculation
>
> the other is to add a periodic field and at the end make the  
> periodic to infinite (long wave appriximation). Vanderbilt also made  
> a proposal using the Berry phase approach,

third, DFPT (restricted to the linear, or low-order) regime

>  My question is in PWSCF how the electronic field is added ,

through either of the first two methods. the third is implemented in  
PHONON

> and whether the method can be used in metal system ?

homogeneous electric fields in a metal? for that a computer code is  
not enough. One should modify Maxwell's equations!

SB

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html






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From yuminqian at gmail.com  Fri Oct 10 08:48:18 2008
From: yuminqian at gmail.com (yumin qian)
Date: Fri, 10 Oct 2008 14:48:18 +0800
Subject: [Pw_forum] Perturbation in electronic field
In-Reply-To: <084A79E6-AEFC-4160-984A-DEC38B5D1983@sissa.it>
References: <aa128b2c0810091858j61ec12c3wc5b324473e70daa6@mail.gmail.com>
	<084A79E6-AEFC-4160-984A-DEC38B5D1983@sissa.it>
Message-ID: <aa128b2c0810092348x634d9b24i85cd72952bcd4bc6@mail.gmail.com>

thanks for your reply

2008/10/10 Stefano Baroni <baroni at sissa.it>

>
>  On Oct 10, 2008, at 3:58 AM, yumin qian wrote:
>
>   There is one problem I am not clear about DFPT in external
>> electronmagnetic field. How to switch on the external field since the field
>> will distroy the translational symmetry(periodic boundary condition ).
>
>
> please, take the time to have a glance at:
> S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Phonons and
> related crystal properties from density-functional perturbation theory, Rev.
> Mod. Phys. 73, 515 (2001).
>
>
>
>
>> There a two way right now : one is add a dipole layer in vaccum layers ,
>> this method can only be used in slab calculation
>
>
>
>> the other is to add a periodic field and at the end make the periodic to
>> infinite (long wave appriximation). Vanderbilt also made a proposal using
>> the Berry phase approach,
>
>
> third, DFPT (restricted to the linear, or low-order) regime
>
>   My question is in PWSCF how the electronic field is added ,
>
>
> through either of the first two methods. the third is implemented in PHONON
>
>  and whether the method can be used in metal system ?
>
>
> homogeneous electric fields in a metal? for that a computer code is not
> enough. One should modify Maxwell's equations!
>
> SB
>
>    ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
>  La morale est une logique de l'action comme la logique est une morale de
> la pens?e - Jean Piaget
>
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From degironc at sissa.it  Fri Oct 10 10:19:09 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 10 Oct 2008 10:19:09 +0200
Subject: [Pw_forum] k point convergence of dielectric properties
In-Reply-To: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>
References: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>
Message-ID: <48EF0FFD.5050605@sissa.it>

Dear Dario,

this is an issue related to the fact that a shifted grid in the fcc  
Bravais lattice has  lower symmetry than cubic... just think of the  
simplest 
1 1 1 1 1 1 grid that should contains one single point  L=(1/2 1/2 1/2) 
but actually represents  the 4 (rotationally but not translationally)
equivalent points (1/2 1/2 1/2), (-1/2,-1/2,1/2), 
(-1/2,1/2,-1/2),(1/2,-1/2,-1/2) . The argument can be easily extended to 
denser grids and shows that the shifted grid represents 4*N^3 points in 
the fcc BZ.
This explains why the shifted grid appears more accurate (it is actually 
denser than you think) and why the number of points it contains is 
larger than you may have thought ... In fact avoiding high symmetry 
points like the Gamma point,  contained in the unshifted grid, should 
help reducing the number of inequivalent points while instead the number 
of  shifted points for a given nominal density is larger than the number 
of unshifted ones... true, but the corresponding parent grid is actually 
4 times denser than you may have thought...and the "symmetry reductions"
factor is indeed larger for the shifted grid
for example:
shifted     4*4*4 -> 256 points in the full BZ -> 10 points in the IW 
=>  sym. red. fact. = 25.6
unshifted 4*4*4 ->  64 points in the full BZ ->   8 points in the IW =>  
sym. red. fact. = 8
 
Some time (especially if your system does not have much symmetry to 
start with) you don't really care about sampling the BZ according to a 
fully cubic symmetry but a regular grid in the 3 directions is enough.. 
in this case the use of shifted grids may results in a large amount of  
"un-needed" k-points which you may want NOT to include in the 
calculation... this annoying fact is the origin of the infamous 
nosym=.true. options that much confusion generates in most users until 
they realize what its meaning and purpose really is ... there are many 
threads on that in the archive....

As to the fact that total energy are less sensitive than dielectric 
properties to k-points sampling this is a well known fact
[see for instance  S.Baroni and R. Resta, PRB 33, 7017 (1986)]

Hope this helps,

stefano
--

Stefano de Gironcoli - SISSA and DEMOCRITOS


dario rocca wrote:
> Dear Users
> I have an issue related to the convergence of the static dielectric  
> matrix using the PH code. I have performed calculations
> on bulk silicon using different k point meshes and I have obtained the 
> following results:
>
> k grid              diagonal component of      number of k points in
>                          the dielectric tensor           the 
> irreducible Brillouin zone
>
> 4*4*4                   23.668350065                        8
>  6 *6*6                16.297485614                       16
> 8 *8*8                  14.044830694                       29
> 10 *10*10             13.288531964                     47
> 12*12*12              13.029602882                     72
> 16 *16*16             12.908820645                    145
> 20 *20*20             12.894538380                    256
>
> k grid+ 1 1 1 shift              diagonal component of      number of 
> k points in
>                                             the dielectric 
> tensor           the irreducible Brillouin zone
>
> 4*4*4                                      13.840844632 
>                           10
> 6*6*6                                     
> 12.997009732                           28
> 8*8*8                                     
> 12.903849607                           60
> 10*10*10                               
> 12.893711596                         110
> 12*12*12                               
> 12.892685597                         182
> 16*16*16                               
> 12.892482798                         408
> 20*20*20                               
> 12.892537346                         770
>  
> I was surprised of the improvement in the convergence due to the shift 
> of the grid. I don't think this is related to the number of k points
> in the IBZ (at least not exclusively).
> I have observed a similar behavior in diamond.
> The ground state energy convergence also benefits from the shift, but 
> the improvement is not so striking.
> Does someone has any hint on why the shift of the grid improves the 
> calculation of the dielectric properties of silicon?
> Thanks a lot
> Dario Rocca, dept. of chemistry, UC Davis
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From prasenjit.jnc at gmail.com  Fri Oct 10 10:21:04 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 10 Oct 2008 10:21:04 +0200
Subject: [Pw_forum] k point convergence of dielectric properties
In-Reply-To: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>
References: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>
Message-ID: <627e0ffa0810100121wa8aae7arbc89f45f62519d26@mail.gmail.com>

Dear Dario,

For calculation of dielectric properties you need to do integrations over
the BZ. For high symmetry lattices, a shifted k-point mesh (specially a k-pt
mesh without Gamma pt.) without the high symmetry points should be used. In
that way you have a better sampling of your BZ and hence a improvement in
the results. I also found similar improvements of convergence when I tested
for convergence of adsorption energy wrt k-point mesh.

Prasenjit.

2008/10/10 dario rocca <roccad at gmail.com>

>
> Dear Users
> I have an issue related to the convergence of the static dielectric  matrix
> using the PH code. I have performed calculations
> on bulk silicon using different k point meshes and I have obtained the
> following results:
>
> k grid              diagonal component of      number of k points in
>                          the dielectric tensor           the irreducible
> Brillouin zone
>
> 4*4*4                   23.668350065                        8
>  6 *6*6                16.297485614                       16
> 8 *8*8                  14.044830694                       29
> 10 *10*10             13.288531964                     47
> 12*12*12              13.029602882                     72
> 16 *16*16             12.908820645                    145
> 20 *20*20             12.894538380                    256
>
> k grid+ 1 1 1 shift              diagonal component of      number of k
> points in
>                                             the dielectric tensor
> the irreducible Brillouin zone
>
> 4*4*4                                      13.840844632
>                           10
> 6*6*6
> 12.997009732                           28
> 8*8*8
> 12.903849607                           60
> 10*10*10                               12.893711596
> 110
> 12*12*12                               12.892685597
> 182
> 16*16*16                               12.892482798
> 408
> 20*20*20                               12.892537346
> 770
>
> I was surprised of the improvement in the convergence due to the shift of
> the grid. I don't think this is related to the number of k points
> in the IBZ (at least not exclusively).
> I have observed a similar behavior in diamond.
> The ground state energy convergence also benefits from the shift, but the
> improvement is not so striking.
> Does someone has any hint on why the shift of the grid improves the
> calculation of the dielectric properties of silicon?
> Thanks a lot
> Dario Rocca, dept. of chemistry, UC Davis
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From giannozz at democritos.it  Fri Oct 10 10:43:54 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 10:43:54 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
 working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
Message-ID: <48EF15CA.6020506@democritos.it>

xu yuehua wrote:

> "error couldn't change working directory to "Y/xc_23632": 
>  no such file or directory"

likely you did something wrong during installation. Remove
everything and try to reinstall

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Fri Oct 10 10:46:50 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 10:46:50 +0200
Subject: [Pw_forum] about relaxation
In-Reply-To: <719081.81629.qm@web31403.mail.mud.yahoo.com>
References: <719081.81629.qm@web31403.mail.mud.yahoo.com>
Message-ID: <48EF167A.9000500@democritos.it>

meghdad saeedian wrote:

> i get the famous error  message: "not orthogonal oporation"
> i do  use the symmetry-conserving Wentzecovic algorithm.
> so what's the point?

what's the version of the code?

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From marzari at MIT.EDU  Fri Oct 10 11:16:05 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 10 Oct 2008 12:16:05 +0300
Subject: [Pw_forum] k point convergence of dielectric properties
In-Reply-To: <48EF0FFD.5050605@sissa.it>
References: <cb6486310810092341x12845ba3m7d71e1271c865163@mail.gmail.com>
	<48EF0FFD.5050605@sissa.it>
Message-ID: <48EF1D55.1000904@mit.edu>



Dario,


great detective work - and more remarkable than I would have
guessed (although I've been a fan for years of the shifted grids).

What Stefano said so clearly is related to the original idea of Alfonso
Baldereschi (PRB 7, 5121 (1973)) and generalized by Chadi and Cohen (PRB
8, 5747 (1973) - interestingly written in Paris VI Jussieu) - i.e. how 
to choose a single, special k-point (Baldereschi) or meshes of them
(Chadi and Cohen) in order to get the most accurate average. Basically,
a function f(k) that has the symmetry f the crystal, fourier expanded in
plane waves exp (i k.R) (R lattice vectors), can be rewritten as a
linear combination of symmetrized stars of plane waves (you bunch
together all the plane waves that have the same modulus for R, paying
some attention to degenerate shells that have different symmetry). By
choosing k's such that the largest number of those symmetrized stars
(sum exp (i k.R), sum over the R of a star) are zero, you have a recipe
that gives accurate integrals

Stefano de Gironcoli wrote:
> ... this annoying fact is the origin of the infamous 
> nosym=.true. options that much confusion generates in most users until 
> they realize what its meaning and purpose really is ... there are many 
> threads on that in the archive....

A god-blessing ! Try it - instead of using a 2x2x2 shifted mesh (4 
k-points, if no symmetry is present beside time reversal) use only 1
point, and stop the code from symmetrizing it using nosym=true.

The results will be very close to the full mesh, at 1/4 of the cost.

				nicola

---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From arunmanna at jncasr.ac.in  Fri Oct 10 11:21:23 2008
From: arunmanna at jncasr.ac.in (Arun Kumar Manna)
Date: Fri, 10 Oct 2008 13:21:23 +0400 (RET)
Subject: [Pw_forum] Regarding raman intensity
Message-ID: <41042.172.16.1.1.1223630483.squirrel@172.16.1.1>



Dear All,
        Could anyone please tell me how to get raman intensity values
from raman tensors those are calculated at gamma point?. For 2 atom per unit
cell, I have 6 no. of tensors matrices. I have confusion that in 2 dimension
there should be only 4 optical phonons and corresponding 4 no. of raman
tensor matrices, but i am getting 6 tensors matrices.
     Please help me..
  Thanks,
   Arun
-- 
PhD Student
JNCASR, Bangalore-560064
India

From tone.kokalj at ijs.si  Fri Oct 10 11:38:09 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 10 Oct 2008 11:38:09 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
	working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
Message-ID: <1223631489.5216.2.camel@walk.ijs.si>

On Fri, 2008-10-10 at 10:44 +0800, xu yuehua wrote:
> hi everyone here:
> i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux
> system .and when I ran   xcrysden, the
>  graphic interface can appear, but could open any file ,when i open
> some file ,the error message is below "error couldn't change working
> directory to "Y/xc_23632": no such file or directory"
> AND  i found out the Y  directory is generated automatically  in the
> directory  where the software is running . 

You have specified relative pathname for XCRYSDEN_SCRATCH. A very bad
idea. Thatwhy the "Y" directory is created in current directory. Please
set XCRYSDEN_SCRATCH as absolute pathname, e.g., something
like /scratch/$USER/xcrys_tmp

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From prasenjit.jnc at gmail.com  Fri Oct 10 11:53:43 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 10 Oct 2008 11:53:43 +0200
Subject: [Pw_forum] Regarding raman intensity
In-Reply-To: <41042.172.16.1.1.1223630483.squirrel@172.16.1.1>
References: <41042.172.16.1.1.1223630483.squirrel@172.16.1.1>
Message-ID: <627e0ffa0810100253k696fcb1am5888e66c5ae58cfa@mail.gmail.com>

Your system may be 2-d (eg. surface), but you are doing the calculations in
a three dimensional space.
Therefore you get (2x3=) 6 phonon modes.

>   I have confusion that in 2 dimension there should be only 4 optical
phonons
 For a 2-d system with 2 atoms per unit cell, there will be (2x2=) 4 phonon
modes, out of which 2 should be acoustic and 2 optical.

Prasenjit.


and corresponding 4 no. of raman
> tensor matrices, but i am getting 6 tensors matrices.
>     Please help me..
>  Thanks,
>   Arun
> --
> PhD Student
> JNCASR, Bangalore-560064
> India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From njuxuyuehua at gmail.com  Fri Oct 10 12:09:48 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 18:09:48 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <1223631489.5216.2.camel@walk.ijs.si>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
Message-ID: <aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>

en,en
i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills  is
the problem
of pre-compile ? i  found the errors are the same whether i run the
./xcconfire or not (directly run xcrysden after tar xf the package).

the bashrc :

ulimit -s unlimited
export PATH=~/bin/:$PATH
alias q=qstat
#------------------------------------------------------------------------
# this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
# Fri Oct 10 09:32:28 UTC 2008
#------------------------------------------------------------------------
XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util"


2008/10/10 Tone Kokalj <tone.kokalj at ijs.si>

> On Fri, 2008-10-10 at 10:44 +0800, xu yuehua wrote:
> > hi everyone here:
> > i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux
> > system .and when I ran   xcrysden, the
> >  graphic interface can appear, but could open any file ,when i open
> > some file ,the error message is below "error couldn't change working
> > directory to "Y/xc_23632": no such file or directory"
> > AND  i found out the Y  directory is generated automatically  in the
> > directory  where the software is running .
>
> You have specified relative pathname for XCRYSDEN_SCRATCH. A very bad
> idea. Thatwhy the "Y" directory is created in current directory. Please
> set XCRYSDEN_SCRATCH as absolute pathname, e.g., something
> like /scratch/$USER/xcrys_tmp
>
> Regards, Tone
>
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From tone.kokalj at ijs.si  Fri Oct 10 12:27:58 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 10 Oct 2008 12:27:58 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
	working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
Message-ID: <1223634478.5216.9.camel@walk.ijs.si>

On Fri, 2008-10-10 at 18:09 +0800, xu yuehua wrote:
> en,en  
> i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills
> is the problem 
> of pre-compile ? i  found the errors are the same whether i run
> the ./xcconfire or not (directly run xcrysden after tar xf the
> package).
>  
> the bashrc :
> 
> ulimit -s unlimited
> export PATH=~/bin/:$PATH
> alias q=qstat
> #------------------------------------------------------------------------
> # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
> # Fri Oct 10 09:32:28 UTC 2008
> #------------------------------------------------------------------------
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
> PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:
> $XCRYSDEN_TOPDIR/util"

This definition is not compatible with "error couldn't change working
directory to "Y/xc_23632"

Can you execute: env | grep XCRYSDEN

You should get something like:

XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From giannozz at democritos.it  Fri Oct 10 12:51:55 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 12:51:55 +0200
Subject: [Pw_forum] k-points mismatch
In-Reply-To: <829678.87709.qm@web65715.mail.ac4.yahoo.com>
References: <829678.87709.qm@web65715.mail.ac4.yahoo.com>
Message-ID: <48EF33CB.6040302@democritos.it>

Eyvaz Isaev wrote:

> [...]  first I did phonon calculations for a base centered 
> orthorhombic cell (ibrav=9) using 4x2x2 mesh (10 q-points) 
> and got an error message from q2r.x "q not allowed" [...]
> Then I tried to generate q-points using kpoints.x which stated 
> that 4x2x2 mesh "has not the correct symmetry" and gave only 
>  6 q-points. OK, I used 4x3x3 to generate q-points and got 10
> q-points without any message from kpoints.x. But when I started
> phonons with 4x3x3 q-mesh, the ph.x program generated 14 q-points.
> 
> Can someone explain such kind discrepancy between two programs 
> generating q-points? 

I cannot (yet) explain why the two programs behave in a wrong
but different way, but I have half an idea of what triggers this
bug. With this Bravais lattice (which, by the way, kpoints.f90
incorrectly reports as "orthor 1-(fco)"), axis 1 and 2 have the
same length, different from the length of axis 3. So you should
use a 2x2x4 mesh, or a 3x3x4, not the ones you used. I don't see
why this confuses the logic of the symmetry check, though, since
there are no symmetry operations sending axis 1 into 2.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From zdw2000 at gmail.com  Fri Oct 10 13:49:31 2008
From: zdw2000 at gmail.com (Wei Zhou)
Date: Fri, 10 Oct 2008 04:49:31 -0700
Subject: [Pw_forum] is there a pseduo potential about the C
	Perdew-Burke-Ernzerhof (PBE) NC ?
Message-ID: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>

dear all users
                    I want to do some calcuations about some structures
related to the element I and C ,however ,I only found one element I pseudo
potential in the pw pseudo potential libary ,which is Perdew-Burke-Ernzerhof
(PBE)  NC potential , and I cannot find the corresponding pseudo potential C
, would some one can help me give the matching pseudo potential ? I  pseudo
potential or  Perdew-Burke-Ernzerhof (PBE)  NC carbon potential.
any help will be appreciated .
best wishes


-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From umari at democritos.it  Fri Oct 10 14:34:04 2008
From: umari at democritos.it (umari at democritos.it)
Date: Fri, 10 Oct 2008 14:34:04 +0200
Subject: [Pw_forum] unit of the polarization (Paolo Umari)
Message-ID: <20081010143404.h2rgwd3wg08cs04w@mail.democritos.it>

Dear Chen,

The electric field is treated in Rydberg atomic units in pw.x
in this way:

1)The polarization P(\Psi) is calculated as sqrt(2.)*<\Psi|r|\Psi>/Omega
where \Psi is the slater determinant of the KS wavefunctions, Omega is 
the valume of the simulation cell,
and the expectation value of the position operator r  is calculated
through the Berry's phase formulation. This assures that for the same
wavefunctions the "numerical value" of the polarization is sqrt(2.) times
larger then that calculated for the case of Hartree atomic units.

The KS Hamiltonian in the presence of the electric field E  contains a term
proportional to Omega*E*\partial P(\Psi) /\partial \Psi
= E* sqrt(2) *\partial *<\Psi|r|\Psi> /\partial \Psi
This is the factor sqrt(2.) appearing in the routine h_epsi_her_set.f90

If you want to calculate the ratio P/E you must use
both values in Rydberg atomic units: the electric dipole as reported
by the code (in Rydberg atomic units) and the input numerical value of 
the electric field which is also given in Rydberg atomic units
(see Example 31)

Note that to obtain the corresponding  numerical value of the electric
field in Hartree atomic units you must divide by a factor of sqrt(2.)

Best regards,

Paolo Umari, DEMOCRITOS


> Dear PWSCF users,
>     I have a question about the polarization unit which has confused me for
> a long time.
>     The atomic unit of electric field is: e/a0^2 where 'e' is the electron
> charge and a0 is the Bohr radius. The unit of polarization (i.e. dipole per
> unit volume) should have the same unit as electric field. However from the
> source code c_phase_field.f90(version4.0.2), the output of dipole per cell
> has a factor sqrt(2) which is the electron in the Ry units. So 'e' becomes
> sqrt(2).
>    Then if I want to calculate P/E which is dimensionless, shall I convert
> the output of P into P/sqrt(2). Note when we input the electric field E, E
> is in the atomic unit, i.e. 'e' is not converted into sqrt(2).
>    I am just confused that since you use atomic unit, why you explicitly
> convert 'e' into sqrt(2) rather than implicitly retain it in the unit?
>
> Hanghui Chen
> Department of Physics,
> Yale University


----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.


From njuxuyuehua at gmail.com  Fri Oct 10 14:54:45 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 20:54:45 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <1223634478.5216.9.camel@walk.ijs.si>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
Message-ID: <aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>

yes ,i get the information :
jdong at sgi4700:~> env | grep XCRYSDEN
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static



2008/10/10 Tone Kokalj <tone.kokalj at ijs.si>

> On Fri, 2008-10-10 at 18:09 +0800, xu yuehua wrote:
> > en,en
> > i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills
> > is the problem
> > of pre-compile ? i  found the errors are the same whether i run
> > the ./xcconfire or not (directly run xcrysden after tar xf the
> > package).
> >
> > the bashrc :
> >
> > ulimit -s unlimited
> > export PATH=~/bin/:$PATH
> > alias q=qstat
> > #------------------------------------------------------------------------
> > # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
> > # Fri Oct 10 09:32:28 UTC 2008
> > #------------------------------------------------------------------------
> > XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> > XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
> > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:
> > $XCRYSDEN_TOPDIR/util"
>
> This definition is not compatible with "error couldn't change working
> directory to "Y/xc_23632"
>
> Can you execute: env | grep XCRYSDEN
>
> You should get something like:
>
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
>
>  Regards, Tone
>
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From paulatto at sissa.it  Fri Oct 10 14:55:55 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 10 Oct 2008 14:55:55 +0200
Subject: [Pw_forum] is there a pseduo potential about the
 C	Perdew-Burke-Ernzerhof (PBE) NC ?
In-Reply-To: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>
References: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>
Message-ID: <48EF50DB.3040007@sissa.it>

Wei Zhou ha scritto:
>  I  pseudo potential or  Perdew-Burke-Ernzerhof (PBE)  NC carbon
> potential.
Dear Wei Zhou,
there are several matching pseudopotentials in the library. Rememeber
that it is perfectly safe to mix norm-conserving (NC) and ultrasoft
pseudopotentials, as long as they use the same functional.

regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From degironc at sissa.it  Fri Oct 10 14:57:47 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 10 Oct 2008 14:57:47 +0200
Subject: [Pw_forum] is there a pseduo potential about the
 C	Perdew-Burke-Ernzerhof (PBE) NC ?
In-Reply-To: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>
References: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>
Message-ID: <48EF514B.20209@sissa.it>

Dear Wei Zhou,
   please notice that you can mix NC and US pseudo-potentials in PWscf....
   Iodine is an sp element in the forth row and it is likely to need an 
only moderate cutoff  (22 Ry in the paper by Brandon Wood and Nicola 
Marzari quoted in the "details" entry on the pseudo-potential web-page) 
... Carbon is a first-row element that in the NC form would require 
significantly larger cut-offs  (50-60 Ry at least). With an ultrasoft 
pseudo-potential instead a cutoff of the order of 30 Ry is typically enough.
There are several PBE US pseudo-potentials for Carbon in the 
pseudo-potential library.

 Hope this helps,
  stefano

PS: Don't forget to test convergence of the calculation for your 
specific case.
-
Stefano de Gironcoli - SISSA and DEMOCRITOS

Wei Zhou wrote:
> dear all users
>                     I want to do some calcuations about some 
> structures related to the element I and C ,however ,I only found one 
> element I pseudo potential in the pw pseudo potential libary ,which is 
> Perdew-Burke-Ernzerhof (PBE)  NC potential , and I cannot find the 
> corresponding pseudo potential C , would some one can help me give the 
> matching pseudo potential ? I  pseudo 
> potential or  Perdew-Burke-Ernzerhof (PBE)  NC carbon potential.
> any help will be appreciated .
> best wishes
>  
>
> -- 
> ZhouDawei
> JiLin Universiyt ,ChangChun ,China
> zdw2000 at gmail.com <mailto:zdw2000 at gmail.com>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From tone.kokalj at ijs.si  Fri Oct 10 15:09:14 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 10 Oct 2008 15:09:14 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
	working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
Message-ID: <1223644154.5216.34.camel@walk.ijs.si>

On Fri, 2008-10-10 at 20:54 +0800, xu yuehua wrote:
> yes ,i get the information :
> jdong at sgi4700:~> env | grep XCRYSDEN
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static

This looks OK. 

Are you sure you still get "Y/xc_***: no such file or directory" message
or is the message different now?

or does it says: "/disk2/jdong/xyh/xcrys_tmp/xc_***: ... no such file or
directory"

If it is the latter, it can be the problem related to write permission
of /disk2/jdong/xyh/xcrys_tmp or to full disk.

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From njuxuyuehua at gmail.com  Fri Oct 10 15:28:37 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 21:28:37 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <1223644154.5216.34.camel@walk.ijs.si>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
	<1223644154.5216.34.camel@walk.ijs.si>
Message-ID: <aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>

the former.
the problem is so strange. Y is what ?
i have not specify any directory named  as  "Y"
 and i
ls  -al  found the
 drwxr-xr-x 4  jdong phys    96 2008-10-10 17:56 Y
and the same  xcryden software in another machine is rather ok.and the ls
-al

drwxrwxr-x  46 xyh  xyh      4096 Oct 10 10:07 xcrys_tmp

maybe the reason is Y.where is Y ???

2008/10/10 Tone Kokalj <tone.kokalj at ijs.si>

> On Fri, 2008-10-10 at 20:54 +0800, xu yuehua wrote:
> > yes ,i get the information :
> > jdong at sgi4700:~> env | grep XCRYSDEN
> > XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> > XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
>
> This looks OK.
>
> Are you sure you still get "Y/xc_***: no such file or directory" message
> or is the message different now?
>
> or does it says: "/disk2/jdong/xyh/xcrys_tmp/xc_***: ... no such file or
> directory"
>
> If it is the latter, it can be the problem related to write permission
> of /disk2/jdong/xyh/xcrys_tmp or to full disk.
>
> Regards, Tone
>
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at democritos.it  Fri Oct 10 15:35:15 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 15:35:15 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
 working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>	<1223631489.5216.2.camel@walk.ijs.si>	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>	<1223634478.5216.9.camel@walk.ijs.si>	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>	<1223644154.5216.34.camel@walk.ijs.si>
	<aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
Message-ID: <48EF5A13.2080805@democritos.it>

xu yuehua wrote:

> the problem is so strange. Y is what ?
> i have not specify any directory named  as  "Y"

sure? really? didn't you answer "Y" to any question
during installation?

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From tone.kokalj at ijs.si  Fri Oct 10 15:38:49 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 10 Oct 2008 15:38:49 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
	working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
	<1223644154.5216.34.camel@walk.ijs.si>
	<aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
Message-ID: <1223645929.5216.47.camel@walk.ijs.si>

On Fri, 2008-10-10 at 21:28 +0800, xu yuehua wrote:
> the former.
> the problem is so strange. Y is what ?

Probably a symbol for "unknown" ...#@!#...

> i have not specify any directory named  as  "Y"
>  and i  
> ls  -al  found the 
>  drwxr-xr-x 4  jdong phys    96 2008-10-10 17:56 Y
> 
> and the same  xcryden software in another machine is rather ok.and the
> ls -al 
> 
> drwxrwxr-x  46 xyh  xyh      4096 Oct 10 10:07 xcrys_tmp
>  
> maybe the reason is Y.where is Y ???

This is very awkward!

Wait, both Y and xcrys_tmp seems like a relative paths. From which
dirrectory you executed "ls" command?

What about the owenrship of scratch directory. On onw machine it is
jdongh:phys on the other xyh:xyh. Note that each user should create its
own scratch directory.

Regards, Tone

PS: Let us try to solve this via private channel not to populate
pw_forum too much ...

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From njuxuyuehua at gmail.com  Fri Oct 10 16:13:33 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 22:13:33 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <48EF5A13.2080805@democritos.it>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
	<1223644154.5216.34.camel@walk.ijs.si>
	<aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
	<48EF5A13.2080805@democritos.it>
Message-ID: <aca2feb20810100713v2da37eedqb4a315c0705e2d6e@mail.gmail.com>

 the whole progress of installation:

 jdong at sgi4700:~/xyh/XCrySDen-pre1.5bbin-static> ./xcConfigure
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
Press <Enter>  to continue ...
   I am about to create the $HOME/.xcrysden directory and copy XCRYSDEN
   definition/customization files to it. See the XCRYSDEN  documentation
   for further instructions about XCRYSDEN customization.
   Press <Enter> to continue ...
   ------------------------------------------------------------------------
                 Please answer to following QUESTIONS!!!
   ------------------------------------------------------------------------

CRYSTAL-95/98/03 is an electronic structure program for periodic systems.
(http://www.crystal.unito.it/)
Do you have a CRYSTAL-95/98/03 package ([y]es/[n]o): n
Specify printing command (default: lpr -h):
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
Do you want to enable the "babel" program ([y]es/[n]o): n
Do you want to enable the ImageMagick's "convert" program ([y]es/[n]o): n
Do you want to enable the "whirlgif" program ([y]es/[n]o): n
Do you want to enable the "mpeg_encode" program ([y]es/[n]o): n

 ========================================================================
           You have specified the following definitions:
 ========================================================================
Print Command:                 lpr -h
Is this correct ([y]es/[n]o): y
creating /disk2/jdong/.xcrysden/custom-definitions ... OK
Would you like to edit ~/.xcrysden/custom-definitions file now
([y]es/[n]o):n
copying /disk2/jdong/xyh/XCrySDen-pre1.5bbin-static/Tcl/Xcrysden_defaults
... OK
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
------------------------------------------------------------------------------------------------------
is there any other  problem ?



2008/10/10 Paolo Giannozzi <giannozz at democritos.it>

> xu yuehua wrote:
>
> > the problem is so strange. Y is what ?
> > i have not specify any directory named  as  "Y"
>
> sure? really? didn't you answer "Y" to any question
> during installation?
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
>  Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From smogunov at sissa.it  Fri Oct 10 14:55:49 2008
From: smogunov at sissa.it (Alexander)
Date: Fri, 10 Oct 2008 14:55:49 +0200
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <Pine.GSO.4.21.0810092319250.25585-100000@neptune.phys.ufl.edu>
References: <Pine.GSO.4.21.0810092319250.25585-100000@neptune.phys.ufl.edu>
Message-ID: <200810101455.49286.smogunov@sissa.it>

Dear Manoj

On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> Any follow ups on the message below? Alexander?
>
> Regards,
> Manoj
>
> On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > Dear All,
> >  Is any body familiar with the scatter_forw.f90 subroutine of PWCOND? I
> > think there is a bug in this subroutine at the place where you calculate
> > intw2, which is z integration of nonlocal wavefunction with beta
> > function. I have looked up the necessary formulae in the Choi & Ihm's
> > paper (PRB 59, 2267, Jan 1999). In the paper, nonlocal wavefunction has 3
> > terms, one of which contains beta function, say W. The other two parts
> > dont have any W in them, rather they are just plane wave solution.
> > (Please have a look at equation 24 and 26 of the paper ). So, when we are
> > doing z integration of nonlocal wavefunction with beta function W, we
> > should have three terms, one of which should contain two W, but rest
> > should just have one W. On the other hand in the code all three terms
> > contain two beta functions!! (please have a look at line 228 of
> > scatter_forw.f90). I am wondering if my understanding is right?

Your understanding is wrong. On the line 228 you add to the integral ONLY
contribution with two beta functions (from the 1st term in the nonlocal 
function, see Eq. 24) but on the line 393 the contribution from the 2nd term 
is added too. There is no 3rd term since every step you rotate your local 
solutions \psi_n in such a way that b_{\lambda \alpha lm} vanish (see the 
paragraph after Eq. 37). 

 > > I have one more question in the later part of the same subroutine. What
> > does the lapack subroutine
> > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > do?
> > I tried to look it up and i got the idea that it is trying to solve
> > amat*x=xmat, with amat and xmat known and x unknown, and at the end of
> > calculation it stores x in xmat.
> > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it changes
> > the structure of xmat from what is defined in 'constructs matrices'
> > part. Is it correct?

Here, you are right.

> > Also, afterwards in this code where  it 'rotates integrals' is not very
> > clear to me.
> > Could somebody please tell me in little detail, what is going on
> > here? 
As I explained before rotation means that every step (at each slab)
you make a linear combination of local solutions \psi_n with the 
transformation matrix  h_{nn'} (see the last paragraph on the p. 2270).
so that the new solutions have the property: 
b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions have
b_{\lambda \alpha lm}=0. Doing this transformation of local and nonlocal
solutions you should also perform the corresponding transformations
of the integrals.

> > Also, is this subroutine written just on the basis of Choi and Ihm 
> > paper, or are there more reference to it? If yes, would someone mind
> > mentioning them?
Unfortunately, the paper of Choi and Ihm is very detail, and in the 
PWCOND code we followed it very closely, so no more references
are needed. In our papers we just extended those ideas to ultrasoft
pseudopotentials, magnetism, spin-orbit coupling and so on.
  
Hope this helped you,
regards, Alexander 

> >
> > Regards,
> > Manoj Srivastava
> > Physics Graduate Student
> > University of Florida,
> > Gainesville,FL, USA
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Fri Oct 10 16:21:22 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 10 Oct 2008 16:21:22 +0200
Subject: [Pw_forum] xcrysden problem "error couldn't change
 working	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <aca2feb20810100713v2da37eedqb4a315c0705e2d6e@mail.gmail.com>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>	<1223631489.5216.2.camel@walk.ijs.si>	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>	<1223634478.5216.9.camel@walk.ijs.si>	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>	<1223644154.5216.34.camel@walk.ijs.si>	<aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>	<48EF5A13.2080805@democritos.it>
	<aca2feb20810100713v2da37eedqb4a315c0705e2d6e@mail.gmail.com>
Message-ID: <48EF64E2.10509@democritos.it>

xu yuehua wrote:

> the whole progress of installation:

I do not see where XCRYSDEN_SCRATCH is set. You need to:
- remove everything Xcrysden-related from everywhere,
   including .bashrc
- reinstall from scratch

> [..] is there any other problem ?

I have no problem at all! (well, actually I have one:
some genius has cut the electricity and the mail server
of the physics department is down...)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From janbeck at gmail.com  Fri Oct 10 16:23:10 2008
From: janbeck at gmail.com (Jan Beck)
Date: Fri, 10 Oct 2008 08:23:10 -0600
Subject: [Pw_forum] Bug in axsf generation?
Message-ID: <f9fbbdf30810100723x75bed882i1a74d2188a2d8e1c@mail.gmail.com>

I have an axsf file that I have generated with quantum espresso's cppp. I
have checked with the specification of the axsf file format, and the
output from quantum espresso is consistent with that.

My file starts with:
 ANIMSTEPS         100
 CRYSTAL
 PRIMVEC           1
 8.466835337    0.000000000    0.000000000
 0.000000000    8.466835337    0.000000000
 0.000000000    0.000000000    4.233417669
 CONVVEC           1
 8.466835337    0.000000000    0.000000000
 0.000000000    8.466835337    0.000000000
 0.000000000    0.000000000    4.233417669
 PRIMCOORD           1
       96           1
 8       1.375860742    0.000000000    0.000000000
 8       0.687930371   -0.687930371    0.000000000

and on the xcrysden website, http://www.xcrysden.org/doc/XSF.html ,
the specification for Variable-cell animated XSF gives this example:

 ANIMSTEPS 2
 CRYSTAL
 PRIMVEC 1
 2.7100000    2.7100000    0.00000000
 2.7100000    0.0000000    2.71000000
 0.0000000    2.7100000    2.71000000
 CONVVEC 1
 5.4200000    0.0000000    0.00000000
 0.0000000    5.4200000    0.00000000
 0.0000000    0.0000000    5.42000000
 PRIMCOORD 1
 2 1
 16      0.0000000     0.0000000     0.00000000
 30      1.3550000    -1.3550000    -1.35500000


so the output seems to conform to the standard. However, as soon as I
load the file with the command:

xcrysden --axsf c6h6.axsf

I get the following output

Executing: /home/jan/XCrySDen-1.4.1s/bin/ftnunit

*** the hardware does not support the stereo ***

Number of Atoms:  0
Number of Frames: 0
Estimated number of bonds = 0
sInfo(dim) = 3; periodic(dim) = 3
Executing: /home/jan/XCrySDen-1.4.1s/bin/gengeom 0 1 11 1 1 1 1
xc_gengeom.24392 /home/jan/xcrys_tmp/xc_24392/c6h6.axsf.raw.1.raw
Executing: /home/jan/XCrySDen-1.4.1s/bin/gengeom 2 1 11 1 1 1 1
/home/jan/xcrys_tmp/xc_24392/xc_struc.24392
/home/jan/xcrys_tmp/xc_24392/c6h6.axsf.raw.1.raw
Number of Atoms:  236
Number of Frames: 12
WARNING: Atom 2 and atom 6 overlap !!!
      Atom 6 deleted !!!
WARNING: Atom 2 and atom 10 overlap !!!
      Atom 10 deleted !!!


Has anyone else seen this type of problem?

Thank you for your time,


Jan Beck
TXL Group, El Paso, TX

From njuxuyuehua at gmail.com  Fri Oct 10 16:38:42 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 10 Oct 2008 22:38:42 +0800
Subject: [Pw_forum] xcrysden problem "error couldn't change working
	directory to "Y/xc_23632": no such file or directory
In-Reply-To: <48EF64E2.10509@democritos.it>
References: <aca2feb20810091944mb46eb55pff0b0da76cddf5a7@mail.gmail.com>
	<1223631489.5216.2.camel@walk.ijs.si>
	<aca2feb20810100309jdf2184cm6b0c996f0ca0b4c1@mail.gmail.com>
	<1223634478.5216.9.camel@walk.ijs.si>
	<aca2feb20810100554o6358922bw30bc127afebafef@mail.gmail.com>
	<1223644154.5216.34.camel@walk.ijs.si>
	<aca2feb20810100628s36415c3crdc5fa5df4774b717@mail.gmail.com>
	<48EF5A13.2080805@democritos.it>
	<aca2feb20810100713v2da37eedqb4a315c0705e2d6e@mail.gmail.com>
	<48EF64E2.10509@democritos.it>
Message-ID: <aca2feb20810100738i7c335be7g98a2a6ab769d6bd0@mail.gmail.com>

thank  you for your kindly help (even if in the condition of  the server is
down. )
2008/10/10 Paolo Giannozzi <giannozz at democritos.it>

> xu yuehua wrote:
>
> > the whole progress of installation:
>
> I do not see where XCRYSDEN_SCRATCH is set. You need to:
> - remove everything Xcrysden-related from everywhere,
>   including .bashrc
> - reinstall from scratch
>
> > [..] is there any other problem ?
>
> I have no problem at all! (well, actually I have one:
> some genius has cut the electricity and the mail server
> of the physics department is down...)
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From ski2 at mail.uh.edu  Fri Oct 10 17:49:13 2008
From: ski2 at mail.uh.edu (ski2 at mail.uh.edu)
Date: Fri, 10 Oct 2008 10:49:13 -0500
Subject: [Pw_forum] Use different type of PP
Message-ID: <f5a39f751db11.48ef3329@mail.uh.edu>

Dear all,

I have a quick question about utilization of pseudopentials.

Is it possible to use Vanderbilt ultrasoft PPs with? Martins-Troullier PPs in an electronic structure calculation?
For example: I.pbe-mt_bw.UPF and O.pbe-van_bm.UPF

Best Wishes,
Sang-Hwan


Department of Chemistry
University of Houston
136 Fleming Building
Houston, TX 77204-5003
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From prasenjit.jnc at gmail.com  Fri Oct 10 17:58:53 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 10 Oct 2008 17:58:53 +0200
Subject: [Pw_forum] Use different type of PP
In-Reply-To: <f5a39f751db11.48ef3329@mail.uh.edu>
References: <f5a39f751db11.48ef3329@mail.uh.edu>
Message-ID: <627e0ffa0810100858n5c8cbe1ex2b42cf2c9a7a745@mail.gmail.com>

As long as the Exchange correlation function of the two pseudopotentials are
same you cam use it.

Prasenjit.

2008/10/10 <ski2 at mail.uh.edu>

> Dear all,
>
> I have a quick question about utilization of pseudopentials.
>
> Is it possible to use Vanderbilt ultrasoft PPs with  Martins-Troullier PPs
> in an electronic structure calculation?
> For example: I.pbe-mt_bw.UPF<http://www.quantum-espresso.org/pseudo/1.3/UPF/I.pbe-mt_bw.UPF>and
> O.pbe-van_bm.UPF<http://www.quantum-espresso.org/pseudo/1.3/UPF/O.pbe-van_bm.UPF>
>
> Best Wishes,
> Sang-Hwan
>
>
> Department of Chemistry
> University of Houston
> 136 Fleming Building
> Houston, TX 77204-5003
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
             +39 3807528672 (M)
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From janos.kiss at theochem.ruhr-uni-bochum.de  Fri Oct 10 19:15:48 2008
From: janos.kiss at theochem.ruhr-uni-bochum.de (Janos Kiss)
Date: Fri, 10 Oct 2008 19:15:48 +0200
Subject: [Pw_forum] WFC convergence in NEB calculation
Message-ID: <200810101915.49136.janos.kiss@theochem.ruhr-uni-bochum.de>

Dear PWSCF community,

I already asked these questions a good while ago, but unfortunately 
none of the resposes solved my problem. This would be the following:

I want to study relative 'simple' proton transfer reaction on a ZnO surface 
(surface slab represented with a  hexagonal supercell and ultrasoft psp). 
When i do an NEB calculation, the wfc for those images, which are close either 
to the reactant, or the product converge really nicely within 7-12 SCF steps.
Such an example, if i make a band with 17 images (15 movable 2 fixed), than 
the wfc for images 2->6 and 9->15 converges flawlessly and really fast. 
Now, for images 7-8-9 i cannot manage to get the wfc to converge, no matter 
what i do. Of course, one could argue, that the position of the nuclei in 
these configuration are way too far from equilibrium. I completely agree with 
this, but if i visualize them, they are completely meaningful TS 
configurations, where an OH group is elongated to around 1.6 A and this 
proton is oriented towards a 'target' C or O atom, which would give me the 
product. What is even more puzzling, is that after the first linear 
interpolation (when the nuclear positions are the worse possible) the wfc 
does converge for all images most of the time. After 4-10 iterations with the 
band the barrier nicely goes down to around 2-3 eV, because the path is 
getting better and better. This is exactly the point, when this strange 
behavior in the wfc convergence kicks in. For images 7-8-9 the Total Energy 
and the gradient on the wfc will just fluctuate up and down within a given 
range, without achieving convergence ever.

What i tried up to now: decrease mixing_beta to values as low as 0.1, tried 
all the mixing modes (my default was mixing mode=?local-TF?), increased 
mixing ndim to 12, increased ecutrho to 5 times ecutwfc. Altough, the ZnO slab 
should be semiconductor, just to try to get a converged wfc i added around 
extra 20% empty bands and a broadening. This did not help, either. Because of 
the available memory i do not really wanna play around to crank up the cutoff, 
but if one say that this gonna help, i can give it a try. Just for testing, i 
plugged the same geometries with the same VDB psp with the same cutoff values 
into CPMD. Although the achieving self-consistency was slow as well, but 
still i could obtain a converged wfc and calculate the forces for these 
configurations without too much additional effort/trick. My point here is not 
that CPMD is better/worse, but the fact that the given configurations were 
not completely nonsense, and the whole setup and set of psp is reasonable.

Is this behavior completely normal in an NEB calculation with PWSCF, or this 
is an issue with my particular system/setup only? 
What else could one try, to get the wfc somehow converged?
Another question: when i restart an NEB calculation, how can i restart the wfc 
for those images, which were already converged for a given NEB iteration?
The output file indicates, that the initial density and the Starting wfc were 
read in 'from file'. I would have expected, that once this is done, the wfc 
will converge within 1-2 iterations, because the already self-consistent wfc 
was written out in the respective *.wfc files. Apparently this is not the 
case, because even for those images, where the wfc was converged, i still 
nead to spend again like 5-9 SCF cycles/image. 

What am i doing wrong?

Yours Sincerely,
 Janos.

 ==================================================================
   Janos Kiss   e-mail: janos.kiss at theochem.ruhr-uni-bochum.de       
 Lehrstuhl fuer Theoretische Chemie  Phone: +49 (0)234/32-26485 
 NC 03/297                                  +49 (0)234 32 26754
 Ruhr-Universitaet Bochum            Fax:   +49 (0)234/32-14045
 D-44780 Bochum            http://www.theochem.ruhr-uni-bochum.de
 ==================================================================



From marzari at MIT.EDU  Fri Oct 10 19:39:10 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 10 Oct 2008 20:39:10 +0300
Subject: [Pw_forum] WFC convergence in NEB calculation
In-Reply-To: <200810101915.49136.janos.kiss@theochem.ruhr-uni-bochum.de>
References: <200810101915.49136.janos.kiss@theochem.ruhr-uni-bochum.de>
Message-ID: <48EF933E.5080309@mit.edu>



Dear Janos,


the only thing that jumps out is the ecutrho - for ultrasoft
I'd go for 8 times the ecutwfc, as a starting point. You mention
that you raised it to 5 times (presumably from 4) - this is still too
little.

Second, try decreasing mixing beta below 0.1 .

A few extra bands (but not remotely 20% more) and some boradening
might indeed help is there are some level-crossing states in the gap.

No other suggestions I could think of.

Out of curiosity, you could try the same identical system, and
converge it using the CP code - either using damped dynamics on
the electrons (very robust, a bit slow) or conjugate-gradients.

			nicola

---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From tone.kokalj at ijs.si  Sat Oct 11 00:22:34 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Sat, 11 Oct 2008 00:22:34 +0200
Subject: [Pw_forum] Bug in axsf generation?
In-Reply-To: <f9fbbdf30810100723x75bed882i1a74d2188a2d8e1c@mail.gmail.com>
References: <f9fbbdf30810100723x75bed882i1a74d2188a2d8e1c@mail.gmail.com>
Message-ID: <1223677354.23688.4.camel@walk.ijs.si>

On Fri, 2008-10-10 at 08:23 -0600, Jan Beck wrote:
> I have an axsf file that I have generated with quantum espresso's cppp. I
> have checked with the specification of the axsf file format, and the
> output from quantum espresso is consistent with that.
> so the output seems to conform to the standard. However, as soon as I
> load the file with the command:
> 
> xcrysden --axsf c6h6.axsf
> 
> I get the following output

Please provide your c6h6.axsf file, and then somebody may help you.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From nakhmanson at anl.gov  Sat Oct 11 00:33:35 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Fri, 10 Oct 2008 17:33:35 -0500
Subject: [Pw_forum] Should I scrap the nonanalytic part of DM in
 electroded thin films?
In-Reply-To: <1D8CFCA6-C407-46DC-AA84-65FDE2AD3E4E@sissa.it>
References: <48EBD865.8020701@anl.gov>
	<1D8CFCA6-C407-46DC-AA84-65FDE2AD3E4E@sissa.it>
Message-ID: <48EFD83F.4000606@anl.gov>

Stefano, Nicola,

Thank you for your comments -- this is some good food for thought!
Making electrodes an explicit part of the calculation will
surely be necessary in the case of thin-ish films, but it
opens its own big can of worms (band alignment between components
with DFT band gaps, etc; I bet you know the issues very well)
I do not want to deal with in this particular project. For
the case of thick-ish films with assumed perfect screening
I could probably guesstimate things around Gamma by taking an
"honest" bulk case as a reference and then playing with phonon
postprocessing routines (easy, since no new time-consuming DM
calculations are required).

But, I guess, the thought of how to add screening to this
process in a more rigorous fashion is worth some additional
thinking.

THX,

Serge

Stefano Baroni wrote:
> Dear Serge:
> 
>>
>> I understand that in bulk calculations the dynamical
>> matrices at small q are split into analytic and
>> nonanalytic parts, with the latter accounting for the
>> effects of macroscopic electric field. However, if
>> we want to study phonons in a model representing an
>> electroded thin film instead of a bulk crystal (i.e.,
>> the electrodes are not explicitly included in such a
>> calculation), we should assume that such an electric
>> field will be screened out by the free charges and
>> its influence onto ionic vibrations should not be
>> considered.
>>
>> I am under an impression that to achieve this in pwscf
>> I need to block the calls to nonanal(...) subroutine
>> in dynmat and matdyn, while leaving everything else
>> intact. Would this work out or could it possibly be not
>> as trivial as I imagine it?
> 
> I am afraid it is indeed not as trivial as you imagine it ... I am no 
> longer familiar with the guts of the code, but the only thing the code 
> can possibly do is to make the phonons calculated at q=0 equal to the 
> values that the phonon branches would have in the long-wavelength limit 
> (and those depend in a non trivial way on the combination of 
> wavevector/polarization, because of the long range character of the 
> Coulomb interaction). I think that, in the presence of free carriers, 
> the results of the code are in principle correct whenever the phonon 
> wavelength is smaller that the screening length. At q=0 just setting the 
> effective charges equal to zero (which is what you would presumably get 
> by commenting out some appropriate routine calls) should do the job, but 
> you would then get frequencies that are inconsistent with those 
> calculated at finite q. To get fully consistent results, I think that 
> screening from free carriers should be explicitly accounted for in the 
> calculation of the dynamical matrix. Possible, but "not as trivial as 
> one could imagine".
> 
> Cheers - stefano
> 


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From zdw2000 at gmail.com  Sat Oct 11 12:27:13 2008
From: zdw2000 at gmail.com (Wei Zhou)
Date: Sat, 11 Oct 2008 03:27:13 -0700
Subject: [Pw_forum] is there a pseduo potential about the C
	Perdew-Burke-Ernzerhof (PBE) NC ?
In-Reply-To: <48EF514B.20209@sissa.it>
References: <3e36a8fc0810100449x7fdcc84dueeefda66c5eeef2e@mail.gmail.com>
	<48EF514B.20209@sissa.it>
Message-ID: <3e36a8fc0810110327w7cd87cdek81ad36bedca39b31@mail.gmail.com>

thank you for your quickly reply in details ,It is very helpful for my work.
best wishes


2008/10/10, Stefano de Gironcoli <degironc at sissa.it>:
>
> Dear Wei Zhou,
>   please notice that you can mix NC and US pseudo-potentials in PWscf....
>   Iodine is an sp element in the forth row and it is likely to need an
> only moderate cutoff  (22 Ry in the paper by Brandon Wood and Nicola
> Marzari quoted in the "details" entry on the pseudo-potential web-page)
> ... Carbon is a first-row element that in the NC form would require
> significantly larger cut-offs  (50-60 Ry at least). With an ultrasoft
> pseudo-potential instead a cutoff of the order of 30 Ry is typically
> enough.
> There are several PBE US pseudo-potentials for Carbon in the
> pseudo-potential library.
>
> Hope this helps,
> stefano
>
> PS: Don't forget to test convergence of the calculation for your
> specific case.
> -
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> Wei Zhou wrote:
> > dear all users
> >                     I want to do some calcuations about some
> > structures related to the element I and C ,however ,I only found one
> > element I pseudo potential in the pw pseudo potential libary ,which is
> > Perdew-Burke-Ernzerhof (PBE)  NC potential , and I cannot find the
> > corresponding pseudo potential C , would some one can help me give the
> > matching pseudo potential ? I  pseudo
> > potential or  Perdew-Burke-Ernzerhof (PBE)  NC carbon potential.
> > any help will be appreciated .
> > best wishes
> >
> >
> > --
> > ZhouDawei
> > JiLin Universiyt ,ChangChun ,China
> > zdw2000 at gmail.com <mailto:zdw2000 at gmail.com>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From marzari at MIT.EDU  Sat Oct 11 14:20:59 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sat, 11 Oct 2008 15:20:59 +0300
Subject: [Pw_forum] Should I scrap the nonanalytic part of DM in
 electroded thin films?
In-Reply-To: <48EFD83F.4000606@anl.gov>
References: <48EBD865.8020701@anl.gov>	<1D8CFCA6-C407-46DC-AA84-65FDE2AD3E4E@sissa.it>
	<48EFD83F.4000606@anl.gov>
Message-ID: <48F09A2B.7060409@mit.edu>




Dear Serge,


I think I've found the perfect reference: vibrational
properties of a BN sheet deposited over different metals:
http://prola.aps.org/abstract/PRL/v79/i23/p4609_1

(and indeed different metals lead to a different properties,
with Ni having perfect screening, and LO/TO degeneracy).

				nicola



Serge Nakhmanson wrote:
> Stefano, Nicola,
> 
> Thank you for your comments -- this is some good food for thought!
> Making electrodes an explicit part of the calculation will
> surely be necessary in the case of thin-ish films, but it
> opens its own big can of worms (band alignment between components
> with DFT band gaps, etc; I bet you know the issues very well)
> I do not want to deal with in this particular project. For
> the case of thick-ish films with assumed perfect screening
> I could probably guesstimate things around Gamma by taking an
> "honest" bulk case as a reference and then playing with phonon
> postprocessing routines (easy, since no new time-consuming DM
> calculations are required).
> 
> But, I guess, the thought of how to add screening to this
> process in a more rigorous fashion is worth some additional
> thinking.
> 
> THX,
> 
> Serge
> 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From w2agz at pacbell.net  Mon Oct 13 01:47:52 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Sun, 12 Oct 2008 16:47:52 -0700
Subject: [Pw_forum] Getting DOS at Fermi Energy
Message-ID: <000001c92cc4$f1bc9550$d535bff0$@net>

There must be an easier way to get the density-of-states at the Fermi level
then what I'm doing now, viz., using dos.x or the la2f flag and
interpolating through the output.  I note that pp.x has a feature "plot_num
= 3" which purports to give the "local density of states at e_fermi," but I
see no way of configuring the &plot namelist to yield other than a plot
file.and of course the DOS at Ef is just a number.  I tried scanning through
the fortran source and just got more confused.  Does a simple tool exist to
extract this number from a full DOS calculation?  If not, I might consider
writing one.

BTW, Happy Columbus Day to All!

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/> 
 
 


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From w2agz at pacbell.net  Mon Oct 13 01:56:17 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Sun, 12 Oct 2008 16:56:17 -0700
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
Message-ID: <000501c92cc6$1f5ac940$5e105bc0$@net>

How does one make an animated axsf file using XCrySDen directly?  For
example, suppose I want save in an axsf file the animation of an isosurface
of charge density moving through a given unit cell.  I can save the
"situation" as an .xcrysden script file for play back, but on loading it
doesn't raise the Modify -> Animation Controls option.  Only an .axsf file
apparently does this.  Do I have to go through the script file inserting
"ANIMSTEPS" by hand?

I note that the XCrySDen forum archives has had no entries since April.Is
PW_Forum now the appropriate target for XCrySDen issues?

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/> 
 
 


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From akohlmey at cmm.chem.upenn.edu  Mon Oct 13 02:17:44 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 12 Oct 2008 20:17:44 -0400 (EDT)
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <000501c92cc6$1f5ac940$5e105bc0$@net>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
Message-ID: <Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>

On Sun, 12 Oct 2008, Paul M. Grant wrote:

hi paul,

not sure whether this is helpful, but i managed to do something
similar to what you describe with VMD (granted VMD is still missing
a lot of features for crystals etc. so it may not work as well for you).

the problem is that usually volumetric data sets are not associated
with the individual time step of an animation. the VMD script works
because it is loading a sequence of cube files with a 1:1 correlation
of coordinate and volumetric data and then makes the correlation by
replacing the volumetric data sets through a callback hook to the 
animation loop frame number variable (standard tcl method). see:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect6

for more complicated scenarios (e.g. i have dome some nice movies of 
the fluctuations of spin densities of electron pairs in the cavities 
of an electride-like compound) one has to write more complicated tcl 
scripts.

i would assume that there may be similar scripts possible with xcrysden, 
provided the script API is flexible enough... (never tried it).

cheers,
   axel.


PG> How does one make an animated axsf file using XCrySDen directly?  For
PG> example, suppose I want save in an axsf file the animation of an isosurface
PG> of charge density moving through a given unit cell.  I can save the
PG> "situation" as an .xcrysden script file for play back, but on loading it
PG> doesn't raise the Modify -> Animation Controls option.  Only an .axsf file
PG> apparently does this.  Do I have to go through the script file inserting
PG> "ANIMSTEPS" by hand?
PG> 
PG> I note that the XCrySDen forum archives has had no entries since April.Is
PG> PW_Forum now the appropriate target for XCrySDen issues?
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com <http://www.w2agz.com/> 
PG>  
PG>  
PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From w2agz at pacbell.net  Mon Oct 13 06:37:13 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Sun, 12 Oct 2008 21:37:13 -0700
Subject: [Pw_forum] k-point grids...and all that
In-Reply-To: <CF518C85-3B9F-43B1-A853-7462CEEEFFC7@democritos.it>
References: <020401c916e3$571a2bd0$054e8370$@net>
	<CF518C85-3B9F-43B1-A853-7462CEEEFFC7@democritos.it>
Message-ID: <001601c92ced$5e170cd0$1a452670$@net>

Not to be tedious, but let me raise this question again.  First of all,
k-point.f90 is a routine I've been writing for my own education, and in the
bleariness of a late evening posting, I subliminally substituted it for
kpoints.f.  I did have a quick look at the latter code beforehand, but when
I saw the phrase "special points," I took it to refer to the
Bouckaert-Smolukowski-Wigner notation for high symmetry BZ "special points"
I learned in my younger years (this is the sort of stuff you can find on the
Bilbao website these days).  I do see now the usage of the term in kpoints.f
indeed means the calculation of an MP mesh.  Thanks, Paolo.

What I was most concerned about was the generation of k-point meshes or nets
for use as input to pw.x (nscf) for subsequent post-processing calculations,
such as the computation of Fermi surfaces or optical properties. For
example, the routine kvecs_FS.x appears to fill the reciprocal lattice of
its input structure with uniformly spaced, equally weighted, point
coordinates, whereas the method used to calculate the mesh used for the
aluminum example of epsilon.x is unclear (at least to me).  There is a
warning in the documentation for epsilon.x that "reduction of the k-points
grid into the irreducible BZ" is not supported.  I also note that the
conventional unit cell (ibrav = 1), not the Bravais or primitive fcc (ibrav
= 2) coordinates are used in the example.  Does this mean one can compute
the mesh for epsilon.x using kvecs_FS.x and the "conventional" reciprocal
cell coordinates?

Finally, on the point of mesh visualization.  I use XCrySDen a lot,
especially for BZ and charge-potential visualizations.  But I don't know how
to configure or generate a .xsf file for a 3D mesh of discrete points.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Monday, September 15, 2008 1:33 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] k-point grids...and all that

On Sep 15, 2008, at 5:30 , Paul M. Grant wrote:
> The ability to compute weighted 1st BZ grids according to the  
> Monkhorst-Pack scheme is included somewhere within espresso-4.0,  
> but exactly where is unclear (k-points.f90?  No).
>
of course no, since it is non-existent:
$ ls -l */k-points.f90
ls: */k-points.f90: No such file or directory
There is however an auxiliary code, pwtools/kpoints.f, that produces  
Monkhorst-Pack
grids with weights (executable: kpoints.x).

Inside q-e, there are several routines for the generation of  
automatic k-point grids.
See PW/setup.f90, under
   !
   ! ... Automatic generation of k-points (if required)
   !
Routines kpoint_grid_efield and kp_strings are specific for  
macroscopic field
and Berry phase calculations; kpoint_grid and setupkpoint (undocumented)
take care of the typical scf case. The difference between the two is  
just
aesthetic.
> Finally, is there a visualization tool to display the k-point  
> distribution within the  1st BZ?  XcrysDen?
>
for sure: see http://www.xcrysden.org/img/xcrysden-in-action.png,  
first picture

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From w2agz at pacbell.net  Mon Oct 13 06:53:06 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Sun, 12 Oct 2008 21:53:06 -0700
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
	<Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>
Message-ID: <002301c92cef$952c3cc0$bf84b640$@net>

Axel, thanks for getting back on this.  Let me think about your suggestion
and see what others have to comment as well.

Reflecting on "animation" in general a little more, I wonder if there's a
Linux screen capture tool available somewhere analogous to KDE Ksnapshot for
jpeg images, but which could capture motion in addition resulting in an mpeg
file.  Now that would be a handy and nifty gadget for lots of purposes!

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Axel Kohlmeyer
Sent: Sunday, October 12, 2008 5:18 PM
To: Paul M. Grant
Cc: 'PWSCF Forum'
Subject: Re: [Pw_forum] On making a *.axsf file with XCrySDen

On Sun, 12 Oct 2008, Paul M. Grant wrote:

hi paul,

not sure whether this is helpful, but i managed to do something
similar to what you describe with VMD (granted VMD is still missing
a lot of features for crystals etc. so it may not work as well for you).

the problem is that usually volumetric data sets are not associated
with the individual time step of an animation. the VMD script works
because it is loading a sequence of cube files with a 1:1 correlation
of coordinate and volumetric data and then makes the correlation by
replacing the volumetric data sets through a callback hook to the 
animation loop frame number variable (standard tcl method). see:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#c
hap7_sect6

for more complicated scenarios (e.g. i have dome some nice movies of 
the fluctuations of spin densities of electron pairs in the cavities 
of an electride-like compound) one has to write more complicated tcl 
scripts.

i would assume that there may be similar scripts possible with xcrysden, 
provided the script API is flexible enough... (never tried it).

cheers,
   axel.


PG> How does one make an animated axsf file using XCrySDen directly?  For
PG> example, suppose I want save in an axsf file the animation of an
isosurface
PG> of charge density moving through a given unit cell.  I can save the
PG> "situation" as an .xcrysden script file for play back, but on loading it
PG> doesn't raise the Modify -> Animation Controls option.  Only an .axsf
file
PG> apparently does this.  Do I have to go through the script file inserting
PG> "ANIMSTEPS" by hand?
PG> 
PG> I note that the XCrySDen forum archives has had no entries since
April.Is
PG> PW_Forum now the appropriate target for XCrySDen issues?
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com <http://www.w2agz.com/> 
PG>  
PG>  
PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From mansourehp at gmail.com  Mon Oct 13 07:49:58 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Mon, 13 Oct 2008 09:19:58 +0330
Subject: [Pw_forum] About LDA+U
In-Reply-To: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
References: <7085520.195881223537668198.JavaMail.coremail@bj126app52.126.com>
Message-ID: <cbe1626b0810122249k418b1840xaf8c5864c940323a@mail.gmail.com>

Dear Wang
you can find the way of U calculation in first Vlab in lecture part and
Matteo Cococcioni'
thesis.
good luck
Mansoureh
On Thu, Oct 9, 2008 at 11:04 AM, wangqj1 <wangqj1 at 126.com> wrote:

>
>  Dear Mansoureh
>       I have not got U for this system ,So I want to caculate it .Can you
> give some advice and examples ? Thank you !
>
>
>
>
>
>
>  Dear Wang
> have you got U for this system?or do you want to calculate it?
> Mansoureh
>
> >*
> *>*  Dear pwscf users
> *>*
> *>*     I want to do some LDA+U caculations of Mn adoped ZnO, but I don't
> know
> *>* how to set
> *>*
> *>* the parameter of Hubbard_U(I) , *Does anyone know the Hubbard U
> parameter
> *>* of ZnO and Mn ?*
> *>* *   *
> *>*  *Any help will be greatly appreciated.*
> *>* **
> *>*
> *>* Sincerely.
> *>*
> *>* Wang
> *>* **
> *>*
> *
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From marcello.rosini at unimore.it  Mon Oct 13 10:03:45 2008
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Mon, 13 Oct 2008 10:03:45 +0200
Subject: [Pw_forum] XCRYSDEN problem readinf PW4 output
Message-ID: <48F300E1.1020304@unimore.it>

Hi everybody,
I had a problem with xcrysden when reading the output of a pw 4.* 
relaxation. The problem is that in the output also the fixed flags of 
the atom coordinates are present, while it was not so in the previous 
versions.
I modified few lines in the source code, in order to make xcrysden able 
to work in this case.
You can find the modified code here:
http://cdm.unimo.it/home/fisica/rosini.marcello/scr.tar.gz

One you have installed xcrysden, extract the modified files in the 
directory "scripts" of the xcrysden root directory and it should work.

Marcello

From giannozz at democritos.it  Mon Oct 13 10:54:46 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Oct 2008 10:54:46 +0200
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <000001c92cc4$f1bc9550$d535bff0$@net>
References: <000001c92cc4$f1bc9550$d535bff0$@net>
Message-ID: <F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>

On Oct 13, 2008, at 1:47 , Paul M. Grant wrote:

> There must be an easier way to get the density-of-states at the  
> Fermi level
>

I think that the simplest way is to use function dos_ef,
in PH/elphon.f90

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From asaaravindh at yahoo.co.in  Mon Oct 13 13:28:30 2008
From: asaaravindh at yahoo.co.in (asa aravindh)
Date: Mon, 13 Oct 2008 16:58:30 +0530 (IST)
Subject: [Pw_forum] scf-convergence
Message-ID: <720108.21446.qm@web7907.mail.in.yahoo.com>

Dear all..
I am trying to do scf calculation of an fe/co nanowire along the bcc (110) direction.
However the calculation is not getting converged..after even 100 iterations.. the scf accuarcy is not reached and suddenly the program stops ...
can anybody pls tell me if anything is wrong with my input file...
the input file is attached
any reply would be greatly appreciated
regards,
asa


      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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From giannozz at democritos.it  Mon Oct 13 16:21:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Oct 2008 16:21:33 +0200
Subject: [Pw_forum] k-point grids...and all that
In-Reply-To: <001601c92ced$5e170cd0$1a452670$@net>
References: <020401c916e3$571a2bd0$054e8370$@net>
	<CF518C85-3B9F-43B1-A853-7462CEEEFFC7@democritos.it>
	<001601c92ced$5e170cd0$1a452670$@net>
Message-ID: <ABCD170C-ACF8-425A-9809-423FEB0389C5@democritos.it>


On Oct 13, 2008, at 6:37 , Paul M. Grant wrote:

> [...] the method used to calculate the mesh used for the
> aluminum example of epsilon.x is unclear (at least to me).

which aluminum example of epsilon.x you are referring to?

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From nguyenhalvt at yahoo.com  Mon Oct 13 16:15:59 2008
From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha)
Date: Mon, 13 Oct 2008 07:15:59 -0700 (PDT)
Subject: [Pw_forum] String method example?
Message-ID: <840628.72382.qm@web31006.mail.mud.yahoo.com>

Dear PWscf users,
I like using SMD and Metadynamics to investigate free energy suface (That implemented in PWscf code) but I see there are so few of examples for SMD. 
For testing purpose only with phase_space = 'coarse-grained', I'm still failed.
Here is my input:
...
 &IONS
                ion_dynamics = 'damp' ,
                 phase_space = 'coarse-grained' ,
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
            remove_rigid_rot = .false. ,
               num_of_images = 5 ,
                  opt_scheme = 'langevin' ,
                    temp_req = 298 ,
                          ds = 1. ,
                    path_thr = 0.1D0 ,
                use_freezing = .false. ,
                  use_masses = .true. ,
 /
ATOMIC_SPECIES
    H    1.00794  HUSPBE.RRKJ3 
ATOMIC_POSITIONS angstrom 
first_image
    H     -2.416592653    0.000000000    0.000000000    1  0  0 
    H      0.000000000    0.000000000    0.000000000    0  0  0 
    H      0.824334341    0.000000000    0.000000000    1  0  0 
last_image
    H     -0.824334341    0.000000000    0.000000000 
    H      0.000000000    0.000000000    0.000000000 
    H      2.416592653    0.000000000    0.000000000 
K_POINTS gamma 

Then I get the following message:
...
    from read_cards : error #         1
    wrong number of columns in ATOMIC_POSITIONS
...

I don't know what's wrong with my input (why is ATOMIC_POSITIONS indicated?)
 
Thank you for your help.


Nguyen, Ngoc Ha
Hanoi National University of Education
Faculty of Chemistry
Department of Physical Chemistry
Tel: Office: 04/8330842
Home: 04/7891674
Mobile: 0989133436


      

From giannozz at democritos.it  Mon Oct 13 16:59:05 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Oct 2008 16:59:05 +0200
Subject: [Pw_forum] WFC convergence in NEB calculation
In-Reply-To: <200810101915.49136.janos.kiss@theochem.ruhr-uni-bochum.de>
References: <200810101915.49136.janos.kiss@theochem.ruhr-uni-bochum.de>
Message-ID: <6C74E7C5-9809-4A15-BF3A-E55BF20CDD44@democritos.it>


On Oct 10, 2008, at 19:15 , Janos Kiss wrote:

> Is this behavior completely normal in an NEB calculation with  
> PWSCF, or this
> is an issue with my particular system/setup only?

the latter you say, and a bit of the former as well: your particular  
system seems
to be a nasty one, and NEB typically explores strange geometrical  
configurations
that are sometimes hard to converge.

> What else could one try, to get the wfc somehow converged?

hard to say (especially withouth the ouput). Are you sure that spin  
polarization
is not a source of trouble close to the transition state?

One possible trick could be to go on with the calculation even if not  
converged.
I am actually considering adding yet another option  
("sloppy_convergence"?)
doing exactly this. It should be easy: in PW/electrons.f90, set  
"conv_elec" to
.true. at the last iteration, after the call to "mix_rho". No warranty.

> Another question: when i restart an NEB calculation, how can i  
> restart the wfc
> for those images, which were already converged for a given NEB  
> iteration?
> [...] even for those images, where the wfc was converged, i still  
> need to
> spend again like 5-9 SCF cycles/image.

are you sure that the code is using the same set of coordinates that  
were used
in the previous calculation? Maybe the restart doesn't work as expected.

> What am i doing wrong?

maybe nothing. NEB is relatively new and its application may  
encounter some
difficulties, until more experience is gathered (and better  
algorithms implemented).

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From giannozz at democritos.it  Mon Oct 13 17:02:09 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Oct 2008 17:02:09 +0200
Subject: [Pw_forum] String method example?
In-Reply-To: <840628.72382.qm@web31006.mail.mud.yahoo.com>
References: <840628.72382.qm@web31006.mail.mud.yahoo.com>
Message-ID: <984D48D0-41E4-4AB2-9F7C-0B8C2C10C1F7@democritos.it>


On Oct 13, 2008, at 16:15 , Nguyen Ngoc Ha wrote:

> ATOMIC_POSITIONS angstrom
> first_image
>     H     -2.416592653    0.000000000    0.000000000    1  0  0
>     H      0.000000000    0.000000000    0.000000000    0  0  0
>     H      0.824334341    0.000000000    0.000000000    1  0  0
> last_image
>     H     -0.824334341    0.000000000    0.000000000
>     H      0.000000000    0.000000000    0.000000000
>     H      2.416592653    0.000000000    0.000000000
> K_POINTS gamma
>
> Then I get the following message:
> ...
>     from read_cards : error #         1
>     wrong number of columns in ATOMIC_POSITIONS
> ...
>
> I don't know what's wrong with my input (why is ATOMIC_POSITIONS  
> indicated?)

because the error is there. I think the code doesn't like that you have
7 columns for atomic positions (+ constraints) in the first image,
4 columns (i.e. no constraints) in the last image

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From akohlmey at cmm.chem.upenn.edu  Mon Oct 13 18:11:10 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 12:11:10 -0400 (EDT)
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <002301c92cef$952c3cc0$bf84b640$@net>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
	<Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>
	<002301c92cef$952c3cc0$bf84b640$@net>
Message-ID: <Pine.LNX.4.64.0810131040320.2352@localhost.localdomain>

On Sun, 12 Oct 2008, Paul M. Grant wrote:

paul,

PG> Axel, thanks for getting back on this.  Let me think about your suggestion
PG> and see what others have to comment as well.

it is actually quite difficult to give a recommendation, 
since everybody uses a different nomenclature when it comes
to visualization and animations, based on background, software
being used and ability to put visual ideas in words (which i 
always found very difficult). 

PG> Reflecting on "animation" in general a little more, I wonder if there's a
PG> Linux screen capture tool available somewhere analogous to KDE Ksnapshot for
PG> jpeg images, but which could capture motion in addition resulting in an mpeg
PG> file.  Now that would be a handy and nifty gadget for lots of purposes!

there is a number of ways to do this and it depends on whether
you want a "realtime" capture or just "one frame per update"
type animations. the former could in principle be done on any 
x11 based machine with some smart shell scripting using the
xwd utility after figuring out the x window id of the display
window. the latter is a method that is been used by many "movie maker"
tools that are integrated into visualization programs.

in both cases you assemble a sequence of snapshots and then use
tools like ppmtompeg, mencoder, convert, gifsicle and so on 
to turn them into an mpeg, avi, or animated gif movie. 

please note that "realtime" capture (for mpeg) would require a 
screenshot frequency of up to 30 snapshots per second which is
probably beyond the capability of most hardware, not to mention
the limitations of the X protocol... but then again, it would
reduced the load and hardware requirements at playback time a lot.

it should be possible to write a proof-of-concept code based on
existing tools rather quickly. i'll put it on my (ever growing)
TODO list and will get back to you if i have something that is
worth trying out.

cheers,
   axel.

PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com
PG> ?
PG> ?
PG> 
PG> 
PG> -----Original Message-----
PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
PG> Behalf Of Axel Kohlmeyer
PG> Sent: Sunday, October 12, 2008 5:18 PM
PG> To: Paul M. Grant
PG> Cc: 'PWSCF Forum'
PG> Subject: Re: [Pw_forum] On making a *.axsf file with XCrySDen
PG> 
PG> On Sun, 12 Oct 2008, Paul M. Grant wrote:
PG> 
PG> hi paul,
PG> 
PG> not sure whether this is helpful, but i managed to do something
PG> similar to what you describe with VMD (granted VMD is still missing
PG> a lot of features for crystals etc. so it may not work as well for you).
PG> 
PG> the problem is that usually volumetric data sets are not associated
PG> with the individual time step of an animation. the VMD script works
PG> because it is loading a sequence of cube files with a 1:1 correlation
PG> of coordinate and volumetric data and then makes the correlation by
PG> replacing the volumetric data sets through a callback hook to the 
PG> animation loop frame number variable (standard tcl method). see:
PG> 
PG> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#c
PG> hap7_sect6
PG> 
PG> for more complicated scenarios (e.g. i have dome some nice movies of 
PG> the fluctuations of spin densities of electron pairs in the cavities 
PG> of an electride-like compound) one has to write more complicated tcl 
PG> scripts.
PG> 
PG> i would assume that there may be similar scripts possible with xcrysden, 
PG> provided the script API is flexible enough... (never tried it).
PG> 
PG> cheers,
PG>    axel.
PG> 
PG> 
PG> PG> How does one make an animated axsf file using XCrySDen directly?  For
PG> PG> example, suppose I want save in an axsf file the animation of an
PG> isosurface
PG> PG> of charge density moving through a given unit cell.  I can save the
PG> PG> "situation" as an .xcrysden script file for play back, but on loading it
PG> PG> doesn't raise the Modify -> Animation Controls option.  Only an .axsf
PG> file
PG> PG> apparently does this.  Do I have to go through the script file inserting
PG> PG> "ANIMSTEPS" by hand?
PG> PG> 
PG> PG> I note that the XCrySDen forum archives has had no entries since
PG> April.Is
PG> PG> PW_Forum now the appropriate target for XCrySDen issues?
PG> PG> 
PG> PG> Paul M. Grant, PhD
PG> PG> Principal, W2AGZ Technologies
PG> PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> PG> EPRI Science Fellow (Retired)
PG> PG> IBM Research Staff Member Emeritus
PG> PG> w2agz at pacbell.net
PG> PG> http://www.w2agz.com <http://www.w2agz.com/> 
PG> PG>  
PG> PG>  
PG> PG> 
PG> PG> 
PG> PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From tone.kokalj at ijs.si  Mon Oct 13 19:19:42 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 13 Oct 2008 19:19:42 +0200
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <000501c92cc6$1f5ac940$5e105bc0$@net>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
Message-ID: <1223918382.19497.29.camel@walk.ijs.si>

On Sun, 2008-10-12 at 16:56 -0700, Paul M. Grant wrote:
> How does one make an animated axsf file using XCrySDen directly?  For
> example, suppose I want save in an axsf file the animation of an
> isosurface of charge density moving through a given unit cell. 

The *.axsf file is meant for specifying several snapshots of 
structures (e.g. evolution of MD run or geometry optimization) and for
for "animating" the charge density.

>  I can save the ?situation? as an .xcrysden script file for play back,
> but on loading it doesn?t raise the Modify -> Animation Controls
> option.  Only an .axsf file apparently does this.

I believe the answer above answers also this question.

> I note that the XCrySDen forum archives has had no entries since
> April?Is PW_Forum now the appropriate target for XCrySDen issues?

xcrysden forum is not very active indeed. Either people ask question on
pw_forum or directly to me. But otherwise xcrysden forum should be the
appropriate target.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Mon Oct 13 19:41:11 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 13 Oct 2008 19:41:11 +0200
Subject: [Pw_forum] XCRYSDEN problem readinf PW4 output
In-Reply-To: <48F300E1.1020304@unimore.it>
References: <48F300E1.1020304@unimore.it>
Message-ID: <1223919671.19497.46.camel@walk.ijs.si>

On Mon, 2008-10-13 at 10:03 +0200, Marcello Rosini wrote:
> Hi everybody,
> I had a problem with xcrysden when reading the output of a pw 4.* 
> relaxation. The problem is that in the output also the fixed flags of 
> the atom coordinates are present, while it was not so in the previous 
> versions.

Indeed so. The xcrysden 1.4.* version cannot handle it due to the reason
you describe, but the "latest-snapshot" version can
http://www.xcrysden.org/download/xc-latest-linuxPC-semishared.tar.gz

> I modified few lines in the source code, in order to make xcrysden able 
> to work in this case.
> You can find the modified code here:
> http://cdm.unimo.it/home/fisica/rosini.marcello/scr.tar.gz

Very good!

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Mon Oct 13 19:50:47 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 13 Oct 2008 19:50:47 +0200
Subject: [Pw_forum] String method example?
In-Reply-To: <984D48D0-41E4-4AB2-9F7C-0B8C2C10C1F7@democritos.it>
References: <840628.72382.qm@web31006.mail.mud.yahoo.com>
	<984D48D0-41E4-4AB2-9F7C-0B8C2C10C1F7@democritos.it>
Message-ID: <1223920248.19497.55.camel@walk.ijs.si>

On Mon, 2008-10-13 at 17:02 +0200, Paolo Giannozzi wrote:
> On Oct 13, 2008, at 16:15 , Nguyen Ngoc Ha wrote:
> 
> > ATOMIC_POSITIONS angstrom
> > first_image
> >     H     -2.416592653    0.000000000    0.000000000    1  0  0
> >     H      0.000000000    0.000000000    0.000000000    0  0  0
> >     H      0.824334341    0.000000000    0.000000000    1  0  0
> > last_image
> >     H     -0.824334341    0.000000000    0.000000000
> >     H      0.000000000    0.000000000    0.000000000
> >     H      2.416592653    0.000000000    0.000000000
> > K_POINTS gamma
> >
> > Then I get the following message:
> > ...
> >     from read_cards : error #         1
> >     wrong number of columns in ATOMIC_POSITIONS
> > ...
> >
> > I don't know what's wrong with my input (why is ATOMIC_POSITIONS  
> > indicated?)
> 
> because the error is there. I think the code doesn't like that you have
> 7 columns for atomic positions (+ constraints) in the first image,
> 4 columns (i.e. no constraints) in the last image


I am not sure for SMD, but for NEB this is how it should be: 7 columns
for the first image and 4 for the rest. What is your value of nat
variable (i.e. number of atoms). Please post the whole input, so that
one may try and see what is giong on.

Why are you fixing the middle atom? I believe in this example you don't
need to fix any atom (I assume its a reaction H2+H = H+H2, right?).

Regards, Tone

> 
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From janos.kiss at theochem.ruhr-uni-bochum.de  Mon Oct 13 21:54:45 2008
From: janos.kiss at theochem.ruhr-uni-bochum.de (Janos Kiss)
Date: Mon, 13 Oct 2008 21:54:45 +0200
Subject: [Pw_forum] WFC convergence in NEB calculation
Message-ID: <200810132154.45883.janos.kiss@theochem.ruhr-uni-bochum.de>

J K wrote:

>> What else could one try, to get the wfc somehow converged?

Paolo Giannozzi wrote:

>hard to say (especially withouth the ouput). Are you sure that spin  
>polarization
>is not a source of trouble close to the transition state?

I have not tried this up to now, because i would suspect that in a reaction 
where a proton/hydride transfer is involved most species should be more like 
ions and not radicals (of course i might be plain wrong here). 
I was also concerned about this aspect, but when i did a quick and 
rough test calculation, the wfc convergence was not particularly better, and 
one SCF step took a lot longer time. Therefore, i just killed it impatiently 
iirc.

Paolo Giannozzi wrote:

>One possible trick could be to go on with the calculation even if not  
>converged.
>I am actually considering adding yet another option  
>("sloppy_convergence"?)
>doing exactly this. It should be easy: in PW/electrons.f90, set  
>"conv_elec" to
>.true. at the last iteration, after the call to "mix_rho". No warranty.

I have done this right after your first response, and recompiled the code with 
the modified routine. I set the maximum number of SCF steps to 150, expecting  
that either the wfc gonna converge in this 150 iterations, or i get 
the forces with that wfc what i have in the given moment after 
150 step. Insted of this i just got a crash and a core dump.

For my case this workaround is not really good anyway, because the wfc is so 
bad (the total energy fluctuates in the very first decimal), that the forces 
would not really make any physical sense. 

J K wrote:

>> Another question: when i restart an NEB calculation, how can i  
>> restart the wfc
>> for those images, which were already converged for a given NEB  
>> iteration?
>> [...] even for those images, where the wfc was converged, i still  
>> need to
>> spend again like 5-9 SCF cycles/image.

Paolo Giannozzi wrote:

>are you sure that the code is using the same set of coordinates that  
>were used
>in the previous calculation? Maybe the restart doesn't work as expected.

I have looked into this, and i think you are completely right, because the 
code restarts the nuclear positions from the *.path file, which in a case of 
a crash contains the coordinates from the previous NEB iteration. I was 
thinking that it is updated after the convergence is achieved on any movable 
image, and not just after a successfull NEB optimization step.

I tried to use the cg scheme for those images where the wfc convergence was 
tricky, but it was not successfull. I am really afraid, that somehow i 
managed to misscompile the code, because if i try to crank up the density 
cutoff above 5 times the pwcutoff, the code crashes right after the wfc 
initialization in the wfc diagonalization. I think this is a really bad sign.
In fact, i completely forgot to mention, that i was able to produce a relative 
stable binary with mkl 8.1 only. With newer mkl versions in a geometry 
optimization after several successfull steps when the nuclei were close to 
the minimum  geometry the code crashed very often in chdiag. This was 
reproduceable for a TiO2 and a Cu slab as well. With mkl 10 it was a pain to 
actually produce somehow a binary (i had to modify some flags to get it 
working), but the binary crashed right after the wfc initialisation for all 
my test calculations. 
Than i have seen in the forum, that mkl 10 does not give any gain compared 
to older mkl versions, so i gave up on it. Of course, to clarify this i should 
attache all the config files, the machine architecture, the ifc compiler and 
mkl versions and so on. 
Apparently i am not alone having this issue on the new quad core Intel Xeon 
machines. For example, on dual Opteron i produced a rock solid binary with 
Atlas and with mkl 9.0 as well. Now someone could say, that i am not really 
supposed to use mkl on an Opteron, but it worked. It was only around 4% 
slower than the Atlas version, and the numbers were looking the same (within 
the numerical noise). Of course, i would prefer to use the dual Quad Xeon 
machines, because they are faster. I would suspect, that this is more like an 
issue with the Quad Xeon architecture, or with our particular system 
environment/installation.

Yours Sincerely,
   Janos.

 ==================================================================
   Janos Kiss   e-mail: janos.kiss at theochem.ruhr-uni-bochum.de       
 Lehrstuhl fuer Theoretische Chemie  Phone: +49 (0)234/32-26485 
 NC 03/297                                  +49 (0)234 32 26754
 Ruhr-Universitaet Bochum            Fax:   +49 (0)234/32-14045
 D-44780 Bochum            http://www.theochem.ruhr-uni-bochum.de
 ==================================================================



From janbeck at gmail.com  Mon Oct 13 23:13:30 2008
From: janbeck at gmail.com (Jan Beck)
Date: Mon, 13 Oct 2008 15:13:30 -0600
Subject: [Pw_forum] Bug in axsf generation?
In-Reply-To: <f9fbbdf30810101543x17b9125fy9ccec0df803f0af7@mail.gmail.com>
References: <f9fbbdf30810101543x17b9125fy9ccec0df803f0af7@mail.gmail.com>
Message-ID: <f9fbbdf30810131413n2f49b22aodd7e7b018f141244@mail.gmail.com>

Gladly,

this is my third attempt at posting this reply, I cannot paste the
.axsf file or attach it, because its too large. The message bounces
back to me with a "moderator approval pending" message. I think
approval is still pending, so I apologize for making you download the
file from a 3rd party site:

http://rapidshare.com/files/153722255/data.axsf.html



 Thanks for taking the time,

 Jan Beck, TXL   Group El Paso, TX

To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <1223677354.23688.4.camel at walk.ijs.si>
Content-Type: text/plain

On Fri, 2008-10-10 at 08:23 -0600, Jan Beck wrote:
> I have an axsf file that I have generated with quantum espresso's cppp. I
> have checked with the specification of the axsf file format, and the
> output from quantum espresso is consistent with that.
> so the output seems to conform to the standard. However, as soon as I
> load the file with the command:
>
> xcrysden --axsf c6h6.axsf
>
> I get the following output

Please provide your c6h6.axsf file, and then somebody may help you.

Regards, Tone
--
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

From akohlmey at cmm.chem.upenn.edu  Mon Oct 13 23:14:53 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 17:14:53 -0400
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <002301c92cef$952c3cc0$bf84b640$@net>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
	<Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>
	<002301c92cef$952c3cc0$bf84b640$@net>
Message-ID: <7b6913e90810131414p18311738te41173cd31522995@mail.gmail.com>

On Mon, Oct 13, 2008 at 12:53 AM, Paul M. Grant <w2agz at pacbell.net> wrote:
> Axel, thanks for getting back on this.  Let me think about your suggestion
> and see what others have to comment as well.
>
> Reflecting on "animation" in general a little more, I wonder if there's a
> Linux screen capture tool available somewhere analogous to KDE Ksnapshot for
> jpeg images, but which could capture motion in addition resulting in an mpeg
> file.  Now that would be a handy and nifty gadget for lots of purposes!

paul,

to follow up on this. something along those lines already _does_ exist.

the "import" utility of ImageMagick allows to make automated sequences
of snapshots of any given window or screen area of any x11 desktop it
can access.

to get a movie, all you have to do is:

- start xcrysden and set up what you want to monitor.
- launch xwininfo from an xterm and click on the xcrysden window
  to get its window id, e.g. 0x3200045
- launch: import -snaps 20 -pause 1 -window 0x3200045 snap.jpg
- this will produce 20 snapshots of that window, one per second
  named snap-1.jpg snap-2.jpg and so on...
to make a gif animation: convert snap-?.jpg snap-??.jpg snaps-movie.gif
to make an mpeg-1 movie you should make snapshots more frequently and
use, e.g, ppmtompeg (i can send you a parameter file and some info on how
to script using it).

this is all a bit clumsy and should be adapted to your specific needs.
one could even consider integrating it into xcrysden at some point. the
the nice thing is, that there is no hacking of low level code involved,
which would be most important if speed up the capture needs to be
improved.

cheers,
     axel.







>
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com
>
>
>
>


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From akohlmey at cmm.chem.upenn.edu  Mon Oct 13 23:32:01 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 17:32:01 -0400 (EDT)
Subject: [Pw_forum] WFC convergence in NEB calculation
In-Reply-To: <200810132154.45883.janos.kiss@theochem.ruhr-uni-bochum.de>
References: <200810132154.45883.janos.kiss@theochem.ruhr-uni-bochum.de>
Message-ID: <Pine.LNX.4.64.0810131710540.2352@localhost.localdomain>

On Mon, 13 Oct 2008, Janos Kiss wrote:

hi janos,

JK> I was also concerned about this aspect, but when i did a quick and 
JK> rough test calculation, the wfc convergence was not particularly better, and 
JK> one SCF step took a lot longer time. Therefore, i just killed it impatiently 
JK> iirc.

please don't discard nicola marzari's suggestion to use the cp.x code
with damped dynamics. with difficult to converge wavefunctions, this
is actually quite competitive (and the reason why i added it to CPMD 
not so long ago. mind you the CPMD implementation is less sophisticated 
than the one in cp.x).

[...]

JK> I tried to use the cg scheme for those images where the wfc convergence was 
JK> tricky, but it was not successfull. I am really afraid, that somehow i 
JK> managed to misscompile the code, because if i try to crank up the density 
JK> cutoff above 5 times the pwcutoff, the code crashes right after the wfc 
JK> initialization in the wfc diagonalization. I think this is a really bad sign.

... or a sign, that you have an overly paranoid sysadmin that does not
allow increasing the stack size sufficiently. 

JK> In fact, i completely forgot to mention, that i was able to produce a relative 
JK> stable binary with mkl 8.1 only. With newer mkl versions in a geometry 

i would not expect that you see bad behavior because of the MKL version.
miscopilation because of bad compiler version or overoptimization is
_much_ more likely.

JK> optimization after several successfull steps when the nuclei were close to 
JK> the minimum  geometry the code crashed very often in chdiag. This was 

JK> reproduceable for a TiO2 and a Cu slab as well. With mkl 10 it was a pain to 
JK> actually produce somehow a binary (i had to modify some flags to get it 

compiling Q-E properly with mkl-10 has been discussed on this list N+1 
times, please check the mailing list archives. it is actually not that
difficult if you understand how mkl is structured, and _that_ is 
explained in the mkl documentation. 

JK> working), but the binary crashed right after the wfc initialisation for all 
JK> my test calculations. 
JK> Than i have seen in the forum, that mkl 10 does not give any gain compared 
JK> to older mkl versions, so i gave up on it. Of course, to clarify this i should 

that is usually a sign of not using mkl correctly. particularly when
using the threaded version, but not enforcing OMP_NUM_THREADS=1 on _all_ 
parallel nodes. again, this has been discussed plenty of times here.

JK> attache all the config files, the machine architecture, the ifc compiler and 
JK> mkl versions and so on. 
JK> Apparently i am not alone having this issue on the new quad core Intel Xeon 
JK> machines. For example, on dual Opteron i produced a rock solid binary with 
JK> Atlas and with mkl 9.0 as well. Now someone could say, that i am not really 
JK> supposed to use mkl on an Opteron, but it worked. It was only around 4% 

mkl works well on opteron and is - as of recent versions - also 
validated from intel for opteron. the mapping PGI compiler-> AMD CPU
and Intel compiler -> Intel CPU is mostly due to marketing myths and 
incompetent or lazy sysadmins. 

JK> slower than the Atlas version, and the numbers were looking the same (within 
JK> the numerical noise). Of course, i would prefer to use the dual Quad Xeon 
JK> machines, because they are faster. I would suspect, that this is more like an 
JK> issue with the Quad Xeon architecture, or with our particular system 
JK> environment/installation.

i'm having no problems with Q-E on a cluster of dual quad-core xeon 
using intel mkl-10 and 10.1 compilers. once mostly has to make sure
to have recent patchlevels and compile/link with the proper flags.

cheers,
    axel.

p.s.: here are the flags that i'm using on our machine running a
clone of RHEL 5.1.

FFLAGS         = -O2 -assume byterecl -march=pentiumpro -mtune=core2 -pc64 -unroll 
FFLAGS_NOOPT   = -O0 -assume byterecl

the mkl linking is done in a somewhat atypical way, because i don't 
want to have to set up LD_LIBRARY_PATH globally, so i am encoding it 
into the binaries directly using -rpath (see the manpage for "ld"). 
i'm also explicitly linking the non-threaded version (for details 
see the mkl docs). please note that this only works with mkl 10.

BLAS_LIBS      = -Wl,-rpath,/cmm/pkg/intel/mkl/default/lib/em64t \
-L/cmm/pkg/intel/mkl/default/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core


JK> 
JK> Yours Sincerely,
JK>    Janos.
JK> 
JK>  ==================================================================
JK>    Janos Kiss   e-mail: janos.kiss at theochem.ruhr-uni-bochum.de       
JK>  Lehrstuhl fuer Theoretische Chemie  Phone: +49 (0)234/32-26485 
JK>  NC 03/297                                  +49 (0)234 32 26754
JK>  Ruhr-Universitaet Bochum            Fax:   +49 (0)234/32-14045
JK>  D-44780 Bochum            http://www.theochem.ruhr-uni-bochum.de
JK>  ==================================================================
JK> 
JK> 
JK> _______________________________________________
JK> Pw_forum mailing list
JK> Pw_forum at pwscf.org
JK> http://www.democritos.it/mailman/listinfo/pw_forum
JK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From w2agz at pacbell.net  Tue Oct 14 00:33:45 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 13 Oct 2008 15:33:45 -0700
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>
References: <000001c92cc4$f1bc9550$d535bff0$@net>
	<F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>
Message-ID: <008801c92d83$c1bc7950$45356bf0$@net>

Look in the PH directory and not PW or PP?  How obvious!  Should'a thought
about that myself (just kidding, ;-)!

I knew that e-p calculations produced a table of N(Ef) as a function of
broadening parameter, but figured that route was even more clumsy than the
ones I've been pursuing...and anyway, ph.x bombs for spin-correlated band
states and it's such compounds in which I'm mainly interested (is anyone
working on adding this feature?).

However, thanks for pointing to the dos_ef function in elphon.f90 (which
also needs the external routine w0gauss.f90).  I'll try applying my feeble
1970s era Fortran skills to build a standalone module.  I think my main
challenge will be to figure out how to extract the arrays et and wk from the
nefarious *.save folders.  Maybe you can point me to some routines where
this task is handled...and for spin polarized states as well?  I'm currently
looking at epsilon.f90 for inspiration, and in fact, may first try to imbed
something like dos_ef as an additional option.

To begin with, let me see if I understand some of the basics of the *.save
folders:
1.  pw.x with the scf option saves the scf charge density and spin data in
two binaries named charge-density.dat and spin-polarization.dat (is there a
utility that displays the info therein in readable, or even hex, form?
OS/360 had a lot of such tools.), in addition to the PPs employed, and an
array of k-point folders, presumably reflecting the MP grid employed, each
with two xml files containing eigenvalues for each spin respectively.
2.  pw.x with nscf option only rewrites the k-points folders.

Wish me luck.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Monday, October 13, 2008 1:55 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Getting DOS at Fermi Energy

On Oct 13, 2008, at 1:47 , Paul M. Grant wrote:

> There must be an easier way to get the density-of-states at the  
> Fermi level
>

I think that the simplest way is to use function dos_ef,
in PH/elphon.f90

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From w2agz at pacbell.net  Tue Oct 14 00:46:42 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 13 Oct 2008 15:46:42 -0700
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <7b6913e90810131414p18311738te41173cd31522995@mail.gmail.com>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>	<Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>	<002301c92cef$952c3cc0$bf84b640$@net>
	<7b6913e90810131414p18311738te41173cd31522995@mail.gmail.com>
Message-ID: <008901c92d85$90a19a60$b1e4cf20$@net>

Thanks, again, Axel.

You probably know ImageMagick can be incorporated into XCrySDen, along with
the "animation tools" Whirlgif and mpeg_encode.  However, the latter two
will not be "raised" by XCrySDen unless the file type is axsf.  You're
suggestion to use ImageMagick is a good one and I'll have a look.

BTW, it seems there's a plethora of mpeg screen capture tools for Linux...go
have a look at:
http://www.linux.com/feature/38221

-Paul

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Axel Kohlmeyer
Sent: Monday, October 13, 2008 2:15 PM
To: Paul M. Grant
Cc: PWSCF Forum
Subject: Re: [Pw_forum] On making a *.axsf file with XCrySDen

On Mon, Oct 13, 2008 at 12:53 AM, Paul M. Grant <w2agz at pacbell.net> wrote:
> Axel, thanks for getting back on this.  Let me think about your suggestion
> and see what others have to comment as well.
>
> Reflecting on "animation" in general a little more, I wonder if there's a
> Linux screen capture tool available somewhere analogous to KDE Ksnapshot
for
> jpeg images, but which could capture motion in addition resulting in an
mpeg
> file.  Now that would be a handy and nifty gadget for lots of purposes!

paul,

to follow up on this. something along those lines already _does_ exist.

the "import" utility of ImageMagick allows to make automated sequences
of snapshots of any given window or screen area of any x11 desktop it
can access.

to get a movie, all you have to do is:

- start xcrysden and set up what you want to monitor.
- launch xwininfo from an xterm and click on the xcrysden window
  to get its window id, e.g. 0x3200045
- launch: import -snaps 20 -pause 1 -window 0x3200045 snap.jpg
- this will produce 20 snapshots of that window, one per second
  named snap-1.jpg snap-2.jpg and so on...
to make a gif animation: convert snap-?.jpg snap-??.jpg snaps-movie.gif
to make an mpeg-1 movie you should make snapshots more frequently and
use, e.g, ppmtompeg (i can send you a parameter file and some info on how
to script using it).

this is all a bit clumsy and should be adapted to your specific needs.
one could even consider integrating it into xcrysden at some point. the
the nice thing is, that there is no hacking of low level code involved,
which would be most important if speed up the capture needs to be
improved.

cheers,
     axel.







>
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com
>
>
>
>


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From akohlmey at cmm.chem.upenn.edu  Tue Oct 14 00:44:01 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 18:44:01 -0400 (EDT)
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <008801c92d83$c1bc7950$45356bf0$@net>
References: <000001c92cc4$f1bc9550$d535bff0$@net>
	<F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>
	<008801c92d83$c1bc7950$45356bf0$@net>
Message-ID: <Pine.LNX.4.64.0810131833340.2352@localhost.localdomain>

On Mon, 13 Oct 2008, Paul M. Grant wrote:

paul,

PG> To begin with, let me see if I understand some of the basics of the *.save
PG> folders:
PG> 1.  pw.x with the scf option saves the scf charge density and spin data in
PG> two binaries named charge-density.dat and spin-polarization.dat (is there a
PG> utility that displays the info therein in readable, or even hex, form?

please see the attached shell script that will instruct the hexdump 
command (part of the ulti-linux package that should be installed on 
almost any current linux machine) to spit out a more traditionally 
formatted hexdump akin to a nice program that i was using loooong ago 
on 6502 processor code (we all have our "war time" experiences... ;-) ).

a more practical approach to accessing the .save directory 
would be to compile the PP/qexml.f90 code and use the API provided 
in there and link the resulting code with libiotk.a from the QE installation. 
the two .dat file you mention and others are written in an xml-like 
format either in binary or in text mode. easy to tell from the 
hexviewer, of course. ;-)

i would assume that you can program from there on pretty much
in f77 style. you'd just have to add "USE qexml_module" at the
very beginning of your code and each subroutine using the interface
and compile with an f90 compiler.

good luck,
    axel.


PG> OS/360 had a lot of such tools.), in addition to the PPs employed, and an
PG> array of k-point folders, presumably reflecting the MP grid employed, each
PG> with two xml files containing eigenvalues for each spin respectively.
PG> 2.  pw.x with nscf option only rewrites the k-points folders.
PG> 
PG> Wish me luck.
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com
PG> ?
PG> ?
PG> 
PG> 
PG> -----Original Message-----
PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
PG> Behalf Of Paolo Giannozzi
PG> Sent: Monday, October 13, 2008 1:55 AM
PG> To: PWSCF Forum
PG> Subject: Re: [Pw_forum] Getting DOS at Fermi Energy
PG> 
PG> On Oct 13, 2008, at 1:47 , Paul M. Grant wrote:
PG> 
PG> > There must be an easier way to get the density-of-states at the  
PG> > Fermi level
PG> >
PG> 
PG> I think that the simplest way is to use function dos_ef,
PG> in PH/elphon.f90
PG> 
PG> P.
PG> ---
PG> Paolo Giannozzi, Dept of Physics, University of Udine
PG> via delle Scienze 208, 33100 Udine, Italy
PG> Phone +39-0432-558216, fax +39-0432-558222
PG> 
PG> 
PG> 
PG> _______________________________________________
PG> Pw_forum mailing list
PG> Pw_forum at pwscf.org
PG> http://www.democritos.it/mailman/listinfo/pw_forum
PG> 
PG> _______________________________________________
PG> Pw_forum mailing list
PG> Pw_forum at pwscf.org
PG> http://www.democritos.it/mailman/listinfo/pw_forum
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
-------------- next part --------------
#!/bin/sh

if [ $# -lt 1 ] 
then
   echo usage: $0 filename
   exit 1
fi

cat > /tmp/hexdump-fmt-$$ <<EOF
"%06.6_ax "  16/1 "%02x "
"\t" "%_p"
"\n"

EOF

hexdump -f /tmp/hexdump-fmt-$$ $* | ${PAGER-less}
rm -f /tmp/hexdump-fmt-$$


From akohlmey at cmm.chem.upenn.edu  Tue Oct 14 01:10:50 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 19:10:50 -0400 (EDT)
Subject: [Pw_forum] On making a *.axsf file with XCrySDen
In-Reply-To: <008901c92d85$90a19a60$b1e4cf20$@net>
References: <000501c92cc6$1f5ac940$5e105bc0$@net>
	<Pine.LNX.4.64.0810122004440.2352@localhost.localdomain>
	<002301c92cef$952c3cc0$bf84b640$@net>
	<7b6913e90810131414p18311738te41173cd31522995@mail.gmail.com>
	<008901c92d85$90a19a60$b1e4cf20$@net>
Message-ID: <Pine.LNX.4.64.0810131847130.2352@localhost.localdomain>

On Mon, 13 Oct 2008, Paul M. Grant wrote:

PG> Thanks, again, Axel.
PG> 
PG> You probably know ImageMagick can be incorporated into XCrySDen, along with
PG> the "animation tools" Whirlgif and mpeg_encode.  However, the latter two
PG> will not be "raised" by XCrySDen unless the file type is axsf.  You're
PG> suggestion to use ImageMagick is a good one and I'll have a look.
PG> 
PG> BTW, it seems there's a plethora of mpeg screen capture tools for Linux...go
PG> have a look at:
PG> http://www.linux.com/feature/38221

xvidcap looks like the application that i had initially in mind
(basically an extended version of the X11 standard tool "xwd")
with some conversion and audio export integrated directly. due to
its nature, it may have problems dumping the output of OpenGL 
windows, but if that works (which is most likely the case if you 
don't have a fully 3d-accelerated OpenGL card (nvidia or ati/amd) 
with the corresponding vendor provided driver), it should be more
efficient as imagemagick's import. 

the vnc method is interesting, but actually not that surprising,
since vnc does export whole desktops and one just has to dump the
(compressed) data simply to a file and then decode and convert it
after the fact. i'm actually using VNC right now to have the desktop 
of my laptop exported to my desktop (i'm writing mails almost 
exclusively from the laptop). vnc only supports minimal OpenGL 
functionality, too.

cheers,
   axel.

p.s.: as shown on the xvidcap homepage. using screen captures generated
like this could be a very interesting way to add to a potential on-line
tutorial for Q-E and make Q-E tutorials possible for larger/diverse 
groups  as people can study at their own pace, and have demonstrations 
repeated as many times as they wish, without wearing out the patience 
of the tutor. ;-)

PG> 
PG> -Paul
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com
PG> ?
PG> ?
PG> 
PG> 
PG> -----Original Message-----
PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
PG> Behalf Of Axel Kohlmeyer
PG> Sent: Monday, October 13, 2008 2:15 PM
PG> To: Paul M. Grant
PG> Cc: PWSCF Forum
PG> Subject: Re: [Pw_forum] On making a *.axsf file with XCrySDen
PG> 
PG> On Mon, Oct 13, 2008 at 12:53 AM, Paul M. Grant <w2agz at pacbell.net> wrote:
PG> > Axel, thanks for getting back on this.  Let me think about your suggestion
PG> > and see what others have to comment as well.
PG> >
PG> > Reflecting on "animation" in general a little more, I wonder if there's a
PG> > Linux screen capture tool available somewhere analogous to KDE Ksnapshot
PG> for
PG> > jpeg images, but which could capture motion in addition resulting in an
PG> mpeg
PG> > file.  Now that would be a handy and nifty gadget for lots of purposes!
PG> 
PG> paul,
PG> 
PG> to follow up on this. something along those lines already _does_ exist.
PG> 
PG> the "import" utility of ImageMagick allows to make automated sequences
PG> of snapshots of any given window or screen area of any x11 desktop it
PG> can access.
PG> 
PG> to get a movie, all you have to do is:
PG> 
PG> - start xcrysden and set up what you want to monitor.
PG> - launch xwininfo from an xterm and click on the xcrysden window
PG>   to get its window id, e.g. 0x3200045
PG> - launch: import -snaps 20 -pause 1 -window 0x3200045 snap.jpg
PG> - this will produce 20 snapshots of that window, one per second
PG>   named snap-1.jpg snap-2.jpg and so on...
PG> to make a gif animation: convert snap-?.jpg snap-??.jpg snaps-movie.gif
PG> to make an mpeg-1 movie you should make snapshots more frequently and
PG> use, e.g, ppmtompeg (i can send you a parameter file and some info on how
PG> to script using it).
PG> 
PG> this is all a bit clumsy and should be adapted to your specific needs.
PG> one could even consider integrating it into xcrysden at some point. the
PG> the nice thing is, that there is no hacking of low level code involved,
PG> which would be most important if speed up the capture needs to be
PG> improved.
PG> 
PG> cheers,
PG>      axel.
PG> 
PG> 
PG> 
PG> 
PG> 
PG> 
PG> 
PG> >
PG> > Paul M. Grant, PhD
PG> > Principal, W2AGZ Technologies
PG> > Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> > EPRI Science Fellow (Retired)
PG> > IBM Research Staff Member Emeritus
PG> > w2agz at pacbell.net
PG> > http://www.w2agz.com
PG> >
PG> >
PG> >
PG> >
PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From nguyenhalvt at yahoo.com  Tue Oct 14 02:10:03 2008
From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha)
Date: Mon, 13 Oct 2008 17:10:03 -0700 (PDT)
Subject: [Pw_forum] String method example?
In-Reply-To: <mailman.797.1223937242.1801.pw_forum@pwscf.org>
Message-ID: <108194.57159.qm@web31003.mail.mud.yahoo.com>

Here is my input
 &CONTROL
                 calculation = 'smd' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/hthp/Desktop/TMP/' ,
                  pseudo_dir = '/home/hthp/Desktop/QUANTUM/espresso-4.0.2/pseudo/' ,
                      prefix = 'H2+H' ,
 /
 &SYSTEM
                       ibrav = 14,
                           A = 6.3501240000 ,
                           B = 2.6458850000 ,
                           C = 2.6458850000 ,
                       cosAB = 0. ,
                       cosAC = 0. ,
                       cosBC = 0. ,
                         nat = 3,
                        ntyp = 1,
                     ecutwfc = 20.0D0 ,
                     ecutrho = 100.0D0 ,
                 occupations = 'smearing' ,
                     degauss = 0.03D0 ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.5,
 /
 &ELECTRONS
                    conv_thr = 1.D-8 ,
                 mixing_beta = 0.3D0 ,
 /
 &IONS
                ion_dynamics = 'damp' ,
                 phase_space = 'coarse-grained' ,
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
            remove_rigid_rot = .false. ,
               num_of_images = 5 ,
                  opt_scheme = 'langevin' ,
                    temp_req = 298 ,
                          ds = 1 ,
                    path_thr = 0.1D0 ,
                use_freezing = .false. ,
                  use_masses = .true. ,
 /
ATOMIC_SPECIES
    H    1.00794  HUSPBE.RRKJ3 
ATOMIC_POSITIONS angstrom 
first_image
    H     -2.416592653    0.000000000    0.000000000    1  0  0 
    H      0.000000000    0.000000000    0.000000000    0  0  0 
    H      0.824334341    0.000000000    0.000000000    1  0  0 
intermediate_image
    H     -1.730204529    0.000000000    0.000000000 
    H      0.000000000    0.000000000    0.000000000 
    H      0.841944334    0.000000000    0.000000000 
intermediate_image
    H     -1.054499302    0.000000000    0.000000000 
    H      0.000000000    0.000000000    0.000000000 
    H      1.054497022    0.000000000    0.000000000 
intermediate_image
    H     -0.841942510    0.000000000    0.000000000 
    H      0.000000000    0.000000000    0.000000000 
    H      1.730201743    0.000000000    0.000000000 
last_image
    H     -0.824334341    0.000000000    0.000000000 
    H      0.000000000    0.000000000    0.000000000 
    H      2.416592653    0.000000000    0.000000000 
K_POINTS gamma 

It's a reaction H2+H = H+H2, the reaction chosen to be test but please note that phase_space = coarse-grained.
> Why are you fixing the middle atom? I believe in this
> example you don't
> need to fix any atom (I assume its a reaction H2+H = H+H2,
> right?).
Tone, you are right, before posting I've tested all case with or without any kind of constraints but I couldn't get any result.

Thank you for your help,

Nguyen, Ngoc Ha
Hanoi National University of Education
Faculty of Chemistry
Department of Physical Chemistry
Tel: Office: 04/8330842
Home: 04/7891674
Mobile: 0989133436





      

From leommj at usp.br  Tue Oct 14 02:21:40 2008
From: leommj at usp.br (Leonardo Matheus)
Date: Mon, 13 Oct 2008 21:21:40 -0300
Subject: [Pw_forum] Atomic rho
In-Reply-To: <c09ad1e50810131442h40eb3b01xe0c96374c61f7afe@mail.gmail.com>
References: <c09ad1e50810131442h40eb3b01xe0c96374c61f7afe@mail.gmail.com>
Message-ID: <c09ad1e50810131721x17abdcybb600078d25c8a22@mail.gmail.com>

Hello,

I'm trying to calculate Hirshfeld charges as a postprocess. To do so,
I need to obtain the atomic rho for each atom, in real space. I've
seen that "atomic_rho.f90" calculates the total rho as a superposition
of the individual atomic ones, obtained from the pseudopotentials.
But I couldn't understand how this superposition is done, as the
internal loop is based on atomic types, and not on individual atoms. I
couldn't also find how the atomic coordinates are used (to "center"
the charge on the atomic position), and which variable stores them. I
saw that it was all done in reciprocal space, and probably this is
where I'm confusing myself.
Can someone please give me a hand?

Thanks,

Leonardo Matheus
Doctorate student - Physics Institute, University of S?o Paulo, Brazil
Nanomol group - http://nanomol.if.usp.br

From akohlmey at cmm.chem.upenn.edu  Tue Oct 14 02:58:10 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 20:58:10 -0400 (EDT)
Subject: [Pw_forum] String method example?
In-Reply-To: <108194.57159.qm@web31003.mail.mud.yahoo.com>
References: <108194.57159.qm@web31003.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0810132053550.2352@localhost.localdomain>

On Mon, 13 Oct 2008, Nguyen Ngoc Ha wrote:

NNH> It's a reaction H2+H = H+H2, the reaction chosen to be test but please note that phase_space = coarse-grained.
NNH> > Why are you fixing the middle atom? I believe in this
NNH> > example you don't
NNH> > need to fix any atom (I assume its a reaction H2+H = H+H2,
NNH> > right?).

NNH> Tone, you are right, before posting I've tested all case with or 
NNH> without any kind of constraints but I couldn't get any result.

because you cannot combine meta-dynamics with SMD (or NEB).

for details have a look at Modules/read_cards.f90

the code chokes on the "first_image" lines which has only 1 column
istead of the expected 4, 7 (or 8 in case if SIC) columns.

axel.

NNH> 
NNH> Thank you for your help,
NNH> 
NNH> Nguyen, Ngoc Ha
NNH> Hanoi National University of Education
NNH> Faculty of Chemistry
NNH> Department of Physical Chemistry
NNH> Tel: Office: 04/8330842
NNH> Home: 04/7891674
NNH> Mobile: 0989133436
NNH> 
NNH> 
NNH> 
NNH> 
NNH> 
NNH>       
NNH> _______________________________________________
NNH> Pw_forum mailing list
NNH> Pw_forum at pwscf.org
NNH> http://www.democritos.it/mailman/listinfo/pw_forum
NNH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From akohlmey at cmm.chem.upenn.edu  Tue Oct 14 03:27:55 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 13 Oct 2008 21:27:55 -0400 (EDT)
Subject: [Pw_forum] Atomic rho
In-Reply-To: <c09ad1e50810131721x17abdcybb600078d25c8a22@mail.gmail.com>
References: <c09ad1e50810131442h40eb3b01xe0c96374c61f7afe@mail.gmail.com>
	<c09ad1e50810131721x17abdcybb600078d25c8a22@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810132058220.2352@localhost.localdomain>

On Mon, 13 Oct 2008, Leonardo Matheus wrote:

LM> Hello,

hello leonardo,

LM> I'm trying to calculate Hirshfeld charges as a postprocess. To do so,
LM> I need to obtain the atomic rho for each atom, in real space. I've
LM> seen that "atomic_rho.f90" calculates the total rho as a superposition
LM> of the individual atomic ones, obtained from the pseudopotentials.
LM> But I couldn't understand how this superposition is done, as the
LM> internal loop is based on atomic types, and not on individual atoms. I

well, for practical reasons it is more efficient to loop over
atom types and atoms per atom type. per atom-type parameters 
only need to be computed once this way.

LM> couldn't also find how the atomic coordinates are used (to "center"
LM> the charge on the atomic position), and which variable stores them. I
LM> saw that it was all done in reciprocal space, and probably this is
LM> where I'm confusing myself.

i suggest you first have a look into textbook material 
explaining the implementation of electronic structure
calculation with plane wave pseudopotentials (e.g. the 
books by jorge kohnoff or richard martin). and then
read the marx / hutter review which also gives an overview
on how the implementation can be done (on the example of
the CPMD code, which is not that different as far as the 
basic principles are concerned). the CPMD code actually 
does have an implementation of hirshfeld charges determination, 
but only for norm-conserving pseudopotentials, IIRC, so you
can look up how the implementation principles.

for implementing it into QE you'll have to figure out
how to handle ultra-soft psps contribution to the atomic
density on top of everything else.

good luck,
   axel.


LM> Can someone please give me a hand?
LM> 
LM> Thanks,
LM> 
LM> Leonardo Matheus
LM> Doctorate student - Physics Institute, University of S?o Paulo, Brazil
LM> Nanomol group - http://nanomol.if.usp.br
LM> _______________________________________________
LM> Pw_forum mailing list
LM> Pw_forum at pwscf.org
LM> http://www.democritos.it/mailman/listinfo/pw_forum
LM> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From yuminqian at gmail.com  Tue Oct 14 05:21:05 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 14 Oct 2008 11:21:05 +0800
Subject: [Pw_forum] question about output of SCF
Message-ID: <aa128b2c0810132021r6193963bvc6f8e4d82c6dd01@mail.gmail.com>

I have done a scf calculation of ground state Pbnm CaCrO3 crystal , the
total band nbnd=101
there are 152 irreducible k-points  ,but the output file in X.save directory
only contians 76 folders : K00001-K00076, and the charge-desity.xml only
contains <z.1> to <z.72> , what is the relation between charge desity grid,
and the number of K000XX folders.

   I also do not know why we define Main grid and wavefunction grid
respectively ? Since the grid number are determined by the same ecutwfc ,
could someone explain more clearly about the all the grids system (include
FFT grid, and charge density grid in real or G-space) in DFT ?

  Many thanks

-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
-------------- next part --------------
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From giannozz at democritos.it  Tue Oct 14 08:29:47 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 14 Oct 2008 08:29:47 +0200
Subject: [Pw_forum] Bug in axsf generation?
In-Reply-To: <f9fbbdf30810131413n2f49b22aodd7e7b018f141244@mail.gmail.com>
References: <f9fbbdf30810101543x17b9125fy9ccec0df803f0af7@mail.gmail.com>
	<f9fbbdf30810131413n2f49b22aodd7e7b018f141244@mail.gmail.com>
Message-ID: <48F43C5B.1090209@democritos.it>

Jan Beck wrote:

> this is my third attempt at posting this reply, I cannot paste the
> .axsf file or attach it, because its too large. The message bounces
> back to me with a "moderator approval pending" message. I think
> approval is still pending

apparently you didn't notice the "Important notice" here: 
http://www.quantum-espresso.org/wiki/index.php/Introduction#Contacts
Executive summary:
---
Messages "waiting for moderator approval" are automatically
deleted with no further processing (sorry, too much spam)
---
> so I apologize for making you download the
> file from a 3rd party site:
> 
> http://rapidshare.com/files/153722255/data.axsf.html

you shouldn't apologize: this is the correct way to send
large files, in my opinion.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Oct 14 08:40:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 14 Oct 2008 08:40:16 +0200
Subject: [Pw_forum] question about output of SCF
In-Reply-To: <aa128b2c0810132021r6193963bvc6f8e4d82c6dd01@mail.gmail.com>
References: <aa128b2c0810132021r6193963bvc6f8e4d82c6dd01@mail.gmail.com>
Message-ID: <48F43ED0.7090003@democritos.it>

yumin qian wrote:

> I have done a scf calculation of ground state Pbnm CaCrO3 crystal , the 
> total band nbnd=101 
> there are 152 irreducible k-points  ,but the output file in X.save 
> directory only contians 76 folders : K00001-K00076

so there are 76 irreducible k-points, and since you are using
LSDA, the code doubles the number of k-points during the
calculation, so that you have 76 k-points for spin-up states
and 76 for spin-down. At the end, when results are saved,
spin-up and spin-down states are collected into a single
folder.

> I also do not know why we define Main grid and wavefunction grid 
> respectively ? Since the grid number are determined by the same 
> ecutwfc

not for USPP or PAW

> , could someone explain more clearly about the all the grids system 
> (include FFT grid, and charge density grid in real or G-space) in DFT ?

the best explanations I managed to produce are reported in
the 3rd paper listed here:
http://www.quantum-espresso.org/wiki/index.php/Ref:_First-principles_Molecular_Dynamics
You can get a copy here:
http://www.fisica.uniud.it/~giannozz/Papers/JCP_57.pdf

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Oct 14 09:24:46 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 14 Oct 2008 09:24:46 +0200
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <008801c92d83$c1bc7950$45356bf0$@net>
References: <000001c92cc4$f1bc9550$d535bff0$@net>	<F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>
	<008801c92d83$c1bc7950$45356bf0$@net>
Message-ID: <48F4493E.1060508@democritos.it>

Paul M. Grant wrote:

> Look in the PH directory and not PW or PP?  How obvious!

it is the only part of the entire distribution where the DOS
at E_F is presently used. There is a reason for everything in
Q-E.  Sometimes it is not a good reason, or it is an obsolete
reason, or nobody knows any longer what the reason was, but
there is always a reason...

> However, thanks for pointing to the dos_ef function in elphon.f90 
> (which also needs the external routine w0gauss.f90)

it is in PW/w0gauss.f90 and is used in many other places

> I think my main challenge will be to figure out how to extract
> the arrays et and wk from the nefarious *.save folders.
>  Maybe you can point me to some routines where this task
> is handled...and for spin polarized states as well?

if you start from scratch, it will take a lot of time. I think
the minimum energy path here is one of the following:
- add a call to dos_ef in the main pw.x code, whenever the Fermi
   energy is calculated (PW/weights.f90) ;
- modify any of the codes in PP/ that read the nefarious .save
   folders. They typically rebuild the structure of variables as
   used in pw.x ;
- build upon the "qexml" library, as suggested by Axel, but
   beware: I am not sure it is updated

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From tone.kokalj at ijs.si  Tue Oct 14 10:45:24 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 14 Oct 2008 10:45:24 +0200
Subject: [Pw_forum] Bug in axsf generation?
In-Reply-To: <f9fbbdf30810100723x75bed882i1a74d2188a2d8e1c@mail.gmail.com>
References: <f9fbbdf30810100723x75bed882i1a74d2188a2d8e1c@mail.gmail.com>
Message-ID: <1223973924.1455.9.camel@walk.ijs.si>

On Fri, 2008-10-10 at 08:23 -0600, Jan Beck wrote:
> I have an axsf file that I have generated with quantum espresso's cppp. I
> have checked with the specification of the axsf file format, and the
> output from quantum espresso is consistent with that.

> WARNING: Atom 2 and atom 6 overlap !!!
>       Atom 6 deleted !!!
> WARNING: Atom 2 and atom 10 overlap !!!
>       Atom 10 deleted !!!

I have looked at your file. It is nothing wrong with its syntax, but the
structure is a complete mass: there are many overlapping atoms (look
into the file). Therefore you receive the atom-deleted warnings!

Either your original cp.x file already contains massy structure, or the
cppp utility has a bug (i never used the latter).

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From w2agz at pacbell.net  Tue Oct 14 17:38:05 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Tue, 14 Oct 2008 08:38:05 -0700
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <48F4493E.1060508@democritos.it>
References: <000001c92cc4$f1bc9550$d535bff0$@net>	<F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>	<008801c92d83$c1bc7950$45356bf0$@net>
	<48F4493E.1060508@democritos.it>
Message-ID: <00c401c92e12$da3d28a0$8eb779e0$@net>

..."there is always a reason"...sounds like some sort of creationist mantra
to me!

Thanks for the insight into pw.x...maybe in a few light-years I'll be able
to contribute to the cause.

I'll have a look at method you suggest, but last night I think I've found a
straightforward (relatively) way to hack epsilon.f90 with a dos_ef like
option.  Let you know how it turns out.  BTW, have you had a chance to look
at the k-points file for aluminum I sent?

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Tuesday, October 14, 2008 12:25 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Getting DOS at Fermi Energy

Paul M. Grant wrote:

> Look in the PH directory and not PW or PP?  How obvious!

it is the only part of the entire distribution where the DOS
at E_F is presently used. There is a reason for everything in
Q-E.  Sometimes it is not a good reason, or it is an obsolete
reason, or nobody knows any longer what the reason was, but
there is always a reason...

> However, thanks for pointing to the dos_ef function in elphon.f90 
> (which also needs the external routine w0gauss.f90)

it is in PW/w0gauss.f90 and is used in many other places

> I think my main challenge will be to figure out how to extract
> the arrays et and wk from the nefarious *.save folders.
>  Maybe you can point me to some routines where this task
> is handled...and for spin polarized states as well?

if you start from scratch, it will take a lot of time. I think
the minimum energy path here is one of the following:
- add a call to dos_ef in the main pw.x code, whenever the Fermi
   energy is calculated (PW/weights.f90) ;
- modify any of the codes in PP/ that read the nefarious .save
   folders. They typically rebuild the structure of variables as
   used in pw.x ;
- build upon the "qexml" library, as suggested by Axel, but
   beware: I am not sure it is updated

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From manoj at phys.ufl.edu  Tue Oct 14 17:49:46 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Tue, 14 Oct 2008 11:49:46 -0400 (EDT)
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <200810101455.49286.smogunov@sissa.it>
Message-ID: <Pine.GSO.4.21.0810141133180.12583-100000@neptune.phys.ufl.edu>

Dear Alexader, 

 Thank you very much for your reply. I was out of town and could not see
the message till yesterday. I have some questions on it, it would be great
if you could answer them.
On Fri, 10 Oct 2008, Alexander wrote:

> Dear Manoj
> 
> On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > Any follow ups on the message below? Alexander?
> >
> > Regards,
> > Manoj
> >
> > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > Dear All,
> > >  Is any body familiar with the scatter_forw.f90 subroutine of PWCOND? I
> > > think there is a bug in this subroutine at the place where you calculate
> > > intw2, which is z integration of nonlocal wavefunction with beta
> > > function. I have looked up the necessary formulae in the Choi & Ihm's
> > > paper (PRB 59, 2267, Jan 1999). In the paper, nonlocal wavefunction has 3
> > > terms, one of which contains beta function, say W. The other two parts
> > > dont have any W in them, rather they are just plane wave solution.
> > > (Please have a look at equation 24 and 26 of the paper ). So, when we are
> > > doing z integration of nonlocal wavefunction with beta function W, we
> > > should have three terms, one of which should contain two W, but rest
> > > should just have one W. On the other hand in the code all three terms
> > > contain two beta functions!! (please have a look at line 228 of
> > > scatter_forw.f90). I am wondering if my understanding is right?
> 
> Your understanding is wrong. On the line 228 you add to the integral ONLY
> contribution with two beta functions (from the 1st term in the nonlocal 
> function, see Eq. 24) but on the line 393 the contribution from the 2nd term 
> is added too. There is no 3rd term since every step you rotate your local 
> solutions \psi_n in such a way that b_{\lambda \alpha lm} vanish (see the 
> paragraph after Eq. 37).
  I believe that the equations 40, 41 and 42 implemented in the code are
in the momentum space. In the code, intw2 has 3 terms. We can tell this by
looking at the subroutine integrals.f90, where int2d is defined. Now, by
looking at the choi& Ihm 's paper, the very first term of psi{alpha,l,m}
has f{lambda,alpha,l,m}(equation26).And, if we substitute this in equation
40, we should just get one term. I am just confuesd on the fact that how
come this one term in paper gets transformed into 3 terms of the code!
Would you mind explaining? Also, the integrals that are defined in the
code are only in the slabs (nz1), so how are you taking the integration in
the region (0,d), which we need according to equations 40, 41 and 42 ?

> 
>  > > I have one more question in the later part of the same subroutine. What
> > > does the lapack subroutine
> > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > do?
> > > I tried to look it up and i got the idea that it is trying to solve
> > > amat*x=xmat, with amat and xmat known and x unknown, and at the end of
> > > calculation it stores x in xmat.
> > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it changes
> > > the structure of xmat from what is defined in 'constructs matrices'
> > > part. Is it correct?
> 
> Here, you are right.
> 
> > > Also, afterwards in this code where  it 'rotates integrals' is not very
> > > clear to me.
> > > Could somebody please tell me in little detail, what is going on
> > > here? 
> As I explained before rotation means that every step (at each slab)
> you make a linear combination of local solutions \psi_n with the 
> transformation matrix  h_{nn'} (see the last paragraph on the p. 2270).
> so that the new solutions have the property: 
> b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions have
> b_{\lambda \alpha lm}=0. Doing this transformation of local and nonlocal
> solutions you should also perform the corresponding transformations
> of the integrals.
> 
> > > Also, is this subroutine written just on the basis of Choi and Ihm 
> > > paper, or are there more reference to it? If yes, would someone mind
> > > mentioning them?
> Unfortunately, the paper of Choi and Ihm is very detail, and in the 
> PWCOND code we followed it very closely, so no more references
> are needed. In our papers we just extended those ideas to ultrasoft
> pseudopotentials, magnetism, spin-orbit coupling and so on.
>   
> Hope this helped you,
> regards, Alexander 
> 
> > >
> > > Regards,
> > > Manoj Srivastava
> > > Physics Graduate Student
> > > University of Florida,
> > > Gainesville,FL, USA
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

Once again thank you very much for your help. I appreciate it. 

Regards, 
Manoj Srivastava


From giannozz at democritos.it  Tue Oct 14 18:18:06 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 14 Oct 2008 18:18:06 +0200
Subject: [Pw_forum] Getting DOS at Fermi Energy
In-Reply-To: <00c401c92e12$da3d28a0$8eb779e0$@net>
References: <000001c92cc4$f1bc9550$d535bff0$@net>	<F114B431-E1C5-42E7-B0DB-B2CE1FE064E0@democritos.it>	<008801c92d83$c1bc7950$45356bf0$@net>	<48F4493E.1060508@democritos.it>
	<00c401c92e12$da3d28a0$8eb779e0$@net>
Message-ID: <48F4C63E.3070703@democritos.it>

Paul M. Grant wrote:

> BTW, have you had a chance to look
> at the k-points file for aluminum I sent?

it looks like a uniform unshifted 12x12x12 grid in a simple
cubic lattice. You should get it (or an equivalent one)
directly from pw.x using options nosym=.true., noinv=.true.
(the latter is undocumented: removes q=>-q symmetry) and
K_POINT {automatic}
12 12 12 0 0 0
or else, from kpoints.x, answering 'T' to the question
   write all k? [f] >>
I am not aware of any limitation to the simple cubic grid,
but this should be asked to the authors of epsilon.x

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From deyulu at yahoo.com  Tue Oct 14 19:31:13 2008
From: deyulu at yahoo.com (Deyu Lu)
Date: Tue, 14 Oct 2008 10:31:13 -0700 (PDT)
Subject: [Pw_forum] k-point grids...and all that
Message-ID: <624316.28375.qm@web56604.mail.re3.yahoo.com>

>Finally, on the point of mesh visualization.  I use XCrySDen a lot,
>especially for BZ and charge-potential visualizations.  But I don't know how
>to configure or generate a .xsf file for a 3D mesh of discrete points.

W.r.t. visualization of k-points, if the coordinates of k-points and the boundary
of the BZ are known, they can be visualized in VMD with the .xyz file format.
Below is an example of the 10 fcc special k-points (blue spheres) in the 
irreducible wedge (white spheres).

http://picasaweb.google.com/deyu.lu/Misc#5257056499972518002

Best
Deyu Lu


***************************************************************************
Deyu Lu (Ph.D)
190 Chemistry Building
University of California, Davis 
One Shields Avenue
Davis, CA 95616
Office phone: (530) 754-9663
Group Webpage: http://angstrom.ucdavis.edu/
***************************************************************************



      

From leommj at usp.br  Tue Oct 14 21:57:43 2008
From: leommj at usp.br (Leonardo Matheus)
Date: Tue, 14 Oct 2008 17:57:43 -0200
Subject: [Pw_forum] Atomic rho
In-Reply-To: <Pine.LNX.4.64.0810132058220.2352@localhost.localdomain>
References: <c09ad1e50810131442h40eb3b01xe0c96374c61f7afe@mail.gmail.com>
	<c09ad1e50810131721x17abdcybb600078d25c8a22@mail.gmail.com>
	<Pine.LNX.4.64.0810132058220.2352@localhost.localdomain>
Message-ID: <c09ad1e50810141257s32176cd1h8e99ed0686d518fe@mail.gmail.com>

Thanks for your reply Axel.

> well, for practical reasons it is more efficient to loop over
> atom types and atoms per atom type. per atom-type parameters
> only need to be computed once this way.

I understand why the calculation is like this, but still couldn't find
this "atoms per atom type" loop.

> i suggest you first have a look into textbook material
> explaining the implementation of electronic structure
> calculation with plane wave pseudopotentials (e.g. the
> books by jorge kohnoff or richard martin). and then
> read the marx / hutter review which also gives an overview
> on how the implementation can be done (on the example of
> the CPMD code, which is not that different as far as the
> basic principles are concerned). the CPMD code actually
> does have an implementation of hirshfeld charges determination,
> but only for norm-conserving pseudopotentials, IIRC, so you
> can look up how the implementation principles.

I've already read the book by Kohanoff, and now I'm waiting for the
licence to download the CPMD code, to see how Hirshfeld charges are
implemented there, thanks for the hint. ABINIT code also has Hirshfeld
charges implemented, I'm looking there too.

> for implementing it into QE you'll have to figure out
> how to handle ultra-soft psps contribution to the atomic
> density on top of everything else.

I'm also using the SaX code, which accepts just NC PPs, so I haven't
thought deeply on this, but I would first try to adapt the "addusdens"
subroutine to the individual atomic densities (at least, this is what
I understood the subroutine does).

Actually, I've based most of my code on the "voronoy" program, so what
I really need now is just to obtain the individual atomic rho, the
rest (I think) is mostly done.

> good luck,
>   axel.

Thanks

Leonardo Matheus
Doctorate student - Physics Institute, University of S?o Paulo, Brazil
Nanomol group - http://nanomol.if.usp.br

From eyvaz_isaev at yahoo.com  Tue Oct 14 22:13:03 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 14 Oct 2008 13:13:03 -0700 (PDT)
Subject: [Pw_forum] scf-convergence
In-Reply-To: <720108.21446.qm@web7907.mail.in.yahoo.com>
Message-ID: <932553.34163.qm@web65708.mail.ac4.yahoo.com>

Dear Asa,

A few comments on your input file.

1. UsXCrysDen have shown that, presumably, what you study is not a monowire, it looks quite strange. Be sure that you have correct structure.

2. You use UltraSoft pseudopotentials, so ecutwfc should be around 10-12 times of ecutrho.

3. Again, you mean you have body centered orthorhombic structure, but looking at the structure (by XCrysDen) there is no cell center.

Bests,
Eyvaz.


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Mon, 10/13/08, asa aravindh <asaaravindh at yahoo.co.in> wrote:

> From: asa aravindh <asaaravindh at yahoo.co.in>
> Subject: [Pw_forum] scf-convergence
> To: pw_forum at pwscf.org
> Date: Monday, October 13, 2008, 3:28 PM
> Dear all..
> I am trying to do scf calculation of an fe/co nanowire
> along the bcc (110) direction.
> However the calculation is not getting converged..after
> even 100 iterations.. the scf accuarcy is not reached and
> suddenly the program stops ...
> can anybody pls tell me if anything is wrong with my input
> file...
> the input file is attached
> any reply would be greatly appreciated
> regards,
> asa
> 
> 
>       Add more friends to your messenger and enjoy! Go to
> http://messenger.yahoo.com/invite/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From degironc at sissa.it  Tue Oct 14 22:36:36 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 14 Oct 2008 22:36:36 +0200
Subject: [Pw_forum] Atomic rho
In-Reply-To: <c09ad1e50810141257s32176cd1h8e99ed0686d518fe@mail.gmail.com>
References: <c09ad1e50810131442h40eb3b01xe0c96374c61f7afe@mail.gmail.com>
	<c09ad1e50810131721x17abdcybb600078d25c8a22@mail.gmail.com>
	<Pine.LNX.4.64.0810132058220.2352@localhost.localdomain>
	<c09ad1e50810141257s32176cd1h8e99ed0686d518fe@mail.gmail.com>
Message-ID: <20081014223636.yzyxxftjvsokc8ks@webmail.sissa.it>

In reciprocal space the sum of atomic densities is

sum_rho_at(G) = \sum_ityp S_ityp(G) rho_atomic_ityp(G)

where rho_atomic_ityp(G) is the Fourier trasform of the atomic charge  
density for atomic type ityp and S_ityp(G) is the strcuture factor for  
that atomic type

S_ityp(G) = \sum_{na such that ityp_of_na=ityp) esp(-i G tau_na) / Omega

If you want a single atom charge density you simply need to use the  
espression above with

S_ityp(G) =  esp(-i G tau_na_you_want) / Omega

this is actually a periodic charge density corresponding to atom  
na_you_want plus its
periodic images ... so the cell must be large enough that these images  
do not overlap.

Hope this helps,

  stefano


Quoting Leonardo Matheus <leommj at usp.br>:

> Thanks for your reply Axel.
>
>> well, for practical reasons it is more efficient to loop over
>> atom types and atoms per atom type. per atom-type parameters
>> only need to be computed once this way.
>
> I understand why the calculation is like this, but still couldn't find
> this "atoms per atom type" loop.
>
>> i suggest you first have a look into textbook material
>> explaining the implementation of electronic structure
>> calculation with plane wave pseudopotentials (e.g. the
>> books by jorge kohnoff or richard martin). and then
>> read the marx / hutter review which also gives an overview
>> on how the implementation can be done (on the example of
>> the CPMD code, which is not that different as far as the
>> basic principles are concerned). the CPMD code actually
>> does have an implementation of hirshfeld charges determination,
>> but only for norm-conserving pseudopotentials, IIRC, so you
>> can look up how the implementation principles.
>
> I've already read the book by Kohanoff, and now I'm waiting for the
> licence to download the CPMD code, to see how Hirshfeld charges are
> implemented there, thanks for the hint. ABINIT code also has Hirshfeld
> charges implemented, I'm looking there too.
>
>> for implementing it into QE you'll have to figure out
>> how to handle ultra-soft psps contribution to the atomic
>> density on top of everything else.
>
> I'm also using the SaX code, which accepts just NC PPs, so I haven't
> thought deeply on this, but I would first try to adapt the "addusdens"
> subroutine to the individual atomic densities (at least, this is what
> I understood the subroutine does).
>
> Actually, I've based most of my code on the "voronoy" program, so what
> I really need now is just to obtain the individual atomic rho, the
> rest (I think) is mostly done.
>
>> good luck,
>>   axel.
>
> Thanks
>
> Leonardo Matheus
> Doctorate student - Physics Institute, University of S?o Paulo, Brazil
> Nanomol group - http://nanomol.if.usp.br
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From lanhaiping at gmail.com  Wed Oct 15 09:39:31 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 15 Oct 2008 15:39:31 +0800
Subject: [Pw_forum] scf-convergence
In-Reply-To: <932553.34163.qm@web65708.mail.ac4.yahoo.com>
References: <720108.21446.qm@web7907.mail.in.yahoo.com>
	<932553.34163.qm@web65708.mail.ac4.yahoo.com>
Message-ID: <c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>

On Wed, Oct 15, 2008 at 4:13 AM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Dear Asa,
>
> A few comments on your input file.
>
> 1. UsXCrysDen have shown that, presumably, what you study is not a
> monowire, it looks quite strange. Be sure that you have correct structure.
>
> 2. You use UltraSoft pseudopotentials, so ecutwfc should be around 10-12
> times of ecutrho.


  Hi, Eyvaz, I think you mistook  ecutwfc and  ecutrho .
In US scheme, ecutrho should be four times of ecutwfc
by default in QE.


> 3. Again, you mean you have body centered orthorhombic structure, but
> looking at the structure (by XCrysDen) there is no cell center.
>
> Bests,
> Eyvaz.
>
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Mon, 10/13/08, asa aravindh <asaaravindh at yahoo.co.in> wrote:
>
> > From: asa aravindh <asaaravindh at yahoo.co.in>
> > Subject: [Pw_forum] scf-convergence
> > To: pw_forum at pwscf.org
> > Date: Monday, October 13, 2008, 3:28 PM
> > Dear all..
> > I am trying to do scf calculation of an fe/co nanowire
> > along the bcc (110) direction.
> > However the calculation is not getting converged..after
> > even 100 iterations.. the scf accuarcy is not reached and
> > suddenly the program stops ...
> > can anybody pls tell me if anything is wrong with my input
> > file...
> > the input file is attached
> > any reply would be greatly appreciated
> > regards,
> > asa
> >
> >
> >       Add more friends to your messenger and enjoy! Go to
> >
> http://messenger.yahoo.com/invite/_______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From giannozz at democritos.it  Wed Oct 15 09:58:02 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Oct 2008 09:58:02 +0200
Subject: [Pw_forum] scf-convergence
In-Reply-To: <c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>
References: <720108.21446.qm@web7907.mail.in.yahoo.com>	<932553.34163.qm@web65708.mail.ac4.yahoo.com>
	<c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>
Message-ID: <48F5A28A.60609@democritos.it>

lan haiping wrote:

> In US scheme, ecutrho should be four times of ecutwfc
> by default in QE.

this is the default and it is perfectly appropriate for
norm-conserving pseudopotentials, but for USPP, very
often you should choose ecutrho > 4*ecutwfc.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From smogunov at sissa.it  Wed Oct 15 08:45:24 2008
From: smogunov at sissa.it (Alexander)
Date: Wed, 15 Oct 2008 08:45:24 +0200
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <Pine.GSO.4.21.0810141133180.12583-100000@neptune.phys.ufl.edu>
References: <Pine.GSO.4.21.0810141133180.12583-100000@neptune.phys.ufl.edu>
Message-ID: <200810150845.24935.smogunov@sissa.it>

Dear Manoj

On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> Dear Alexader,
>
>  Thank you very much for your reply. I was out of town and could not see
> the message till yesterday. I have some questions on it, it would be great
> if you could answer them.
>
> On Fri, 10 Oct 2008, Alexander wrote:
> > Dear Manoj
> >
> > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > Any follow ups on the message below? Alexander?
> > >
> > > Regards,
> > > Manoj
> > >
> > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > Dear All,
> > > >  Is any body familiar with the scatter_forw.f90 subroutine of PWCOND?
> > > > I think there is a bug in this subroutine at the place where you
> > > > calculate intw2, which is z integration of nonlocal wavefunction with
> > > > beta function. I have looked up the necessary formulae in the Choi &
> > > > Ihm's paper (PRB 59, 2267, Jan 1999). In the paper, nonlocal
> > > > wavefunction has 3 terms, one of which contains beta function, say W.
> > > > The other two parts dont have any W in them, rather they are just
> > > > plane wave solution. (Please have a look at equation 24 and 26 of the
> > > > paper ). So, when we are doing z integration of nonlocal wavefunction
> > > > with beta function W, we should have three terms, one of which should
> > > > contain two W, but rest should just have one W. On the other hand in
> > > > the code all three terms contain two beta functions!! (please have a
> > > > look at line 228 of scatter_forw.f90). I am wondering if my
> > > > understanding is right?
> >
> > Your understanding is wrong. On the line 228 you add to the integral ONLY
> > contribution with two beta functions (from the 1st term in the nonlocal
> > function, see Eq. 24) but on the line 393 the contribution from the 2nd
> > term is added too. There is no 3rd term since every step you rotate your
> > local solutions \psi_n in such a way that b_{\lambda \alpha lm} vanish
> > (see the paragraph after Eq. 37).
>
>   I believe that the equations 40, 41 and 42 implemented in the code are
> in the momentum space. In the code, intw2 has 3 terms. We can tell this by
> looking at the subroutine integrals.f90, where int2d is defined. Now, by
> looking at the choi& Ihm 's paper, the very first term of psi{alpha,l,m}
> has f{lambda,alpha,l,m}(equation26).And, if we substitute this in equation
> 40, we should just get one term. I am just confuesd on the fact that how
> come this one term in paper gets transformed into 3 terms of the code!

intw2(alpha,beta) is the integral of nonlocal solution (24) with w functions,
intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr, where
alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO 
contributions from the first and second terms of (24), the one from the third 
term vanishes as I explained before. These two contributions are calculated
on the lines  228  and 393 of the code. The integrals intw1
(alpha,n)=\int_{0,d} w_{alpha}(r)*psi_{n}(r)dr are the integrals of local 
solutions (17) with the same projector functions w. 
The integrals intw2 and intw1 have nothing to do with boundary conditions 
(40). They enter in (11) and are needed to construct the final solutions 
according to Eq.(10). Substituting the form of this solution (10) in the 
boundary conditions (40) you will be led to the generalized eigenvalue 
problem, AX=exp(ikd) BX, with known matrices A and B and unknown
coefficients X={a_n,C_{alpha,l,m}} defining the resulting solution (10).

> Would you mind explaining? Also, the integrals that are defined in the
> code are only in the slabs (nz1), so how are you taking the integration in
> the region (0,d), which we need according to equations 40, 41 and 42 ?

When you go over slabs you add new contributions to the integrals intw1 and 
intw2 (see the line 228 for the first contribution to intw2 and the part "add 
to the integrals" for another contribution to intw2 and contributions to 
intw1) so at the end you obtain integrals over all the region.

Regards,
Alexander

>
> >  > > I have one more question in the later part of the same subroutine.
> >  > > What
> > > >
> > > > does the lapack subroutine
> > > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > > do?
> > > > I tried to look it up and i got the idea that it is trying to solve
> > > > amat*x=xmat, with amat and xmat known and x unknown, and at the end
> > > > of calculation it stores x in xmat.
> > > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it
> > > > changes the structure of xmat from what is defined in 'constructs
> > > > matrices' part. Is it correct?
> >
> > Here, you are right.
> >
> > > > Also, afterwards in this code where  it 'rotates integrals' is not
> > > > very clear to me.
> > > > Could somebody please tell me in little detail, what is going on
> > > > here?
> >
> > As I explained before rotation means that every step (at each slab)
> > you make a linear combination of local solutions \psi_n with the
> > transformation matrix  h_{nn'} (see the last paragraph on the p. 2270).
> > so that the new solutions have the property:
> > b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions have
> > b_{\lambda \alpha lm}=0. Doing this transformation of local and nonlocal
> > solutions you should also perform the corresponding transformations
> > of the integrals.
> >
> > > > Also, is this subroutine written just on the basis of Choi and Ihm
> > > > paper, or are there more reference to it? If yes, would someone mind
> > > > mentioning them?
> >
> > Unfortunately, the paper of Choi and Ihm is very detail, and in the
> > PWCOND code we followed it very closely, so no more references
> > are needed. In our papers we just extended those ideas to ultrasoft
> > pseudopotentials, magnetism, spin-orbit coupling and so on.
> >
> > Hope this helped you,
> > regards, Alexander
> >
> > > > Regards,
> > > > Manoj Srivastava
> > > > Physics Graduate Student
> > > > University of Florida,
> > > > Gainesville,FL, USA
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> Once again thank you very much for your help. I appreciate it.
>
> Regards,
> Manoj Srivastava
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From eyvaz_isaev at yahoo.com  Wed Oct 15 10:24:01 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 15 Oct 2008 01:24:01 -0700 (PDT)
Subject: [Pw_forum] scf-convergence
In-Reply-To: <c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>
Message-ID: <265767.43283.qm@web65710.mail.ac4.yahoo.com>

Hi,
 
--- On Wed, 10/15/08, lan haiping <lanhaiping at gmail.com> wrote:

> > 2. You use UltraSoft pseudopotentials, so ecutwfc
> should be around 10-12
> > times of ecutrho.
> 
> I think you mistook  ecutwfc and  ecutrho .
> In US scheme, ecutrho should be four times of ecutwfc
> by default in QE.
> 

Yes, you are right, I have mixed up (overlooked) ecutwfc and ecutrho, but for US PsPs usually ecutrho is 10-12 times of ecutwfc. What you mean is for norm-conserving PsPs.

Bests,
Eyvaz. 
 
> -------------------------------------------------------------------
> > Prof. Eyvaz Isaev,
> > Theoretical Physics Department, Moscow State Institute
> of Steel & Alloys,
> > Russia,
> > Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University,
> > Sweden
> > Condensed Matter Theory Group, Uppsala University,
> Sweden
> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com
> >
 


      

From lanhaiping at gmail.com  Wed Oct 15 11:39:48 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 15 Oct 2008 17:39:48 +0800
Subject: [Pw_forum] scf-convergence
In-Reply-To: <265767.43283.qm@web65710.mail.ac4.yahoo.com>
References: <c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>
	<265767.43283.qm@web65710.mail.ac4.yahoo.com>
Message-ID: <c92002fa0810150239o1f3dfapa46c01ce734dd6a7@mail.gmail.com>

Thanks for clarification .

Regards
H.P

On Wed, Oct 15, 2008 at 4:24 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Hi,
>
> --- On Wed, 10/15/08, lan haiping <lanhaiping at gmail.com> wrote:
>
> > > 2. You use UltraSoft pseudopotentials, so ecutwfc
> > should be around 10-12
> > > times of ecutrho.
> >
> > I think you mistook  ecutwfc and  ecutrho .
> > In US scheme, ecutrho should be four times of ecutwfc
> > by default in QE.
> >
>
> Yes, you are right, I have mixed up (overlooked) ecutwfc and ecutrho, but
> for US PsPs usually ecutrho is 10-12 times of ecutwfc. What you mean is for
> norm-conserving PsPs.
>
> Bests,
> Eyvaz.
>
> > -------------------------------------------------------------------
> > > Prof. Eyvaz Isaev,
> > > Theoretical Physics Department, Moscow State Institute
> > of Steel & Alloys,
> > > Russia,
> > > Department of Physics, Chemistry, and Biology (IFM),
> > Linkoping University,
> > > Sweden
> > > Condensed Matter Theory Group, Uppsala University,
> > Sweden
> > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> > eyvaz_isaev at yahoo.com
> > >
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From nazari at iasbs.ac.ir  Wed Oct 15 16:08:34 2008
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Wed, 15 Oct 2008 15:08:34 +0100 (BST)
Subject: [Pw_forum] scf-convergence
In-Reply-To: <48F5A28A.60609@democritos.it>
References: <720108.21446.qm@web7907.mail.in.yahoo.com>
	<932553.34163.qm@web65708.mail.ac4.yahoo.com>
	<c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>
	<48F5A28A.60609@democritos.it>
Message-ID: <17094.213.176.122.17.1224079714.squirrel@mail.iasbs.ac.ir>


 Dear All,

 I have upgrade os to  SUSE  11 and when i compile the
 pwscf 4 I face with the following error:
./configure  F90=ifort cc=icc MPIF90=ifort F77=ifort
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for Fortran 77 compiler default output file name... configure:
error: Fortran 77 compiler cannot create executables
See `config.log' for more details.

  Would you please let me know how I can compile the program.
 Regards
 Fariba Nazari
 IASBS



From giannozz at democritos.it  Wed Oct 15 14:46:00 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Oct 2008 14:46:00 +0200
Subject: [Pw_forum] scf-convergence
In-Reply-To: <17094.213.176.122.17.1224079714.squirrel@mail.iasbs.ac.ir>
References: <720108.21446.qm@web7907.mail.in.yahoo.com>	<932553.34163.qm@web65708.mail.ac4.yahoo.com>	<c92002fa0810150039h36fc84dbk3b1cd4a2bca4230a@mail.gmail.com>	<48F5A28A.60609@democritos.it>
	<17094.213.176.122.17.1224079714.squirrel@mail.iasbs.ac.ir>
Message-ID: <48F5E608.907@democritos.it>

nazari at iasbs.ac.ir wrote:

>  I have upgrade os to  SUSE  11  and when i compile the
>  pwscf 4 I face with the following error:
> ./configure  F90=ifort cc=icc MPIF90=ifort F77=ifort
> checking build system type... x86_64-unknown-linux-gnu
> checking architecture... amd64
> checking for Fortran 77 compiler default output file name... configure:
> error: Fortran 77 compiler cannot create executables

0) please use a subject that reflects the contents of your message
1) the above means that your compiler is not working

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From ski2 at mail.uh.edu  Thu Oct 16 06:02:14 2008
From: ski2 at mail.uh.edu (ski2 at mail.uh.edu)
Date: Wed, 15 Oct 2008 23:02:14 -0500
Subject: [Pw_forum] DOS plot
Message-ID: <f5faf79e4b8e.48f67676@mail.uh.edu>

Dear All, 

I have two simple questions about Fermi level and DOS.
For insulator electronic structure calculations, is the Fermi level evaluated set to the top of a valence band? 
When DOS plotted, is the Fermi level manually set to zero by shifting the value achieved self consistently in a scf.out file?

Best Wishes,
Sang-Hwan


Department of Chemistry
University of Houston
136 Fleming Building
Houston, TX 77204-5003
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From lanhaiping at gmail.com  Thu Oct 16 08:05:22 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 16 Oct 2008 14:05:22 +0800
Subject: [Pw_forum] DOS plot
In-Reply-To: <f5faf79e4b8e.48f67676@mail.uh.edu>
References: <f5faf79e4b8e.48f67676@mail.uh.edu>
Message-ID: <c92002fa0810152305r78769332q6c4c60bb65c0f200@mail.gmail.com>

Hi,
Actually, you should align with fermi level yourself when preparing  DOS
plot.

Regards


On Thu, Oct 16, 2008 at 12:02 PM, <ski2 at mail.uh.edu> wrote:

> Dear All,
>
> I have two simple questions about Fermi level and DOS.
> For insulator electronic structure calculations, is the Fermi level
> evaluated set to the top of a valence band?
> When DOS plotted, is the Fermi level manually set to zero by shifting the
> value achieved self consistently in a scf.out file?
>
> Best Wishes,
> Sang-Hwan
>
>
> Department of Chemistry
> University of Houston
> 136 Fleming Building
> Houston, TX 77204-5003
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From lfhuang at theory.issp.ac.cn  Thu Oct 16 10:34:00 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 16 Oct 2008 16:34:00 +0800
Subject: [Pw_forum] =?utf-8?q?DOS_plot?=
Message-ID: <20081016083400.17249.qmail@ms.hfcas.ac.cn>

Dear Sang-Hwan:
    In addition to Lan Haiping's words, I introduce you a easy method to plot DOS with Ef=0eV:
    (1) Find the Ef in the output file of self consistent calculation(e.g. Ef=0.0345Ry);
    (2) plot DOS with gnuplot : plot '*.DOS'  using ($1-0.0345):2 with line
         where the 1st column should be Energy and the 2nd column should be the corresponding DOS.
         with ($1-0.0345), the all energy values will go down for 0.0345Ry together, letting the fermi level coincide
         with 0 Ry in the graph.

Best Wishes!

                                                                    Yours Sincerely
                                                                        L.F.Huang 
------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn    (website of our institute)
======================================================================


> Date: Wed, 15 Oct 2008 23:02:14 -0500
> From: ski2 at mail.uh.edu
> Subject: [Pw_forum] DOS plot
> To: pw_forum at pwscf.org
> Message-ID: 
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear All, 
> 
> I have two simple questions about Fermi level and DOS.
> For insulator electronic structure calculations, is the Fermi level evaluated set to the top of a valence band? 
> When DOS plotted, is the Fermi level manually set to zero by shifting the value achieved self consistently in a scf.out file?
> 
> Best Wishes,
> Sang-Hwan
> 
> 
> Department of Chemistry
> University of Houston
> 136 Fleming Building
> Houston, TX 77204-5003
> -------------- next part --------------
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> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 16 Oct 2008 14:05:22 +0800
> From: "lan haiping" 
> Subject: Re: [Pw_forum] DOS plot
> To: "PWSCF Forum" 
> Message-ID:
> 	
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi,
> Actually, you should align with fermi level yourself when preparing  DOS
> plot.
> 
> Regards
> 
> 
> On Thu, Oct 16, 2008 at 12:02 PM,  wrote:
> 
> > Dear All,
> >
> > I have two simple questions about Fermi level and DOS.
> > For insulator electronic structure calculations, is the Fermi level
> > evaluated set to the top of a valence band?
> > When DOS plotted, is the Fermi level manually set to zero by shifting the
> > value achieved self consistently in a scf.out file?
> >
> > Best Wishes,
> > Sang-Hwan
> >
> >
> > Department of Chemistry
> > University of Houston
> > 136 Fleming Building
> > Houston, TX 77204-5003
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> 
> 
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
> -------------- next part --------------
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> 


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From greatnaol at gmail.com  Thu Oct 16 11:21:38 2008
From: greatnaol at gmail.com (Naol Regassa)
Date: Thu, 16 Oct 2008 12:21:38 +0300
Subject: [Pw_forum] Antiferro
Message-ID: <97e4b88e0810160221n79a0586i96288409c85cc169@mail.gmail.com>

Dear sir we were doing our scf calculation on peroviskites (CaMnO3)
and we know that it is fcc or orthorohmbic G-type antiferro with 10
atoms. When we prepare our input try to excute it tells us that we
have an error like 'wrong atomic positions(coordinates)' or 'existance
of overlaping of atoms'. What should we do to find(guess) the atomic
positions.

From greatnaol at gmail.com  Thu Oct 16 11:21:53 2008
From: greatnaol at gmail.com (Naol Regassa)
Date: Thu, 16 Oct 2008 12:21:53 +0300
Subject: [Pw_forum] Antiferro
Message-ID: <97e4b88e0810160221t4583e14dnf2dd3e90b2a4ec00@mail.gmail.com>

Dear sir we were doing our scf calculation on peroviskites (CaMnO3)
and we know that it is fcc or orthorohmbic G-type antiferro with 10
atoms. When we prepare our input try to excute it tells us that we
have an error like 'wrong atomic positions(coordinates)' or 'existance
of overlaping of atoms'. What should we do to find(guess) the atomic
positions?

From hande at newton.physics.metu.edu.tr  Thu Oct 16 11:35:41 2008
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Thu, 16 Oct 2008 12:35:41 +0300 (EEST)
Subject: [Pw_forum] Antiferro
In-Reply-To: <97e4b88e0810160221t4583e14dnf2dd3e90b2a4ec00@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0810161232390.3514-100000@newton.physics.metu.edu.tr>

Dear Naol,

Your problem is probably what it says in the error, that is you have
overlapping atoms. You have either put in wrong atomic positions or are
confused about how to use parameters and options such as celldm, alat
etc. In either case I suggest using xcrysden to visualize your structure
before submitting it. Atomic positions should not be guessed but should be
taken from some preexisting data, try someting like :

    http://cst-www.nrl.navy.mil/lattice/

Best,
Hande

On Thu, 16 Oct 2008, Naol Regassa wrote:

> Dear sir we were doing our scf calculation on peroviskites (CaMnO3)
> and we know that it is fcc or orthorohmbic G-type antiferro with 10
> atoms. When we prepare our input try to excute it tells us that we
> have an error like 'wrong atomic positions(coordinates)' or 'existance
> of overlaping of atoms'. What should we do to find(guess) the atomic
> positions?
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 
Hande Toffoli
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande


From baroni at sissa.it  Thu Oct 16 16:25:40 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 16 Oct 2008 16:25:40 +0200
Subject: [Pw_forum] post doc opening in Padova
References: <200810161419.m9GEJV5S005376@lxpd05.pd.infn.it>
Message-ID: <E9743B5A-A77B-467C-9E24-76D2E0766283@sissa.it>

    A POSTDOCTORAL POSITION of 2 YEARS
    (with the possibility of renewal)
    is available from February/March 2009 at the
    Group of Theoretical Condensed-Matter Physics,
    Department of Physics "Galileo Galilei"
    of the University of Padova, Italy.

    APPLICATION DEADLINE: Dic 08, 2008

    RESPONSIBILITIES:
    To investigate with ab initio computational methods
    surface processes, such as physisorption of rare gas atom
    on metal surface, molecule adsorption,
    and interaction of water with hydrophobic/hdrophilic
    surfaces. Ab initio methods will be based
    on Density Functional Theory with inclusion of
    Wan der Waals effects (see Phys. Rev. Lett., 100, 053002 (2008)).
    The research group, which is part of the
    DEMOCRITOS  National Simulation Center (Trieste, Italy),
    is currently composed
    of three professors of the University of Padova (Flavio Toigo,
    Francesco Ancilotto, and Pier Luigi Silvestrelli).

    Applications should be accompanied by a detailed CV and a
    publication list (recommendation letters are appreciated).
    After a preliminary, informal selection, suitable candidate(s)
    will be invited to submit a formal application to the
    University of Padova in order to be evaluated with a
    colloquium/seminar at our Institute, in January 2009.
    N.B. Travel expenses cannot be reimbursed.

    REQUIREMENTS:
    Dynamic and motivated scientist with Ph.D. in theoretical
    physics, chemistry or related fields.
    Candidates with a documented experience in scientific programming,
    high-performance computing,
    and application of ab initio packages, such as
    Quantum-ESPRESSO(PWscf) and CPMD, are strongly preferred.

    SALARY:
    about 1450 Euro per month (net).

    CONTACT: Prof. Pier Luigi Silvestrelli
    E-mail: psil at pd.infn.it
    Phone: +39 049 8277171
    Fax: +39 049 8277102
    Address: Department of Physics "Galileo Galilei",
    University of Padova, Via Marzolo 8, 35131 Padova, Italy



From janbeck at gmail.com  Thu Oct 16 18:42:35 2008
From: janbeck at gmail.com (Jan Beck)
Date: Thu, 16 Oct 2008 10:42:35 -0600
Subject: [Pw_forum] Bug in axsf generation?
Message-ID: <f9fbbdf30810160942l7ba0598x808a2c65b3ee4453@mail.gmail.com>

Thank you for taking the time. My cp.x file was bad to begin with.
Sorry to pollute the list like that.


Jan Beck
Txl Group

> Date: Tue, 14 Oct 2008 10:45:24 +0200
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [Pw_forum] Bug in axsf generation?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1223973924.1455.9.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Fri, 2008-10-10 at 08:23 -0600, Jan Beck wrote:
>> I have an axsf file that I have generated with quantum espresso's cppp. I
>> have checked with the specification of the axsf file format, and the
>> output from quantum espresso is consistent with that.
>
>> WARNING: Atom 2 and atom 6 overlap !!!
>>       Atom 6 deleted !!!
>> WARNING: Atom 2 and atom 10 overlap !!!
>>       Atom 10 deleted !!!
>
> I have looked at your file. It is nothing wrong with its syntax, but the
> structure is a complete mass: there are many overlapping atoms (look
> into the file). Therefore you receive the atom-deleted warnings!
>
> Either your original cp.x file already contains massy structure, or the
> cppp utility has a bug (i never used the latter).
>
> Regards, Tone
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
>

From huihh.tang at gmail.com  Thu Oct 16 21:01:14 2008
From: huihh.tang at gmail.com (Hui Tang)
Date: Thu, 16 Oct 2008 15:01:14 -0400
Subject: [Pw_forum] Total energy diverges in cell relaxation
Message-ID: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>

Dear all,

I'm trying to do cell relaxation on my Mg-Boron systems. For some of the
structures, I got extremely strange results. The total energy diverges
starting from some ionic step. For example, here are the total energy in
each ionic step for one of the problematic run:

!    total energy              =   -24.47168660 Ry
!    total energy              =   -35.02062718 Ry
!    total energy              =   -38.37822321 Ry
!    total energy              =   -40.20237747 Ry
!    total energy              =   -40.96387007 Ry
!    total energy              =   -41.20956341 Ry
!    total energy              =   -41.41389316 Ry
!    total energy              =   -41.46640700 Ry
!    total energy              =   -41.49930067 Ry
!    total energy              =   -41.51263104 Ry
!    total energy              =   -41.53987139 Ry
!    total energy              =   -41.59139496 Ry
!    total energy              =   -41.55162726 Ry
!    total energy              =   -41.64537650 Ry
!    total energy              =   -41.67440874 Ry
!    total energy              =   -41.73712135 Ry
!    total energy              =   -51.60413428 Ry
!    total energy              =  -688.94041793 Ry
!    total energy              =  -817.40812316 Ry
!    total energy              =  -914.65691139 Ry
!    total energy              =  -980.98769592 Ry
!    total energy              = -1145.13424734 Ry
!    total energy              = -1079.87331043 Ry
!    total energy              = -1148.61890203 Ry
!    total energy              = -1147.67898328 Ry
!    total energy              = -1147.50188067 Ry
!    total energy              = -1148.72218340 Ry
!    total energy              = -1149.83861471 Ry
!    total energy              = -1690.39538237 Ry
!    total energy              = -2822.35642442 Ry
!    total energy              = -2718.63827111 Ry
!    total energy              = -2790.48198795 Ry
!    total energy              = -2823.74590405 Ry
!    total energy              = -2878.31317290 Ry
!    total energy              = -4478.65409327 Ry
!    total energy              = -5464.15854938 Ry
!    total energy              =-14818.93675687 Ry
!    total energy              =-17158.30103958 Ry
!    total energy              =-18287.28161766 Ry

and the forces:

     Total force =    39.327209     Total SCF correction =     0.000071
     Total force =    11.517813     Total SCF correction =     0.000029
     Total force =     8.564152     Total SCF correction =     0.000058
     Total force =     3.973671     Total SCF correction =     0.000035
     Total force =     1.056249     Total SCF correction =     0.000106
     Total force =     0.617165     Total SCF correction =     0.000092
     Total force =     0.326250     Total SCF correction =     0.000046
     Total force =     0.416678     Total SCF correction =     0.000033
     Total force =     0.227223     Total SCF correction =     0.000033
     Total force =     0.501912     Total SCF correction =     0.000042
     Total force =     0.269395     Total SCF correction =     0.000104
     Total force =     0.369080     Total SCF correction =     0.000049
     Total force =     0.334142     Total SCF correction =     0.000026
     Total force =     0.148318     Total SCF correction =     0.000034
     Total force =     0.145030     Total SCF correction =     0.000012
     Total force =     0.143331     Total SCF correction =     0.000064
     Total force =   116.856723     Total SCF correction =     0.000084
     Total force =    65.417648     Total SCF correction =     0.000066
     Total force =   171.381517     Total SCF correction =     0.000070
     Total force =   155.577114     Total SCF correction =     0.000070
     Total force =   184.877111     Total SCF correction =     0.000057
     Total force =   109.156982     Total SCF correction =     0.000037
     Total force =   142.602012     Total SCF correction =     0.000080
     Total force =    88.522593     Total SCF correction =     0.000117
     Total force =   127.562744     Total SCF correction =     0.000058
     Total force =    92.956163     Total SCF correction =     0.000108
     Total force =    88.462372     Total SCF correction =     0.000117
     Total force =    84.376621     Total SCF correction =     0.000056
     Total force =   134.526750     Total SCF correction =     0.000106
     Total force =   282.688334     Total SCF correction =     0.000132
     Total force =   600.035535     Total SCF correction =     0.000078
     Total force =   224.477965     Total SCF correction =     0.000122
     Total force =   398.869729     Total SCF correction =     0.000123
     Total force =   396.502768     Total SCF correction =     0.000149
     Total force =   420.885999     Total SCF correction =     0.000136
     Total force =   443.182054     Total SCF correction =     0.000031
     Total force =  3819.452849     Total SCF correction =     0.000261
     Total force =  1265.093632     Total SCF correction =     0.000207
     Total force =  1027.278240     Total SCF correction =     0.000338

For this problematic system, this behavior is very stable. No matter I use
'cg' or 'david', change the mixing parameter from 0.9 to 0.1, I still get
similar problem.

I cannot find anything relevant in the archive. I wonder if anyone knows
what's going on here and can help me get rid of this annoying problem.

btw, the input, output files and pseudo-potentials can be found at:
http://volga.eng.yale.edu/hui/MgonBS.tar.gz




Thank you very much,
---------------------------------------------
Hui Tang
Graduate Student
Department of Applied Physics
Yale University
Email: hui.tang at yale.edu
Phone: 1-203-432-7763
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From marzari at MIT.EDU  Thu Oct 16 21:09:44 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 16 Oct 2008 22:09:44 +0300
Subject: [Pw_forum] Total energy diverges in cell relaxation
In-Reply-To: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>
References: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>
Message-ID: <48F79178.1030703@mit.edu>

Hui Tang wrote:
> Dear all,
> 
> I'm trying to do cell relaxation on my Mg-Boron systems. For some of the 
> structures, I got extremely strange results. The total energy diverges 
> starting from some ionic step. For example, here are the total energy in 
> each ionic step for one of the problematic run:
> 

Two suggestions

1) are atoms overlapping much more than they should ? I.e. are these
new configurations reasonable, or are core overlaps very significant ?
The pseudopotential approximation breaks down if cores overlap (a lot).

2) is it a bug/memory overrun ? Take the first configuration with
much lower energy, and rerun that from scratch. Do you get an
energy that looks like -41.7 Ry, or much lower ?

			nic



---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From huihh.tang at gmail.com  Thu Oct 16 21:39:54 2008
From: huihh.tang at gmail.com (Hui Tang)
Date: Thu, 16 Oct 2008 15:39:54 -0400
Subject: [Pw_forum] Total energy diverges in cell relaxation
In-Reply-To: <48F79178.1030703@mit.edu>
References: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>
	<48F79178.1030703@mit.edu>
Message-ID: <edd968890810161239y216560ap801d7bbe80e969e1@mail.gmail.com>

Hi Nic,

1)  I have tested the pseudo-potentials (psps) with small atomic
separations. The pseudo-potentials give reasonable till two atoms are as
close as 0.8 A. When the total energy starts to diverge, which is about
Ionic iteration 17, the smallest inter-atomic distance is about 1.4 A. So I
do not think the breakdown of the psps is the trigger of this divergence of
the total energy, although it should be the reason for the enormous large
negative energies.

2) I have tried to restart the calculation from where the divergence starts.
Once I did that, the first scf calculation would give a reasonable energy
around -41.7 Ry, and the calculation could run smoothly till the total
energy converges most of the times. So what I deal with this problem right
now is to restart calculations from where they start to have diverged total
energies and it's been working well. However, I hope this is not the optimal
way to solve this problem. :)

Thank you very much,
Hui

On Thu, Oct 16, 2008 at 3:09 PM, Nicola Marzari <marzari at mit.edu> wrote:

> Hui Tang wrote:
> > Dear all,
> >
> > I'm trying to do cell relaxation on my Mg-Boron systems. For some of the
> > structures, I got extremely strange results. The total energy diverges
> > starting from some ionic step. For example, here are the total energy in
> > each ionic step for one of the problematic run:
> >
>
> Two suggestions
>
> 1) are atoms overlapping much more than they should ? I.e. are these
> new configurations reasonable, or are core overlaps very significant ?
> The pseudopotential approximation breaks down if cores overlap (a lot).
>
> 2) is it a bug/memory overrun ? Take the first configuration with
> much lower energy, and rerun that from scratch. Do you get an
> energy that looks like -41.7 Ry, or much lower ?
>
>                        nic
>
>
>
> ---------------------------------------------------------------------
> Prof Nicola Marzari   Department of Materials Science and Engineering
> 13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
> tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From akohlmey at cmm.chem.upenn.edu  Thu Oct 16 22:00:06 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 16 Oct 2008 16:00:06 -0400 (EDT)
Subject: [Pw_forum] Total energy diverges in cell relaxation
In-Reply-To: <edd968890810161239y216560ap801d7bbe80e969e1@mail.gmail.com>
References: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>
	<48F79178.1030703@mit.edu>
	<edd968890810161239y216560ap801d7bbe80e969e1@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810161547300.2352@localhost.localdomain>

On Thu, 16 Oct 2008, Hui Tang wrote:

hi hui,

your cell is expanding quite a bit and your cutoff is not 
that large. with an expanding cell, your _effective_ cutoff 
becomes much smaller as the number of plane waves remains
constant during a variable cell calculation. have you tested 
the stess tensor convergence vs. the cutoff? you basically
have to figure out how many plane waves you need for a well
converged stress tensor at the largest expansion of your cell 
and then you have to set the cutoff at the beginning so that 
it results in the same number of plane waves...

that would explain why it works (better) if you restart.

also, did you test the pseudopotentials for ghost states?

cheers,
   axel.

p.s.: please provide an affiliation. thanks.

HT> Hi Nic,
HT> 
HT> 1)  I have tested the pseudo-potentials (psps) with small atomic
HT> separations. The pseudo-potentials give reasonable till two atoms are as
HT> close as 0.8 A. When the total energy starts to diverge, which is about
HT> Ionic iteration 17, the smallest inter-atomic distance is about 1.4 A. So I
HT> do not think the breakdown of the psps is the trigger of this divergence of
HT> the total energy, although it should be the reason for the enormous large
HT> negative energies.
HT> 
HT> 2) I have tried to restart the calculation from where the divergence starts.
HT> Once I did that, the first scf calculation would give a reasonable energy
HT> around -41.7 Ry, and the calculation could run smoothly till the total
HT> energy converges most of the times. So what I deal with this problem right
HT> now is to restart calculations from where they start to have diverged total
HT> energies and it's been working well. However, I hope this is not the optimal
HT> way to solve this problem. :)
HT> 
HT> Thank you very much,
HT> Hui
HT> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From manoj at phys.ufl.edu  Thu Oct 16 23:15:13 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Thu, 16 Oct 2008 17:15:13 -0400 (EDT)
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <200810150845.24935.smogunov@sissa.it>
Message-ID: <Pine.GSO.4.21.0810161700280.16794-100000@neptune.phys.ufl.edu>

Dear Alexandar, 
 Thank you very much. Your answers make sense and now i have better
understanding of the subroutine scatter_forw.f90.  I have one question
about poten.f90 subroutine, where you calculate the V(p,gper) in each
slices of the slab(equation 15). I have a question about Gz, which is
2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the line
60, you have Gz multiplied with bg(3,3). I kind of understand this is
because 3rd direction is perpendicular to xy plane, but not totally clear
about it. Would you mind explaining? my other question is when reciprocal
space vectors b1, b2 and b3 are not orhogonal to each other, which is
more general case, then should not we take bg(1,3) and bg(2,3) in there
too? 
 Thank you once again for listening to my questions and i hope i am
not bothering you too much.

Regards, 
Manoj Srivastava 
Physics Graduate Student 
Department of Physics 
Gainesville, FL, USA.


have  On Wed, 15 Oct 2008, Alexander wrote:

> Dear Manoj
> 
> On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > Dear Alexader,
> >
> >  Thank you very much for your reply. I was out of town and could not see
> > the message till yesterday. I have some questions on it, it would be great
> > if you could answer them.
> >
> > On Fri, 10 Oct 2008, Alexander wrote:
> > > Dear Manoj
> > >
> > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > Any follow ups on the message below? Alexander?
> > > >
> > > > Regards,
> > > > Manoj
> > > >
> > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > Dear All,
> > > > >  Is any body familiar with the scatter_forw.f90 subroutine of PWCOND?
> > > > > I think there is a bug in this subroutine at the place where you
> > > > > calculate intw2, which is z integration of nonlocal wavefunction with
> > > > > beta function. I have looked up the necessary formulae in the Choi &
> > > > > Ihm's paper (PRB 59, 2267, Jan 1999). In the paper, nonlocal
> > > > > wavefunction has 3 terms, one of which contains beta function, say W.
> > > > > The other two parts dont have any W in them, rather they are just
> > > > > plane wave solution. (Please have a look at equation 24 and 26 of the
> > > > > paper ). So, when we are doing z integration of nonlocal wavefunction
> > > > > with beta function W, we should have three terms, one of which should
> > > > > contain two W, but rest should just have one W. On the other hand in
> > > > > the code all three terms contain two beta functions!! (please have a
> > > > > look at line 228 of scatter_forw.f90). I am wondering if my
> > > > > understanding is right?
> > >
> > > Your understanding is wrong. On the line 228 you add to the integral ONLY
> > > contribution with two beta functions (from the 1st term in the nonlocal
> > > function, see Eq. 24) but on the line 393 the contribution from the 2nd
> > > term is added too. There is no 3rd term since every step you rotate your
> > > local solutions \psi_n in such a way that b_{\lambda \alpha lm} vanish
> > > (see the paragraph after Eq. 37).
> >
> >   I believe that the equations 40, 41 and 42 implemented in the code are
> > in the momentum space. In the code, intw2 has 3 terms. We can tell this by
> > looking at the subroutine integrals.f90, where int2d is defined. Now, by
> > looking at the choi& Ihm 's paper, the very first term of psi{alpha,l,m}
> > has f{lambda,alpha,l,m}(equation26).And, if we substitute this in equation
> > 40, we should just get one term. I am just confuesd on the fact that how
> > come this one term in paper gets transformed into 3 terms of the code!
> 
> intw2(alpha,beta) is the integral of nonlocal solution (24) with w functions,
> intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr, where
> alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO 
> contributions from the first and second terms of (24), the one from the third 
> term vanishes as I explained before. These two contributions are calculated
> on the lines  228  and 393 of the code. The integrals intw1
> (alpha,n)=\int_{0,d} w_{alpha}(r)*psi_{n}(r)dr are the integrals of local 
> solutions (17) with the same projector functions w. 
> The integrals intw2 and intw1 have nothing to do with boundary conditions 
> (40). They enter in (11) and are needed to construct the final solutions 
> according to Eq.(10). Substituting the form of this solution (10) in the 
> boundary conditions (40) you will be led to the generalized eigenvalue 
> problem, AX=exp(ikd) BX, with known matrices A and B and unknown
> coefficients X={a_n,C_{alpha,l,m}} defining the resulting solution (10).
> 
> > Would you mind explaining? Also, the integrals that are defined in the
> > code are only in the slabs (nz1), so how are you taking the integration in
> > the region (0,d), which we need according to equations 40, 41 and 42 ?
> 
> When you go over slabs you add new contributions to the integrals intw1 and 
> intw2 (see the line 228 for the first contribution to intw2 and the part "add 
> to the integrals" for another contribution to intw2 and contributions to 
> intw1) so at the end you obtain integrals over all the region.
> 
> Regards,
> Alexander
> 
> >
> > >  > > I have one more question in the later part of the same subroutine.
> > >  > > What
> > > > >
> > > > > does the lapack subroutine
> > > > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > > > do?
> > > > > I tried to look it up and i got the idea that it is trying to solve
> > > > > amat*x=xmat, with amat and xmat known and x unknown, and at the end
> > > > > of calculation it stores x in xmat.
> > > > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it
> > > > > changes the structure of xmat from what is defined in 'constructs
> > > > > matrices' part. Is it correct?
> > >
> > > Here, you are right.
> > >
> > > > > Also, afterwards in this code where  it 'rotates integrals' is not
> > > > > very clear to me.
> > > > > Could somebody please tell me in little detail, what is going on
> > > > > here?
> > >
> > > As I explained before rotation means that every step (at each slab)
> > > you make a linear combination of local solutions \psi_n with the
> > > transformation matrix  h_{nn'} (see the last paragraph on the p. 2270).
> > > so that the new solutions have the property:
> > > b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions have
> > > b_{\lambda \alpha lm}=0. Doing this transformation of local and nonlocal
> > > solutions you should also perform the corresponding transformations
> > > of the integrals.
> > >
> > > > > Also, is this subroutine written just on the basis of Choi and Ihm
> > > > > paper, or are there more reference to it? If yes, would someone mind
> > > > > mentioning them?
> > >
> > > Unfortunately, the paper of Choi and Ihm is very detail, and in the
> > > PWCOND code we followed it very closely, so no more references
> > > are needed. In our papers we just extended those ideas to ultrasoft
> > > pseudopotentials, magnetism, spin-orbit coupling and so on.
> > >
> > > Hope this helped you,
> > > regards, Alexander
> > >
> > > > > Regards,
> > > > > Manoj Srivastava
> > > > > Physics Graduate Student
> > > > > University of Florida,
> > > > > Gainesville,FL, USA
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > Once again thank you very much for your help. I appreciate it.
> >
> > Regards,
> > Manoj Srivastava
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From huihh.tang at gmail.com  Thu Oct 16 23:25:53 2008
From: huihh.tang at gmail.com (Hui Tang)
Date: Thu, 16 Oct 2008 17:25:53 -0400
Subject: [Pw_forum] Total energy diverges in cell relaxation
In-Reply-To: <Pine.LNX.4.64.0810161547300.2352@localhost.localdomain>
References: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>
	<48F79178.1030703@mit.edu>
	<edd968890810161239y216560ap801d7bbe80e969e1@mail.gmail.com>
	<Pine.LNX.4.64.0810161547300.2352@localhost.localdomain>
Message-ID: <edd968890810161425qad649ffs1352393280268a4f@mail.gmail.com>

Hi Axel,

I have used a much larger cutoff energy to rerun a problematic calculation.
This rerun does not have the divergence problem any more. I'm going to do a
few more runs to confirm this.

I think it's just as what you said that the effective cutoff energy becomes
smaller as the cell expands. So I probably should check the convergence of
stresses in my largest cell with respect to the number of plane waves.

btw, I did ghost states tests for my pseudo-potentials and there isn't any.


p.s., I remember to put on my affiliation this time. :)


Thank you very much,
---------------------------------------------
Hui Tang
Graduate Student
Department of Applied Physics
Yale University
Email: hui.tang at yale.edu
Phone: 1-203-432-7763



On Thu, Oct 16, 2008 at 4:00 PM, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu
> wrote:

> On Thu, 16 Oct 2008, Hui Tang wrote:
>
> hi hui,
>
> your cell is expanding quite a bit and your cutoff is not
> that large. with an expanding cell, your _effective_ cutoff
> becomes much smaller as the number of plane waves remains
> constant during a variable cell calculation. have you tested
> the stess tensor convergence vs. the cutoff? you basically
> have to figure out how many plane waves you need for a well
> converged stress tensor at the largest expansion of your cell
> and then you have to set the cutoff at the beginning so that
> it results in the same number of plane waves...
>
> that would explain why it works (better) if you restart.
>
> also, did you test the pseudopotentials for ghost states?
>
> cheers,
>   axel.
>
> p.s.: please provide an affiliation. thanks.
>
> HT> Hi Nic,
> HT>
> HT> 1)  I have tested the pseudo-potentials (psps) with small atomic
> HT> separations. The pseudo-potentials give reasonable till two atoms are
> as
> HT> close as 0.8 A. When the total energy starts to diverge, which is about
> HT> Ionic iteration 17, the smallest inter-atomic distance is about 1.4 A.
> So I
> HT> do not think the breakdown of the psps is the trigger of this
> divergence of
> HT> the total energy, although it should be the reason for the enormous
> large
> HT> negative energies.
> HT>
> HT> 2) I have tried to restart the calculation from where the divergence
> starts.
> HT> Once I did that, the first scf calculation would give a reasonable
> energy
> HT> around -41.7 Ry, and the calculation could run smoothly till the total
> HT> energy converges most of the times. So what I deal with this problem
> right
> HT> now is to restart calculations from where they start to have diverged
> total
> HT> energies and it's been working well. However, I hope this is not the
> optimal
> HT> way to solve this problem. :)
> HT>
> HT> Thank you very much,
> HT> Hui
> HT>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From lfhuang at theory.issp.ac.cn  Fri Oct 17 04:57:16 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Fri, 17 Oct 2008 10:57:16 +0800
Subject: [Pw_forum] =?utf-8?q?How_to_obtain_the_deformation_potentials?=
Message-ID: <20081017025716.25599.qmail@ms.hfcas.ac.cn>


Hello everyone:
    I want to obtain the deformation potential for further calculation of transport properties, but in some
complicated cases(e.g. doped systems), gama and lamda seems not enough for me to induce the value
of deformation potentials. Then I have two questions to ask:
    (1) Anyone knows how to extract the deformation potential for certain vibrational mode and certain
         electronic state from the "*.vscf" file?
    (2)Or if I want to use Frozen Phonon approach after knowning vibrational modes, how could I obtain
         the deformation potential from the changes of electronic structure? Does there some formulas
         or REFERENCES? 
I would like to greatly appreciate any kindly hearted person and any help! 
 
------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn (website of our institute)
======================================================================


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From giannozz at democritos.it  Fri Oct 17 14:06:49 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Oct 2008 14:06:49 +0200
Subject: [Pw_forum] Total energy diverges in cell relaxation
In-Reply-To: <edd968890810161425qad649ffs1352393280268a4f@mail.gmail.com>
References: <edd968890810161201k56cf3ddao849345eaad71cb51@mail.gmail.com>	<48F79178.1030703@mit.edu>	<edd968890810161239y216560ap801d7bbe80e969e1@mail.gmail.com>	<Pine.LNX.4.64.0810161547300.2352@localhost.localdomain>
	<edd968890810161425qad649ffs1352393280268a4f@mail.gmail.com>
Message-ID: <48F87FD9.7070100@democritos.it>

Hui Tang wrote:

> I think it's just as what you said that the effective cutoff energy 
> becomes smaller as the cell expands. So I probably should check the 
> convergence of stresses in my largest cell with respect to the number 
> of plane waves.

no, you should check your input data first. You didn't check them
with xcrysden, did you? (I did: you have two atoms at d<0.4A)

Wrong input data typically leads to quick crashes. In this peculiar
case,  I suspect that the overlapping "core charges" for nonlinear
core corrections lead to weird results

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From njuxuyuehua at gmail.com  Fri Oct 17 15:40:55 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 17 Oct 2008 21:40:55 +0800
Subject: [Pw_forum] can the results of relax calculation be accepted?
Message-ID: <aca2feb20810170640o626b314fw770373a48d340326@mail.gmail.com>

hi all here :
 i am doing the relax job ,and the final force and stress is below:
i think the force is OK, but i am wondering the stress, is it OK ? please
give me some hints about the stress!
i will be appreciated
    atom   1 type  1   force =     0.00007018    0.00002245    0.00006498
     atom   2 type  1   force =     0.00005086   -0.00008932   -0.00000841
     atom   3 type  1   force =    -0.00007008    0.00002623   -0.00000841
     atom   4 type  1   force =    -0.00006425    0.00004599    0.00003014
     atom   5 type  1   force =    -0.00002315    0.00000809   -0.00001995
     atom   6 type  1   force =    -0.00003537   -0.00001800    0.00000374
     atom   7 type  1   force =     0.00005869    0.00001524    0.00000622
     atom   8 type  1   force =    -0.00000484   -0.00004491   -0.00000012
     atom   9 type  1   force =    -0.00001452    0.00004794   -0.00006021
     atom  10 type  1   force =     0.00003603   -0.00000450    0.00000211
     atom  11 type  1   force =     0.00002750    0.00001320   -0.00005575
     atom  12 type  1   force =    -0.00002557    0.00001401    0.00001566
     atom  13 type  1   force =     0.00009605   -0.00002151    0.00005370
     atom  14 type  1   force =     0.00003301   -0.00007073   -0.00003975
     atom  15 type  2   force =     0.00000298    0.00000041   -0.00001313
     atom  16 type  2   force =    -0.00005178   -0.00000168   -0.00001090
     atom  17 type  2   force =    -0.00000155    0.00001193    0.00002975
     atom  18 type  2   force =    -0.00001487    0.00000621    0.00001093
     atom  19 type  2   force =    -0.00001029    0.00000516   -0.00004670
     atom  20 type  2   force =     0.00002293   -0.00000863    0.00000876
     atom  21 type  2   force =    -0.00008195    0.00004243    0.00003734

     Total force =     0.000303     Total SCF correction =     0.000006


     entering subroutine stress ...

          total   stress  (Ry/bohr**3)                   (kbar)     P=
-0.32
  -0.00000304  -0.00000004   0.00000024         -0.45     -0.01      0.04
  -0.00000004  -0.00000332   0.00000004         -0.01     -0.49      0.01
   0.00000024   0.00000004  -0.00000020          0.04      0.01     -0.03


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at democritos.it  Fri Oct 17 16:06:26 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Oct 2008 16:06:26 +0200
Subject: [Pw_forum] can the results of relax calculation be accepted?
In-Reply-To: <aca2feb20810170640o626b314fw770373a48d340326@mail.gmail.com>
References: <aca2feb20810170640o626b314fw770373a48d340326@mail.gmail.com>
Message-ID: <48F89BE2.5020605@democritos.it>

xu yuehua wrote:

> please give me some hints about the stress!

avoid it :-)

Seriously: with a rough estimate of the elastic constants,
you can calculate how much the volume changes if you apply
a 0.32 KBar pressure. My guess is "very little".

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Fri Oct 17 17:07:15 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Oct 2008 17:07:15 +0200
Subject: [Pw_forum] k-points mismatch
In-Reply-To: <48EF33CB.6040302@democritos.it>
References: <829678.87709.qm@web65715.mail.ac4.yahoo.com>
	<48EF33CB.6040302@democritos.it>
Message-ID: <48F8AA23.5020308@democritos.it>

Paolo Giannozzi wrote:

> I don't see why this confuses the logic of the symmetry check,
> though, since there are no symmetry operations sending axis 1
> into 2.

sure there are! I don't know yet why the code contained in
pw.x yields a different number of k-points wrt kpoints.x,
but this is quite irrelevant: the 4,2,2 grid doesn't have
the correct symmetry and should be discarded by pw.x

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From cruzrojas at gmail.com  Fri Oct 17 21:20:31 2008
From: cruzrojas at gmail.com (=?ISO-8859-1?Q?Jes=FAs_Cruz?=)
Date: Fri, 17 Oct 2008 12:20:31 -0700
Subject: [Pw_forum] running paw on 4.0.1
Message-ID: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>

Hello
    I'm trying to use Quantum Espresso to perform a PAW calculation. Does
any one have some examples I can run to make sure my installation is working
right? I'm using version 4.0.1 and this is what I have done so far:

     I was trying to make a Bulk Copper Calculation to determine the lattice
constant.

     1) I generated the Cu paw potential using the input file in
/atomic_doc/paw_library/input

     2) Run pwscf.x with this pseudopotential, 1 atom per u.c. ibrav = 2
ecutwfc = 25 ecutrho=4*ecutwfc

     3) pwscf.x exited with a segmentation fault while reading the
potential, the problem, the two scalars nqlc and nwfc, the vector lll, and
the matrix dion were not writen into the UPF file when generated. So I
modified pwscf to fill these values while reading the potential.

      4) vary the lattice constant and plot energy vs lattice constant.
problem: by varying the lattice constant I don't get a smotth surface like
in the case of ultrasoft pseudopotential in the same lattice constant range.

      5) Increase the ecutwfc, to 30, 50, 75 and 90. Same noise plots were
obtained.

     What would you recomend to do next? or what do you think might be the
problme? What is the current state of PAW in version 4.0.1? does anyone have
a Cu paw UPF which is not incomplete?

Best Regards
Jesus Cruz
ILP Georgetown University
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From paulatto at sissa.it  Sat Oct 18 14:32:21 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 18 Oct 2008 14:32:21 +0200 (CEST)
Subject: [Pw_forum] running paw on 4.0.1
In-Reply-To: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
References: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
Message-ID: <60339.151.65.45.183.1224333141.squirrel@webmail.sissa.it>

On Ven, Ottobre 17, 2008 21:20, Jes?s Cruz wrote:
>  Hello
>      I'm trying to use Quantum Espresso to perform a PAW calculation. Does
>  any one have some examples I can run to make sure my installation is
>  working right? I'm using version 4.0.1 and this is what I have done so
>  far:

Dear Jes?s,
I have dozens of them, but cannot access them befor monday. I'll send them
one if still needed.

>       1) I generated the Cu paw potential using the input file in
>  /atomic_doc/paw_library/input

I'm not really sure that it is good, I've only a couple simple tests on it.

>       2) Run pwscf.x with this pseudopotential, 1 atom per u.c. ibrav = 2
>  ecutwfc = 25 ecutrho=4*ecutwfc

It should be ok.

>       3) pwscf.x exited with a segmentation fault while reading the
>  potential, the problem, the two scalars nqlc and nwfc, the vector lll,
> and the matrix dion were not writen into the UPF file when generated. So I
>  modified pwscf to fill these values while reading the potential.

Very strange, dion are a fundamental part of the psudopotential; I'm 100%
sure that they are written to and read from the UPF file: nothing would
work otherwise.

This is a showstopper: I cannot go any deeper with you question until I've
found out what's happening here.

I will try to run your exact scenario, but I suspect the problem is
somehow platform-dependent. Have you tried upgrading to 4.0.2? It should
not be relevant, but it may help.

Can you please provide more information on your system? e.g. compiler
version, architecture. If you can gzip the UPF file and send it to me
(privately) I will have a look at it.

regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



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From alex.mazheika at gmail.com  Sun Oct 19 23:40:54 2008
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Mon, 20 Oct 2008 01:40:54 +0400
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <ec86c07d0810191425v75754251y724bd1143433ec42@mail.gmail.com>
References: <ec86c07d0810191425v75754251y724bd1143433ec42@mail.gmail.com>
Message-ID: <ec86c07d0810191440h6511f97cq9d9c23a03853a3f2@mail.gmail.com>

Dear all

I perform the calculations of surface with adsorbed cluster Ag4/TiO2 and
have a problem with convergence during SCF-procedure. It does not converge.
In order to eliminate it I tried the shown methods in the user_guide: to
decrease mixing beta, to increase mixing ndim, to increase ecutwfc and
ecutrho. But it didn't help me. Is there any other methods to solve such
problem? The input file is here attached.

Best regards
Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
Belarus
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From amigliore at cmm.upenn.edu  Mon Oct 20 00:41:06 2008
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Sun, 19 Oct 2008 18:41:06 -0400 (EDT)
Subject: [Pw_forum] problem with convergence during SCF-procedure
Message-ID: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>

Hello Alex

Since, you have transition metals in your system, it could help you to
introduce an electronic smearing and then progressively  reduce it until
you get the solution without any orbital fractional occupations.
Then, from the attached file I saw that you are using  mixing_beta =
0.7D0. Did you try something like mixing_beta = 0.5 or similar (perhaps
you already did, but I don?t know) and also mixing_mode = ?plain?
(although I know that the local_TF mode may be good for highly
inhomogeneous systems).
Finally, your system includes Ti atoms, which have d electrons. Have you
tried to use the Hubbard U correction scheme implemented in pwscf? Also
irrespective of your convergence problem, it could provide you with a
better description of the electronic structure (indeed, I don?t have
direct experience on Ti, but I have on Fe, and the Hubbard U correction
term works well).
I hope something I said can help you.

Best regards,
Agostino Migliore
CMM, Department of Chemistry, Philadelphia


Quoting Alexej Mazheika <alex.mazheika at gmail.com>:

> Dear all
>
> I perform the calculations of surface with adsorbed cluster Ag4/TiO2 and
> have a problem with convergence during SCF-procedure. It does not converge.
> In order to eliminate it I tried the shown methods in the user_guide: to
> decrease mixing beta, to increase mixing ndim, to increase ecutwfc and
> ecutrho. But it didn't help me. Is there any other methods to solve such
> problem? The input file is here attached.
>
> Best regards
> Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
> Belarus
>



From nazari at iasbs.ac.ir  Mon Oct 20 10:17:22 2008
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Mon, 20 Oct 2008 09:17:22 +0100 (BST)
Subject: [Pw_forum] Stop job/ Davidson diagonalization with overlap
In-Reply-To: <60339.151.65.45.183.1224333141.squirrel@webmail.sissa.it>
References: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
	<60339.151.65.45.183.1224333141.squirrel@webmail.sissa.it>
Message-ID: <41523.213.176.122.17.1224490642.squirrel@mail.iasbs.ac.ir>

 Dear all,

 when I do scf or relax calculation  job starts the first iteration but

  stop immedietly.  with this line in output:

    iteration #  1     ecut=    30.00 Ry     beta=0.70
     Davidson diagonalization with overlap

 any suggestion?

 regards
 Fariba nazari
 IASBS



From giannozz at democritos.it  Mon Oct 20 08:45:18 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Oct 2008 08:45:18 +0200
Subject: [Pw_forum] Stop job/ Davidson diagonalization with overlap
In-Reply-To: <41523.213.176.122.17.1224490642.squirrel@mail.iasbs.ac.ir>
References: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>	<60339.151.65.45.183.1224333141.squirrel@webmail.sissa.it>
	<41523.213.176.122.17.1224490642.squirrel@mail.iasbs.ac.ir>
Message-ID: <48FC28FE.5060101@democritos.it>

nazari at iasbs.ac.ir wrote:

>  when I do scf or relax calculation  job starts the first iteration but
>   stop immedietly.  with this line in output:
> 
>     iteration #  1     ecut=    30.00 Ry     beta=0.70
>      Davidson diagonalization with overlap

as a first guess I would say "out of memory"

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Mon Oct 20 08:49:39 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Mon, 20 Oct 2008 12:19:39 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
Message-ID: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>

Hi all,

     I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0 with
GNU compilers ( gcc-4.1.2 & gfortran-4.1.2) succeessfully.

But the same installation is failing on Rocks-4.2 cluster either with GNU
compilers or pathscale compilers.
The error is:

configure:2314: WARNING: serial/parallel compiler mismatch detected
configure:2316: WARNING: parallel compiler  uses gfortran, but serial
compiler is /usr/bin/gfortran
...
configure:2983: /usr/bin/gcc4 -E  conftest.c
conftest.c:9:28: error: ac_nonexistent.h: No such file or directory
configure:2989: $? = 1
....
configure:4172:  --version </dev/null >&5
./configure: line 4173: --version: command not found
configure:4175: $? = 127
configure:4177:  -v </dev/null >&5
./configure: line 4178: -v: command not found
configure:4180: $? = 127
configure:4182:  -V </dev/null >&5
./configure: line 4183: -V: command not found
configure:4185: $? = 127
configure:4193: checking whether we are using the GNU Fortran 77 compiler
configure:4207:  -c  conftest.F >&5
./configure: line 4208: -c: command not found
configure:4213: $? = 127
....

The GNU version of Rocks 4.2 is 4.1.0 but in Rocks 5.0 it is 4.1.2.

The strange thing happened with Rocks-4.2 is, if the variables CC, F77 or
MPIF90 did not set to either gcc or pathscale, then configure works fine,
but fails during make.

If set the variables it fails in configure itself.

I'm attaching here the config.log file.

Please let me know if any one has faced this problem or atleast anybody
successful to install QE on Rocks 4.2.

Thanks,
Sangamesh
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From nazari at iasbs.ac.ir  Mon Oct 20 11:43:25 2008
From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir)
Date: Mon, 20 Oct 2008 10:43:25 +0100 (BST)
Subject: [Pw_forum] Stop job/ Davidson diagonalization with overlap
In-Reply-To: <48FC28FE.5060101@democritos.it>
References: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
	<60339.151.65.45.183.1224333141.squirrel@webmail.sissa.it>
	<41523.213.176.122.17.1224490642.squirrel@mail.iasbs.ac.ir>
	<48FC28FE.5060101@democritos.it>
Message-ID: <44343.213.176.122.17.1224495805.squirrel@mail.iasbs.ac.ir>


  Dear Paolo,

 At first I thought so. But at this moment I do not think so because

 I did calculation on 72 atoms rutile and 72 atoms anatas . the 72 atom

 anatas job with ecut 30 ry crash but rutile run.

 regards
 Fariba Nazari
 IASBS




> nazari at iasbs.ac.ir wrote:
>
>>  when I do scf or relax calculation  job starts the first iteration but
>>   stop immedietly.  with this line in output:
>>
>>     iteration #  1     ecut=    30.00 Ry     beta=0.70
>>      Davidson diagonalization with overlap
>
> as a first guess I would say "out of memory"
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



From giannozz at democritos.it  Mon Oct 20 09:17:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Oct 2008 09:17:40 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
Message-ID: <48FC3094.8010707@democritos.it>

Sangamesh B wrote:

>      I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0 

on WHAT?!?

> But the same installation is failing on Rocks-4.2 cluster [..]
> The strange thing happened with Rocks-4.2 is, if the variables CC, F77 
> or MPIF90 did not set to either gcc or pathscale, then configure works 
> fine, but fails during make.

how does it fails?

> If set the variables it fails in configure itself.

because they are not properly set, I guess

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Mon Oct 20 09:39:11 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Mon, 20 Oct 2008 13:09:11 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FC3094.8010707@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FC3094.8010707@democritos.it>
Message-ID: <cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>

Hi Paolo,

On Mon, Oct 20, 2008 at 12:47 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> Sangamesh B wrote:
>
> >      I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0
>
> on WHAT?!?
>
If you asking about Rocks-5.0, then Rocks is a clustering tool which is
built on Cent OS.
The cluster has two nodes, with Dual core, dual AMD64 Opteron processors.

>
> > But the same installation is failing on Rocks-4.2 cluster [..]
> > The strange thing happened with Rocks-4.2 is, if the variables CC, F77
> > or MPIF90 did not set to either gcc or pathscale, then configure works
> > fine, but fails during make.
>
> how does it fails?
>
Right now I don't have that output. In further I'll send it.

>
> > If set the variables it fails in configure itself.
>
> because they are not properly set, I guess
>
I don't think so. Because I set - CC=<path to gcc> F77=<path to gfortran>
and MPIF90=<path to MPICh2's mpif90>

>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From smogunov at sissa.it  Mon Oct 20 08:23:11 2008
From: smogunov at sissa.it (Alexander)
Date: Mon, 20 Oct 2008 08:23:11 +0200
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <Pine.GSO.4.21.0810161700280.16794-100000@neptune.phys.ufl.edu>
References: <Pine.GSO.4.21.0810161700280.16794-100000@neptune.phys.ufl.edu>
Message-ID: <200810200823.11752.smogunov@sissa.it>

Dear Manoj

On Thursday 16 October 2008 23:15, Manoj Srivastava wrote:
> Dear Alexandar,
>  Thank you very much. Your answers make sense and now i have better
> understanding of the subroutine scatter_forw.f90.  I have one question
> about poten.f90 subroutine, where you calculate the V(p,gper) in each
> slices of the slab(equation 15). I have a question about Gz, which is
> 2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the line
> 60, you have Gz multiplied with bg(3,3). I kind of understand this is
> because 3rd direction is perpendicular to xy plane, 
Exactly. As it is implemented now pwcond deals with systems 
having monoclinic unit cell, i.e. such that a3 is perpendicular to both a1 and 
a2 (a1 and a2 are not necessary orthogonal one to another) and the direction 
of transport is a3. This seems to us the most general setup for transport and 
I do not think we should consider at the moment the situation where the a3 is 
not perpendicular to the xy plane.

Best regards, 
Alexander

> but not totally clear 
> about it. Would you mind explaining? my other question is when reciprocal
> space vectors b1, b2 and b3 are not orhogonal to each other, which is
> more general case, then should not we take bg(1,3) and bg(2,3) in there
> too?
>  Thank you once again for listening to my questions and i hope i am
> not bothering you too much.
>
> Regards,
> Manoj Srivastava
> Physics Graduate Student
> Department of Physics
> Gainesville, FL, USA.
>
> have  On Wed, 15 Oct 2008, Alexander wrote:
> > Dear Manoj
> >
> > On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > > Dear Alexader,
> > >
> > >  Thank you very much for your reply. I was out of town and could not
> > > see the message till yesterday. I have some questions on it, it would
> > > be great if you could answer them.
> > >
> > > On Fri, 10 Oct 2008, Alexander wrote:
> > > > Dear Manoj
> > > >
> > > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > > Any follow ups on the message below? Alexander?
> > > > >
> > > > > Regards,
> > > > > Manoj
> > > > >
> > > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > > Dear All,
> > > > > >  Is any body familiar with the scatter_forw.f90 subroutine of
> > > > > > PWCOND? I think there is a bug in this subroutine at the place
> > > > > > where you calculate intw2, which is z integration of nonlocal
> > > > > > wavefunction with beta function. I have looked up the necessary
> > > > > > formulae in the Choi & Ihm's paper (PRB 59, 2267, Jan 1999). In
> > > > > > the paper, nonlocal wavefunction has 3 terms, one of which
> > > > > > contains beta function, say W. The other two parts dont have any
> > > > > > W in them, rather they are just plane wave solution. (Please have
> > > > > > a look at equation 24 and 26 of the paper ). So, when we are
> > > > > > doing z integration of nonlocal wavefunction with beta function
> > > > > > W, we should have three terms, one of which should contain two W,
> > > > > > but rest should just have one W. On the other hand in the code
> > > > > > all three terms contain two beta functions!! (please have a look
> > > > > > at line 228 of scatter_forw.f90). I am wondering if my
> > > > > > understanding is right?
> > > >
> > > > Your understanding is wrong. On the line 228 you add to the integral
> > > > ONLY contribution with two beta functions (from the 1st term in the
> > > > nonlocal function, see Eq. 24) but on the line 393 the contribution
> > > > from the 2nd term is added too. There is no 3rd term since every step
> > > > you rotate your local solutions \psi_n in such a way that b_{\lambda
> > > > \alpha lm} vanish (see the paragraph after Eq. 37).
> > >
> > >   I believe that the equations 40, 41 and 42 implemented in the code
> > > are in the momentum space. In the code, intw2 has 3 terms. We can tell
> > > this by looking at the subroutine integrals.f90, where int2d is
> > > defined. Now, by looking at the choi& Ihm 's paper, the very first term
> > > of psi{alpha,l,m} has f{lambda,alpha,l,m}(equation26).And, if we
> > > substitute this in equation 40, we should just get one term. I am just
> > > confuesd on the fact that how come this one term in paper gets
> > > transformed into 3 terms of the code!
> >
> > intw2(alpha,beta) is the integral of nonlocal solution (24) with w
> > functions, intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr,
> > where alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO
> > contributions from the first and second terms of (24), the one from the
> > third term vanishes as I explained before. These two contributions are
> > calculated on the lines  228  and 393 of the code. The integrals intw1
> > (alpha,n)=\int_{0,d} w_{alpha}(r)*psi_{n}(r)dr are the integrals of local
> > solutions (17) with the same projector functions w.
> > The integrals intw2 and intw1 have nothing to do with boundary conditions
> > (40). They enter in (11) and are needed to construct the final solutions
> > according to Eq.(10). Substituting the form of this solution (10) in the
> > boundary conditions (40) you will be led to the generalized eigenvalue
> > problem, AX=exp(ikd) BX, with known matrices A and B and unknown
> > coefficients X={a_n,C_{alpha,l,m}} defining the resulting solution (10).
> >
> > > Would you mind explaining? Also, the integrals that are defined in the
> > > code are only in the slabs (nz1), so how are you taking the integration
> > > in the region (0,d), which we need according to equations 40, 41 and 42
> > > ?
> >
> > When you go over slabs you add new contributions to the integrals intw1
> > and intw2 (see the line 228 for the first contribution to intw2 and the
> > part "add to the integrals" for another contribution to intw2 and
> > contributions to intw1) so at the end you obtain integrals over all the
> > region.
> >
> > Regards,
> > Alexander
> >
> > > >  > > I have one more question in the later part of the same
> > > >  > > subroutine. What
> > > > > >
> > > > > > does the lapack subroutine
> > > > > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > > > > do?
> > > > > > I tried to look it up and i got the idea that it is trying to
> > > > > > solve amat*x=xmat, with amat and xmat known and x unknown, and at
> > > > > > the end of calculation it stores x in xmat.
> > > > > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it
> > > > > > changes the structure of xmat from what is defined in 'constructs
> > > > > > matrices' part. Is it correct?
> > > >
> > > > Here, you are right.
> > > >
> > > > > > Also, afterwards in this code where  it 'rotates integrals' is
> > > > > > not very clear to me.
> > > > > > Could somebody please tell me in little detail, what is going on
> > > > > > here?
> > > >
> > > > As I explained before rotation means that every step (at each slab)
> > > > you make a linear combination of local solutions \psi_n with the
> > > > transformation matrix  h_{nn'} (see the last paragraph on the p.
> > > > 2270). so that the new solutions have the property:
> > > > b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions
> > > > have b_{\lambda \alpha lm}=0. Doing this transformation of local and
> > > > nonlocal solutions you should also perform the corresponding
> > > > transformations of the integrals.
> > > >
> > > > > > Also, is this subroutine written just on the basis of Choi and
> > > > > > Ihm paper, or are there more reference to it? If yes, would
> > > > > > someone mind mentioning them?
> > > >
> > > > Unfortunately, the paper of Choi and Ihm is very detail, and in the
> > > > PWCOND code we followed it very closely, so no more references
> > > > are needed. In our papers we just extended those ideas to ultrasoft
> > > > pseudopotentials, magnetism, spin-orbit coupling and so on.
> > > >
> > > > Hope this helped you,
> > > > regards, Alexander
> > > >
> > > > > > Regards,
> > > > > > Manoj Srivastava
> > > > > > Physics Graduate Student
> > > > > > University of Florida,
> > > > > > Gainesville,FL, USA
> > > > >
> > > > > _______________________________________________
> > > > > Pw_forum mailing list
> > > > > Pw_forum at pwscf.org
> > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > > Once again thank you very much for your help. I appreciate it.
> > >
> > > Regards,
> > > Manoj Srivastava
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Mon Oct 20 09:49:12 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Oct 2008 09:49:12 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FC3094.8010707@democritos.it>
	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
Message-ID: <48FC37F8.8070505@democritos.it>

Sangamesh B wrote:

> I don't think so. Because I set - CC=<path to gcc> F77=<path to gfortran>
> and MPIF90=<path to MPICh2's mpif90>

if you set those variables, instead of letting configure find them,
you have to set them to the correct values. It looks like MPIF90
is not the correct location of the parallel compiler:

 > configure:2052: checking for /opt/mpich2GNU/bin/mpif90
 > configure:2081: result: no

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Mon Oct 20 12:45:42 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Mon, 20 Oct 2008 16:15:42 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FC37F8.8070505@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FC3094.8010707@democritos.it>
	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
	<48FC37F8.8070505@democritos.it>
Message-ID: <cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>

On Mon, Oct 20, 2008 at 1:19 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> Sangamesh B wrote:
>
> > I don't think so. Because I set - CC=<path to gcc> F77=<path to gfortran>
> > and MPIF90=<path to MPICh2's mpif90>
>
> if you set those variables, instead of letting configure find them,
> you have to set them to the correct values. It looks like MPIF90
> is not the correct location of the parallel compiler:
>
No. I've set it to correct location of the parallel compiler.

I'll send you the output of 'make all' error tomorrow.

What might be the cause? Will it work, If I upgrade the gcc version to
4.3.0?

>
>  > configure:2052: checking for /opt/mpich2GNU/bin/mpif90
>  > configure:2081: result: no
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Mon Oct 20 13:22:36 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Oct 2008 13:22:36 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FC3094.8010707@democritos.it>	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>	<48FC37F8.8070505@democritos.it>
	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
Message-ID: <48FC69FC.2050506@democritos.it>

Sangamesh B wrote:

> No. I've set it to correct location of the parallel compiler.

this is what you think. Based on the file you sent, "configure"
seems to think otherwise.

> I'll send you the output of 'make all' error tomorrow.

if it is a "compiler internal error" or something similar,
please look into the user guide.

> What might be the cause?  

anything: there are pages and pages in the user guide describing
what can go wrong.

> Will it work, If I upgrade the gcc version to 4.3.0? 

hard to predict.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From paulatto at sissa.it  Mon Oct 20 13:41:13 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 20 Oct 2008 13:41:13 +0200
Subject: [Pw_forum] running paw on 4.0.1
In-Reply-To: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
References: <aa63c41c0810171220l675efb77n8494e54195c22215@mail.gmail.com>
Message-ID: <48FC6E59.5000309@sissa.it>

Jes?s Cruz ha scritto:
> Segmentation fault while reading the potential, the problem, the two
> scalars nqlc and nwfc, the vector lll, and the matrix dion were not
> writen into the UPF file when generated. So I modified pwscf to fill
> these values while reading the potential.
I've compiled a fresh and clean 4.0.1 version, generated the Cu pseudo,
run the example01 with it and everything works perfectly fine for me.

Can you please provide some additional information on your platform?

regards



-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From manoj at phys.ufl.edu  Tue Oct 21 00:01:34 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Mon, 20 Oct 2008 18:01:34 -0400 (EDT)
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <200810200823.11752.smogunov@sissa.it>
Message-ID: <Pine.GSO.4.21.0810201748530.1564-100000@neptune.phys.ufl.edu>


Dear Alexander, 
 Thank you very much for your answer. I have one more question, it seems
my list of questions is never gonna end :( 
 this is about init_gper.f90 subroutine. where you calculate
|G+k|^2<Ecut2d. 
the expression - 
norm2=(((il+xyk(1,ik))*bg(1,1)+(jl+xyk(2,ik))*bg(1,2))**2+ &
            ((il+xyk(1,ik))*bg(2,1)+(jl+xyk(2,ik))*bg(2,2))**2)* &

i believe is  |G+k|^2. How do you get above expression in the code for
this? I tried to work it out but could not get this. You even have g.k
term!  I guess i would have more understanding once i understand how did
you define Gper in the fourier transform,
 V(rper,z)=sum(gper)[exp(i*gper*rper) V(gper,z)
Is gper just gx and gy, and then you rotate your axis to get
bg(1,1),bg(1,2), bg(2,1) and bg(2,2)? Would you mind explaining?

Regards, 
Manoj
On Mon, 20 Oct 2008, Alexander wrote:

> Dear Manoj
> 
> On Thursday 16 October 2008 23:15, Manoj Srivastava wrote:
> > Dear Alexandar,
> >  Thank you very much. Your answers make sense and now i have better
> > understanding of the subroutine scatter_forw.f90.  I have one question
> > about poten.f90 subroutine, where you calculate the V(p,gper) in each
> > slices of the slab(equation 15). I have a question about Gz, which is
> > 2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the line
> > 60, you have Gz multiplied with bg(3,3). I kind of understand this is
> > because 3rd direction is perpendicular to xy plane, 
> Exactly. As it is implemented now pwcond deals with systems 
> having monoclinic unit cell, i.e. such that a3 is perpendicular to both a1 and 
> a2 (a1 and a2 are not necessary orthogonal one to another) and the direction 
> of transport is a3. This seems to us the most general setup for transport and 
> I do not think we should consider at the moment the situation where the a3 is 
> not perpendicular to the xy plane.
> 
> Best regards, 
> Alexander
> 
> > but not totally clear 
> > about it. Would you mind explaining? my other question is when reciprocal
> > space vectors b1, b2 and b3 are not orhogonal to each other, which is
> > more general case, then should not we take bg(1,3) and bg(2,3) in there
> > too?
> >  Thank you once again for listening to my questions and i hope i am
> > not bothering you too much.
> >
> > Regards,
> > Manoj Srivastava
> > Physics Graduate Student
> > Department of Physics
> > Gainesville, FL, USA.
> >
> > have  On Wed, 15 Oct 2008, Alexander wrote:
> > > Dear Manoj
> > >
> > > On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > > > Dear Alexader,
> > > >
> > > >  Thank you very much for your reply. I was out of town and could not
> > > > see the message till yesterday. I have some questions on it, it would
> > > > be great if you could answer them.
> > > >
> > > > On Fri, 10 Oct 2008, Alexander wrote:
> > > > > Dear Manoj
> > > > >
> > > > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > > > Any follow ups on the message below? Alexander?
> > > > > >
> > > > > > Regards,
> > > > > > Manoj
> > > > > >
> > > > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > > > Dear All,
> > > > > > >  Is any body familiar with the scatter_forw.f90 subroutine of
> > > > > > > PWCOND? I think there is a bug in this subroutine at the place
> > > > > > > where you calculate intw2, which is z integration of nonlocal
> > > > > > > wavefunction with beta function. I have looked up the necessary
> > > > > > > formulae in the Choi & Ihm's paper (PRB 59, 2267, Jan 1999). In
> > > > > > > the paper, nonlocal wavefunction has 3 terms, one of which
> > > > > > > contains beta function, say W. The other two parts dont have any
> > > > > > > W in them, rather they are just plane wave solution. (Please have
> > > > > > > a look at equation 24 and 26 of the paper ). So, when we are
> > > > > > > doing z integration of nonlocal wavefunction with beta function
> > > > > > > W, we should have three terms, one of which should contain two W,
> > > > > > > but rest should just have one W. On the other hand in the code
> > > > > > > all three terms contain two beta functions!! (please have a look
> > > > > > > at line 228 of scatter_forw.f90). I am wondering if my
> > > > > > > understanding is right?
> > > > >
> > > > > Your understanding is wrong. On the line 228 you add to the integral
> > > > > ONLY contribution with two beta functions (from the 1st term in the
> > > > > nonlocal function, see Eq. 24) but on the line 393 the contribution
> > > > > from the 2nd term is added too. There is no 3rd term since every step
> > > > > you rotate your local solutions \psi_n in such a way that b_{\lambda
> > > > > \alpha lm} vanish (see the paragraph after Eq. 37).
> > > >
> > > >   I believe that the equations 40, 41 and 42 implemented in the code
> > > > are in the momentum space. In the code, intw2 has 3 terms. We can tell
> > > > this by looking at the subroutine integrals.f90, where int2d is
> > > > defined. Now, by looking at the choi& Ihm 's paper, the very first term
> > > > of psi{alpha,l,m} has f{lambda,alpha,l,m}(equation26).And, if we
> > > > substitute this in equation 40, we should just get one term. I am just
> > > > confuesd on the fact that how come this one term in paper gets
> > > > transformed into 3 terms of the code!
> > >
> > > intw2(alpha,beta) is the integral of nonlocal solution (24) with w
> > > functions, intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr,
> > > where alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO
> > > contributions from the first and second terms of (24), the one from the
> > > third term vanishes as I explained before. These two contributions are
> > > calculated on the lines  228  and 393 of the code. The integrals intw1
> > > (alpha,n)=\int_{0,d} w_{alpha}(r)*psi_{n}(r)dr are the integrals of local
> > > solutions (17) with the same projector functions w.
> > > The integrals intw2 and intw1 have nothing to do with boundary conditions
> > > (40). They enter in (11) and are needed to construct the final solutions
> > > according to Eq.(10). Substituting the form of this solution (10) in the
> > > boundary conditions (40) you will be led to the generalized eigenvalue
> > > problem, AX=exp(ikd) BX, with known matrices A and B and unknown
> > > coefficients X={a_n,C_{alpha,l,m}} defining the resulting solution (10).
> > >
> > > > Would you mind explaining? Also, the integrals that are defined in the
> > > > code are only in the slabs (nz1), so how are you taking the integration
> > > > in the region (0,d), which we need according to equations 40, 41 and 42
> > > > ?
> > >
> > > When you go over slabs you add new contributions to the integrals intw1
> > > and intw2 (see the line 228 for the first contribution to intw2 and the
> > > part "add to the integrals" for another contribution to intw2 and
> > > contributions to intw1) so at the end you obtain integrals over all the
> > > region.
> > >
> > > Regards,
> > > Alexander
> > >
> > > > >  > > I have one more question in the later part of the same
> > > > >  > > subroutine. What
> > > > > > >
> > > > > > > does the lapack subroutine
> > > > > > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > > > > > do?
> > > > > > > I tried to look it up and i got the idea that it is trying to
> > > > > > > solve amat*x=xmat, with amat and xmat known and x unknown, and at
> > > > > > > the end of calculation it stores x in xmat.
> > > > > > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right? So, it
> > > > > > > changes the structure of xmat from what is defined in 'constructs
> > > > > > > matrices' part. Is it correct?
> > > > >
> > > > > Here, you are right.
> > > > >
> > > > > > > Also, afterwards in this code where  it 'rotates integrals' is
> > > > > > > not very clear to me.
> > > > > > > Could somebody please tell me in little detail, what is going on
> > > > > > > here?
> > > > >
> > > > > As I explained before rotation means that every step (at each slab)
> > > > > you make a linear combination of local solutions \psi_n with the
> > > > > transformation matrix  h_{nn'} (see the last paragraph on the p.
> > > > > 2270). so that the new solutions have the property:
> > > > > b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions
> > > > > have b_{\lambda \alpha lm}=0. Doing this transformation of local and
> > > > > nonlocal solutions you should also perform the corresponding
> > > > > transformations of the integrals.
> > > > >
> > > > > > > Also, is this subroutine written just on the basis of Choi and
> > > > > > > Ihm paper, or are there more reference to it? If yes, would
> > > > > > > someone mind mentioning them?
> > > > >
> > > > > Unfortunately, the paper of Choi and Ihm is very detail, and in the
> > > > > PWCOND code we followed it very closely, so no more references
> > > > > are needed. In our papers we just extended those ideas to ultrasoft
> > > > > pseudopotentials, magnetism, spin-orbit coupling and so on.
> > > > >
> > > > > Hope this helped you,
> > > > > regards, Alexander
> > > > >
> > > > > > > Regards,
> > > > > > > Manoj Srivastava
> > > > > > > Physics Graduate Student
> > > > > > > University of Florida,
> > > > > > > Gainesville,FL, USA
> > > > > >
> > > > > > _______________________________________________
> > > > > > Pw_forum mailing list
> > > > > > Pw_forum at pwscf.org
> > > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > >
> > > > > _______________________________________________
> > > > > Pw_forum mailing list
> > > > > Pw_forum at pwscf.org
> > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > >
> > > > Once again thank you very much for your help. I appreciate it.
> > > >
> > > > Regards,
> > > > Manoj Srivastava
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From forum.san at gmail.com  Tue Oct 21 08:54:22 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 12:24:22 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FC3094.8010707@democritos.it>
	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
	<48FC37F8.8070505@democritos.it>
	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
	<48FC69FC.2050506@democritos.it>
	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
Message-ID: <cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>

Hi,

     For more clarification, I'm summarising the problem in three scenarios.

Scenario 1:
    In this case, the env variables CC,F77 & MPIf90 were not set. The
configure works fine. It detects pathscale compilers. But during 'make
all', it fails.

Scenario 2:
    I switched to GCC, by setting CC, F77 and MPIF90 to GCC. This
fails in configure itself.

Scenario 3:
   I set the env variables - CC, F77 and MPIF90 to pathscale
binaries. This also fails in configure itself.

Below are the details for the three scenarios. The attachmets are
mentioned for each  scenario.

Thanks,
Sangamesh
Consultant - HPC
Locuz Enterprise Solutions,
Bangalore, India

----------------------------------------------------------------------------------------------

SCENARIO 1:

       No environment variables set.
       ./configure - completes successfully.
       make all - fails

Error during make all:

mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
-I../PH -c iotk_stream.F90 -o iotk_stream.o
pathcc -E -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
-I../include  iotk_str.f90 -o iotk_str.F90
pathcc WARNING: compiler not invoked with language of source file;
will compile with f90 but link with cc
..
....
pathf95-83 pathf90: ERROR IOTK_TOOL_MAN_X, File = iotk_tool.F90, Line
= 475, Column = 1
 This token is missing the " delimiter.
^
pathf95-83 pathf90: ERROR IOTK_TOOL_MAN_X, File = iotk_tool.F90, Line
= 475, Column = 1
 This token is missing the " delimiter.
.......
pathf95-505 pathf90: ERROR IOTK_TOOL_MAN_X, File = iotk_tool.F90, Line
= 475, Column = 1
 Continuation of character context in free source form requires an
"&" as the first nonblank character of the next line.
......
"It also writes informations about the version of the file format
(file_version)."
pathf95-214 pathf90: LIMIT IOTK_TOOL_MAN_X, File = iotk_tool.F90, Line = 475
 The maximum number, 100, of fatal errors has been exceeded.
make[2]: *** [iotk_tool.o] Error 2
make[2]: Leaving directory `/opt/espresso-4.0.2/iotk/src'
make[1]: *** [lib+util] Error 2
make[1]: Leaving directory `/opt/espresso-4.0.2/iotk'
make: *** [libiotk] Error 2

Attachments for this scenario:

make.sys_no-vars-set
make_terminal_out1
config.log_no-vars-set


SCENARIO 2: Setting CC, F90, MPIf90 to GCC

# gcc --version
gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2)
Copyright (C) 2004 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

# gfortran --version
GNU Fortran 95 (GCC) 4.1.0 20060515 (Red Hat 4.1.0-18)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

# /opt/mpich2GNU/bin/mpif90 -show
gfortran -I/opt/mpich2GNU/include -I/opt/mpich2GNU/include
-L/opt/mpich2GNU/lib -lmpichf90 -lmpichf90 -lmpich -lpthread -lrt

# export CC=/usr/bin/gcc
# export CXX=/usr/bin/g++
# export F77=/usr/bin/gfortran
# export MPIF90=/opt/mpich2GNU/bin/mpif90

# ./configure | tee config_GCC_output
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... yes
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /usr/bin/gfortran accepts -g... yes
checking for /opt/mpich2GNU/bin/mpif90... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking version of ... unknown, assuming gfortran
configure: WARNING: serial/parallel compiler mismatch detected
configure: WARNING: parallel compiler  uses gfortran, but serial
compiler is /usr/bin/gfortran
setting F90... /usr/bin/gfortran
setting MPIF90...
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ANSI C... none needed
setting CC... /usr/bin/gcc
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int *... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for /usr/bin/gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
setting F77...
using F90... /usr/bin/gfortran
setting FFLAGS... -O
setting F90FLAGS... $(FFLAGS)
setting FFLAGS_NOOPT... -O0
setting CFLAGS... -O3
setting CPP... cpp
setting CPPFLAGS... -P -traditional
setting LD...
setting LDFLAGS...
setting AR... ar
setting ARFLAGS... ruv
setting ARFLAGS_DYNAMIC...ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... yes
checking how to get verbose linking output from ... configure:
WARNING: compilation failed

checking for Fortran libraries of ...
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... configure: error: cannot
compile a simple Fortran program
See `config.log' for more details.

Attachmets:

config.log_GCC
make.sys_GCC

I observed from make.sys file, mpif90 doesn't have complete path.


SCENARIO 3: SETTING CC, F77, MPIF90 to pathscale

# export CC=/opt/pathscale/bin/pathcc
# export F77=/opt/pathscale/bin/pathf90
# export MPIF90=/opt/mpich2PS/bin/mpif90
# export CXX=/opt/pathscale/bin/pathCC

# pathcc --version
PathScale EKOPath(TM) Compiler Suite: Version 2.4
Built on: 2006-03-24 14:54:44 -0800
Thread model: posix
GNU gcc version 3.3.1 (PathScale 2.4 driver)

Copyright 2000, 2001 Silicon Graphics, Inc.  All Rights Reserved.
Copyright 2002, 2003, 2004, 2005, 2006 PathScale, Inc.  All Rights Reserved.
See complete copyright, patent and legal notices in the
/opt/pathscale/share/doc/pathscale-compilers-2.4/LEGAL.pdf file.

# pathf90 --version
PathScale EKOPath(TM) Compiler Suite: Version 2.4
Built on: 2006-03-24 14:54:44 -0800
Thread model: posix
GNU gcc version 3.3.1 (PathScale 2.4 driver)

Copyright 2000, 2001 Silicon Graphics, Inc.  All Rights Reserved.
Copyright 2002, 2003, 2004, 2005, 2006 PathScale, Inc.  All Rights Reserved.
See complete copyright, patent and legal notices in the
/opt/pathscale/share/doc/pathscale-compilers-2.4/LEGAL.pdf file.

]# ./configure | tee config_out_psc
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... yes
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /opt/pathscale/bin/pathf90 accepts -g... yes
checking for /opt/mpich2PS/bin/mpif90... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking version of ... unknown, assuming gfortran
configure: WARNING: serial/parallel compiler mismatch detected
configure: WARNING: parallel compiler  uses gfortran, but serial
compiler is /opt/pathscale/bin/pathf90
setting F90... /opt/pathscale/bin/pathf90
setting MPIF90...
checking whether we are using the GNU C compiler... yes
checking whether /opt/pathscale/bin/pathcc accepts -g... yes
checking for /opt/pathscale/bin/pathcc option to accept ANSI C... none needed
setting CC... /opt/pathscale/bin/pathcc
checking how to run the C preprocessor... /opt/pathscale/bin/pathcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int *... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for /opt/pathscale/bin/pathf90... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
setting F77...
using F90... /opt/pathscale/bin/pathf90
setting FFLAGS... -O
setting F90FLAGS... $(FFLAGS)
setting FFLAGS_NOOPT... -O0
setting CFLAGS... -O3
setting CPP... cpp
setting CPPFLAGS... -P -traditional
setting LD...
setting LDFLAGS...
setting AR... ar
setting ARFLAGS... ruv
setting ARFLAGS_DYNAMIC...ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... yes
checking how to get verbose linking output from ... configure:
WARNING: compilation failed

checking for Fortran libraries of ...
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... configure: error: cannot
compile a simple Fortran program
See `config.log' for more details.

Attachmets:
config.log_PSC
make.sys_PSC
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From giannozz at democritos.it  Tue Oct 21 09:18:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 09:18:35 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FC3094.8010707@democritos.it>	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>	<48FC37F8.8070505@democritos.it>	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>	<48FC69FC.2050506@democritos.it>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
Message-ID: <48FD824B.9010407@democritos.it>

Sangamesh B wrote:

 > Scenario 1:
>     In this case, the env variables CC,F77 & MPIf90 were not set. The
> configure works fine. It detects pathscale compilers. But during 'make
> all', it fails.

    please replace
CPP            = pathcc -E
    with
CPP            = /lib/cpp  -P -traditional
    and report if it works

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Oct 21 09:25:32 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 09:25:32 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FC3094.8010707@democritos.it>	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>	<48FC37F8.8070505@democritos.it>	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>	<48FC69FC.2050506@democritos.it>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
Message-ID: <48FD83EC.1040309@democritos.it>

..and, by the way, this was documented:

http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Pathscale_compiler

"Versions 2.3 ad 2.4 of the Pathscale compiler crash when compiling 
CPV/phasefactors.f90. Workaround: replace SUM(na(1:nsp)) with nat
(info by Paolo Cazzato; fixed since version 3.1.1).

Version 2.99 of the Pathscale compiler works and is recognized by 
configure for versions later than 4.0.1, but the preprocessing step:

   pathcc -E

causes a mysterious error in compilation of iotk and should be replaced by

   /lib/cpp -P --traditional

The MVAPICH parallel environment with Pathscale compilers also works. 
(info by Paolo Giannozzi, July 2008)"

[note the "--traditional" instead of "-traditional" as I incoprrectly
  wrote in the preceding message]

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Tue Oct 21 09:35:31 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 13:05:31 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FD83EC.1040309@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FC3094.8010707@democritos.it>
	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
	<48FC37F8.8070505@democritos.it>
	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
	<48FC69FC.2050506@democritos.it>
	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
	<48FD83EC.1040309@democritos.it>
Message-ID: <cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>

Hi,

    I set:

  # export CPP="/lib/cpp -P --traditional"

# ./configure | tee config_out
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf90... no
checking for pathf95... pathf95
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... yes
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether pathf95 accepts -g... yes
checking for mpif90... mpif90
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether mpif90 accepts -g... yes
checking version of mpif90... pathf95 2.4
setting F90... pathf95
setting MPIF90... mpif90
checking for pathcc... pathcc
checking whether we are using the GNU C compiler... yes
checking whether pathcc accepts -g... yes
checking for pathcc option to accept ANSI C... none needed
setting CC... pathcc
checking how to run the C preprocessor... /lib/cpp -P --traditional
configure: error: C preprocessor "/lib/cpp -P --traditional" fails sanity check
See `config.log' for more details.

Again its failing.
Please note that, I've not set any other variables, CC, F77.

Do I have to put it in make.sys.

Thanks,
Sangamesh
Consultant - HPC
Locuz Enterprise Solutions

On Tue, Oct 21, 2008 at 12:55 PM, Paolo Giannozzi
<giannozz at democritos.it> wrote:
> ..and, by the way, this was documented:
>
> http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Pathscale_compiler
>
> "Versions 2.3 ad 2.4 of the Pathscale compiler crash when compiling
> CPV/phasefactors.f90. Workaround: replace SUM(na(1:nsp)) with nat
> (info by Paolo Cazzato; fixed since version 3.1.1).
>
> Version 2.99 of the Pathscale compiler works and is recognized by
> configure for versions later than 4.0.1, but the preprocessing step:
>
>   pathcc -E
>
> causes a mysterious error in compilation of iotk and should be replaced by
>
>   /lib/cpp -P --traditional
>
> The MVAPICH parallel environment with Pathscale compilers also works.
> (info by Paolo Giannozzi, July 2008)"
>
> [note the "--traditional" instead of "-traditional" as I incoprrectly
>  wrote in the preceding message]
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Tue Oct 21 09:37:05 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 09:37:05 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FC3094.8010707@democritos.it>	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>	<48FC37F8.8070505@democritos.it>	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>	<48FC69FC.2050506@democritos.it>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>	<48FD83EC.1040309@democritos.it>
	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
Message-ID: <48FD86A1.6020404@democritos.it>

Sangamesh B wrote:

> Do I have to put it in make.sys.

yes
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Tue Oct 21 11:27:40 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 14:57:40 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FD86A1.6020404@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>
	<48FC37F8.8070505@democritos.it>
	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
	<48FC69FC.2050506@democritos.it>
	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
	<48FD83EC.1040309@democritos.it>
	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
	<48FD86A1.6020404@democritos.it>
Message-ID: <cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>

On Tue, Oct 21, 2008 at 1:07 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> Sangamesh B wrote:
>
>> Do I have to put it in make.sys.
>
> yes
> --
Did ./configure

Then set CPP=/lib/cpp -P --traditional in make.sys.

Now its giving different error:

/lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -I../include  scf_mod.f90 -o scf_mod.F90
mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
-I../PH -c scf_mod.F90 -o scf_mod.o

MODULE scf
       ^
pathf95-855 pathf90: ERROR SCF, File = scf_mod.F90, Line = 10, Column = 8
  The compiler has detected errors in module "SCF".  No module
information file will be created for this module.

     REAL(DP),   allocatable :: of_r(:,:)  ! the charge density in R-space
                 ^
pathf95-197 pathf90: ERROR SCF, File = scf_mod.F90, Line = 48, Column = 18
  Unexpected syntax: "POINTER or DIMENSION" was expected but found
"ALLOCATABLE".
                                ^
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 48, Column = 33
  Component "OF_R" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

     COMPLEX(DP),allocatable :: of_g(:,:)  ! the charge density in G-space
                 ^
...
......
pathf95-197 pathf90: ERROR SCF, File = scf_mod.F90, Line = 59, Column = 19
  Unexpected syntax: "POINTER or DIMENSION" was expected but found
"ALLOCATABLE".
                                 ^
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 59, Column = 34
  Component "NS" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

     REAL(DP),    allocatable :: bec(:,:,:) ! PAW corrections to hamiltonian
                  ^
pathf95-197 pathf90: ERROR SCF, File = scf_mod.F90, Line = 60, Column = 19
  Unexpected syntax: "POINTER or DIMENSION" was expected but found
"ALLOCATABLE".
                                 ^
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 60, Column = 34
  Component "BEC" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

pathf95: PathScale(TM) Fortran Version 2.4 (f14) Tue Oct 21, 2008  15:06:55
pathf95: 677 source lines
pathf95: 21 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s)
pathf95: "explain pathf95-message number" gives more information about
each message
make[1]: *** [scf_mod.o] Error 2
make[1]: Leaving directory `/opt/espresso-4.0.2/PW'
make: *** [pw] Error 2

Thanks,
Sangamesh
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From paulatto at sissa.it  Tue Oct 21 11:30:38 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 21 Oct 2008 11:30:38 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<cb60cbc40810200039u3ed0bc90g38cdfacd06cbf1cb@mail.gmail.com>	<48FC37F8.8070505@democritos.it>	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>	<48FC69FC.2050506@democritos.it>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>	<48FD83EC.1040309@democritos.it>	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>	<48FD86A1.6020404@democritos.it>
	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
Message-ID: <48FDA13E.3000200@sissa.it>

Sangamesh B ha scritto:
>   Unexpected syntax: "POINTER or DIMENSION" was expected but found
> "ALLOCATABLE".
>   
Dear Sangamesh,
adding -D__GFORTRAN to the F90FLAGS in make.sys should solve this problem.

regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From forum.san at gmail.com  Tue Oct 21 11:51:09 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 15:21:09 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FDA13E.3000200@sissa.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>
	<48FC69FC.2050506@democritos.it>
	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
	<48FD83EC.1040309@democritos.it>
	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
	<48FD86A1.6020404@democritos.it>
	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
	<48FDA13E.3000200@sissa.it>
Message-ID: <cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>

On Tue, Oct 21, 2008 at 3:00 PM, Lorenzo Paulatto <paulatto at sissa.it> wrote:
> Sangamesh B ha scritto:
>>   Unexpected syntax: "POINTER or DIMENSION" was expected but found
>> "ALLOCATABLE".
>>
> Dear Sangamesh,
> adding -D__GFORTRAN to the F90FLAGS in make.sys should solve this problem.
>
Added -D_GFORTRAN. Still the error persists:

make[1]: Leaving directory `/opt/espresso-4.0.2/flib'
if test -d PW ; then \
( cd PW ; if test "make" = "" ; then make  TLDEPS= all ; \
else make  TLDEPS= all ; fi ) ; fi
make[1]: Entering directory `/opt/espresso-4.0.2/PW'
test -n "" && ( cd .. ; make -w  || exit 1) || :
/lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -I../include  noncol.f90 -o noncol.F90
mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
-I../PH -D__GFORTRAN -c noncol.F90 -o noncol.o
/lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -I../include  pwscf.f90 -o pwscf.F90
mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
-I../PH -D__GFORTRAN -c pwscf.F90 -o pwscf.o
...

MODULE scf
       ^
pathf95-855 pathf90: ERROR SCF, File = scf_mod.F90, Line = 10, Column = 8
  The compiler has detected errors in module "SCF".  No module
information file will be created for this module.

     REAL(DP),   allocatable :: of_r(:,:)  ! the charge density in R-space
                 ^
pathf95-197 pathf90: ERROR SCF, File = scf_mod.F90, Line = 48, Column = 18
  Unexpected syntax: "POINTER or DIMENSION" was expected but found
"ALLOCATABLE".
                                ^
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 48, Column = 33
  Component "OF_R" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

     COMPLEX(DP),allocatable :: of_g(:,:)  ! the charge density in G-space
                 ^
pathf95-197 pathf90: ERROR SCF, File = scf_mod.F90, Line = 49, Column = 18
  Unexpected syntax: "POINTER or DIMENSION" was expected but found
"ALLOCATABLE".

......
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 60, Column = 34
  Component "BEC" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

pathf95: PathScale(TM) Fortran Version 2.4 (f14) Tue Oct 21, 2008  15:41:44
pathf95: 677 source lines
pathf95: 21 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s)
pathf95: "explain pathf95-message number" gives more information about
each message
make[1]: *** [scf_mod.o] Error 2
make[1]: Leaving directory `/opt/espresso-4.0.2/PW'
make: *** [pw] Error 2

I've attached here the make.sys and Makefile. Please have a look at it
for compatibilities.

Thanks,
sangamesh
> regards
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Tue Oct 21 11:55:22 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 11:55:22 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<cb60cbc40810200345q371e4071i5be3695256bec088@mail.gmail.com>	<48FC69FC.2050506@democritos.it>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>	<48FD83EC.1040309@democritos.it>	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>	<48FD86A1.6020404@democritos.it>	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>	<48FDA13E.3000200@sissa.it>
	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
Message-ID: <48FDA70A.7020508@democritos.it>

Sangamesh B wrote:

> Added -D_GFORTRAN. Still the error persists:
> 
> /lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
> -D__MPI -D__PARA -I../include  pwscf.f90 -o pwscf.F90

must be added above, not below ...

> mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
> -D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
> -I../PH -D__GFORTRAN -c pwscf.F90 -o pwscf.o

...where it is useless, since your compiler doesn't perform
preprocessing. It must be added to DFLAGS in make.sys
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Tue Oct 21 12:08:41 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 15:38:41 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FDA70A.7020508@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>
	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>
	<48FD83EC.1040309@democritos.it>
	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
	<48FD86A1.6020404@democritos.it>
	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
	<48FDA13E.3000200@sissa.it>
	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
	<48FDA70A.7020508@democritos.it>
Message-ID: <cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>

On Tue, Oct 21, 2008 at 3:25 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> Sangamesh B wrote:
>
>> Added -D_GFORTRAN. Still the error persists:
>>
>> /lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
>> -D__MPI -D__PARA -I../include  pwscf.f90 -o pwscf.F90
>
> must be added above, not below ...
>
Added here:

DFLAGS         =  -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -D_GFORTRAN
FDFLAGS        = $(DFLAGS)

......
CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -march=auto -O2

.....

Error still persists:

ar: creating ptools.a
a - blockset.o
a - flush_unit.o
a - gridsetup.o
a - ilcm.o
a - indxg2l.o
a - indxg2p.o
a - indxl2g.o
a - infog1l.o
a - infog2l.o
a - localdim.o
a - localindex.o
a - npreroc.o
a - numroc.o
a - ownerof.o
ranlib ptools.a
make[1]: Leaving directory `/opt/espresso-4.0.2/flib'
if test -d PW ; then \
( cd PW ; if test "make" = "" ; then make  TLDEPS= all ; \
else make  TLDEPS= all ; fi ) ; fi
make[1]: Entering directory `/opt/espresso-4.0.2/PW'
test -n "" && ( cd .. ; make -w  || exit 1) || :
/lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -D_GFORTRAN -I../include  noncol.f90 -o noncol.F90
mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA -D_GFORTRAN -I../include  -I./  -I../Modules  -I../iotk/src
-I../PW  -I../PH -c noncol.F90 -o noncol.o
/lib/cpp -P --traditional -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -D_GFORTRAN -I../include  pwscf.f90 -o pwscf.F90

........
MODULE scf
       ^
pathf95-855 pathf90: ERROR SCF, File = scf_mod.F90, Line = 10, Column = 8
  The compiler has detected errors in module "SCF".  No module
information file will be created for this module.

     REAL(DP),   allocatable :: of_r(:,:)  ! the charge density in R-space
                 ^
.......
pathf95-190 pathf90: ERROR SCF, File = scf_mod.F90, Line = 60, Column = 34
  Component "BEC" does not have a POINTER attribute so its dimension
must be an explicit-shape array with constant bounds.

pathf95: PathScale(TM) Fortran Version 2.4 (f14) Tue Oct 21, 2008  16:06:37
pathf95: 677 source lines
pathf95: 21 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s)
pathf95: "explain pathf95-message number" gives more information about
each message
make[1]: *** [scf_mod.o] Error 2
make[1]: Leaving directory `/opt/espresso-4.0.2/PW'
make: *** [pw] Error 2


Thanks,
Sangamesh

>> mpif90 -march=auto -O2 -D__EKO -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
>> -D__PARA -I../include  -I./  -I../Modules  -I../iotk/src -I../PW
>> -I../PH -D__GFORTRAN -c pwscf.F90 -o pwscf.o
>
> ...where it is useless, since your compiler doesn't perform
> preprocessing. It must be added to DFLAGS in make.sys
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Tue Oct 21 12:11:17 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 12:11:17 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<cb60cbc40810202325y7920dfc0q1f7828e9a9fa2eeb@mail.gmail.com>	<cb60cbc40810202354l1f306231q8a36106358fda55b@mail.gmail.com>	<48FD83EC.1040309@democritos.it>	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>	<48FD86A1.6020404@democritos.it>	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>	<48FDA13E.3000200@sissa.it>	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>	<48FDA70A.7020508@democritos.it>
	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
Message-ID: <48FDAAC5.4030507@democritos.it>

Sangamesh B wrote:

>>> Added -D_GFORTRAN. Still the error persists:

__GFORTRAN /= _GFORTRAN
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Tue Oct 21 12:30:16 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 16:00:16 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FDAAC5.4030507@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FD83EC.1040309@democritos.it>
	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>
	<48FD86A1.6020404@democritos.it>
	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
	<48FDA13E.3000200@sissa.it>
	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
	<48FDA70A.7020508@democritos.it>
	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
	<48FDAAC5.4030507@democritos.it>
Message-ID: <cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>

It got installed. Thanks for your support.

Does QE-4.0.2 support make install?

On Tue, Oct 21, 2008 at 3:41 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> Sangamesh B wrote:
>
>>>> Added -D_GFORTRAN. Still the error persists:
>
> __GFORTRAN /= _GFORTRAN
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Tue Oct 21 12:35:20 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 12:35:20 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FD83EC.1040309@democritos.it>	<cb60cbc40810210035p6375bf41r1924f51eede85be4@mail.gmail.com>	<48FD86A1.6020404@democritos.it>	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>	<48FDA13E.3000200@sissa.it>	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>	<48FDA70A.7020508@democritos.it>	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>	<48FDAAC5.4030507@democritos.it>
	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>
Message-ID: <48FDB068.5000201@democritos.it>

Sangamesh B wrote:
> It got installed. Thanks for your support.
> 
> Does QE-4.0.2 support make install?

no, it doesn't. All executables are linked into to the bin/
subdirectory.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From djaithania at hotmail.com  Tue Oct 21 13:08:47 2008
From: djaithania at hotmail.com (hania djani-ait aissa)
Date: Tue, 21 Oct 2008 11:08:47 +0000
Subject: [Pw_forum] about pseudopotentials
Message-ID: <BLU115-W374539D80FA2F55A16F7D0D22E0@phx.gbl>


dears,
can we use for the same structure but for differents atoms USPP and BHS pseudopotentials (Ecut regarding BHS and rhocut regarding USPP)? If no, can someone provide me ultrasoft pseudo for W in LDA approximation?
 thanks a lot
 
Hania djani
PHD student,
center for developement of advanced technologies (CDTA)
Algiers, Algeria
_________________________________________________________________
D?couvrez Windows Live Spaces et cr?ez votre site Web perso en quelques clics !
http://spaces.live.com/signup.aspx
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From forum.san at gmail.com  Tue Oct 21 13:21:38 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 21 Oct 2008 16:51:38 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FDB068.5000201@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FD86A1.6020404@democritos.it>
	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>
	<48FDA13E.3000200@sissa.it>
	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
	<48FDA70A.7020508@democritos.it>
	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
	<48FDAAC5.4030507@democritos.it>
	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>
	<48FDB068.5000201@democritos.it>
Message-ID: <cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>

Hi,

  Its giving segmentation fault for the given examples.

The used example is example01:

output of Serial Run:

# ./run_example | tee run_serial_out

/opt/espresso-4.0.2/examples/example01 : starting

This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.

  executables directory: /opt/espresso-4.0.2/bin
  pseudo directory:      /opt/espresso-4.0.2/pseudo
  temporary directory:   /root/qstemp
  checking that needed directories and files exist... done

  running pw.x as:  /opt/espresso-4.0.2/bin/pw.x
  running bands.x as:  /opt/espresso-4.0.2/bin/bands.x

  cleaning /root/qstemp... done
  running the scf calculation for Si... done
  running the band-structure calculation for Si... done
  running the symmetry analysis for Si bands...

**** Segmentation fault!  Fault address: 0x2bd0

Fault address is 4183088 bytes below the first valid
mapping boundary, which is at 0x400000.

This may have been caused by a struct access through a null pointer.
./run_example: line 77: 10169 Aborted                 $BANDS_COMMAND
<si.bands.in >si.bands.out
 done
  cleaning /root/qstemp... done
  running the scf calculation for Al... done
  running the band-structure calculation for Al... done
  cleaning /root/qstemp... done
  running the scf calculation for Cu... done
  running the band-structure calculation for Cu... done
  running the symmetry analysis for Cu bands...

**** Segmentation fault!  Fault address: 0xa90

Fault address is 4191600 bytes below the first valid
mapping boundary, which is at 0x400000.

This may have been caused by a struct access through a null pointer.
./run_example: line 77: 10182 Aborted                 $BANDS_COMMAND
<cu.bands.in >cu.bands.out
 done
  cleaning /root/qstemp... done
  running the scf calculation for Ni... done
  running the band-structure calculation for Ni... done
  cleaning /root/qstemp... done
  running the scf calculation for Si... done
  running the band-structure calculation for Si... done
  cleaning /root/qstemp... done
  running the scf calculation for Al... done
  running the band-structure calculation for Al... done
  cleaning /root/qstemp... done
  running the scf calculation for Cu... done
  running the band-structure calculation for Cu... done
  cleaning /root/qstemp... done
  running the scf calculation for Ni... done
  running the band-structure calculation for Ni... done

/opt/espresso-4.0.2/examples/example01 : done


Output of parallel job with 4 mpi processes on a single node(dual core
dual processor)

/opt/espresso-4.0.2/examples/example01 : starting

This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.

  executables directory: /opt/espresso-4.0.2/bin
  pseudo directory:      /opt/espresso-4.0.2/pseudo
  temporary directory:   /root/qstemp
  checking that needed directories and files exist... done

  running pw.x as:  /opt/mpich2PS/bin/mpirun -machinefile /root/mach
-np 4  /opt/espresso-4.0.2/bin/pw.x
  running bands.x as:  /opt/mpich2PS/bin/mpirun -machinefile
/root/mach -np 4  /opt/espresso-4.0.2/bin/bands.x

  cleaning /root/qstemp... done
  running the scf calculation for Si...Error condition encountered
during test: exit status = 255
Aborting


Thanks,
Sangamesh
On Tue, Oct 21, 2008 at 4:05 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> Sangamesh B wrote:
>> It got installed. Thanks for your support.
>>
>> Does QE-4.0.2 support make install?
>
> no, it doesn't. All executables are linked into to the bin/
> subdirectory.
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Tue Oct 21 13:32:24 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 21 Oct 2008 13:32:24 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FD86A1.6020404@democritos.it>	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>	<48FDA13E.3000200@sissa.it>	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>	<48FDA70A.7020508@democritos.it>	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>	<48FDAAC5.4030507@democritos.it>	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>	<48FDB068.5000201@democritos.it>
	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
Message-ID: <48FDBDC8.6010605@democritos.it>

Sangamesh B wrote:

>   Its giving segmentation fault for the given examples.

no, only in one specific auxiliary code (bands.x). In any
case, it is a problem of your compiler, with (100-\epsilon)%
probability, and \epsilon quite small.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From eyvaz_isaev at yahoo.com  Tue Oct 21 14:49:25 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 21 Oct 2008 05:49:25 -0700 (PDT)
Subject: [Pw_forum] about pseudopotentials
In-Reply-To: <BLU115-W374539D80FA2F55A16F7D0D22E0@phx.gbl>
Message-ID: <990165.20379.qm@web65715.mail.ac4.yahoo.com>

Dear Hania,

As it was discussed many times in the forum, you can mix any pseudopotential with the same exchange-correlation functional. But in this particular case the choice of the energy cutoff is dictated by NCPsP, as you mix USPP and NCPsP which requires higher cutoff energy. 
I guess you have to perform some tests regarding ecutwfc and ecutrho keeping in mind that  NCPsPs are "harder" compared  with USPP (for which ecutwfc~30Ry), and at the same time USPP requires ecutrho~(8-12)*ecutwfc.
 
Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Tue, 10/21/08, hania djani-ait aissa <djaithania at hotmail.com> wrote:

> From: hania djani-ait aissa <djaithania at hotmail.com>
> Subject: [Pw_forum] about pseudopotentials
> To: pw_forum at pwscf.org
> Date: Tuesday, October 21, 2008, 3:08 PM
> dears,
> can we use for the same structure but for differents atoms
> USPP and BHS pseudopotentials (Ecut regarding BHS and rhocut
> regarding USPP)? If no, can someone provide me ultrasoft
> pseudo for W in LDA approximation?
>  thanks a lot
>  
> Hania djani
> PHD student,
> center for developement of advanced technologies (CDTA)
> Algiers, Algeria
> _________________________________________________________________
> D?couvrez Windows Live Spaces et cr?ez votre site Web
> perso en quelques clics !
> http://spaces.live.com/signup.aspx_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From baris.malcioglu at gmail.com  Tue Oct 21 14:28:11 2008
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Tue, 21 Oct 2008 15:28:11 +0300
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FD86A1.6020404@democritos.it>	<cb60cbc40810210227n40d71637o58ddeb8c2fa53d20@mail.gmail.com>	<48FDA13E.3000200@sissa.it>	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>	<48FDA70A.7020508@democritos.it>	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>	<48FDAAC5.4030507@democritos.it>	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>	<48FDB068.5000201@democritos.it>
	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
Message-ID: <48FDCADB.6020705@gmail.com>

Sangamesh B wrote:
> Hi,
> 
Hello Sangamesh,

>   Its giving segmentation fault for the given examples.

Some compilers suppress allocate() problems silently.

This might also mean that you do not have (access to) enough free memory
on the computer you are running example on.


You might either play with compiler flags depending on your compiler or
try adding something like
if (.not. allocated(some_array_you_are_suspicious_of)) call errore
('allocate','array not properly allocated',1)

in the routines that are responsible allocating memory space for arrays
i.e.:
allocate_fft
allocate_locpot
allocate_nlpot
allocate_wfc
...

Sincerely,

  _______________________________
|                                ``::::%%%%%%%%%HHH|
|  O. Baris Malcioglu                ::::::::%%%%%%|
|                                      ``:::::::::%|
|  SISSA                                     `````:|
|   via Beirut, 2-4    34014 Trieste TS,           |
|                                   ITALY          |
|               T: +39 040 378 73 74               |
|:.                  F: +39 +39 040 3787 528       |
|%:::::::::..                                      |
|%%%%%%::::::::..         mbaris at sissa.it          |
|HHH%%%%%%%%:::::::::......________________________|

From forum.san at gmail.com  Wed Oct 22 08:49:38 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Wed, 22 Oct 2008 12:19:38 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FDCADB.6020705@gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FDA13E.3000200@sissa.it>
	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>
	<48FDA70A.7020508@democritos.it>
	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
	<48FDAAC5.4030507@democritos.it>
	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>
	<48FDB068.5000201@democritos.it>
	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
	<48FDCADB.6020705@gmail.com>
Message-ID: <cb60cbc40810212349g41505f40oa6db9eebe5bfa870@mail.gmail.com>

Hi,

   Today I'm trying to build QE-4.0.2 from GNU compilers. Installed
mpich2-1.0.7 with gcc4 and gfortran.

   When I try to configure QE, its failing. The output of configure is:

[root at deepblue espresso-4.0.2_GNU]# ./configure | tee config_GNU
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... yes
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /usr/bin/gfortran accepts -g... yes
*checking for /opt/mpich2_107_GNU/bin/mpif90... no*

Why its not detecting mpif90?

checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking version of ... unknown, assuming gfortran
configure: WARNING: serial/parallel compiler mismatch detected
configure: WARNING: parallel compiler  uses gfortran, but serial compiler is
/usr/bin/gfortran

I'm not getting why its telling mismatch?

setting F90... /usr/bin/gfortran
setting MPIF90...
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc4 accepts -g... yes
checking for /usr/bin/gcc4 option to accept ANSI C... none needed
setting CC... /usr/bin/gcc4
checking how to run the C preprocessor... /usr/bin/gcc4 -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int *... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for /usr/bin/gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
setting F77...
using F90... /usr/bin/gfortran
setting FFLAGS... -O
setting F90FLAGS... $(FFLAGS)
setting FFLAGS_NOOPT... -O0
setting CFLAGS... -O3
setting CPP... cpp
setting CPPFLAGS... -P -traditional
setting LD...
setting LDFLAGS...
setting AR... ar
setting ARFLAGS... ruv
setting ARFLAGS_DYNAMIC...ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... yes
checking how to get verbose linking output from ... configure: WARNING:
compilation failed

checking for Fortran libraries of ...
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... configure: error: cannot
compile a simple Fortran program
See `config.log' for more details.

Earlier, in the same cluster espresso-3.2 was working fine. I think there
might be a problem with configure script itself.

Thanks,
Sangamesh

On Tue, Oct 21, 2008 at 5:58 PM, O. Baris Malcioglu <
baris.malcioglu at gmail.com> wrote:
> Sangamesh B wrote:
>> Hi,
>>
> Hello Sangamesh,
>
>>   Its giving segmentation fault for the given examples.
>
> Some compilers suppress allocate() problems silently.
>
> This might also mean that you do not have (access to) enough free memory
> on the computer you are running example on.
>
>
> You might either play with compiler flags depending on your compiler or
> try adding something like
> if (.not. allocated(some_array_you_are_suspicious_of)) call errore
> ('allocate','array not properly allocated',1)
>
> in the routines that are responsible allocating memory space for arrays
> i.e.:
> allocate_fft
> allocate_locpot
> allocate_nlpot
> allocate_wfc
> ...
>
> Sincerely,
>
>  _______________________________
> |                                ``::::%%%%%%%%%HHH|
> |  O. Baris Malcioglu                ::::::::%%%%%%|
> |                                      ``:::::::::%|
> |  SISSA                                     `````:|
> |   via Beirut, 2-4    34014 Trieste TS,           |
> |                                   ITALY          |
> |               T: +39 040 378 73 74               |
> |:.                  F: +39 +39 040 3787 528       |
> |%:::::::::..                                      |
> |%%%%%%::::::::..         mbaris at sissa.it          |
> |HHH%%%%%%%%:::::::::......________________________|
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From mansourehp at gmail.com  Wed Oct 22 09:06:48 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Wed, 22 Oct 2008 10:36:48 +0330
Subject: [Pw_forum] correlation function
Message-ID: <cbe1626b0810220006u2adbf9a5g80d907d22b8d7626@mail.gmail.com>

Dear all
I am performing MD with NVT ensemble.how can I find (radial distribution
function) correlation function data  to plot it during a Molecular
 dynamics simulation?
good luck
Mansoureh
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From smogunov at sissa.it  Wed Oct 22 08:23:09 2008
From: smogunov at sissa.it (Alexander)
Date: Wed, 22 Oct 2008 08:23:09 +0200
Subject: [Pw_forum] possible bug in scatter_forw.f90
In-Reply-To: <Pine.GSO.4.21.0810201748530.1564-100000@neptune.phys.ufl.edu>
References: <Pine.GSO.4.21.0810201748530.1564-100000@neptune.phys.ufl.edu>
Message-ID: <200810220823.09244.smogunov@sissa.it>

Dear Manoj

On Tuesday 21 October 2008 00:01, Manoj Srivastava wrote:
> Dear Alexander,
>  Thank you very much for your answer. I have one more question, it seems
> my list of questions is never gonna end :(
It is always a pleasure when there is someone going through
the code written by you and trying to understand what is there 
after all :-).

>  this is about init_gper.f90 subroutine. where you calculate
>
> |G+k|^2<Ecut2d.
>
> the expression -
> norm2=(((il+xyk(1,ik))*bg(1,1)+(jl+xyk(2,ik))*bg(1,2))**2+ &
>             ((il+xyk(1,ik))*bg(2,1)+(jl+xyk(2,ik))*bg(2,2))**2)* &
>
> i believe is  |G+k|^2. How do you get above expression in the code for
> this? 
norm2 is indeed |G_perp+k_perp|^2, where G_perp=il*b_1+jl*b_2 and 2d vector 
k_perp=xyk(1,ik)*b_1+xyk(2,ik)*b_2 and you indeed select out those 
G_perp+k_perp which satisfy (G_perp+k_perp)^2<Ecut2d. 
The number of latters is ngper. Notice that gper array contains 
the cartesian coordinates of these G_perp+k_perp vectors.
> I tried to work it out but could not get this. You even have g.k 
> term!  
> I guess i would have more understanding once i understand how did 
> you define Gper in the fourier transform,
>  V(rper,z)=sum(gper)[exp(i*gper*rper) V(gper,z)
> Is gper just gx and gy, and then you rotate your axis to get
> bg(1,1),bg(1,2), bg(2,1) and bg(2,2)? Would you mind explaining?
The potential V(z,G_perp) is calculated for the full set of 2d G_perp related 
to the real space discretization of r_perp=(x,y). 
V(z,G_perp) <--FFT--> V(z,r_perp).
G_perp=il*b_1+jl*b_2, il=1..nrx, jl=1..nry, where nrx and nry are in fact
nr1s and nr2s of pw.x and are defined by the cut-off ecutwfc.
This potential is then used in the subroutine local.f90.

Hope this helps,
Alexander



>
> Regards,
> Manoj
>
> On Mon, 20 Oct 2008, Alexander wrote:
> > Dear Manoj
> >
> > On Thursday 16 October 2008 23:15, Manoj Srivastava wrote:
> > > Dear Alexandar,
> > >  Thank you very much. Your answers make sense and now i have better
> > > understanding of the subroutine scatter_forw.f90.  I have one question
> > > about poten.f90 subroutine, where you calculate the V(p,gper) in each
> > > slices of the slab(equation 15). I have a question about Gz, which is
> > > 2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the
> > > line 60, you have Gz multiplied with bg(3,3). I kind of understand this
> > > is because 3rd direction is perpendicular to xy plane,
> >
> > Exactly. As it is implemented now pwcond deals with systems
> > having monoclinic unit cell, i.e. such that a3 is perpendicular to both
> > a1 and a2 (a1 and a2 are not necessary orthogonal one to another) and the
> > direction of transport is a3. This seems to us the most general setup for
> > transport and I do not think we should consider at the moment the
> > situation where the a3 is not perpendicular to the xy plane.
> >
> > Best regards,
> > Alexander
> >
> > > but not totally clear
> > > about it. Would you mind explaining? my other question is when
> > > reciprocal space vectors b1, b2 and b3 are not orhogonal to each other,
> > > which is more general case, then should not we take bg(1,3) and bg(2,3)
> > > in there too?
> > >  Thank you once again for listening to my questions and i hope i am
> > > not bothering you too much.
> > >
> > > Regards,
> > > Manoj Srivastava
> > > Physics Graduate Student
> > > Department of Physics
> > > Gainesville, FL, USA.
> > >
> > > have  On Wed, 15 Oct 2008, Alexander wrote:
> > > > Dear Manoj
> > > >
> > > > On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > > > > Dear Alexader,
> > > > >
> > > > >  Thank you very much for your reply. I was out of town and could
> > > > > not see the message till yesterday. I have some questions on it, it
> > > > > would be great if you could answer them.
> > > > >
> > > > > On Fri, 10 Oct 2008, Alexander wrote:
> > > > > > Dear Manoj
> > > > > >
> > > > > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > > > > Any follow ups on the message below? Alexander?
> > > > > > >
> > > > > > > Regards,
> > > > > > > Manoj
> > > > > > >
> > > > > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > > > > Dear All,
> > > > > > > >  Is any body familiar with the scatter_forw.f90 subroutine of
> > > > > > > > PWCOND? I think there is a bug in this subroutine at the
> > > > > > > > place where you calculate intw2, which is z integration of
> > > > > > > > nonlocal wavefunction with beta function. I have looked up
> > > > > > > > the necessary formulae in the Choi & Ihm's paper (PRB 59,
> > > > > > > > 2267, Jan 1999). In the paper, nonlocal wavefunction has 3
> > > > > > > > terms, one of which contains beta function, say W. The other
> > > > > > > > two parts dont have any W in them, rather they are just plane
> > > > > > > > wave solution. (Please have a look at equation 24 and 26 of
> > > > > > > > the paper ). So, when we are doing z integration of nonlocal
> > > > > > > > wavefunction with beta function W, we should have three
> > > > > > > > terms, one of which should contain two W, but rest should
> > > > > > > > just have one W. On the other hand in the code all three
> > > > > > > > terms contain two beta functions!! (please have a look at
> > > > > > > > line 228 of scatter_forw.f90). I am wondering if my
> > > > > > > > understanding is right?
> > > > > >
> > > > > > Your understanding is wrong. On the line 228 you add to the
> > > > > > integral ONLY contribution with two beta functions (from the 1st
> > > > > > term in the nonlocal function, see Eq. 24) but on the line 393
> > > > > > the contribution from the 2nd term is added too. There is no 3rd
> > > > > > term since every step you rotate your local solutions \psi_n in
> > > > > > such a way that b_{\lambda \alpha lm} vanish (see the paragraph
> > > > > > after Eq. 37).
> > > > >
> > > > >   I believe that the equations 40, 41 and 42 implemented in the
> > > > > code are in the momentum space. In the code, intw2 has 3 terms. We
> > > > > can tell this by looking at the subroutine integrals.f90, where
> > > > > int2d is defined. Now, by looking at the choi& Ihm 's paper, the
> > > > > very first term of psi{alpha,l,m} has
> > > > > f{lambda,alpha,l,m}(equation26).And, if we substitute this in
> > > > > equation 40, we should just get one term. I am just confuesd on the
> > > > > fact that how come this one term in paper gets transformed into 3
> > > > > terms of the code!
> > > >
> > > > intw2(alpha,beta) is the integral of nonlocal solution (24) with w
> > > > functions, intw2(alpha,beta) = \int_{0,d}
> > > > w_{alpha}(r)*psi_{beta}(r)dr, where alpha,beta={alpha,l,m} in the
> > > > paper. In each slab it will have TWO contributions from the first and
> > > > second terms of (24), the one from the third term vanishes as I
> > > > explained before. These two contributions are calculated on the lines
> > > >  228  and 393 of the code. The integrals intw1 (alpha,n)=\int_{0,d}
> > > > w_{alpha}(r)*psi_{n}(r)dr are the integrals of local solutions (17)
> > > > with the same projector functions w.
> > > > The integrals intw2 and intw1 have nothing to do with boundary
> > > > conditions (40). They enter in (11) and are needed to construct the
> > > > final solutions according to Eq.(10). Substituting the form of this
> > > > solution (10) in the boundary conditions (40) you will be led to the
> > > > generalized eigenvalue problem, AX=exp(ikd) BX, with known matrices A
> > > > and B and unknown coefficients X={a_n,C_{alpha,l,m}} defining the
> > > > resulting solution (10).
> > > >
> > > > > Would you mind explaining? Also, the integrals that are defined in
> > > > > the code are only in the slabs (nz1), so how are you taking the
> > > > > integration in the region (0,d), which we need according to
> > > > > equations 40, 41 and 42 ?
> > > >
> > > > When you go over slabs you add new contributions to the integrals
> > > > intw1 and intw2 (see the line 228 for the first contribution to intw2
> > > > and the part "add to the integrals" for another contribution to intw2
> > > > and contributions to intw1) so at the end you obtain integrals over
> > > > all the region.
> > > >
> > > > Regards,
> > > > Alexander
> > > >
> > > > > >  > > I have one more question in the later part of the same
> > > > > >  > > subroutine. What
> > > > > > > >
> > > > > > > > does the lapack subroutine
> > > > > > > > ZGESV(2*n2d,2*n2d+norb*npol,amat,2*n2d,ipiv,xmat,2*n2d,info)
> > > > > > > > do?
> > > > > > > > I tried to look it up and i got the idea that it is trying to
> > > > > > > > solve amat*x=xmat, with amat and xmat known and x unknown,
> > > > > > > > and at the end of calculation it stores x in xmat.
> > > > > > > > so, basically it does--  x=[(amat)^(-1)]*xmat. Am i right?
> > > > > > > > So, it changes the structure of xmat from what is defined in
> > > > > > > > 'constructs matrices' part. Is it correct?
> > > > > >
> > > > > > Here, you are right.
> > > > > >
> > > > > > > > Also, afterwards in this code where  it 'rotates integrals'
> > > > > > > > is not very clear to me.
> > > > > > > > Could somebody please tell me in little detail, what is going
> > > > > > > > on here?
> > > > > >
> > > > > > As I explained before rotation means that every step (at each
> > > > > > slab) you make a linear combination of local solutions \psi_n
> > > > > > with the transformation matrix  h_{nn'} (see the last paragraph
> > > > > > on the p. 2270). so that the new solutions have the property:
> > > > > > b_{\lambda n} = \delta_{\lambda n} and the new nonlocal solutions
> > > > > > have b_{\lambda \alpha lm}=0. Doing this transformation of local
> > > > > > and nonlocal solutions you should also perform the corresponding
> > > > > > transformations of the integrals.
> > > > > >
> > > > > > > > Also, is this subroutine written just on the basis of Choi
> > > > > > > > and Ihm paper, or are there more reference to it? If yes,
> > > > > > > > would someone mind mentioning them?
> > > > > >
> > > > > > Unfortunately, the paper of Choi and Ihm is very detail, and in
> > > > > > the PWCOND code we followed it very closely, so no more
> > > > > > references are needed. In our papers we just extended those ideas
> > > > > > to ultrasoft pseudopotentials, magnetism, spin-orbit coupling and
> > > > > > so on.
> > > > > >
> > > > > > Hope this helped you,
> > > > > > regards, Alexander
> > > > > >
> > > > > > > > Regards,
> > > > > > > > Manoj Srivastava
> > > > > > > > Physics Graduate Student
> > > > > > > > University of Florida,
> > > > > > > > Gainesville,FL, USA
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > Pw_forum mailing list
> > > > > > > Pw_forum at pwscf.org
> > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > > >
> > > > > > _______________________________________________
> > > > > > Pw_forum mailing list
> > > > > > Pw_forum at pwscf.org
> > > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > >
> > > > > Once again thank you very much for your help. I appreciate it.
> > > > >
> > > > > Regards,
> > > > > Manoj Srivastava
> > > > >
> > > > > _______________________________________________
> > > > > Pw_forum mailing list
> > > > > Pw_forum at pwscf.org
> > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From giannozz at democritos.it  Wed Oct 22 11:22:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 22 Oct 2008 11:22:40 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810212349g41505f40oa6db9eebe5bfa870@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FDA13E.3000200@sissa.it>	<cb60cbc40810210251j4767a2cel8f99d2f299851c02@mail.gmail.com>	<48FDA70A.7020508@democritos.it>	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>	<48FDAAC5.4030507@democritos.it>	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>	<48FDB068.5000201@democritos.it>	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>	<48FDCADB.6020705@gmail.com>
	<cb60cbc40810212349g41505f40oa6db9eebe5bfa870@mail.gmail.com>
Message-ID: <48FEF0E0.7010004@democritos.it>

Sangamesh B wrote:

> *checking for /opt/mpich2_107_GNU/bin/mpif90... no*
> 
> Why its not detecting mpif90?

either because it is not there, or because it is there and
it doesn't work, or because configure doesn't like the name
with leading path. Put "/opt/mpich2_107_GNU/bin/" first in
your path and let configure detect "mpif90".

> configure: WARNING: serial/parallel compiler mismatch detected
> configure: WARNING: parallel compiler  uses gfortran, but serial 
> compiler is /usr/bin/gfortran
> 
> I'm not getting why its telling mismatch?

again: don't use full paths. I added the warning above for convenience,
to prevent problems in badly installed machines where mpif90 uses a
serial compiler that is not the first found in the path. It is just a
warning, it tells you to pay attention, what do you want more?????

> Earlier, in the same cluster espresso-3.2 was working fine. I think 
> there might be a problem with configure script itself.

then please find the problem, if you can. I am confident that there
is no problem in the configure.ac script, but it cannot detect all
configurations on all machines. And please note that configure has
correctly recognized the pathscale compiler. It is not configure's
fault if the pathscale compiler is, like 99% of the commercial fortran
compilers, a piece of crap that cannot correctly compile a moderately
complex suite of codes. And in any event: Q-E has 1001 pieces, are you
sure that the one that doesn't work with pathscale is the one you
absolutely need?

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From forum.san at gmail.com  Wed Oct 22 11:45:01 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Wed, 22 Oct 2008 15:15:01 +0530
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <48FEF0E0.7010004@democritos.it>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>
	<48FDA70A.7020508@democritos.it>
	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>
	<48FDAAC5.4030507@democritos.it>
	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>
	<48FDB068.5000201@democritos.it>
	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>
	<48FDCADB.6020705@gmail.com>
	<cb60cbc40810212349g41505f40oa6db9eebe5bfa870@mail.gmail.com>
	<48FEF0E0.7010004@democritos.it>
Message-ID: <cb60cbc40810220245rbef5755v8f510730bd06732e@mail.gmail.com>

On Wed, Oct 22, 2008 at 2:52 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> Sangamesh B wrote:
>
>> *checking for /opt/mpich2_107_GNU/bin/mpif90... no*
>>
>> Why its not detecting mpif90?
>
> either because it is not there,
Its there:
# which mpif90
/opt/mpich2_107_GNU/bin/mpif90

# echo $MPIF90


 or because it is there and
> it doesn't work,
It works:
# mpif90 samplempi.f -o sample
# ./sample
 node           0 : Hello world


or because configure doesn't like the name
> with leading path. Put "/opt/mpich2_107_GNU/bin/" first in
Removed MPIF90=/opt/mpich2_107_GNU/bin/mpif90
> your path and let configure detect "mpif90".
>
$PATH is set to MPICH2_GNU.

>> configure: WARNING: serial/parallel compiler mismatch detected
>> configure: WARNING: parallel compiler  uses gfortran, but serial
>> compiler is /usr/bin/gfortran
>>
>> I'm not getting why its telling mismatch?
>
> again: don't use full paths. I added the warning above for convenience,
> to prevent problems in badly installed machines where mpif90 uses a
> serial compiler that is not the first found in the path. It is just a
> warning, it tells you to pay attention, what do you want more?????
>
>> Earlier, in the same cluster espresso-3.2 was working fine. I think
>> there might be a problem with configure script itself.
>
> then please find the problem, if you can. I am confident that there
> is no problem in the configure.ac script, but it cannot detect all
> configurations on all machines. And please note that configure has
> correctly recognized the pathscale compiler. It is not configure's
> fault if the pathscale compiler is, like 99% of the commercial fortran
> compilers, a piece of crap that cannot correctly compile a moderately
> complex suite of codes. And in any event: Q-E has 1001 pieces, are you
> sure that the one that doesn't work with pathscale is the one you
> absolutely need?
>
After doing the the chamges as suggested by you, also the configure is failing:
# ./configure --enable-mpi | tee config_GNU_412_out
checking build system type... x86_64-unknown-linux-gnu
checking architecture... amd64
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... yes
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /usr/bin/gfortran accepts -g... yes
checking for mpif90... mpif90
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether mpif90 accepts -g... yes
checking version of mpif90... unknown, assuming gfortran
configure: WARNING: serial/parallel compiler mismatch detected
configure: WARNING: parallel compiler mpif90 uses gfortran, but serial
compiler is /usr/bin/gfortran
setting F90... /usr/bin/gfortran
setting MPIF90... mpif90
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc4 accepts -g... yes
checking for /usr/bin/gcc4 option to accept ANSI C... none needed
setting CC... /usr/bin/gcc4
checking how to run the C preprocessor... /lib/cpp
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for int *... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for /usr/bin/gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
setting F77...
using F90... /usr/bin/gfortran
setting FFLAGS... -O
setting F90FLAGS... $(FFLAGS)
setting FFLAGS_NOOPT... -O0
setting CFLAGS... -O3
setting CPP... /lib/cpp
setting CPPFLAGS...
setting LD... mpif90
setting LDFLAGS...
setting AR... ar
setting ARFLAGS... ruv
setting ARFLAGS_DYNAMIC...ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... yes
checking how to get verbose linking output from ... configure:
WARNING: compilation failed

checking for Fortran libraries of ...
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... configure: error: cannot
compile a simple Fortran program
See `config.log' for more details.

What you say?
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Wed Oct 22 11:48:27 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 22 Oct 2008 11:48:27 +0200
Subject: [Pw_forum] QE 4.0.2: configure error
In-Reply-To: <cb60cbc40810220245rbef5755v8f510730bd06732e@mail.gmail.com>
References: <cb60cbc40810192349m3e0e67cdocd25d1d912e352d8@mail.gmail.com>	<48FDA70A.7020508@democritos.it>	<cb60cbc40810210308y7d73a794ie7210257e3d071e8@mail.gmail.com>	<48FDAAC5.4030507@democritos.it>	<cb60cbc40810210330o5712d7adxef5676719201213c@mail.gmail.com>	<48FDB068.5000201@democritos.it>	<cb60cbc40810210421h4591415l1f19c74ef8f63b84@mail.gmail.com>	<48FDCADB.6020705@gmail.com>	<cb60cbc40810212349g41505f40oa6db9eebe5bfa870@mail.gmail.com>	<48FEF0E0.7010004@democritos.it>
	<cb60cbc40810220245rbef5755v8f510730bd06732e@mail.gmail.com>
Message-ID: <48FEF6EB.3010601@democritos.it>

Sangamesh B wrote:

> checking whether /usr/bin/gfortran accepts -g... yes

who told configure to look for /usr/bin/gfortran?
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From mansourehp at gmail.com  Wed Oct 22 13:20:05 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Wed, 22 Oct 2008 14:50:05 +0330
Subject: [Pw_forum] g(r)
Message-ID: <cbe1626b0810220420m794d0623yacc4704c8036770@mail.gmail.com>

Dear all
I used the attached program *(*gofr.f*)* to obtain pair correlation function
plot.but I received an error after compiling it (with  gfortran gofr.f -o
gofr)
the error was:

 In file gofr.f:1

 program gdr_real
 1
Error: Non-numeric character in statement label at (1)
 In file gofr.f:1

 program gdr_real
 1
Error: Unclassifiable statement at (1)

 how can I solve this problem?
Thanks in advance
Mansoureh
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From baroni at sissa.it  Wed Oct 22 16:35:17 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 22 Oct 2008 16:35:17 +0200
Subject: [Pw_forum] g(r)
In-Reply-To: <cbe1626b0810220420m794d0623yacc4704c8036770@mail.gmail.com>
References: <cbe1626b0810220420m794d0623yacc4704c8036770@mail.gmail.com>
Message-ID: <CBE7193B-4CA0-4FC9-A38C-B212F63D8F77@sissa.it>

fortran (f77) instructions have to start in column 7, as any fortran  
manual should clearly states
SB

On Oct 22, 2008, at 1:20 PM, Mansoureh Pashangpour wrote:

> Dear all
> I used the attached program (gofr.f) to obtain pair correlation  
> function plot.but I received an error after compiling it (with   
> gfortran gofr.f -o gofr)
> the error was:
>
>  In file gofr.f:1
>
>  program gdr_real
>  1
> Error: Non-numeric character in statement label at (1)
>  In file gofr.f:1
>
>  program gdr_real
>  1
> Error: Unclassifiable statement at (1)
>
>  how can I solve this problem?
> Thanks in advance
> Mansoureh
> <gofr.f>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html




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From djaithania at hotmail.com  Wed Oct 22 17:08:17 2008
From: djaithania at hotmail.com (hania djani-ait aissa)
Date: Wed, 22 Oct 2008 15:08:17 +0000
Subject: [Pw_forum] need for paper
Message-ID: <BLU115-W26A1F11A91C69F0F70D3EAD2290@phx.gbl>


dears,
can someone provides me the  paper:
K.S. Knight, Ferroelectrics 150, 319 (1993)
i'll be grateful,

hania Djani-ait aissa
phd student
CDTA, Algiers Algeria

_________________________________________________________________
Lancez des recherches en toute s?curit? depuis n'importe quelle page Web. T?l?chargez GRATUITEMENT Windows Live Toolbar aujourd'hui !
http://toolbar.live.com
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From alex.mazheika at gmail.com  Wed Oct 22 17:37:36 2008
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Wed, 22 Oct 2008 18:37:36 +0300
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>
References: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>
Message-ID: <ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>

On Mon, Oct 20, 2008 at 1:41 AM, Agostino Migliore
<amigliore at cmm.upenn.edu>wrote:

> Hello Alex
>
> Since, you have transition metals in your system, it could help you to
> introduce an electronic smearing and then progressively  reduce it until
> you get the solution without any orbital fractional occupations.
> Then, from the attached file I saw that you are using  mixing_beta =
> 0.7D0. Did you try something like mixing_beta = 0.5 or similar (perhaps
> you already did, but I don't know) and also mixing_mode = 'plain'
> (although I know that the local_TF mode may be good for highly
> inhomogeneous systems).
> Finally, your system includes Ti atoms, which have d electrons. Have you
> tried to use the Hubbard U correction scheme implemented in pwscf? Also
> irrespective of your convergence problem, it could provide you with a
> better description of the electronic structure (indeed, I don't have
> direct experience on Ti, but I have on Fe, and the Hubbard U correction
> term works well).
> I hope something I said can help you.
>
> Best regards,
> Agostino Migliore
> CMM, Department of Chemistry, Philadelphia
>
>
> Quoting Alexej Mazheika <alex.mazheika at gmail.com>:
>
> > Dear all
> >
> > I perform the calculations of surface with adsorbed cluster Ag4/TiO2 and
> > have a problem with convergence during SCF-procedure. It does not
> converge.
> > In order to eliminate it I tried the shown methods in the user_guide: to
> > decrease mixing beta, to increase mixing ndim, to increase ecutwfc and
> > ecutrho. But it didn't help me. Is there any other methods to solve such
> > problem? The input file is here attached.
> >
> > Best regards
> > Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
> > Belarus
> >
>
>
> I tried to use mixing_beta 0.3, mixing_ndim 10, mixing_mode = 'local-TF'
and I changed the diagonalization to 'diis'. I performed the calculations
with such parameters: occupations = 'smearing', degauss = 3.7D-3, smearing =
'gaussian'. And then the covergance was achieved.
Thank you for recommendations
Best regards
Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
Belarus
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From giannozz at democritos.it  Wed Oct 22 17:53:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 22 Oct 2008 17:53:33 +0200
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>
References: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>
	<ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>
Message-ID: <48FF4C7D.5060309@democritos.it>

Alexej Mazheika wrote:

> I tried to use mixing_beta 0.3, mixing_ndim 10, mixing_mode = 'local-TF' 
> and I changed the diagonalization to 'diis'. 

really? it doesn't exist any longer, since several versions

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From amigliore at cmm.upenn.edu  Wed Oct 22 20:22:12 2008
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Wed, 22 Oct 2008 14:22:12 -0400 (EDT)
Subject: [Pw_forum] diis?
Message-ID: <1361.130.91.67.155.1224699732.squirrel@cmm.upenn.edu>

> and I changed the diagonalization to 'diis'. I performed the calculations
> with such parameters: occupations = 'smearing', degauss = 3.7D-3,
smearing =
> 'gaussian'. And then the covergance was achieved.
> Thank you for recommendations
> Best regards
> Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
> Belarus

Hello Alex

I am happy to hear that you fixed the problem. On the other hand, let me
say something. For what I know, diis doesn't exist anymore in pwscf, so I
wonder if you are using a very old version of the package or if the
program worked anyway (because of the other instructions) and you got just
a warning in the output file because of that instruction. Anyway, please
give a look at that in the output file. Moreover, if you are interested in
energy, and so on, of the ground state, check if with that smearing you
got integer orbital occupations. You can retrieve this information from a
file in the .save directory or directly from your .out file if you used a
high level of verbosity.

Good work. Best,
Agostino

From paulatto at sissa.it  Wed Oct 22 22:02:04 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 22 Oct 2008 22:02:04 +0200
Subject: [Pw_forum] diis?
In-Reply-To: <1361.130.91.67.155.1224699732.squirrel@cmm.upenn.edu>
References: <1361.130.91.67.155.1224699732.squirrel@cmm.upenn.edu>
Message-ID: <48FF86BC.8010106@sissa.it>

Agostino Migliore ha scritto:
>  You can retrieve this information from a
> file in the .save directory or directly from your .out file if you used a
> high level of verbosity.
>   
With the normal level of verbosity you can simply check the smearing
contribution in the output file: if it is zero or little more you only
have integer occupations, otherwise you have some fractionary occupations.


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From oulihui666 at 126.com  Thu Oct 23 03:28:06 2008
From: oulihui666 at 126.com (oulihui666)
Date: Thu, 23 Oct 2008 09:28:06 +0800 (CST)
Subject: [Pw_forum] Frequency of O2 molecule
Message-ID: <8821561.43091224725286381.JavaMail.coremail@bj126app26.126.com>

 Hello, everyone,

    I have a supercell of 14 atoms, 2 of which are a O2 molecule adsorbed on Pt(111) surface of 12 atoms.
I want to calculate frequencies of adsorbed O2 molecule only, not those for substrate atoms.
My input file is displayed as follows: 
 &INPUTPH
                      outdir = '/home/olh/tmp/' ,
                     recover = .false. ,
                      prefix = 'O2-Pt111,
                       ldisp = .false.,
                       trans = .false.,
                       epsil = .false.,
                    amass(1) = 195.1,
                    amass(2) = 16.0,
                    amass(3) = 16.0,
                        elph = .false.,
                      lraman = .false.,
                        elop = .false.,
                        fpol = .false. ,
                    nat_todo = 3 ,
                      tr2_ph = 1.d-6 ,
                      fildyn = 'O2-Pt111.dynG' ,
 /
0.0 0.0 0.0
13 14

unfortunately,when running, error occurred:
 
    negative rho (up, down):  0.249E-05 0.251E-05
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     reading atoms
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
p0_22191:  p4_error: : 0

How can I do this?

My sincere thanks in advance.

 
 

--

======================================
Lihui Ou
PH.D Candidate in Electrochemistry                      
College of Chemistry and Molecular Science            
Wuhan University,430072,Hubei Province,China 
E-mail:oulihui666 at 126.com
======================================
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From vegalew at hotmail.com  Wed Oct 22 18:47:00 2008
From: vegalew at hotmail.com (vega)
Date: Thu, 23 Oct 2008 00:47:00 +0800
Subject: [Pw_forum] Is there any successfull example to explain the TEM
	images of materials using PWSCF?
Message-ID: <BAY124-DS5EA9CC4617F0B13DF7A1AA4280@phx.gbl>

Dear all,

I found pwscf could explain STM images perfectly, and there were quite a lot examples. But there was very few example
with respect to TEM, which was the most powerful and popular tool for materials research. I wonder whether there would be a way to explain something in TEM images using pwscf. 

thank you for reading. and any hints will be appreciated.

vega

=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
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From lanhaiping at gmail.com  Thu Oct 23 07:28:11 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 23 Oct 2008 13:28:11 +0800
Subject: [Pw_forum] Is there any successfull example to explain the TEM
	images of materials using PWSCF?
In-Reply-To: <BAY124-DS5EA9CC4617F0B13DF7A1AA4280@phx.gbl>
References: <BAY124-DS5EA9CC4617F0B13DF7A1AA4280@phx.gbl>
Message-ID: <c92002fa0810222228t17fea3e9q691eacd9f6c9704b@mail.gmail.com>

Then  , what is you expect ?
as far as i know, TEM can give you some images on structure informations and
morphs .
Then, when  doing simulation with pwscf, these knowledge is
the ABC.

On Thu, Oct 23, 2008 at 12:47 AM, vega <vegalew at hotmail.com> wrote:

>  Dear all,
>
> I found pwscf could explain STM images perfectly, and there were quite a
> lot examples. But there was very few example
> with respect to TEM, which was the most powerful and popular tool for
> materials research. I wonder whether there would be a way to explain
> something in TEM images using pwscf.
>
> thank you for reading. and any hints will be appreciated.
>
> vega
>
>
> =================================================================================
> Vega Lew (weijia liu)
> PH.D Candidate in Chemical Engineering
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From giannozz at democritos.it  Thu Oct 23 08:45:39 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Oct 2008 08:45:39 +0200
Subject: [Pw_forum] Frequency of O2 molecule
In-Reply-To: <8821561.43091224725286381.JavaMail.coremail@bj126app26.126.com>
References: <8821561.43091224725286381.JavaMail.coremail@bj126app26.126.com>
Message-ID: <49001D93.2000601@democritos.it>

oulihui666 wrote:

>                     nat_todo = 3 

calculation required for three atoms...

> 13 14

...that is, atoms 13 and 14.

"There are three types of people in the world:
  those who can count, and those who cannot" :-)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From hthp12 at yahoo.com  Thu Oct 23 10:18:24 2008
From: hthp12 at yahoo.com (Ha, Tran Van)
Date: Thu, 23 Oct 2008 01:18:24 -0700 (PDT)
Subject: [Pw_forum] FFTW in PWscf?
Message-ID: <122423.85558.qm@web38405.mail.mud.yahoo.com>

Dear PWscf Users,
When I compile PWscf by a simple ./configure, then I get:
?
The following libraries have been found:
BLAS_LIBS= -lmkl_ia32
LAPACK_LIBS= -lmkl_ia32
FFT_LIBS=
Please check if this is what you expect.

It seems to be not detected FFT_Lib?
Then I make all, I get binaries with them I tested examples and the results are in good agreement with output in refference but I don't know FFTW is still missing in the binaries or using a FFTW version of the PWscf code instead?
How to correct this?
?
Best Regards,
?

Nam, Tran Van
Hanoi University of Technology
Faculty of Chemistry
Department of Physical Chemistry


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From marzari at MIT.EDU  Thu Oct 23 10:30:50 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 23 Oct 2008 11:30:50 +0300
Subject: [Pw_forum] FFTW in PWscf?
In-Reply-To: <122423.85558.qm@web38405.mail.mud.yahoo.com>
References: <122423.85558.qm@web38405.mail.mud.yahoo.com>
Message-ID: <4900363A.60607@mit.edu>



Dear Tran,

It's using the FFTW distributed with pwscf (2.1.3 ?).

This is usually very good - if you know where your fftw has been
installed, you can specify that directly in the make.sys.

			nicola


Ha, Tran Van wrote:
> Dear PWscf Users,
> When I compile PWscf by a simple ./configure, then I get:
>  
> The following libraries have been found:
> BLAS_LIBS= -lmkl_ia32
> LAPACK_LIBS= -lmkl_ia32
> FFT_LIBS=
> Please check if this is what you expect.
> 
> It seems to be not detected FFT_Lib?
> Then I make all, I get binaries with them I tested examples and the 
> results are in good agreement with output in refference but I don't know 
> FFTW is still missing in the binaries or using a FFTW version of the 
> PWscf code instead?
> How to correct this?


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From njuxuyuehua at gmail.com  Thu Oct 23 10:45:57 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 23 Oct 2008 16:45:57 +0800
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
Message-ID: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>

hi all :
i am calculating the phonon at Q=0, my system is one-dimension , so
strictly,there should be 4 zero-frequency. and my result is 0, 24, 31,
38cm-1,
in order to get better result, i add the  asr, and of course, the above 4
modes change to be 0cm-1, but  another mode at  high frequency,changes from
3002 to 2880cm-1,

the difference is big,   and the pwscf forum give me some information :"if
the dynamical matrix is diagonalized with program dynmat.x imposing the ASR,
[image: $ \omega$] should go much closer to 0, with all other modes
virtually unchanged"
so i am wondering, why the mode at 3002cm-1 has so much change ?

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From jdai3 at mail.ustc.edu.cn  Thu Oct 23 10:52:37 2008
From: jdai3 at mail.ustc.edu.cn (Dai)
Date: Thu, 23 Oct 2008 16:52:37 +0800
Subject: [Pw_forum] FFTW in PWscf?
References: <424750364.02159@ustc.edu.cn>
Message-ID: <424751921.31823@ustc.edu.cn>

i guess you're using the internal copy of fftw, plz check the make.sys file after you did the configure. if you have -D__FFTW -D__USE_INTERNAL_FFTW, that means the the internal copy of FFTW is compiled during your installation.


2008-10-23 



Best regards,
Jun Dai

=============================================================
 Jun Dai
 Ph.D. Candidate,
 Hefei National Laboratory For Physical Sciences at the Microscale,
 University of Science and Technology of China,
 Hefei, Anhui, 230026,
 People's Republic of China
 Tel.: 86-551-3606428
 Fax.: 86-551-3602969
 E-mail: jdai3 at mail.ustc.edu.cn
============================================================= 



???? Ha, Tran Van 
????? 2008-10-23  16:26:04 
???? pw_forum 
??? 
??? [Pw_forum] FFTW in PWscf? 
 
Dear PWscf Users,
When I compile PWscf by a simple ./configure, then I get:

The following libraries have been found:
BLAS_LIBS= -lmkl_ia32
LAPACK_LIBS= -lmkl_ia32
FFT_LIBS=
Please check if this is what you expect.

It seems to be not detected FFT_Lib?
Then I make all, I get binaries with them I tested examples and the results are in good agreement with output in refference but I don't know FFTW is still missing in the binaries or using a FFTW version of the PWscf code instead?
How to correct this?

Best Regards,


Nam, Tran Van
Hanoi University of Technology
Faculty of Chemistry
Department of Physical Chemistry



Get your new Email address! 
Grab the Email name you've always wanted before someone else does! 
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From giannozz at democritos.it  Thu Oct 23 10:59:24 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Oct 2008 10:59:24 +0200
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>
Message-ID: <49003CEC.8090206@democritos.it>

xu yuehua wrote:

> in order to get better result, i add the  asr, and of course, the above 
> 4 modes change to be 0cm-1, but  another mode at  high frequency,changes 
> from 3002 to 2880cm-1

simple ASR should set to zero only the three translation modes, not
4 modes. Are you by any chance using ASR="one-dim" ? did you read this?

!                  - 'one-dim': 3 translational asr + 1 rotational asr
!                  imposed by optimized correction of the dyn. mat. (the
!                  rotation axis is the direction of periodicity; it
!                  will work only if this axis considered is one of
!                  the cartesian axis).

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From njuxuyuehua at gmail.com  Thu Oct 23 11:04:16 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 23 Oct 2008 17:04:16 +0800
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <49003CEC.8090206@democritos.it>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>
	<49003CEC.8090206@democritos.it>
Message-ID: <aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>

yes, my system shoule have 3 translation and 1 rotational mode
so i add ASR="one-dim.

2008/10/23 Paolo Giannozzi <giannozz at democritos.it>

> xu yuehua wrote:
>
> > in order to get better result, i add the  asr, and of course, the above
> > 4 modes change to be 0cm-1, but  another mode at  high frequency,changes
> > from 3002 to 2880cm-1
>
> simple ASR should set to zero only the three translation modes, not
> 4 modes. Are you by any chance using ASR="one-dim" ? did you read this?
>
> !                  - 'one-dim': 3 translational asr + 1 rotational asr
> !                  imposed by optimized correction of the dyn. mat. (the
> !                  rotation axis is the direction of periodicity; it
> !                  will work only if this axis considered is one of
> !                  the cartesian axis).
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at democritos.it  Thu Oct 23 11:11:47 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Oct 2008 11:11:47 +0200
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>	<49003CEC.8090206@democritos.it>
	<aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>
Message-ID: <49003FD3.4090005@democritos.it>

xu yuehua wrote:

> yes, my system shoule have 3 translation and 1 rotational mode
> so i add ASR="one-dim.

then try ASR='simple'. If they differ, and if your system is
along one of the cartesian axis, please provide the dynamical
matrix

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From njuxuyuehua at gmail.com  Thu Oct 23 11:54:38 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 23 Oct 2008 17:54:38 +0800
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <49003FD3.4090005@democritos.it>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>
	<49003CEC.8090206@democritos.it>
	<aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>
	<49003FD3.4090005@democritos.it>
Message-ID: <aca2feb20810230254x45915ce2m793307193bfdb63a@mail.gmail.com>

i try the asr='simple', and the high frequency is almost the same with the
situation not add asr.
my system is   quai-one-dimen , like nanotube ,why i can not add "one-dimen"

2008/10/23 Paolo Giannozzi <giannozz at democritos.it>

> xu yuehua wrote:
>
> > yes, my system shoule have 3 translation and 1 rotational mode
> > so i add ASR="one-dim.
>
> then try ASR='simple'. If they differ, and if your system is
> along one of the cartesian axis, please provide the dynamical
> matrix
>
> Paolo
> --
>  Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From lataprem29 at gmail.com  Thu Oct 23 11:57:07 2008
From: lataprem29 at gmail.com (premlata pandit)
Date: Thu, 23 Oct 2008 15:27:07 +0530
Subject: [Pw_forum] problem in phonon calculation of Na2S
Message-ID: <6f289440810230257y6b9764e1t87605ca82e5dcb8a@mail.gmail.com>

Hi users,
I had some problem in Na2S phonon calculation....
The Acoustic modes are comming somewhat unrelevent. I feel there are some
unusual cross-over also.
If anybody just have a look into the graph and comment on it, whether it is
correct or not? I am also sending the na2s.ph.in and na2s.q2r.in file.... Is
there any other parameters, I have to consider for calculation of phonon for
semiconductors like Na2S??


 Thank you

-- 
Premlata Pandit
Ph.d. student,
Barkatullah university,
Bhopal 462026,
MP, India
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From hthp12 at yahoo.com  Thu Oct 23 13:39:25 2008
From: hthp12 at yahoo.com (Ha, Tran Van)
Date: Thu, 23 Oct 2008 04:39:25 -0700 (PDT)
Subject: [Pw_forum] Intel MPI or OpenMPI?
Message-ID: <498790.94938.qm@web38402.mail.mud.yahoo.com>

Thanks Nicola Marzari??and? Jun Dai for help me about FFTW.
Dear Pwscf Users, I have a problem with my new quadcore Q6600 (I had no problem with my old parrallel machine).
I read the messages from our forum, especially http://www.democritos.it/pipermail/pw_forum/2008-February/subject.html#8280
As Axel Kohlmeyer said,?we can get a speedup of roughly 2.5x to 3.5x from
a quad core cpu over a corresponding single core but to me it's very bad! using one core always run faster all 4 cores (the same with gamma point?also k-point).
I used PWscf 4.0.3, Intel compiler 10.1.018 and OpenMPI 1.2.8. I don't know why? Or I can change into using Intel MPI with my Quadcore?
Thank you in advance for your help.


Nam, Tran Van
Hanoi University of Technology
Faculty of Chemistry
Department of Physical Chemistry


      Get your new Email address!
Grab the Email name you&#39;ve always wanted before someone else does!
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From babderre at physics.auth.gr  Thu Oct 23 13:40:47 2008
From: babderre at physics.auth.gr (babderre at physics.auth.gr)
Date: Thu, 23 Oct 2008 14:40:47 +0300
Subject: [Pw_forum] sum selected PDOS sumpdos.x
Message-ID: <1224762047.490062bfcc006@mail.physics.auth.gr>



 Dear PWSCF users,

I want to sum the pdos of selected atoms with sumpdos.x
could anyone give me an example.

Thanks in advance.

Belabbes
http://parsem.physics.auth.gr/belabbes.htm

From marzari at MIT.EDU  Thu Oct 23 13:45:39 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 23 Oct 2008 14:45:39 +0300
Subject: [Pw_forum] Intel MPI or OpenMPI?
In-Reply-To: <498790.94938.qm@web38402.mail.mud.yahoo.com>
References: <498790.94938.qm@web38402.mail.mud.yahoo.com>
Message-ID: <490063E3.2060605@mit.edu>


Dear Tran,

here are the Q-E tests for CP in a Q6600 :
http://quasiamore.mit.edu/pmwiki/index.php?n=Main.CP90Timings

If you get the same performance, things are running ok.

Always set the system varable OMP_NUM_THREADS to 1, otherwise
perfromance can easily decrease by one order of magnitude, on a 4
core job.

				nicola



Ha, Tran Van wrote:
> Thanks Nicola Marzari  and  Jun Dai for help me about FFTW.
> Dear Pwscf Users, I have a problem with my new quadcore Q6600 (I had no 
> problem with my old parrallel machine).
> I read the messages from our forum, especially 
> http://www.democritos.it/pipermail/pw_forum/2008-February/subject.html#8280
> As *Axel Kohlmeyer* said, we can get a speedup of roughly 2.5x to 3.5x from
> a quad core cpu over a corresponding single core but to me it's very 
> bad! using one core always run faster all 4 cores (the same with gamma 
> point also k-point).
> I used PWscf 4.0.3, Intel compiler 10.1.018 and OpenMPI 1.2.8. I don't 
> know why? Or I can change into using Intel MPI with my Quadcore?
> Thank you in advance for your help.
> 
> 
> Nam, Tran Van
> Hanoi University of Technology
> Faculty of Chemistry
> Department of Physical Chemistry
> 
> 
> ------------------------------------------------------------------------
> Get your preferred Email name! 
> <http://sg.rd.yahoo.com/aa/mail/domainchoice/mail/signature/*http://mail.promotions.yahoo.com/newdomains/aa/> 
> 
> Now you can @ymail.com and @rocketmail.com.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From degironc at sissa.it  Thu Oct 23 14:39:28 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 23 Oct 2008 14:39:28 +0200
Subject: [Pw_forum] problem in phonon calculation of Na2S
In-Reply-To: <6f289440810230257y6b9764e1t87605ca82e5dcb8a@mail.gmail.com>
References: <6f289440810230257y6b9764e1t87605ca82e5dcb8a@mail.gmail.com>
Message-ID: <49007080.70502@sissa.it>

premlata pandit wrote:
> Hi users,
> I had some problem in Na2S phonon calculation....
> The Acoustic modes are comming somewhat unrelevent. I feel there are 
> some unusual cross-over also.
sorry I  don't  understand what you mean by unrelevant ...
the plotting tool is just plotting the phonon bands in order of 
increasing frequency, there is  no symmetry analysis so you do not get 
any level crossing (by definition). If you want a nicer picture use a 
denser grid .
Pay attention to the LO-TO splitting... look for variable epsil in the 
ph.x input.
 
hope this helps,

 Stefano de Gironcoli - SISSA and DEMOCRITOS

> If anybody just have a look into the graph and comment on it, whether 
> it is correct or not? I am also sending the na2s.ph.in 
> <http://na2s.ph.in/> and na2s.q2r.in <http://na2s.q2r.in/> file.... Is 
> there any other parameters, I have to consider for calculation of 
> phonon for semiconductors like Na2S??
>        
>
>  Thank you
>
> -- 
> Premlata Pandit
> Ph.d. student,
> Barkatullah university,
> Bhopal 462026,
> MP, India
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lanhaiping at gmail.com  Thu Oct 23 14:53:13 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 23 Oct 2008 20:53:13 +0800
Subject: [Pw_forum] sum selected PDOS sumpdos.x
In-Reply-To: <1224762047.490062bfcc006@mail.physics.auth.gr>
References: <1224762047.490062bfcc006@mail.physics.auth.gr>
Message-ID: <c92002fa0810230553w69cd5bd7ud0e569f74478bad4@mail.gmail.com>

Dear  Belabbes,
for states related to your selected atoms,
you can give the names of related files, and list these
in asccii file, a name per line.
Then, just run ./sumdos.x -f  states-list >sumdos.txt

good luck
On Thu, Oct 23, 2008 at 7:40 PM, <babderre at physics.auth.gr> wrote:

>
>
>  Dear PWSCF users,
>
> I want to sum the pdos of selected atoms with sumpdos.x
> could anyone give me an example.
>
> Thanks in advance.
>
> Belabbes
> http://parsem.physics.auth.gr/belabbes.htm
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From reboredofa at ornl.gov  Thu Oct 23 14:50:01 2008
From: reboredofa at ornl.gov (Fernando A Reboredo)
Date: Thu, 23 Oct 2008 08:50:01 -0400
Subject: [Pw_forum] postdocs in DFT and QMC
References: <6f289440810230257y6b9764e1t87605ca82e5dcb8a@mail.gmail.com>
	<49007080.70502@sissa.it>
Message-ID: <448601c9350d$dcc90ba0$acf45ba0@ornl.gov>

We are offering two postdoctoral positions in the area of Density Functional 
Theory (DFT) and Quantum Monte Carlo (QMC) in the Theory Group of the 
Materials Science and Technology Division (MSTD) of Oak Ridge National 
Laboratory (ORNL). The appointees will work with the support of a strong 
scientific team, in ORNL and around USA, developing new approximations for 
DFT from QMC generated data in highly inhomogeneous electronic systems. The 
support team includes F. A. Reboredo (MSTD-ORNL), J. Kim (National Center of 
Supercomputer Applications, Urbana-Champain), M. Eisenbach (Center for 
Computational Sciences, ORNL), R. Q. Hood (Lawrence Livermore National 
Laboratory), D. Nicholson (Computer Science and Mathematics-ORNL), P. R. C. 
Kent (CNMS-ORNL), and G. M. Stocks (MSTD-ORNL). In addition, the appointees 
could carry out a second project involving applications of either QMC or DFT 
methods to materials to be discussed among several possibilities according 
with the research interests of the applicants and local funding.



For details on the application process please refer to

QMC http://orise.orau.gov/sep/needs/files/ORNL09-02-MSTD.pdf

DFT http://orise.orau.gov/sep/needs/files/ORNL09-04-MSTD.pdf).

For inquiries contact

Fernando A. Reboredo

at reboredofa at ornl.gov


From giannozz at democritos.it  Thu Oct 23 15:01:13 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Oct 2008 15:01:13 +0200
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <aca2feb20810230254x45915ce2m793307193bfdb63a@mail.gmail.com>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>	<49003CEC.8090206@democritos.it>	<aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>	<49003FD3.4090005@democritos.it>
	<aca2feb20810230254x45915ce2m793307193bfdb63a@mail.gmail.com>
Message-ID: <49007599.1070206@democritos.it>

xu yuehua wrote:

> my system is   quai-one-dimen , like nanotube ,why i can not add "one-dimen"

once again: is your system aligned along the x or y opr z axis?
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From alex.mazheika at gmail.com  Thu Oct 23 15:05:47 2008
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Thu, 23 Oct 2008 16:05:47 +0300
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <48FF4C7D.5060309@democritos.it>
References: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>
	<ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>
	<48FF4C7D.5060309@democritos.it>
Message-ID: <ec86c07d0810230605m33492769nf635c6a784629507@mail.gmail.com>

On Wed, Oct 22, 2008 at 6:53 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> Alexej Mazheika wrote:
>
> > I tried to use mixing_beta 0.3, mixing_ndim 10, mixing_mode = 'local-TF'
> > and I changed the diagonalization to 'diis'.
>
> really? it doesn't exist any longer, since several versions
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


Yes, really. I use the version 4.0.1, there are such options in this
version.

Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
Belarus
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From lifei.edu.cn at gmail.com  Thu Oct 23 15:52:42 2008
From: lifei.edu.cn at gmail.com (=?GB2312?B?wO63yQ==?=)
Date: Thu, 23 Oct 2008 21:52:42 +0800
Subject: [Pw_forum] Fwd: A unexpected band-structure calculation result
In-Reply-To: <538fd6b50810230642g5e55129byae502991c0fb7622@mail.gmail.com>
References: <538fd6b50810230642g5e55129byae502991c0fb7622@mail.gmail.com>
Message-ID: <538fd6b50810230652u21aac9fj5ea7c7954b18b632@mail.gmail.com>

I'm a software engineering student. I'm doing some theoretical physics
calculation work for my thesis recently.  I haven't learned any physics
course and I just read some books.

My targets are band-structure and dos. I got my band-structure calculation
result (http://pkm.yi.org/lf/temp/band.png) yesterday.

I find there is no curve on the left part. Moreover, the band-structure
shows my target material is one of semiconductor ones. but what i want is
some intermediate bands in the a gap. that will show my dopping action make
it work.

Any suggestion (*about pseudo, occupation,CELL_PARAMETERS,ATOMIC_POSITIONS,
K_POINT and all*) is welcomed. Thank you for reply.

My input file begin:

&CONTROL
                 calculation = "scf",
                 pseudo_dir  = "../pseudo",
                 wfcdir      = "../tmp",
                 outdir      = "../out",
                 restart_mode= 'from_scratch',
                 prefix      = 'SrTiO3' ,
                     disk_io = 'minimal' ,
                   verbosity = 'high' ,
                       nstep = 1000 ,
                     tstress = .true. ,
                     tprnfor = .true. ,
                          dt = 100 ,

/
&SYSTEM
                       ibrav = 0,
                         nat = 10,
                        ntyp = 4,
                     ecutwfc = 40 ,
                 occupations = 'tetrahedra' ,
                     degauss = 0.005 ,
                    smearing = 'methfessel-paxton' ,
 /
&electrons
            electron_maxstep = 100,
                    conv_thr = 1E-5 ,
                 startingpot = 'atomic' ,
                 startingwfc = 'atomic' ,
                 mixing_mode = 'plain' ,
                 mixing_beta = 0.2 ,
             diagonalization = 'david' ,
 /
CELL_PARAMETERS cubic
15.104837196  0.00000000  0.00000000
0.0000000000  7.67288736  0.00000000
0.0000000000  0.00000000  7.67288736
ATOMIC_SPECIES
O  15.9994  O.pbe-van_ak.UPF
Ti 47.867   Ti.pbe-sp-van_ak.UPF
Ni 58.6934  Ni.pbe-nd-rrkjus.UPF
Sr 87.62    Sr.pbe-nsp-van.UPF
ATOMIC_POSITIONS (crystal)
O            1.1102230246E-16  5.0000000000E-01  5.0000000000E-01
O            5.0000000000E-01  5.0000000000E-01  5.0000000000E-01
O            2.5667504920E-01  2.2958874039E-41  5.0000000000E-01
O            7.4332495080E-01 -2.2958874039E-41  5.0000000000E-01
O            2.5667504920E-01  5.0000000000E-01  2.2958874039E-41
O            7.4332495080E-01  5.0000000000E-01 -2.2958874039E-41
Ti           2.5625323521E-01  5.0000000000E-01  5.0000000000E-01
Ti           7.4374676479E-01  5.0000000000E-01  5.0000000000E-01
Ni           5.0000000000E-01  0.0000000000E+00  0.0000000000E+00
Sr           1.1102230246E-16  0.0000000000E+00  0.0000000000E+00
K_POINTS  (automatic)
  8 8 8 0 0 0

################################################################################
Band.in
################################################################################
&CONTROL
                 calculation = "bands",
                 pseudo_dir  = "../pseudo",
                 wfcdir      = "../tmp",
                 outdir      = "../out",
                 restart_mode= 'from_scratch',
                 prefix      = 'SrTiO3' ,
                     disk_io = 'minimal' ,
                 wf_collect   = .true.,
                   verbosity = 'high' ,
/
&SYSTEM
                       ibrav = 0,
                         nat = 10,
                        ntyp = 4,
                     ecutwfc = 40 ,
                        nbnd = 60,
                 occupations = 'tetrahedra' ,
                     degauss = 0.005 ,
                    smearing = 'methfessel-paxton' ,
 /
&electrons
                    conv_thr = 1E-5 ,
 /
CELL_PARAMETERS cubic
15.104837196  0.00000000  0.00000000
0.0000000000  7.67288736  0.00000000
0.0000000000  0.00000000  7.67288736
ATOMIC_SPECIES
O  15.9994  O.pbe-van_ak.UPF
Ti 47.867   Ti.pbe-sp-van_ak.UPF
Ni 58.6934  Ni.pbe-nd-rrkjus.UPF
Sr 87.62    Sr.pbe-nsp-van.UPF
ATOMIC_POSITIONS (crystal)
O            1.1102230246E-16  5.0000000000E-01  5.0000000000E-01
O            5.0000000000E-01  5.0000000000E-01  5.0000000000E-01
O            2.5667504920E-01  2.2958874039E-41  5.0000000000E-01
O            7.4332495080E-01 -2.2958874039E-41  5.0000000000E-01
O            2.5667504920E-01  5.0000000000E-01  2.2958874039E-41
O            7.4332495080E-01  5.0000000000E-01 -2.2958874039E-41
Ti           2.5625323521E-01  5.0000000000E-01  5.0000000000E-01
Ti           7.4374676479E-01  5.0000000000E-01  5.0000000000E-01
Ni           5.0000000000E-01  0.0000000000E+00  0.0000000000E+00
Sr           1.1102230246E-16  0.0000000000E+00  0.0000000000E+00
K_POINTS
57
0.5000  0.2500  0.7500 1.0000
0.5000  0.2250  0.6750 1.0000
0.5000  0.2000  0.6000 1.0000
0.5000  0.1750  0.5250 1.0000
0.5000  0.1500  0.4500 1.0000
0.5000  0.1250  0.3750 1.0000
0.5000  0.1000  0.3000 1.0000
0.5000  0.0750  0.2250 1.0000
0.5000  0.0500  0.1500 1.0000
0.5000  0.0250  0.0750 1.0000
0.5000  0.0000  0.0000 1.0000
0.4583  0.0000  0.0000 1.0000
0.4167  0.0000  0.0000 1.0000
0.3750  0.0000  0.0000 1.0000
0.3333  0.0000  0.0000 1.0000
0.2917  0.0000  0.0000 1.0000
0.2500  0.0000  0.0000 1.0000
0.2083  0.0000  0.0000 1.0000
0.1667  0.0000  0.0000 1.0000
0.1250  0.0000  0.0000 1.0000
0.0833  0.0000  0.0000 1.0000
0.0417  0.0000  0.0000 1.0000
0.0000  0.0000  0.0000 1.0000
0.0278  0.0000  0.0278 1.0000
0.0556  0.0000  0.0556 1.0000
0.0833  0.0000  0.0833 1.0000
0.1111  0.0000  0.1111 1.0000
0.1389  0.0000  0.1389 1.0000
0.1667  0.0000  0.1667 1.0000
0.1944  0.0000  0.1944 1.0000
0.2222  0.0000  0.2222 1.0000
0.2500  0.0000  0.2500 1.0000
0.2778  0.0000  0.2778 1.0000
0.3056  0.0000  0.3056 1.0000
0.3333  0.0000  0.3333 1.0000
0.3611  0.0000  0.3611 1.0000
0.3889  0.0000  0.3889 1.0000
0.4167  0.0000  0.4167 1.0000
0.4444  0.0000  0.4444 1.0000
0.4722  0.0000  0.4722 1.0000
0.5000  0.0000  0.5000 1.0000
0.5000  0.0313  0.5313 1.0000
0.5000  0.0625  0.5625 1.0000
0.5000  0.0938  0.5938 1.0000
0.5000  0.1250  0.6250 1.0000
0.5000  0.1563  0.6563 1.0000
0.5000  0.1875  0.6875 1.0000
0.5000  0.2188  0.7188 1.0000
0.5000  0.2500  0.7500 1.0000
0.4375  0.2188  0.6563 1.0000
0.3750  0.1875  0.5625 1.0000
0.3125  0.1563  0.4688 1.0000
0.2500  0.1250  0.3750 1.0000
0.1875  0.0938  0.2813 1.0000
0.1250  0.0625  0.1875 1.0000
0.0625  0.0313  0.0938 1.0000
0.0000  0.0000  0.0000 1.0000
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From giannozz at democritos.it  Thu Oct 23 16:17:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Oct 2008 16:17:40 +0200
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <ec86c07d0810230605m33492769nf635c6a784629507@mail.gmail.com>
References: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>	<ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>	<48FF4C7D.5060309@democritos.it>
	<ec86c07d0810230605m33492769nf635c6a784629507@mail.gmail.com>
Message-ID: <49008784.1040206@democritos.it>

Alexej Mazheika wrote:

> Yes, really. I use the version 4.0.1, there are such options in this 
> version.

well, no. More exactly, there are, but they are fake. Try

   diagonalization='whatever funny algorithm you can think of'

and the code will work. Of course it will not use whatever funny
algorithm you inserted there, but will use the default, i.e.
Davidson diagonalization (with parallel subspace diagonalization).
Only the following keywords do something different from the default:
'cg', 'cg-serial', 'cg+serial', 'david-serial', 'david+serial'.
The documentation is rather unclear on this point.
Anyway: you used Davidson, and that's fine.

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From njuxuyuehua at gmail.com  Thu Oct 23 16:56:23 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 23 Oct 2008 22:56:23 +0800
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <49007599.1070206@democritos.it>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>
	<49003CEC.8090206@democritos.it>
	<aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>
	<49003FD3.4090005@democritos.it>
	<aca2feb20810230254x45915ce2m793307193bfdb63a@mail.gmail.com>
	<49007599.1070206@democritos.it>
Message-ID: <aca2feb20810230756r76e89417k63546f89da33424d@mail.gmail.com>

z axis, the z axis is the rotate axis

2008/10/23 Paolo Giannozzi <giannozz at democritos.it>

> xu yuehua wrote:
>
> > my system is   quai-one-dimen , like nanotube ,why i can not add
> "one-dimen"
>
> once again: is your system aligned along the x or y opr z axis?
> --
>  Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From regassa_dhassa at yahoo.com  Fri Oct 24 08:02:11 2008
From: regassa_dhassa at yahoo.com (Regassa Dhasaa)
Date: Thu, 23 Oct 2008 23:02:11 -0700 (PDT)
Subject: [Pw_forum] takes time but converges
Message-ID: <959295.75730.qm@web62305.mail.re1.yahoo.com>

Sir we are calculating antiferro orthorhmbic face centered (CaMnO3 attached with the mail), but at the biggning of the output it says:
WARNING ...not compatable with FFT or something and shows some matrix. Does this affect the converged result which we found ~2hr later.Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{mso-style-parent:"";
	margin:0in;
	margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	mso-hyphenate:none;
	font-size:12.0pt;
	font-family:"Times New Roman";
	mso-fareast-font-family:"Times New Roman";
	mso-fareast-language:AR-SA;}
@page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.25in 1.0in 1.25in;
	mso-header-margin:.5in;
	mso-footer-margin:.5in;
	mso-paper-source:0;}
div.Section1
	{page:Section1;}
--

The other question is about the
'relax' calculation for FCC (CaMnO3) it starts well by showing some six atomic position relaxations at the output but finnally it says "charge is wrong" and stops. I am starting working with the mixing beta = 0.5. What else can I try?
Sir Is it possible to create simpler G-type antiferro, so that I can reduce the time spent in hours?

Thank you for your response!



      
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From giannozz at democritos.it  Fri Oct 24 08:25:51 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 24 Oct 2008 08:25:51 +0200
Subject: [Pw_forum] takes time but converges
In-Reply-To: <959295.75730.qm@web62305.mail.re1.yahoo.com>
References: <959295.75730.qm@web62305.mail.re1.yahoo.com>
Message-ID: <49016A6F.1040208@democritos.it>

Regassa Dhasaa wrote:

> WARNING ...not compatable with FFT or something and shows some matrix. 
> Does this affect the converged result which we found ~2hr later.

no

> The other question is about the 'relax' calculation for FCC (CaMnO3) it 
> starts well by showing some six atomic position relaxations at the 
> output but finnally it says "charge is wrong" and stops. I am starting 
> working with the mixing beta = 0.5. What else can I try?

gaussian broadening instead of fixed occupations

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Fri Oct 24 08:26:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 24 Oct 2008 08:26:52 +0200
Subject: [Pw_forum] why the ASR change the mode in the high frequency ?
In-Reply-To: <aca2feb20810230756r76e89417k63546f89da33424d@mail.gmail.com>
References: <aca2feb20810230145w7dc7c107n68b9ce7667a459c4@mail.gmail.com>	<49003CEC.8090206@democritos.it>	<aca2feb20810230204k5d2da135j27312fe7e3bda623@mail.gmail.com>	<49003FD3.4090005@democritos.it>	<aca2feb20810230254x45915ce2m793307193bfdb63a@mail.gmail.com>	<49007599.1070206@democritos.it>
	<aca2feb20810230756r76e89417k63546f89da33424d@mail.gmail.com>
Message-ID: <49016AAC.7040700@democritos.it>

xu yuehua wrote:

> z axis, the z axis is the rotate axis

then polease provide the dynamical matrix. Maybe somebody
will have a look at it

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From carl.leblond at iup.edu  Fri Oct 24 14:16:53 2008
From: carl.leblond at iup.edu (Carl R LeBlond)
Date: Fri, 24 Oct 2008 08:16:53 -0400
Subject: [Pw_forum] problems computing cholesky decomposition
Message-ID: <web-4622153@embe2.iup.edu>

Hello - I've seem to run into this cholesky error.  I've attached my 
input file below which when run on a Cray XT3 MPP gives the following 
error (pasted below).  I've tried a number of suggestions I found on 
this forum, however none of them seem to work in my case.  Even 
switching from davidson to cg did not alleviate the problem.  The 
problem began to appear after I increased my k points from 4 4 1 1 1 1 
too 8 8 8 1 1 1.  Any help would be greatly appreciated.  Probably 
something blatantly obvious to a seasoned veteran.
thanks much!
Carl

Carl LeBlond
Assistant Professor of Chemistry
Indiana University of PA
Indiana, PA 15705



......
     G cutoff =  320.4806  ( 961271 G-vectors)     FFT grid: 
(108,108,240)
      G cutoff =  160.2403  ( 339703 G-vectors)  smooth grid: ( 72, 
72,180)

      Largest allocated arrays     est. size (Mb)     dimensions
         Kohn-Sham Wavefunctions         7.00 Mb     (   5331,  86)
         NL pseudopotentials            31.24 Mb     (   5331, 384)
         Each V/rho on FFT grid          5.34 Mb     ( 349920)
         Each G-vector array             0.92 Mb     ( 120159)
         G-vector shells                 0.88 Mb     ( 115730)
      Largest temporary arrays     est. size (Mb)     dimensions
         Auxiliary wavefunctions        55.97 Mb     (   5331, 688)
         Each subspace H/S matrix        7.22 Mb     (    688, 688)
         Each <psi_i|beta_j> matrix      0.50 Mb     (    384,  86)
         Arrays for rho mixing          42.71 Mb     ( 349920,   8)

      Initial potential from superposition of free atoms

      starting charge  143.87569, renormalised to  144.00000

      negative rho (up, down):  0.750E-04 0.000E+00
      Starting wfc are  192 atomic wfcs

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from  pzpotrf  : error #        49
       problems computing cholesky decomposition
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...






####
  &CONTROL
                        title = 'CH4 + Al(111)' ,
                  calculation = 'relax' ,
                   pseudo_dir = '/usr/users/8/leblond/pseudo/',
                   outdir = '/scratcha/leblond/' ,
                       prefix = 'Al111' ,
                      disk_io = 'default' ,
                    verbosity = 'default' ,
                      tprnfor = .true. ,
			nstep = 200 ,
  /
  &SYSTEM
                        ibrav = 0,
                    celldm(1) = 7.65339026,
                          nat = 48,
                         ntyp = 1,
                      ecutwfc = 27.0000000000 ,
                      ecutrho = 216.0000000000 ,
                        nosym = .true. ,
                  occupations = 'smearing' ,
                      degauss = 0.03 ,
                     smearing = 'methfessel-paxton' ,
  /
  &ELECTRONS
             electron_maxstep = 100,
                     conv_thr = 1.0e-08 ,
                  startingpot = 'atomic' ,
                  startingwfc = 'atomic' ,
                  mixing_mode = 'local-TF' ,
                  mixing_beta = 0.300000000 ,
                  mixing_ndim = 8,
              diagonalization = 'david' ,
             diago_david_ndim = 8,
  /
  &IONS
                 ion_dynamics = 'damp' ,	
		trust_radius_max = 0.8D0 ,
		trust_radius_ini = 0.5D0 ,
/
CELL_PARAMETERS hexagonal
2.8284271	0.0000000	0.0000000
1.4142136	2.4494897	0.0000000
2.8284271	0.8164966	-5.7735027
ATOMIC_SPECIES
    Al    26.9815  Al.pbe-rrkj.UPF
ATOMIC_POSITIONS angstrom
Al      0.000000000000000      0.000000000000000 
     0.000000000000000 0 0 0
Al      2.863782463805517      0.000000000000000 
     0.000000000000000 0 0 0
Al      5.727564927611034      0.000000000000000 
     0.000000000000000 0 0 0
Al      8.591347391416551      0.000000000000000 
     0.000000000000000 0 0 0
Al      1.431891231902759      2.480108364567967 
     0.000000000000000 0 0 0
Al      4.295673695708276      2.480108364567967 
     0.000000000000000 0 0 0
Al      7.159456159513793      2.480108364567967 
     0.000000000000000 0 0 0
Al     10.023238623319310      2.480108364567967 
     0.000000000000000 0 0 0
Al      2.863782463805517      4.960216729135935 
     0.000000000000000 0 0 0
Al      5.727564927611034      4.960216729135935 
     0.000000000000000 0 0 0
Al      8.591347391416551      4.960216729135935 
     0.000000000000000 0 0 0
Al     11.455129855222069      4.960216729135935 
     0.000000000000000 0 0 0
Al      4.295673695708276      7.440325093703902 
     0.000000000000000 0 0 0
Al      7.159456159513793      7.440325093703902 
     0.000000000000000 0 0 0
Al     10.023238623319310      7.440325093703902 
     0.000000000000000 0 0 0
Al     12.887021087124827      7.440325093703902 
     0.000000000000000 0 0 0
Al      1.431891231902759      0.826702788189322 
    -2.338268590217984 0 0 0
Al      4.295673695708276      0.826702788189322 
    -2.338268590217984 0 0 0
Al      7.159456159513793      0.826702788189322 
    -2.338268590217984 0 0 0
Al     10.023238623319310      0.826702788189322 
    -2.338268590217984 0 0 0
Al      2.863782463805517      3.306811152757290 
    -2.338268590217984 0 0 0
Al      5.727564927611034      3.306811152757290 
    -2.338268590217984 0 0 0
Al      8.591347391416551      3.306811152757290 
    -2.338268590217984 0 0 0
Al     11.455129855222069      3.306811152757290 
    -2.338268590217984 0 0 0
Al      4.295673695708276      5.786919517325257 
    -2.338268590217984 0 0 0
Al      7.159456159513793      5.786919517325257 
    -2.338268590217984 0 0 0
Al     10.023238623319310      5.786919517325257 
    -2.338268590217984 0 0 0
Al     12.887021087124827      5.786919517325257 
    -2.338268590217984 0 0 0
Al      5.727564927611034      8.267027881893224 
    -2.338268590217984 0 0 0
Al      8.591347391416551      8.267027881893224 
    -2.338268590217984 0 0 0
Al     11.455129855222069      8.267027881893224 
    -2.338268590217984 0 0 0
Al     14.318912319027586      8.267027881893224 
    -2.338268590217984 0 0 0
Al      2.863782463805517      1.653405576378645 
    -4.676537180435969 1 1 1
Al      5.727564927611034      1.653405576378645 
    -4.676537180435969 1 1 1
Al      8.591347391416551      1.653405576378645 
    -4.676537180435969 1 1 1
Al     11.455129855222069      1.653405576378645 
    -4.676537180435969 1 1 1
Al      4.295673695708276      4.133513940946612 
    -4.676537180435969 1 1 1
Al      7.159456159513793      4.133513940946612 
    -4.676537180435969 1 1 1
Al     10.023238623319310      4.133513940946612 
    -4.676537180435969 1 1 1
Al     12.887021087124827      4.133513940946612 
    -4.676537180435969 1 1 1
Al      5.727564927611034      6.613622305514579 
    -4.676537180435969 1 1 1
Al      8.591347391416551      6.613622305514579 
    -4.676537180435969 1 1 1
Al     11.455129855222069      6.613622305514579 
    -4.676537180435969 1 1 1
Al     14.318912319027586      6.613622305514579 
    -4.676537180435969 1 1 1
Al      7.159456159513793      9.093730670082547 
    -4.676537180435969 1 1 1
Al     10.023238623319310      9.093730670082547 
    -4.676537180435969 1 1 1
Al     12.887021087124827      9.093730670082547 
    -4.676537180435969 1 1 1
Al     15.750803550930344      9.093730670082547 
    -4.676537180435969 1 1 1
K_POINTS automatic
   8 8 8   1 1 1
######

From akohlmey at cmm.chem.upenn.edu  Fri Oct 24 17:18:54 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 24 Oct 2008 11:18:54 -0400 (EDT)
Subject: [Pw_forum] problems computing cholesky decomposition
In-Reply-To: <web-4622153@embe2.iup.edu>
References: <web-4622153@embe2.iup.edu>
Message-ID: <Pine.LNX.4.64.0810241105180.2352@localhost.localdomain>

On Fri, 24 Oct 2008, Carl R LeBlond wrote:

hello carl,


CL> Hello - I've seem to run into this cholesky error.  I've attached my 
CL> input file below which when run on a Cray XT3 MPP gives the following 
CL> error (pasted below).  I've tried a number of suggestions I found on 

there are a number of details missing to have a full assessment of
the situation. how did you compile the code (compilers, libraries) 
and which version or Q-E?

i remember that some versions of ACML have problems and also
PGI is not exactly known as a reliable compiler...

i presume you are running on the PSC machine, right? 
they have multiple compiler versions and ACLM versions
selectable as "modules". their defaults are usually 
overly conservative. :-( 

CL> this forum, however none of them seem to work in my case.  Even 
CL> switching from davidson to cg did not alleviate the problem.  The 
CL> problem began to appear after I increased my k points from 4 4 1 1 1 1 
CL> too 8 8 8 1 1 1.  Any help would be greatly appreciated.  Probably 
CL> something blatantly obvious to a seasoned veteran.


i made a check on a different machine, and your input runs
fine for me, so it is not an intrinsic problem of the input
or the code, but more likely related to libraries and compiler.

you may want to check out using disk_io='none' and 
wf_collect=.true. for optimal use of resources.

also it looks as if you don't take advantage of the 
-npools flag. which should help speeding up things 
even more. the G-space parallelization is far less
efficient than parallelizing over k-space (and you
have a lot of k-points to parallelize over).

cheers,
   axel.


CL> thanks much!
CL> Carl
CL> 
CL> Carl LeBlond
CL> Assistant Professor of Chemistry
CL> Indiana University of PA
CL> Indiana, PA 15705
CL> 
CL> 
CL> 
CL> ......
CL>      G cutoff =  320.4806  ( 961271 G-vectors)     FFT grid: 
CL> (108,108,240)
CL>       G cutoff =  160.2403  ( 339703 G-vectors)  smooth grid: ( 72, 
CL> 72,180)
CL> 
CL>       Largest allocated arrays     est. size (Mb)     dimensions
CL>          Kohn-Sham Wavefunctions         7.00 Mb     (   5331,  86)
CL>          NL pseudopotentials            31.24 Mb     (   5331, 384)
CL>          Each V/rho on FFT grid          5.34 Mb     ( 349920)
CL>          Each G-vector array             0.92 Mb     ( 120159)
CL>          G-vector shells                 0.88 Mb     ( 115730)
CL>       Largest temporary arrays     est. size (Mb)     dimensions
CL>          Auxiliary wavefunctions        55.97 Mb     (   5331, 688)
CL>          Each subspace H/S matrix        7.22 Mb     (    688, 688)
CL>          Each <psi_i|beta_j> matrix      0.50 Mb     (    384,  86)
CL>          Arrays for rho mixing          42.71 Mb     ( 349920,   8)
CL> 
CL>       Initial potential from superposition of free atoms
CL> 
CL>       starting charge  143.87569, renormalised to  144.00000
CL> 
CL>       negative rho (up, down):  0.750E-04 0.000E+00
CL>       Starting wfc are  192 atomic wfcs
CL> 
CL>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
CL>       from  pzpotrf  : error #        49
CL>        problems computing cholesky decomposition
CL>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
CL> 
CL>       stopping ...
CL> 
CL> 
CL> 
CL> 
CL> 
CL> 
CL> ####
CL>   &CONTROL
CL>                         title = 'CH4 + Al(111)' ,
CL>                   calculation = 'relax' ,
CL>                    pseudo_dir = '/usr/users/8/leblond/pseudo/',
CL>                    outdir = '/scratcha/leblond/' ,
CL>                        prefix = 'Al111' ,
CL>                       disk_io = 'default' ,
CL>                     verbosity = 'default' ,
CL>                       tprnfor = .true. ,
CL> 			nstep = 200 ,
CL>   /
CL>   &SYSTEM
CL>                         ibrav = 0,
CL>                     celldm(1) = 7.65339026,
CL>                           nat = 48,
CL>                          ntyp = 1,
CL>                       ecutwfc = 27.0000000000 ,
CL>                       ecutrho = 216.0000000000 ,
CL>                         nosym = .true. ,
CL>                   occupations = 'smearing' ,
CL>                       degauss = 0.03 ,
CL>                      smearing = 'methfessel-paxton' ,
CL>   /
CL>   &ELECTRONS
CL>              electron_maxstep = 100,
CL>                      conv_thr = 1.0e-08 ,
CL>                   startingpot = 'atomic' ,
CL>                   startingwfc = 'atomic' ,
CL>                   mixing_mode = 'local-TF' ,
CL>                   mixing_beta = 0.300000000 ,
CL>                   mixing_ndim = 8,
CL>               diagonalization = 'david' ,
CL>              diago_david_ndim = 8,
CL>   /
CL>   &IONS
CL>                  ion_dynamics = 'damp' ,	
CL> 		trust_radius_max = 0.8D0 ,
CL> 		trust_radius_ini = 0.5D0 ,
CL> /
CL> CELL_PARAMETERS hexagonal
CL> 2.8284271	0.0000000	0.0000000
CL> 1.4142136	2.4494897	0.0000000
CL> 2.8284271	0.8164966	-5.7735027
CL> ATOMIC_SPECIES
CL>     Al    26.9815  Al.pbe-rrkj.UPF
CL> ATOMIC_POSITIONS angstrom
CL> Al      0.000000000000000      0.000000000000000 
CL>      0.000000000000000 0 0 0
CL> Al      2.863782463805517      0.000000000000000 
CL>      0.000000000000000 0 0 0
CL> Al      5.727564927611034      0.000000000000000 
CL>      0.000000000000000 0 0 0
CL> Al      8.591347391416551      0.000000000000000 
CL>      0.000000000000000 0 0 0
CL> Al      1.431891231902759      2.480108364567967 
CL>      0.000000000000000 0 0 0
CL> Al      4.295673695708276      2.480108364567967 
CL>      0.000000000000000 0 0 0
CL> Al      7.159456159513793      2.480108364567967 
CL>      0.000000000000000 0 0 0
CL> Al     10.023238623319310      2.480108364567967 
CL>      0.000000000000000 0 0 0
CL> Al      2.863782463805517      4.960216729135935 
CL>      0.000000000000000 0 0 0
CL> Al      5.727564927611034      4.960216729135935 
CL>      0.000000000000000 0 0 0
CL> Al      8.591347391416551      4.960216729135935 
CL>      0.000000000000000 0 0 0
CL> Al     11.455129855222069      4.960216729135935 
CL>      0.000000000000000 0 0 0
CL> Al      4.295673695708276      7.440325093703902 
CL>      0.000000000000000 0 0 0
CL> Al      7.159456159513793      7.440325093703902 
CL>      0.000000000000000 0 0 0
CL> Al     10.023238623319310      7.440325093703902 
CL>      0.000000000000000 0 0 0
CL> Al     12.887021087124827      7.440325093703902 
CL>      0.000000000000000 0 0 0
CL> Al      1.431891231902759      0.826702788189322 
CL>     -2.338268590217984 0 0 0
CL> Al      4.295673695708276      0.826702788189322 
CL>     -2.338268590217984 0 0 0
CL> Al      7.159456159513793      0.826702788189322 
CL>     -2.338268590217984 0 0 0
CL> Al     10.023238623319310      0.826702788189322 
CL>     -2.338268590217984 0 0 0
CL> Al      2.863782463805517      3.306811152757290 
CL>     -2.338268590217984 0 0 0
CL> Al      5.727564927611034      3.306811152757290 
CL>     -2.338268590217984 0 0 0
CL> Al      8.591347391416551      3.306811152757290 
CL>     -2.338268590217984 0 0 0
CL> Al     11.455129855222069      3.306811152757290 
CL>     -2.338268590217984 0 0 0
CL> Al      4.295673695708276      5.786919517325257 
CL>     -2.338268590217984 0 0 0
CL> Al      7.159456159513793      5.786919517325257 
CL>     -2.338268590217984 0 0 0
CL> Al     10.023238623319310      5.786919517325257 
CL>     -2.338268590217984 0 0 0
CL> Al     12.887021087124827      5.786919517325257 
CL>     -2.338268590217984 0 0 0
CL> Al      5.727564927611034      8.267027881893224 
CL>     -2.338268590217984 0 0 0
CL> Al      8.591347391416551      8.267027881893224 
CL>     -2.338268590217984 0 0 0
CL> Al     11.455129855222069      8.267027881893224 
CL>     -2.338268590217984 0 0 0
CL> Al     14.318912319027586      8.267027881893224 
CL>     -2.338268590217984 0 0 0
CL> Al      2.863782463805517      1.653405576378645 
CL>     -4.676537180435969 1 1 1
CL> Al      5.727564927611034      1.653405576378645 
CL>     -4.676537180435969 1 1 1
CL> Al      8.591347391416551      1.653405576378645 
CL>     -4.676537180435969 1 1 1
CL> Al     11.455129855222069      1.653405576378645 
CL>     -4.676537180435969 1 1 1
CL> Al      4.295673695708276      4.133513940946612 
CL>     -4.676537180435969 1 1 1
CL> Al      7.159456159513793      4.133513940946612 
CL>     -4.676537180435969 1 1 1
CL> Al     10.023238623319310      4.133513940946612 
CL>     -4.676537180435969 1 1 1
CL> Al     12.887021087124827      4.133513940946612 
CL>     -4.676537180435969 1 1 1
CL> Al      5.727564927611034      6.613622305514579 
CL>     -4.676537180435969 1 1 1
CL> Al      8.591347391416551      6.613622305514579 
CL>     -4.676537180435969 1 1 1
CL> Al     11.455129855222069      6.613622305514579 
CL>     -4.676537180435969 1 1 1
CL> Al     14.318912319027586      6.613622305514579 
CL>     -4.676537180435969 1 1 1
CL> Al      7.159456159513793      9.093730670082547 
CL>     -4.676537180435969 1 1 1
CL> Al     10.023238623319310      9.093730670082547 
CL>     -4.676537180435969 1 1 1
CL> Al     12.887021087124827      9.093730670082547 
CL>     -4.676537180435969 1 1 1
CL> Al     15.750803550930344      9.093730670082547 
CL>     -4.676537180435969 1 1 1
CL> K_POINTS automatic
CL>    8 8 8   1 1 1
CL> ######
CL> _______________________________________________
CL> Pw_forum mailing list
CL> Pw_forum at pwscf.org
CL> http://www.democritos.it/mailman/listinfo/pw_forum
CL> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From alex.mazheika at gmail.com  Sat Oct 25 00:00:13 2008
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Sat, 25 Oct 2008 02:00:13 +0400
Subject: [Pw_forum] problem with convergence during SCF-procedure
In-Reply-To: <49008784.1040206@democritos.it>
References: <3085.130.91.67.155.1224456066.squirrel@cmm.upenn.edu>
	<ec86c07d0810220837q54997d19tad19f75b2d7b81d4@mail.gmail.com>
	<48FF4C7D.5060309@democritos.it>
	<ec86c07d0810230605m33492769nf635c6a784629507@mail.gmail.com>
	<49008784.1040206@democritos.it>
Message-ID: <ec86c07d0810241500m67d35893ydcc59aaa595f702@mail.gmail.com>

On 10/23/08, Paolo Giannozzi <giannozz at democritos.it> wrote:
>
> Alexej Mazheika wrote:
>
> > Yes, really. I use the version 4.0.1, there are such options in this
> > version.
>
>
> well, no. More exactly, there are, but they are fake. Try
>
>    diagonalization='whatever funny algorithm you can think of'
>
> and the code will work. Of course it will not use whatever funny
> algorithm you inserted there, but will use the default, i.e.
> Davidson diagonalization (with parallel subspace diagonalization).
> Only the following keywords do something different from the default:
> 'cg', 'cg-serial', 'cg+serial', 'david-serial', 'david+serial'.
> The documentation is rather unclear on this point.
> Anyway: you used Davidson, and that's fine.
>
> Paolo
>
> --
>
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________


I use the program PWGUI for the building of my input files. There is the
keyword 'diis' in PWGUI, and so I thought that
such algorithm is present in Espresso-4.0.1 too. During the
calculations it does not write anything about 'unrecognized word' both
in output file and in Linux-console, so I really considered that the
'diis' algorithm is embedded in Espresso. Then it means that the
changing of occupation
and mixing data helped to solve the problem with covergance. That's fine.

Alex Mazheika, Research Institute for phys. and chem. problems, Minsk,
Belarus
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From beaudet at illinois.edu  Sat Oct 25 02:25:29 2008
From: beaudet at illinois.edu (beaudet at illinois.edu)
Date: Fri, 24 Oct 2008 19:25:29 -0500 (CDT)
Subject: [Pw_forum] post processing with occupations defined from input
Message-ID: <20081024192529.BLU69874@expms2.cites.uiuc.edu>

pwscf users,

I'm usinge QE 4.0. I've done scf (pw.x) calculations at on a molecule (25 bohr cube, gamma point only) where I have defined the occupations, i.e. occupations = 'from_input'. I would like to visualize the molecular orbitals. My input file for pp.x is as follows:

&INPUTPP
   prefix        = 'filename',
   outdir        = '.',
   plot_num      = 7,
   kband         = 1,
/
&PLOT
   iflag         = 3,
   output_format = 3,
/

However I get the following error:


     Program POST-PROC v.4.0    starts ...
     Today is 24Oct2008 at 18:52:21 

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from postproc : error #         1
     Post-processing with constrained magnetization is not available yet
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Is there a workaround for this?

Thanks

Todd Beaudet

From yuminqian at gmail.com  Sun Oct 26 02:48:23 2008
From: yuminqian at gmail.com (yumin qian)
Date: Sun, 26 Oct 2008 09:48:23 +0800
Subject: [Pw_forum] pseudopotentials type
Message-ID: <aa128b2c0810251848k1504873an6c0bc0485fa24c63@mail.gmail.com>

>
>  generally pseudopotetials can be divided into two classes GGA and LDA  by
> the exchange correlation   type,but there are many way to do it .the mostly
> used form are  USPP , NCPP ; TM,HGH, etc.

   My question are
   1   How to discern the downloaded psudopotentials from the PWSCF web site
,is it GGA  or LDA?
   2   Can I mix NCPP with USPP or PAW, or mix TM with HGH ,for different
types of atom in a multi-type atoms crystal calculation ?





-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From akohlmey at cmm.chem.upenn.edu  Sun Oct 26 03:44:16 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 25 Oct 2008 22:44:16 -0400 (EDT)
Subject: [Pw_forum] pseudopotentials type
In-Reply-To: <aa128b2c0810251848k1504873an6c0bc0485fa24c63@mail.gmail.com>
References: <aa128b2c0810251848k1504873an6c0bc0485fa24c63@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0810252237380.2352@localhost.localdomain>

On Sun, 26 Oct 2008, yumin qian wrote:

YQ> >
YQ> >  generally pseudopotetials can be divided into two classes GGA and LDA  by
YQ> > the exchange correlation   type,but there are many way to do it .the mostly
YQ> > used form are  USPP , NCPP ; TM,HGH, etc.
YQ> 
YQ>    My question are
YQ>    1   How to discern the downloaded psudopotentials from the PWSCF web site
YQ> ,is it GGA  or LDA?

by looking at the name or inspecting the functional code in the 
PP_HEADER section. if you have the NOGX and NOGC flags set, you
have an LDA type pseudopotential.

YQ>    2   Can I mix NCPP with USPP or PAW, or mix TM with HGH ,for different
YQ> types of atom in a multi-type atoms crystal calculation ?

please have a closer look at the F.A.Q. in the quantum espresso wiki
at http://www.quantum-espresso.org/

axel.


YQ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From akohlmey at cmm.chem.upenn.edu  Sun Oct 26 04:12:37 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 25 Oct 2008 23:12:37 -0400 (EDT)
Subject: [Pw_forum] post processing with occupations defined from input
In-Reply-To: <20081024192529.BLU69874@expms2.cites.uiuc.edu>
References: <20081024192529.BLU69874@expms2.cites.uiuc.edu>
Message-ID: <Pine.LNX.4.64.0810251225120.2352@localhost.localdomain>

On Fri, 24 Oct 2008, beaudet at illinois.edu wrote:

todd,

TB> pwscf users,
TB> 
TB> I'm usinge QE 4.0. I've done scf (pw.x) calculations at on a 
TB> molecule (25 bohr cube, gamma point only) where I have defined the 
TB> occupations, i.e. occupations = 'from_input'. I would like to 
TB> visualize the molecular orbitals. My input file for pp.x is as 
TB> follows:

TB>      Program POST-PROC v.4.0    starts ...
TB>      Today is 24Oct2008 at 18:52:21 
TB> 
TB>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
TB>      from postproc : error #         1
TB>      Post-processing with constrained magnetization is not available yet
TB>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
TB> 
TB>      stopping ...
TB> 
TB> Is there a workaround for this?

you mean other than implementing it yourself??

the question is, do you _need_ to set the occupations explicitly?

if yes, then you can take advantage of using open source software, 
and you have the great opportunity to make something good better.

cheers,
   axel.

TB> 
TB> Thanks
TB> 
TB> Todd Beaudet
TB> _______________________________________________
TB> Pw_forum mailing list
TB> Pw_forum at pwscf.org
TB> http://www.democritos.it/mailman/listinfo/pw_forum
TB> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From giannozz at democritos.it  Sun Oct 26 19:29:49 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 26 Oct 2008 19:29:49 +0100
Subject: [Pw_forum] pseudopotentials type
In-Reply-To: <aa128b2c0810251848k1504873an6c0bc0485fa24c63@mail.gmail.com>
References: <aa128b2c0810251848k1504873an6c0bc0485fa24c63@mail.gmail.com>
Message-ID: <553DD37F-4145-421D-892E-B275481936B6@democritos.it>


On Oct 26, 2008, at 2:48 , yumin qian wrote:

>  generally pseudopotetials can be divided into two classes GGA and LDA
>  by the exchange correlation   type,but there are many way to do it .
>  the mostly used form are  USPP , NCPP ; TM,HGH, etc.

please do not confuse
- the XC functional upon which a PP is based
- the different types of pseudization (ultrasoft/normconserving)
- the different ways to produce a required type of pseudization
(TM, RRKJ, HGH etc)
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From giannozz at democritos.it  Mon Oct 27 09:42:26 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 27 Oct 2008 09:42:26 +0100
Subject: [Pw_forum] post processing with occupations defined from input
In-Reply-To: <20081024192529.BLU69874@expms2.cites.uiuc.edu>
References: <20081024192529.BLU69874@expms2.cites.uiuc.edu>
Message-ID: <49057EF2.3080200@democritos.it>

beaudet at illinois.edu wrote:

>      from postproc : error #         1
>      Post-processing with constrained magnetization is not available yet
>[...] 
> Is there a workaround for this?

implement what is missing, or else try to remove the check and see what
happens. Maybe the specific plot you are interested in will display
correctly (or maybe not, or maybe the code will crash)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From lily_physics at yahoo.com.sg  Mon Oct 27 16:26:26 2008
From: lily_physics at yahoo.com.sg (Lily Anh)
Date: Mon, 27 Oct 2008 22:26:26 +0700 (ICT)
Subject: [Pw_forum] Bond analysis through Born effective charges calculation
Message-ID: <945165.72352.qm@web76104.mail.sg1.yahoo.com>

Dear all,
I am doing a high pressure study on CaO and I want to investigate the bond property under compression. The Born effective tensor of cubic CaO has only one independent component. The Born effective charge for Ca are larger than 2 and increase with pressure. Does this mean the bond become more ionic or more covalent? 
Any reply will be appreciated.
Thanks and regards.
Lily



      Get your new Email address!
Grab the Email name you&#39;ve always wanted before someone else does!
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From beaudet at illinois.edu  Mon Oct 27 20:42:54 2008
From: beaudet at illinois.edu (beaudet at illinois.edu)
Date: Mon, 27 Oct 2008 14:42:54 -0500 (CDT)
Subject: [Pw_forum] post processing with occupations defined from input
Message-ID: <20081027144254.BLX54851@expms2.cites.uiuc.edu>

I had tried commenting out the check and recompiling. However, pp.x still another error (I forget what it was).

Todd Beaudet

---- Original message ----
>Date: Mon, 27 Oct 2008 09:42:26 +0100
>From: Paolo Giannozzi <giannozz at democritos.it>  
>Subject: Re: [Pw_forum] post processing with occupations defined from input  
>To: PWSCF Forum <pw_forum at pwscf.org>
>
>beaudet at illinois.edu wrote:
>
>>      from postproc : error #         1
>>      Post-processing with constrained magnetization is not available yet
>>[...] 
>> Is there a workaround for this?
>
>implement what is missing, or else try to remove the check and see what
>happens. Maybe the specific plot you are interested in will display
>correctly (or maybe not, or maybe the code will crash)
>
>Paolo
>-- 
>Paolo Giannozzi, Democritos and University of Udine, Italy
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum

From ding.y1ding at gmail.com  Tue Oct 28 08:27:35 2008
From: ding.y1ding at gmail.com (ding yi)
Date: Tue, 28 Oct 2008 15:27:35 +0800
Subject: [Pw_forum] a bug in the bands_FS.f90
Message-ID: <b06ffd370810280027v7629b447u62cfe8af066b235c@mail.gmail.com>

I find that there is a mistake in the bands_FS.f90. In the bands_FS.f90,
line 310," backspace(5) " should be replace by "! back nlines+1 positions
(number of eigenvalues lines plus one blank line) ! do k=1,nlines+1
backspace(5) enddo !
"
The bands_FS counts the lines of the spin-polarized calculations, while for
the non-spin-polarised case it forgets to counts.


Yi Ding, Ph.D Candidate Department of Physics, Tsinghua University Beijing
100084, P.R.China
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From lily_physics at yahoo.com.sg  Tue Oct 28 08:43:12 2008
From: lily_physics at yahoo.com.sg (Lily Anh)
Date: Tue, 28 Oct 2008 15:43:12 +0800 (SGT)
Subject: [Pw_forum] Bond property analysis through Born effective charges
	calculation
Message-ID: <335114.34813.qm@web76104.mail.sg1.yahoo.com>

Dear all,

I am doing a high pressure study on CaO and I want to investigate the bond property under compression. The Born effective tensor of cubic CaO has only one independent component. The Born effective charge for Ca are larger than the nominal ionic charge +2 and increase with pressure. Does this mean the bond become more ionic or more covalent?  Since the it increase with pressure, can we say that more charge transfer from Ca to O in this case?
Any reply will be appreciated.
Thanks and regards.
Lily


      Try cool new skins, plus more space for friends. 
Download Singapore Yahoo! Messenger now!
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From giannozz at democritos.it  Tue Oct 28 08:48:54 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Oct 2008 08:48:54 +0100
Subject: [Pw_forum] Bond property analysis through Born effective
 charges calculation
In-Reply-To: <335114.34813.qm@web76104.mail.sg1.yahoo.com>
References: <335114.34813.qm@web76104.mail.sg1.yahoo.com>
Message-ID: <4906C3E6.50709@democritos.it>

Lily Anh wrote:

> I am doing a high pressure study on CaO and I want to investigate the 
> bond property under compression. The Born effective tensor of cubic CaO 
> has only one independent component. The Born effective charge for Ca are 
> larger than the nominal ionic charge +2 and increase with pressure. Does 
> this mean the bond become more ionic or more covalent?  Since the it 
> increase with pressure, can we say that more charge transfer from Ca to 
> O in this case?

effective charges are dynamical quantities, expressing the response to
a perturbation, and should not be identified with ionicity, a static
quantity expressing the amount of charge around an atom. More in the
relevant literature

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From yuminqian at gmail.com  Tue Oct 28 10:12:41 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 28 Oct 2008 17:12:41 +0800
Subject: [Pw_forum] Raman and IR spectral
Message-ID: <aa128b2c0810280212p5ea6c6f2mf2ddf35e9786c457@mail.gmail.com>

>
>
>  Dear Prof.

    I have encontered a problems in calculation of Raman and IR spectroscopy
,using ph.x
    the crystal is metallic, so it can not be done ,
   1 Why the IR or Raman calcualtion should only limited to the insulating
system .
   2 How should I do if the system is metallic.



-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From bilica at ihpc.a-star.edu.sg  Tue Oct 28 12:46:23 2008
From: bilica at ihpc.a-star.edu.sg (Ante Bilic)
Date: Tue, 28 Oct 2008 19:46:23 +0800
Subject: [Pw_forum] phonon dispersion jagged
In-Reply-To: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB53@shared-svc-exch.shared-svc.local>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB47@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4A@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4C@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB50@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB51@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB53@shared-svc-exch.shared-svc.local>
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB5A@shared-svc-exch.shared-svc.local>

Hello,

I've tried to calculate the phonon spectrum of a cubic perovskite
using PWSCF. All the input files (and *.freq output)  are in the
attached archive. Basically, I followed the AlAs example06 that is
provided with the distribution. At first I used the 4x4x4 grid to evaluate
the density matrices. The calculated dispersion curves were in
very good agreement with those in the literature, except they look
shockingly ugly! For some reason they are not smooth, but rather
jagged. I thought a denser mesh might fix that so I tried 6x6x6, and
then 8x8x8 but the curves looked just as ugly (if not uglier).

I believe the SCF calculation for the bulk was of a good quality, with ecut=36.4 Ry,
and ecutrho=300 Ry, k-point grid was 6x6x6, and all the convergency
requirements were rather strict, for both SCF and phonon calculations.

Could you please have a look into the provided files, perhaps you can spot
some inappropriate settings etc.

Thanks in anticipation,
-Ante

This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
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From nakhmanson at anl.gov  Tue Oct 28 16:44:05 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 28 Oct 2008 10:44:05 -0500
Subject: [Pw_forum] My phonon dispersion curves are jagged too
Message-ID: <49073345.2070207@anl.gov>

Dear All,

I am learning how to compute phonon dispersion curves across the BZ and
right now I am trying to reproduce the results of a simple calculation
for cubic perovskites that Philippe, Karin and company have done a long
time ago [PRB 60, 836 (1999)].

I take cubic (Pm-3m) PbTiO3 five-atom cell relaxed to zero forces (these
are exactly zero by symmetry) and stresses, and compute DM(k) on a 6x6x6
k-point grid. Going from Gamma to X (0,0,1/2), such grid gives 0, 1/6,
2/6, 3/6 = 1/2.

I do the Gamma --> X --> M --> Gamma --> R BZ route (see the middle panel
of Fig 1). The grid used in the paper is a bit worse than mine but all
the dispersion curves are smooth with no breaks anywhere.

Again, after I get all the DM(k) on the grid, I FFT them into an IFCM(r),
which can be used to compute phonons at any k-point. I use it to draw the
dispersion curves. Here's what I get (this is a 2.7 Mb file):

http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_GXMGR.pdf

or the xmgrace source (~1Mb):

http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_GXMGR.xmgr

Here the dispersion curves between each pair of high-symmetry k-points are
computed using IFCM(r) on a grid of a 1000 k-points (which is probably an
insane resolution that works out just for this tiny sample calculation)
without any interpolations involved. As you can see, there are numerous
"breaks" in the dispersion curves, which are aligned vertically at certain
k-points. The one at ~100 cm-1 around M-point looks pretty ugly. My
impression is that breaks happen at k-points where two levels cross each
other, i.e., my DM(k) has some degenerate eigenvalues (of certain symmetry?),
which suggests a numerical instability in a routine that diagonalizes the DMs
or, possibly, a routine that constructs the DM(k) prior to its diagonalization.

So my question is: are such breaks in dispersion curves something to be
expected or something unusual? If the former is true, then I'm wondering
what kind of postprocessing I should do to get rid of them and produce nice
plots? For example, are coarser grids (say 20 points instead of 1000) +
spline interpolation the method of choice?

If the latter is true, the problem could be in my lapack library. I am
using ifort 10.1.015 with MKL 10.0.4.023 and FFTW 2.1.5 to compile
matdyn.x; make.sys is here:

http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/make.sys

but I will now try linking against something else to see if this problem
goes away.

My whole calculation (pw_scf+ph+q2r+matdyn+xmgrace_plot) is here:

http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_phonon_dispersion.tgz

I have asked a few friends about that, and the general consensus is that
such breaks in dispersion curves should not happen no matter what. However,
since many members of this forum are experts in such calculations, I would
very much appreciate your comments on this.

Finally, PLZ note that the lattice consts here and in Philippe's paper
are used in a somewhat different spirit, so that I am not worried
too much that our results are not identical.

Thank you very much,

Serge


-- 
*********************************************************
   Serge M. Nakhmanson               phone: (630) 252-5205
   Assistant Scientist                 fax: (630) 252-4798
   MSD-212, Rm. C-224
   Argonne National Laboratory
   9700 S. Cass Ave.
   Argonne, IL 60439
*********************************************************


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From marzari at MIT.EDU  Tue Oct 28 17:48:52 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 28 Oct 2008 17:48:52 +0100
Subject: [Pw_forum] My phonon dispersion curves are jagged too
In-Reply-To: <49073345.2070207@anl.gov>
References: <49073345.2070207@anl.gov>
Message-ID: <49074274.6090805@mit.edu>



Dear Serge,


in the past we encountered a problem in the cubic perovskites,
in which the davidson algorithm would converge the top band
at some k-points to an "excited state". This is, afaik, a problem
with some algorithms (much more so with diis); a simple
solution was to use "atomic+random" as a starting point, and maybe
use "cg" as the minimization strategy in the scf calculation,
with a very tight tolerance.

Try that, maybe without redoing the phonons, just to see if the
calculations converge to the same ground state, or to a lower one.

					nicola




Serge Nakhmanson wrote:
> Dear All,
> 
> I am learning how to compute phonon dispersion curves across the BZ and
> right now I am trying to reproduce the results of a simple calculation
> for cubic perovskites that Philippe, Karin and company have done a long
> time ago [PRB 60, 836 (1999)].
> 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From nakhmanson at anl.gov  Tue Oct 28 18:34:08 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 28 Oct 2008 12:34:08 -0500
Subject: [Pw_forum] My phonon dispersion curves are jagged too
In-Reply-To: <49074274.6090805@mit.edu>
References: <49073345.2070207@anl.gov> <49074274.6090805@mit.edu>
Message-ID: <49074D10.4090309@anl.gov>

Hi Nicola,

Thanks for your comment. Actually, following Davide Ceresoli's
advice, I always use "cg" as my minimization algorithm. I just
redid my calculation with startingwfc = 'random' instead of
'atomic' and with conv_thr = 1.e-12 instead of 1.e-10. The
results of the new calculation are identical to the "old" one
(i.e., the one that was used to compute phonons in my example).
Anyway, I have other phonon calculations where the symmetry is
reduced from Pm-3m to, e.g., P4/mmm (not sure, though, that this
symmetry is low enough to avoid the problem you mention below),
and the dispersion-curve breaks are present there too.


THX,

Serge

Nicola Marzari wrote:
> 
> Dear Serge,
> 
> 
> in the past we encountered a problem in the cubic perovskites,
> in which the davidson algorithm would converge the top band
> at some k-points to an "excited state". This is, afaik, a problem
> with some algorithms (much more so with diis); a simple
> solution was to use "atomic+random" as a starting point, and maybe
> use "cg" as the minimization strategy in the scf calculation,
> with a very tight tolerance.
> 
> Try that, maybe without redoing the phonons, just to see if the
> calculations converge to the same ground state, or to a lower one.
> 
> 					nicola
> 
> 
> 
> 
> Serge Nakhmanson wrote:
>> Dear All,
>>
>> I am learning how to compute phonon dispersion curves across the BZ and
>> right now I am trying to reproduce the results of a simple calculation
>> for cubic perovskites that Philippe, Karin and company have done a long
>> time ago [PRB 60, 836 (1999)].
>>
-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From giannozz at democritos.it  Tue Oct 28 18:52:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Oct 2008 18:52:48 +0100
Subject: [Pw_forum] Raman and IR spectral
In-Reply-To: <aa128b2c0810280212p5ea6c6f2mf2ddf35e9786c457@mail.gmail.com>
References: <aa128b2c0810280212p5ea6c6f2mf2ddf35e9786c457@mail.gmail.com>
Message-ID: <49075170.9000604@democritos.it>

yumin qian wrote:

>     I have encontered a problems in calculation of Raman and IR 
> spectroscopy ,using ph.x
>     the crystal is metallic, so it can not be done ,
>    1 Why the IR or Raman calcualtion should only limited to the 
> insulating system .
>    2 How should I do if the system is metallic.

please search the pw_forum archive for "raman metals"

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From nakhmanson at anl.gov  Tue Oct 28 22:31:03 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 28 Oct 2008 16:31:03 -0500
Subject: [Pw_forum] My phonon dispersion curves are jagged too (an
	update)
In-Reply-To: <49073345.2070207@anl.gov>
References: <49073345.2070207@anl.gov>
Message-ID: <49078497.3060908@anl.gov>

A short update. I tried using matdyn.x compiled with internal copies
of blas, lapack and fft and no optimization instead if the one
compiled with MKL and fftw2. However, this binary still produces
phonon dispersion curves that are broken, i.e., it looks like this
problem does not stem from bad mathematical libraries.

BTW: I am using espresso 4.0.2.

Serge

Serge Nakhmanson wrote:
> Dear All,
> 
> I am learning how to compute phonon dispersion curves across the BZ and
> right now I am trying to reproduce the results of a simple calculation
> for cubic perovskites that Philippe, Karin and company have done a long
> time ago [PRB 60, 836 (1999)].
> 
> I take cubic (Pm-3m) PbTiO3 five-atom cell relaxed to zero forces (these
> are exactly zero by symmetry) and stresses, and compute DM(k) on a 6x6x6
> k-point grid. Going from Gamma to X (0,0,1/2), such grid gives 0, 1/6,
> 2/6, 3/6 = 1/2.
> 
> I do the Gamma --> X --> M --> Gamma --> R BZ route (see the middle panel
> of Fig 1). The grid used in the paper is a bit worse than mine but all
> the dispersion curves are smooth with no breaks anywhere.
> 
> Again, after I get all the DM(k) on the grid, I FFT them into an IFCM(r),
> which can be used to compute phonons at any k-point. I use it to draw the
> dispersion curves. Here's what I get (this is a 2.7 Mb file):
> 
> http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_GXMGR.pdf
> 
> or the xmgrace source (~1Mb):
> 
> http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_GXMGR.xmgr
> 
> Here the dispersion curves between each pair of high-symmetry k-points are
> computed using IFCM(r) on a grid of a 1000 k-points (which is probably an
> insane resolution that works out just for this tiny sample calculation)
> without any interpolations involved. As you can see, there are numerous
> "breaks" in the dispersion curves, which are aligned vertically at certain
> k-points. The one at ~100 cm-1 around M-point looks pretty ugly. My
> impression is that breaks happen at k-points where two levels cross each
> other, i.e., my DM(k) has some degenerate eigenvalues (of certain symmetry?),
> which suggests a numerical instability in a routine that diagonalizes the DMs
> or, possibly, a routine that constructs the DM(k) prior to its diagonalization.
> 
> So my question is: are such breaks in dispersion curves something to be
> expected or something unusual? If the former is true, then I'm wondering
> what kind of postprocessing I should do to get rid of them and produce nice
> plots? For example, are coarser grids (say 20 points instead of 1000) +
> spline interpolation the method of choice?
> 
> If the latter is true, the problem could be in my lapack library. I am
> using ifort 10.1.015 with MKL 10.0.4.023 and FFTW 2.1.5 to compile
> matdyn.x; make.sys is here:
> 
> http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/make.sys
> 
> but I will now try linking against something else to see if this problem
> goes away.
> 
> My whole calculation (pw_scf+ph+q2r+matdyn+xmgrace_plot) is here:
> 
> http://home.comcast.net/~sercat/Work_Files/c-PbTiO3_pd/PbTiO3_cp_phonon_dispersion.tgz
> 
> I have asked a few friends about that, and the general consensus is that
> such breaks in dispersion curves should not happen no matter what. However,
> since many members of this forum are experts in such calculations, I would
> very much appreciate your comments on this.
> 
> Finally, PLZ note that the lattice consts here and in Philippe's paper
> are used in a somewhat different spirit, so that I am not worried
> too much that our results are not identical.
> 
> Thank you very much,
> 
> Serge
> 
> 


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From cruzrojas at gmail.com  Wed Oct 29 00:48:24 2008
From: cruzrojas at gmail.com (=?ISO-8859-1?Q?Jes=FAs_Cruz?=)
Date: Tue, 28 Oct 2008 16:48:24 -0700
Subject: [Pw_forum] Paw pseudo-potential for Ti
Message-ID: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>

Dear pwscf users   Does anyone have generated a paw pseudopotential for Ti?
would you share the UPF file and/or the ld1 input file.

Best Regards
Jesus Cruz
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From mighfar at jncasr.ac.in  Wed Oct 29 07:16:04 2008
From: mighfar at jncasr.ac.in (Mighfar  Imam)
Date: Wed, 29 Oct 2008 11:46:04 +0530 (IST)
Subject: [Pw_forum] full-relativistic PP
Message-ID: <42519.172.16.1.1.1225260964.squirrel@172.16.1.1>

Dear pwscf users,
I need fully relativistic pseudopotentials for these elements:
Rh, Fe, Ni, Ag, Cd and Au.
I would be grateful If anybody has any of them and willing to share.

Thanx n regards,

Mighfar Imam




From zl.liu.caep at gmail.com  Wed Oct 29 09:35:45 2008
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Wed, 29 Oct 2008 16:35:45 +0800
Subject: [Pw_forum] no scalar fft driver specified errors
Message-ID: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>

Dear PWSCF users,

      When I run the pw.x code, I confronted with the the cfft3d errors
which reads

"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  cfft3d  : error #         1
      no scalar fft driver specified
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ..."

  I checked the pw forum and the userguide, and found no answers. Some
people in the forum said it is because of the intel compiler.
But I used IBM xlf90 fortran compiler and successfully compiled the the code
with "make pwall". The following is my make.sys file.
Any suggestions would be greatly appreciated. Thanks in advance!

Best

Z. Liu


--
Institute of Atomic and Molecular Physics, College of Physical
Science and Technology, Sichuan University, Chengdu 610065, China
E-mail: zl.liu.caep at gmail.com



====================================================================
make.sys file:
# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
#  $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
#  $(CPP) $(CPPFLAGS) $< -o $*.F90
# $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
 $(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
 $(F77) $(FFLAGS) -c $<

.c.o:
 $(CC) $(CFLAGS)  -c $<


# DFLAGS  = precompilation options (possible arguments to -D and -U)
#           used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas

DFLAGS         = -D__XLF
FDFLAGS        = -D__XLF

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
# If loading an external FFTW library, add the location of FFTW include
files

IFLAGS         = -I../include

# MODFLAGS = flag used by f90 compiler to locate modules
# You need to search for modules in ./, in ../iotk/src, in ../Modules
# Some applications also need modules in ../PW and ../PH

MODFLAGS       = -I./  -I../Modules  -I../iotk/src \
                 -I../PW  -I../PH

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90         = xlf90_r
#F90           = xlf90_r
CC             = xlc_r
F77            = xlf_r

# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS

CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)

# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate
syntax

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -qfree=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O4 -qsuffix=cpp=f90 -qdpc -qalias=nointptr -Q

# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack

FFLAGS_NOOPT   = -O0

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty

LD             = xlf90_r
LDFLAGS        =
LD_LIBS        =

# External Libraries (if any) : blas, lapack, fft, MPI

# If you have nothing better, use the local copy : ../flib/blas.a

BLAS_LIBS      =

# The following lapack libraries will be available in flib/ :
# ../flib/lapack.a : contains all needed routines
# ../flib/lapack_atlas.a: only routines not present in the Atlas library
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    = ../flib/lapack.a

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW -D__USE_INTERNAL_FFTW in DFLAGS)

FFT_LIBS       = -lessl

# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS       =

# IBM-specific: MASS libraries, if available and if -D__MASS is defined in
FDFLAGS

MASS_LIBS      =

# pgplot libraries (used by some post-processing tools)

PGPLOT_LIBS    =

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
# ARFLAGS_DYNAMIC is used in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMIC = $(ARFLAGS)

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo

RANLIB         = ranlib

# all internal and external libraries - do not modify

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a
../iotk/src/libiotk.a
LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS)
$(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)
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From paulatto at sissa.it  Wed Oct 29 11:05:41 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 29 Oct 2008 11:05:41 +0100
Subject: [Pw_forum] Paw pseudo-potential for Ti
In-Reply-To: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>
References: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>
Message-ID: <49083575.3020100@sissa.it>

Jes?s Cruz ha scritto:
> Dear pwscf users
>    Does anyone have generated a paw pseudopotential for Ti? would you
> share the UPF file and/or the ld1 input file.

I have one with semicore state in valence. I'm running some basic tests
on it right now, then I'll send it to you.

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From oulihui666 at 126.com  Wed Oct 29 10:53:15 2008
From: oulihui666 at 126.com (oulihui666)
Date: Wed, 29 Oct 2008 17:53:15 +0800 (CST)
Subject: [Pw_forum] Espresso-4.0.2 compilation problem
Message-ID: <14622184.263161225273995547.JavaMail.coremail@bj126app104.126.com>

 Dear PWscf user:

I am trying to compile Espresso-4.0.2 using the Portland Complier, PGI 7.0-4 in 64
bit mode. The cluster that I am trying to run it on has an x86-64 architecture
with AMD opteron CPUs. When I run the configure script it reads as follows:
============================================================================
The following libraries have been found:
  BLAS_LIBS=-lacml
  LAPACK_LIBS=-lacml
  FFT_LIBS= -lfftw
Please check if this is what you expect.
If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
  ./configure LIBDIRS="list of directories, separated by spaces"
Parallel environment detected successfully.
Configured for compilation of parallel executables.
For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
--------------------------------------------------------------------
configure: success
=============================================================================
But, when I try the "make all" command, it gave me the following error message:
====================================================================================
mpif90 -fast -r8 -D__PGI -D__FFTW -D__MPI -D__PARA -I../include   -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c iotk_dat+LOGICAL4_6.F90 -o iotk_dat+LOGICAL4_6.o
cpp -P -traditional -D__PGI -D__FFTW -D__MPI -D__PARA -I../include   iotk_dat+REAL1_0.f90 -o iotk_dat+REAL1_0.F90
mpif90 -fast -r8 -D__PGI -D__FFTW -D__MPI -D__PARA -I../include   -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c iotk_dat+REAL1_0.F90 -o iotk_dat+REAL1_0.o
/tmp/pgf90Ry5gbK3rFq_1.s: Assembler messages:
/tmp/pgf90Ry5gbK3rFq_1.s:4465: Error: no such instruction: `movntss %xmm0,-28(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4468: Error: no such instruction: `movntss %xmm1,-24(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4472: Error: no such instruction: `movntss %xmm0,-20(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4474: Error: no such instruction: `movntss %xmm1,-16(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4478: Error: no such instruction: `movntss %xmm0,-12(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4480: Error: no such instruction: `movntss %xmm1,-8(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4484: Error: no such instruction: `movntss %xmm0,-4(%rdx)'
/tmp/pgf90Ry5gbK3rFq_1.s:4486: Error: no such instruction: `movntss %xmm1,(%rdx)'
make[2]: *** [iotk_dat+REAL1_0.o] Error 2
make[2]: Leaving directory `/home/olh/espresso-4.0.2/iotk/src'
make[1]: *** [lib+util] Error 2
make[1]: Leaving directory `/home/olh/espresso-4.0.2/iotk'
make: *** [libiotk] Error 2
=====================================================================================
Does anyone have an idea on how to proceed? I have already checked the PWscf
list, but I could not find any answers for this problem.

Thanks for your help
Lihui Ou


 
 
 

--

======================================
Lihui Ou
PH.D Candidate in Electrochemistry                      
College of Chemistry and Molecular Science            
Wuhan University,430072,Hubei Province,China 
E-mail:oulihui666 at 126.com
======================================
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From giannozz at democritos.it  Wed Oct 29 12:59:18 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Oct 2008 12:59:18 +0100
Subject: [Pw_forum] Espresso-4.0.2 compilation problem
In-Reply-To: <14622184.263161225273995547.JavaMail.coremail@bj126app104.126.com>
References: <14622184.263161225273995547.JavaMail.coremail@bj126app104.126.com>
Message-ID: <38C30C8C-689E-41AC-9DB6-9C9609825C12@democritos.it>


On Oct 29, 2008, at 10:53 , oulihui666 wrote:

> mpif90 -fast -r8 -D__PGI -D__FFTW -D__MPI -D__PARA -I../include   - 
> I./  -I./Modules  -I../iotk/src -I../PW  -I../PH -c iotk_dat 
> +REAL1_0.F90 -o iotk_dat+REAL1_0.o
> /tmp/pgf90Ry5gbK3rFq_1.s: Assembler messages:
> /tmp/pgf90Ry5gbK3rFq_1.s:4465: Error: no such instruction: `movntss  
> %xmm0,-28(%rdx)'

this falls into the category "internal compiler error" and has the  
same solution:
get a compiler that works

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From giannozz at democritos.it  Wed Oct 29 13:04:11 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Oct 2008 13:04:11 +0100
Subject: [Pw_forum] no scalar fft driver specified errors
In-Reply-To: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>
References: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>
Message-ID: <B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>


On Oct 29, 2008, at 9:35 , Zhong-Li Liu wrote:

>      from  cfft3d  : error #         1
>       no scalar fft driver specified

if you have ESSL, you need -D__ESSL (or -D__LINUX_ESSL
if you have one of those strange recent IBM machines)

> The following is my make.sys file.

produced by "configure"? if so, please provide details of
the version of q-e you are using, of your machine, and
the config.log file

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From asafis at yahoo.com.br  Wed Oct 29 14:15:45 2008
From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=)
Date: Wed, 29 Oct 2008 06:15:45 -0700 (PDT)
Subject: [Pw_forum] Pseudopotential for Co
Message-ID: <529074.46770.qm@web52306.mail.re2.yahoo.com>

Dear pwscf users,
I need fully relativistic pseudopotentials for Co. I tried to build one, but it has not been good. If anyone can help me, I would be grateful.   

????????????????????? Sincerely, A. S. Santos


      Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com.
http://br.new.mail.yahoo.com/addresses
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From giannozz at democritos.it  Wed Oct 29 16:47:58 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Oct 2008 16:47:58 +0100
Subject: [Pw_forum] phonon dispersion jagged
In-Reply-To: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB5A@shared-svc-exch.shared-svc.local>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB47@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4A@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4C@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB50@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB51@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB53@shared-svc-exch.shared-svc.local>
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB5A@shared-svc-exch.shared-svc.local>
Message-ID: <B2DBEEB0-A848-4F1C-B849-E8F5CC4C1B60@democritos.it>


On Oct 28, 2008, at 12:46 , Ante Bilic wrote:

> The calculated dispersion curves were in very good agreement
> with those in the literature, except they look shockingly ugly! For
> some reason they are not smooth, but rather jagged.

are you by any chance running a version later than July 1st (v.4.0.1
and later)? I am afraid that a change I recently made:
http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/PH/rigid.f90
in order to fix a possible bug and to speedup calculations obeyed the
"bug sum rule", i.e. one bug fixed, one new bug added (thanks to
Andrea Dal Corso for noticing this). Please change the two
instructions at lines 92 and 124 of file PH/rigid.f90:
    if (geg > 0.0 .and. geg < gmax ) then
into
   if (geg > 0.0 .and. geg/alph/4.0_DP < gmax ) then
recompile q2r.x, re-run the "q2r.x" part, report if this fixes your (and
Serge's) problem

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From nakhmanson at anl.gov  Wed Oct 29 20:04:26 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Wed, 29 Oct 2008 14:04:26 -0500
Subject: [Pw_forum] phonon dispersion jagged
In-Reply-To: <B2DBEEB0-A848-4F1C-B849-E8F5CC4C1B60@democritos.it>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB47@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4A@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4C@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB50@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB51@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB53@shared-svc-exch.shared-svc.local>
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB5A@shared-svc-exch.shared-svc.local>
	<B2DBEEB0-A848-4F1C-B849-E8F5CC4C1B60@democritos.it>
Message-ID: <4908B3BA.6010900@anl.gov>

Dear Paolo,

I did a very quick test. Yes, now the problem is fixed and the
dispersion curves are smooth again.

Thank you and, I guess, thanks to Andrea as well,

S.


Paolo Giannozzi wrote:
> 
> On Oct 28, 2008, at 12:46 , Ante Bilic wrote:
> 
>> The calculated dispersion curves were in very good agreement
>> with those in the literature, except they look shockingly ugly! For
>> some reason they are not smooth, but rather jagged.
> 
> are you by any chance running a version later than July 1st (v.4.0.1
> and later)? I am afraid that a change I recently made:
> http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/PH/rigid.f90
> in order to fix a possible bug and to speedup calculations obeyed the
> "bug sum rule", i.e. one bug fixed, one new bug added (thanks to
> Andrea Dal Corso for noticing this). Please change the two
> instructions at lines 92 and 124 of file PH/rigid.f90:
>    if (geg > 0.0 .and. geg < gmax ) then
> into
>   if (geg > 0.0 .and. geg/alph/4.0_DP < gmax ) then
> recompile q2r.x, re-run the "q2r.x" part, report if this fixes your (and
> Serge's) problem
> 
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************

From calderin at physics.queensu.ca  Wed Oct 29 21:08:01 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Wed, 29 Oct 2008 16:08:01 -0400 (EDT)
Subject: [Pw_forum] desc_init
Message-ID: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>

Hello everyone,

Is there any special reason for the subroutine desc_init to be in more
than one file ( PW/regterg.f90, PW/cegterg.f90, PW/rotate_wfc_k.f90,
PW/rotate_wfc_gamma.f90) ?

That gives the following errors for linkers that do not accept symbol
multi definition by default.

The errors are (versions 4.0.2 and 4.0.3):

ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file libpw.a(regterg.o)
type=OBJT);
ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file libpw.a(regterg.o)
type=OBJT);
ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file libpw.a(rotate_wfc_k.o)
type=OBJT);
ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file libpw.a(rotate_wfc_k.o)
type=OBJT);
ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file
libpw.a(rotate_wfc_gamma.o) type=OBJT);
ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
        (file libpw.a(cegterg.o) type=OBJT; file
libpw.a(rotate_wfc_gamma.o) type=OBJT);

A work around is to use -z muldefs for ld.


Thanks, L.

-- 
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca

From akohlmey at cmm.chem.upenn.edu  Wed Oct 29 22:24:33 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 29 Oct 2008 17:24:33 -0400 (EDT)
Subject: [Pw_forum] desc_init
In-Reply-To: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>
References: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>
Message-ID: <Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>

On Wed, 29 Oct 2008, Lazaro Calderin wrote:

LC> Hello everyone,
LC> 
LC> Is there any special reason for the subroutine desc_init to be in more
LC> than one file ( PW/regterg.f90, PW/cegterg.f90, PW/rotate_wfc_k.f90,
LC> PW/rotate_wfc_gamma.f90) ?
LC> 
LC> That gives the following errors for linkers that do not accept symbol
LC> multi definition by default.

lazaro,

this looks like a broken compiler (which one? what platform? etc.).

those are "contained" functions, i.e they should not be 
globally visible. 

cheers,
    axel.



LC> 
LC> The errors are (versions 4.0.2 and 4.0.3):
LC> 
LC> ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file libpw.a(regterg.o)
LC> type=OBJT);
LC> ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file libpw.a(regterg.o)
LC> type=OBJT);
LC> ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file libpw.a(rotate_wfc_k.o)
LC> type=OBJT);
LC> ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file libpw.a(rotate_wfc_k.o)
LC> type=OBJT);
LC> ld: fatal: symbol `__DESC_INIT$COOR_IP$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file
LC> libpw.a(rotate_wfc_gamma.o) type=OBJT);
LC> ld: fatal: symbol `__DESC_INIT$RANK$1' is multiply-defined:
LC>         (file libpw.a(cegterg.o) type=OBJT; file
LC> libpw.a(rotate_wfc_gamma.o) type=OBJT);
LC> 
LC> A work around is to use -z muldefs for ld.


not sure if that is a good idea.

LC> 
LC> 
LC> Thanks, L.
LC> 
LC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From schmidt at chem.wisc.edu  Thu Oct 30 02:32:15 2008
From: schmidt at chem.wisc.edu (JR Schmidt)
Date: Wed, 29 Oct 2008 20:32:15 -0500
Subject: [Pw_forum] Pseudo-potential cutoff recommendations
Message-ID: <49090E9F.9070509@chem.wisc.edu>

Is there an simple mechanism that can be used to estimate a reasonable 
cutoff energy for a given pseudo-potential?  I realize that these values 
need to be checked for convergence, but I would like to at least get a 
reasonable starting point.  It appears that there are fields stored in 
the pseudo-potential files that are supposed to give "reasonable" 
defaults for both the wavefunction and density KE cutoffs, but they seem 
to be always zero in every case I have checked.

I'm guessing a possible answer is to run a calculation on the isolated 
atom for each atom type.  However this seems like something that would 
have been done previously for each pseudo-potential and tabulated somewhere.

Please forgive me if this question comes up frequently, but I couldn't 
find an easy mechanism to search the archives.

-- 
J.R. Schmidt
Assistant Professor of Chemistry
Room 8305D
Department of Chemistry
University of Wisconsin-Madison
1101 University Ave
Madison, WI 53706

Phone: (608) 262-2996
Fax: (608) 262-9918
E-mail: schmidt at chem.wisc.edu
http://www.chem.wisc.edu/people/profiles/schmidt.php


From akohlmey at cmm.chem.upenn.edu  Thu Oct 30 03:24:02 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 29 Oct 2008 22:24:02 -0400 (EDT)
Subject: [Pw_forum] Pseudo-potential cutoff recommendations
In-Reply-To: <49090E9F.9070509@chem.wisc.edu>
References: <49090E9F.9070509@chem.wisc.edu>
Message-ID: <Pine.LNX.4.64.0810292209230.2352@localhost.localdomain>

On Wed, 29 Oct 2008, JR Schmidt wrote:

JRS> Is there an simple mechanism that can be used to estimate a reasonable 
JRS> cutoff energy for a given pseudo-potential?  I realize that these values 
JRS> need to be checked for convergence, but I would like to at least get a 
JRS> reasonable starting point.  It appears that there are fields stored in 
JRS> the pseudo-potential files that are supposed to give "reasonable" 
JRS> defaults for both the wavefunction and density KE cutoffs, but they seem 
JRS> to be always zero in every case I have checked.

yep. these cannot be easily detected automatically. one can derive
some estimates during the generation procedure though and UPF files
generated in version 2 file format contain this value.

however, different properties converge differently with the size of 
the basis set (wfc and density cutoffs). and obviously nobody cared 
to edit the old files.

in general there are some rough guidelines:

ultra-soft pseudopotentials require usually about 
30-50 ry wavefunction cutoff and 6-10 times the
density cutoff. 

norm-conserving pseudopotentials generally require
higher wavefunction cutoffs, say, 60-120ry sometimes
even more, sometimes (e.g. Si) less and there is no 
gain from changing the density cutoff.

forces generally converge faster than total energies
or the stress tensor. energy differences also tend
to converge fast.

JRS> I'm guessing a possible answer is to run a calculation on the isolated 
JRS> atom for each atom type.  However this seems like something that would 

usually a good estimate is done with a small bulk system 
with a proper k-point sampling. checking the E/V curve 
for different cutoffs is a frequent test for pseudos.

JRS> have been done previously for each pseudo-potential and tabulated somewhere.

feel free to start such a table. 

JRS> Please forgive me if this question comes up frequently, but I couldn't 
JRS> find an easy mechanism to search the archives.

you can (ab)use google. adding "site:democritos.it" to your query
will search only the server where the mailing list is currently
archived. there also is a FAQ on the wiki at http://www.quantum-espresso.org

cheers,
   axel.

JRS> 
JRS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From bilica at ihpc.a-star.edu.sg  Thu Oct 30 05:06:13 2008
From: bilica at ihpc.a-star.edu.sg (Ante Bilic)
Date: Thu, 30 Oct 2008 12:06:13 +0800
Subject: [Pw_forum] phonon dispersion jagged
In-Reply-To: <B2DBEEB0-A848-4F1C-B849-E8F5CC4C1B60@democritos.it>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB47@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4A@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB4C@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB50@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB51@shared-svc-exch.shared-svc.local>,
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB53@shared-svc-exch.shared-svc.local>
	<EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB5A@shared-svc-exch.shared-svc.local>,
	<B2DBEEB0-A848-4F1C-B849-E8F5CC4C1B60@democritos.it>
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B902C56AFB65@shared-svc-exch.shared-svc.local>

Dear Paolo,

Fantastic! Now it is looking very good indeed.
I think matdyn.x  also needed re-compiling
with those 2 fixes.

Many thanks,

-Ante

________________________________________
From: Paolo Giannozzi [giannozz at democritos.it]
Sent: Wednesday, October 29, 2008 11:47 PM
To: PWSCF Forum
Cc: Serge Nakhmanson; Ante Bilic
Subject: Re: [Pw_forum] phonon dispersion jagged

On Oct 28, 2008, at 12:46 , Ante Bilic wrote:

> The calculated dispersion curves were in very good agreement
> with those in the literature, except they look shockingly ugly! For
> some reason they are not smooth, but rather jagged.

are you by any chance running a version later than July 1st (v.4.0.1
and later)? I am afraid that a change I recently made:
http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/PH/rigid.f90
in order to fix a possible bug and to speedup calculations obeyed the
"bug sum rule", i.e. one bug fixed, one new bug added (thanks to
Andrea Dal Corso for noticing this). Please change the two
instructions at lines 92 and 124 of file PH/rigid.f90:
    if (geg > 0.0 .and. geg < gmax ) then
into
   if (geg > 0.0 .and. geg/alph/4.0_DP < gmax ) then
recompile q2r.x, re-run the "q2r.x" part, report if this fixes your (and
Serge's) problem

Paolo

This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

From calderin at physics.queensu.ca  Thu Oct 30 00:19:33 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Thu, 30 Oct 2008 00:19:33 +0100
Subject: [Pw_forum] desc_init
In-Reply-To: <Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>
References: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>
	<Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>
Message-ID: <1225322373.23670.66.camel@wolfe>

Axel, thank you very much for your answer.

> this looks like a broken compiler (which one? what platform? etc.).

Sun Fire 25000 (UltraSparc IV)
SunOS 5.10 
Sun Clusters Tools 7 (Fortran 95 v. 8.3)

> those are "contained" functions, i.e they should not be 
> globally visible. 

You are right .. I did not see the contains statements before .. however
I still do not understand the need for having exactly the same
subroutine (desc_init) included in different files which, besides, go
into the same library (libpw.a).

Thanks again, cheers Lazaro.

-- 
=============================================================
Lazaro Calderin                     
Department of Physics        
Queen's University 
Kingston, Ontario, K7L 3N6, Canada
+1 613 533 74811 ext 74811
calderin at physics.queensu.ca


From yuminqian at gmail.com  Thu Oct 30 08:36:58 2008
From: yuminqian at gmail.com (yumin qian)
Date: Thu, 30 Oct 2008 15:36:58 +0800
Subject: [Pw_forum] Pseudopotential generation problem
Message-ID: <aa128b2c0810300036i55c2f1adm5e83a77376e4d2dc@mail.gmail.com>

 &input
     title='self generation of pseudopotential'
     atom='Sr',
     iswitch=3,
     dft='PZ',
     nld=3,
     rlderiv=2.5
     eminld=-2.0,
     emaxld=2.0,
     deld=0.05,
     config='[Kr] 4p6 5s2 '
/
 &inputp
     lloc=0,
     pseudotype =3
     nlcc=.true.
     file_pseudopw='38.Sr-LDA-nlcc-uspp-TM.UPF',
     tm=.true.
/
2
4P   4  1    6.00  1.0  2.1  2.4
5S   5  0    2.00  0.0  2.4  2.4
 &test
    pseudotype=3,
    nconf=1,
    configts(1)='4p6 5s2 '
/
4P   4  1    6.00  1.0  2.1  2.4
5S   5  0    2.00  0.0  2.4  2.4


but it crashed with output

     from el_config : error #         9
     wavefunction 4P found too many times

then I remove the line
4P   4  1    6.00  1.0  2.1  2.4

it still have problems

--      from ld1_readin : error #         1
     unbound states must be empty


1  I do know how to generate pseudopotential properly  and is there any
detailled reference or examples about the usage of of the code atomic ?
2  We often use the optimal lattice parameter and the bulk moduli to test
the validity of generated psedopotential , is it save to say ,The more
acurrate of  calculated lattice parameter and bulk moduli compared with
experiment the better of pseudopotential.?
 3 How to test the validity of pseudopotential of liquid elements like Hg,or
gas  such as N and O

Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From giannozz at democritos.it  Thu Oct 30 08:44:20 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Oct 2008 08:44:20 +0100
Subject: [Pw_forum] Pseudopotential generation problem
In-Reply-To: <aa128b2c0810300036i55c2f1adm5e83a77376e4d2dc@mail.gmail.com>
References: <aa128b2c0810300036i55c2f1adm5e83a77376e4d2dc@mail.gmail.com>
Message-ID: <490965D4.7090107@democritos.it>

yumin qian wrote:

>      config='[Kr] 4p6 5s2 '

>      from el_config : error #         9
>      wavefunction 4P found too many times

[Kr] = Kripton electron configuration. If you do not have a
periodic table,  you find one in www.webelements.com

> 1  I do know how to generate pseudopotential properly  and is there any 
> detailed reference or examples about the usage of the code atomic ?

documentation and examples in atomic_doc/
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From zl.liu.caep at gmail.com  Thu Oct 30 14:23:11 2008
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Thu, 30 Oct 2008 21:23:11 +0800
Subject: [Pw_forum] no scalar fft driver specified errors
In-Reply-To: <B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>
References: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>
	<B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>
Message-ID: <8cdd828c0810300623x52800640x84cc3d04397acf84@mail.gmail.com>

Dear Paolo,

   First thank you for your reply. I did produce the "make.sys" by
"configure" and I have also tried
"configure --disable-parallel".  I have tested on several versions of q-e,
3.2.3, 4.0.1, 4.0.2 and the most recent
4.0.3, but I found the same error message. The machine is IBM Power 3
with ESSL libs. The machine was turned
off recently, so I am sorry I can not access to the config.log file right
now.

Z. Liu

--
    Institute of Atomic and Molecular Physics, College of Physical
 Science and Technology, Sichuan University, Chengdu 610065, China
zl.liu.caep at gmail.com


2008/10/29 Paolo Giannozzi <giannozz at democritos.it>

>
> On Oct 29, 2008, at 9:35 , Zhong-Li Liu wrote:
>
> >      from  cfft3d  : error #         1
> >       no scalar fft driver specified
>
> if you have ESSL, you need -D__ESSL (or -D__LINUX_ESSL
> if you have one of those strange recent IBM machines)
>
> > The following is my make.sys file.
>
> produced by "configure"? if so, please provide details of
> the version of q-e you are using, of your machine, and
> the config.log file
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Thu Oct 30 15:37:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Oct 2008 15:37:48 +0100
Subject: [Pw_forum] desc_init
In-Reply-To: <1225322373.23670.66.camel@wolfe>
References: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>	<Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>
	<1225322373.23670.66.camel@wolfe>
Message-ID: <4909C6BC.20905@democritos.it>

Lazaro Calderin wrote:

> I still do not understand the need for having exactly the same
> subroutine (desc_init) included in different files which, besides, 
> go into the same library (libpw.a).

it would be possible, and maybe convenient, to extract a separate
routine, but this would require to pass some more variables that
now are directly accessed (CONTAIN-ed routines have access to all
variables of the containing routine). While I like to say that
"the only line of code that is bug-free is the one that is not
there", I also try not to forget another bit of wisdom:
"if it is not broken, don't fix it"

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Thu Oct 30 15:44:26 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Oct 2008 15:44:26 +0100
Subject: [Pw_forum] no scalar fft driver specified errors
In-Reply-To: <8cdd828c0810300623x52800640x84cc3d04397acf84@mail.gmail.com>
References: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>	<B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>
	<8cdd828c0810300623x52800640x84cc3d04397acf84@mail.gmail.com>
Message-ID: <4909C84A.30307@democritos.it>

Zhong-Li Liu wrote:

>    First thank you for your reply. I did produce the "make.sys" by 
> "configure" and I have also tried "configure --disable-parallel". 
> [..] The machine is IBM Power 3 with ESSL libs. 

I see. Some IBM machines do their best to escape correct detection
by configure. Anyway, the fix is the one I mentioned. Occasionally
I try to make configure more robust, but it is not easy to take into
account all possible cases

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From paulatto at sissa.it  Thu Oct 30 16:21:13 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 30 Oct 2008 16:21:13 +0100
Subject: [Pw_forum] Paw pseudo-potential for Ti
In-Reply-To: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>
References: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>
Message-ID: <4909D0E9.3030305@sissa.it>

Jes?s Cruz ha scritto:
> Dear pwscf users
>    Does anyone have generated a paw pseudopotential for Ti? would you
> share the UPF file and/or the ld1 input file.
I've attached it, it should work fine. Suggested cutoff is about 25 Ry,
but you've better test it and density cutoff accurately. No guarantee is
provided, as usual.

bye

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/


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From giannozz at democritos.it  Thu Oct 30 16:27:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Oct 2008 16:27:52 +0100
Subject: [Pw_forum] no scalar fft driver specified errors
In-Reply-To: <4909C84A.30307@democritos.it>
References: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>	<B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>	<8cdd828c0810300623x52800640x84cc3d04397acf84@mail.gmail.com>
	<4909C84A.30307@democritos.it>
Message-ID: <4909D278.2040408@democritos.it>

Paolo Giannozzi wrote:

> I see. Some IBM machines do their best to escape correct detection
> by configure. 

actually, it was a bug in configure, due to a misspelled variable

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From calderin at physics.queensu.ca  Thu Oct 30 16:48:23 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Thu, 30 Oct 2008 11:48:23 -0400 (EDT)
Subject: [Pw_forum] desc_init
In-Reply-To: <4909C6BC.20905@democritos.it>
References: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>
	<Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>
	<1225322373.23670.66.camel@wolfe> <4909C6BC.20905@democritos.it>
Message-ID: <60940.130.15.24.220.1225381703.squirrel@physics.queensu.ca>

Hi Paolo,

>> I still do not understand the need for having exactly the same
>> subroutine (desc_init) included in different files which, besides,
>> go into the same library (libpw.a).
>
> it would be possible, and maybe convenient, to extract a separate
> routine, but this would require to pass some more variables that
> now are directly accessed (CONTAIN-ed routines have access to all
> variables of the containing routine). While I like to say that
> "the only line of code that is bug-free is the one that is not
> there", I also try not to forget another bit of wisdom:
> "if it is not broken, don't fix it"

Excellent bits of wisdom .. I agree .. it is just the case that for some
reason the sun compiler does not see that subroutine as "contained" and
ends up creating a library with repeated symbols. A workaround is to use
-z muldefs for linking, which is not recommended as Axel pointed out.

Thanks, L.

-- 
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca

From akohlmey at cmm.chem.upenn.edu  Thu Oct 30 16:53:10 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 30 Oct 2008 11:53:10 -0400 (EDT)
Subject: [Pw_forum] desc_init
In-Reply-To: <60940.130.15.24.220.1225381703.squirrel@physics.queensu.ca>
References: <44012.130.15.24.220.1225310881.squirrel@physics.queensu.ca>
	<Pine.LNX.4.64.0810291724260.2352@localhost.localdomain>
	<1225322373.23670.66.camel@wolfe> <4909C6BC.20905@democritos.it>
	<60940.130.15.24.220.1225381703.squirrel@physics.queensu.ca>
Message-ID: <Pine.LNX.4.64.0810301150310.2352@localhost.localdomain>

On Thu, 30 Oct 2008, Lazaro Calderin wrote:

LC> Hi Paolo,
LC> 
LC> > variables of the containing routine). While I like to say that
LC> > "the only line of code that is bug-free is the one that is not
LC> > there", I also try not to forget another bit of wisdom:
LC> > "if it is not broken, don't fix it"
LC> 
LC> Excellent bits of wisdom .. I agree .. it is just the case that for some
LC> reason the sun compiler does not see that subroutine as "contained" and
LC> ends up creating a library with repeated symbols. A workaround is to use
LC> -z muldefs for linking, which is not recommended as Axel pointed out.

another workaround would be to try installing gcc/gfortran 
or g95 and use them instead of the sun compilers. if a compiler
has problems with some (new-ish) language feature, there is a 
high chance that some more problems exist that are not that 
easy to spot.

...and yet another workaround would be to rename the contained
functions and their calls to have different names in each
files, so they don't collide anymore.


cheers,
   axel.


LC> 
LC> Thanks, L.
LC> 
LC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From cruzrojas at gmail.com  Thu Oct 30 18:46:35 2008
From: cruzrojas at gmail.com (=?ISO-8859-1?Q?Jes=FAs_Cruz?=)
Date: Thu, 30 Oct 2008 10:46:35 -0700
Subject: [Pw_forum] Paw pseudo-potential for Ti
In-Reply-To: <4909D0E9.3030305@sissa.it>
References: <aa63c41c0810281648j743b0fd5wcf3a5946a7f87c41@mail.gmail.com>
	<4909D0E9.3030305@sissa.it>
Message-ID: <aa63c41c0810301046l61a3bb6dv10120c3a36a5b6cf@mail.gmail.com>

Dear Lorenzo
   Thank you for your help.
Best Regards
Jesus Cruz

On Thu, Oct 30, 2008 at 8:21 AM, Lorenzo Paulatto <paulatto at sissa.it> wrote:

> Jes?s Cruz ha scritto:
> > Dear pwscf users
> >    Does anyone have generated a paw pseudopotential for Ti? would you
> > share the UPF file and/or the ld1 input file.
> I've attached it, it should work fine. Suggested cutoff is about 25 Ry,
> but you've better test it and density cutoff accurately. No guarantee is
> provided, as usual.
>
> bye
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>
>
>  &input
>    title='Ti',
>    prefix='Ti/ld1'
>    zed=22,
>    config='[Ar] 3d2 4s2 4p0',
>    iswitch=3,
>    dft='PBE',
>    nld=3
>      eminld=-10,
>      emaxld=10,
>      deld=0.01d0
>      rlderiv=2.65
>  /
>  &inputp
>   lloc=-2,
>     rcloc=1.80
>   pseudotype=3,
>   nlcc=.false.
>   !  new_core_ps=.true.
>   !  rcore=1.60
>   file_pseudopw='Ti.pbe-paw_kj-3s3p.UPF'
>   author='"Lorenzo Paulatto" <paulatto at sissa.it>'
>   lpaw = .true.
>     which_augfun='BESSEL'
>     rmatch_augfun=2.10
>   file_screen='Ti/ld1.scr'
>   tm=.true.
> !nX n  l   occ   nrg   rmin   rcut
>  /
> 8
> 3S  1  0  2.00  0.00  1.00  1.90
> 3P  2  1  6.00  0.00  1.00  1.90
> 3D  3  2  2.00  0.00  1.00  2.30
> 3D  3  2  0.00  0.05  1.00  2.30
> 4S  2  0  2.00  0.00  1.00  2.30
> 4S  2  0  0.00  0.50  1.00  2.30
> 4P  3  1  0.00  0.00  1.00  2.30
> 4P  3  1  0.00  0.50  1.00  2.30
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From slgphy at rediffmail.com  Thu Oct 30 18:55:42 2008
From: slgphy at rediffmail.com (Shyam )
Date: 30 Oct 2008 17:55:42 -0000
Subject: [Pw_forum] LO-TO spliting in GaAs
Message-ID: <20081030175542.32165.qmail@f4mail-234-242.rediffmail.com>

Hello all,I am trying to get the LO-TO splitting in GaAs. But I am a bit confused about the pseudo potential to be used.&nbsp; I have done calculations using both the&nbsp;ultrasoft pseudopotential (USPP) &nbsp;and the&nbsp;normconserving (NCPP). The phonon DOS which I have got using&nbsp;USPP is matching with the reported one and that I have got using NCPP is not matching. On the other hand, NCPP is giving the values of LO and TO modes closer to the experimental where as the values obtained using USPP are more deviated from the reported one.Please help me.Thank you.
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From slgphy at rediffmail.com  Thu Oct 30 19:00:12 2008
From: slgphy at rediffmail.com (Shyam )
Date: 30 Oct 2008 18:00:12 -0000
Subject: [Pw_forum] Norm conserving Pseudo potential for Mn and V
Message-ID: <20081030180012.9844.qmail@f4mail214.rediffmail.com>

Hello all,Has someone generated the NC-pseudo potential for manganese (Mn) and vanadium (V)?I will be highly greatful if someone could provide me the same.Thank you.-Slg
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From baroni at sissa.it  Thu Oct 30 19:50:36 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 30 Oct 2008 19:50:36 +0100
Subject: [Pw_forum] LO-TO spliting in GaAs
In-Reply-To: <20081030175542.32165.qmail@f4mail-234-242.rediffmail.com>
References: <20081030175542.32165.qmail@f4mail-234-242.rediffmail.com>
Message-ID: <64394AAF-7F68-42D2-A926-8C6999DAF499@sissa.it>

On Oct 30, 2008, at 6:55 PM, Shyam wrote:

> Hello all,
> I am trying to get the LO-TO splitting in GaAs. But I am a bit  
> confused about the pseudo potential to be used.  I have done  
> calculations using both the ultrasoft pseudopotential (USPP)  and  
> the normconserving (NCPP). The phonon DOS which I have got using  
> USPP is matching with the reported one and that I have got using  
> NCPP is not matching. On the other hand, NCPP is giving the values  
> of LO and TO modes closer to the experimental where as the values  
> obtained using USPP are more deviated from the reported one.
> Please help me.

How could we, without knowing anything of the way you have performed  
your calculations?
Please, do not forget to sign your corespondence to this mailinglist,  
including your current affiliation.

SB



---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html




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From zl.liu.caep at gmail.com  Fri Oct 31 01:01:14 2008
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Fri, 31 Oct 2008 08:01:14 +0800
Subject: [Pw_forum] no scalar fft driver specified errors
In-Reply-To: <4909D278.2040408@democritos.it>
References: <8cdd828c0810290135r2d8fd031j7cd285a585a594d0@mail.gmail.com>
	<B4D3B185-5ADA-4BC6-863F-133F4D873149@democritos.it>
	<8cdd828c0810300623x52800640x84cc3d04397acf84@mail.gmail.com>
	<4909C84A.30307@democritos.it> <4909D278.2040408@democritos.it>
Message-ID: <8cdd828c0810301701g25bb1d83h12ea5b82d3aa39cd@mail.gmail.com>

Dear Paolo,

  I will have a test as you suggested, and I will let you know the result.
Thank you very much!

Z. Liu
-- 
PhD. student of IAMP,  Sichuan University, China
E-mail: zl.liu.caep at gmail.com
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From giannozz at democritos.it  Fri Oct 31 08:19:55 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Oct 2008 08:19:55 +0100
Subject: [Pw_forum] Norm conserving Pseudo potential for Mn and V
In-Reply-To: <20081030180012.9844.qmail@f4mail214.rediffmail.com>
References: <20081030180012.9844.qmail@f4mail214.rediffmail.com>
Message-ID: <490AB19B.7030905@democritos.it>

Shyam wrote:

> Has someone generated the NC-pseudo potential for manganese (Mn)

norm-conserving Mn will be very hard: be prepared for a cutoff
of at least 70 Ry, likely more

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From zewdmes at yahoo.com  Fri Oct 31 08:41:01 2008
From: zewdmes at yahoo.com (mesfin atlaw)
Date: Fri, 31 Oct 2008 00:41:01 -0700 (PDT)
Subject: [Pw_forum] question
Message-ID: <411947.36838.qm@web59613.mail.ac4.yahoo.com>

My name is Mesfin Atlaw from Ethiopia
???? In the making of band structure how to select the special k-points?
??Thanks


      
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From wangqj1 at 126.com  Fri Oct 31 15:12:39 2008
From: wangqj1 at 126.com (wangqj1)
Date: Fri, 31 Oct 2008 22:12:39 +0800 (CST)
Subject: [Pw_forum] about U
Message-ID: <4447705.347721225462359557.JavaMail.coremail@bj126app81.126.com>

 
 Dear Matteo
      In your example of cacualating U of Fe ,with your method ,you get the file U_bcc8 , the file's content is as following :
          8 2.23515829445925
         64 2.76703414230193
         96 2.79787678572939
         96 2.79787678572939
        144 2.81842571395673
         96 2.79787678572939
        144 2.81842571395673
        144 2.81842571395673
        216 2.83209352287300
I know the second column is the U of cacualating ,but I don't know the first column symbolized , is it the numbers of atoms in the suppercell ? Can you tell me ?
Qianjin Wang 

 
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From matteo at umn.edu  Fri Oct 31 16:24:56 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 31 Oct 2008 10:24:56 -0500
Subject: [Pw_forum] about U
In-Reply-To: <4447705.347721225462359557.JavaMail.coremail@bj126app81.126.com>
References: <4447705.347721225462359557.JavaMail.coremail@bj126app81.126.com>
Message-ID: <490B2348.4080406@umn.edu>


Dear Qianjin

yes it is the number of atoms in the supercell.

Matteo


wangqj1 wrote:
> Dear Matteo
> In your example of cacualating U of Fe ,with your method ,you get the 
> file U_bcc8 , the file's content is as following :
> 8 2.23515829445925
> 64 2.76703414230193
> 96 2.79787678572939
> 96 2.79787678572939
> 144 2.81842571395673
> 96 2.79787678572939
> 144 2.81842571395673
> 144 2.81842571395673
> 216 2.83209352287300
> I know the second column is the U of cacualating ,but I don't know the 
> first column symbolized , is it the numbers of atoms in the suppercell 
> ? Can you tell me ?
> Qianjin Wang
>
>
>
> ????????10????,???????????? <http://www.yeah.net>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From zucco at dipteris.unige.it  Fri Oct 31 17:46:01 2008
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Fri, 31 Oct 2008 17:46:01 +0100
Subject: [Pw_forum] about U
In-Reply-To: <490B2348.4080406@umn.edu>
References: <4447705.347721225462359557.JavaMail.coremail@bj126app81.126.com>
	<490B2348.4080406@umn.edu>
Message-ID: <B36CD039-6654-4009-9EDA-397AFD45977C@dipteris.unige.it>

Good morning
... to the sunny (I hope) side of this World,

Matteo does this example is "public"? It doesn't seems to me that it  
is into the QE distribution...or I'm wrong...I'm interested to see  
your method @ work.

Thanks

m.


On 31 Oct 2008, at 16:24, Matteo Cococcioni wrote:

>
> Dear Qianjin
>
> yes it is the number of atoms in the supercell.
>
> Matteo
>
>
> wangqj1 wrote:
>> Dear Matteo
>> In your example of cacualating U of Fe ,with your method ,you get  
>> the file U_bcc8 , the file's content is as following :
>> 8 2.23515829445925
>> 64 2.76703414230193
>> 96 2.79787678572939
>> 96 2.79787678572939
>> 144 2.81842571395673
>> 96 2.79787678572939
>> 144 2.81842571395673
>> 144 2.81842571395673
>> 216 2.83209352287300
>> I know the second column is the U of cacualating ,but I don't know  
>> the first column symbolized , is it the numbers of atoms in the  
>> suppercell ? Can you tell me ?
>> Qianjin Wang
>>
>>
>>
>> ????10??,?????? <http://www.yeah.net>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> <matteo.vcf>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry

DIPartimento per lo studio della TErra e delle sue RISorse -  
Universit?  di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy



From dat36 at cam.ac.uk  Fri Oct 31 18:00:44 2008
From: dat36 at cam.ac.uk (David Tompsett)
Date: Fri, 31 Oct 2008 17:00:44 +0000
Subject: [Pw_forum] Error in Espresso post-installation Test examples
Message-ID: <490B39BC.2080306@cam.ac.uk>

Dear All,
             I have recently compiled the parallel version of Quantum 
Espresso without errors.

But when I try to run some of the post-installation test examples I find 
that each fails with:
Abort on node localhost due to MPI_Abort (Type 2)
So the program is calling abort.

It looks like there is some error from:  read_namelists  : error 
#         1
The output files have:

     Program PWSCF     v.4.0.3  starts ...
     Today is 31Oct2008 at 13:25:44

     Parallel version (MPI)

     Number of processors in use:       2
     K-points division:     npool     =    2

     For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW

     Current dimensions of program pwscf are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3

     from  read_namelists  : error #         1
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%     from  
read_namelists  : error #         1
      reading namelist control
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
bindloe04:0.MPID_Abort: bindloe04:0.MPI Abort by user Aborting program !
bindloe04:0.MPID_CH_Abort: bindloe04:0.Aborting program!
bindloe04:1.MPID_Abort: bindloe04:1.MPI Abort by user Aborting program !
bindloe04:1.MPID_CH_Abort: bindloe04:1.Aborting program!



What could cause this?

Thanks for your help,
David Tompsett.

-- 
David A. Tompsett
Quantum Matter Group
Cavendish Laboratory
J. J. Thomson Avenue
Cambridge CB3 0HE
U.K.
Tel: +44 7907 566351 (mobile)
Fax: +44 1223 337351
http://www-qm.phy.cam.ac.uk/


From matteo at umn.edu  Fri Oct 31 19:55:12 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 31 Oct 2008 13:55:12 -0500
Subject: [Pw_forum] about U
In-Reply-To: <B36CD039-6654-4009-9EDA-397AFD45977C@dipteris.unige.it>
References: <4447705.347721225462359557.JavaMail.coremail@bj126app81.126.com>	<490B2348.4080406@umn.edu>
	<B36CD039-6654-4009-9EDA-397AFD45977C@dipteris.unige.it>
Message-ID: <490B5490.7040405@umn.edu>


Hi Marino,

I think this was part of the Vlab tutorial from summer 2006. It's linked 
from the QE webpage
(or at least it was last time I checked).

Matteo


Marino Vetuschi Zuccolini wrote:
> Good morning
> ... to the sunny (I hope) side of this World,
>
> Matteo does this example is "public"? It doesn't seems to me that it  
> is into the QE distribution...or I'm wrong...I'm interested to see  
> your method @ work.
>
> Thanks
>
> m.
>
>
> On 31 Oct 2008, at 16:24, Matteo Cococcioni wrote:
>
>   
>> Dear Qianjin
>>
>> yes it is the number of atoms in the supercell.
>>
>> Matteo
>>
>>
>> wangqj1 wrote:
>>     
>>> Dear Matteo
>>> In your example of cacualating U of Fe ,with your method ,you get  
>>> the file U_bcc8 , the file's content is as following :
>>> 8 2.23515829445925
>>> 64 2.76703414230193
>>> 96 2.79787678572939
>>> 96 2.79787678572939
>>> 144 2.81842571395673
>>> 96 2.79787678572939
>>> 144 2.81842571395673
>>> 144 2.81842571395673
>>> 216 2.83209352287300
>>> I know the second column is the U of cacualating ,but I don't know  
>>> the first column symbolized , is it the numbers of atoms in the  
>>> suppercell ? Can you tell me ?
>>> Qianjin Wang
>>>
>>>
>>>
>>> ????10??,?????? <http://www.yeah.net>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>       
>> <matteo.vcf>_______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>     
>
>
>
> *******************************************************
> Marino Vetuschi Zuccolini
> zucco at dipteris.unige.it
> Researcher / Geochemist
> Laboratory of Geochemistry
>
> DIPartimento per lo studio della TErra e delle sue RISorse -  
> Universit?  di Genova
> Tel. ++39 010 3538136 Fax. ++39 010 352169
> Corso Europa 26, 16132 - Genova - Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From lanhaiping at gmail.com  Fri Oct 31 21:09:06 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 1 Nov 2008 04:09:06 +0800
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <490B39BC.2080306@cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
Message-ID: <c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>

Hi, David
the error information has clearly shown that
your input file has some wrong tag .
please check it again ,or post to the forum with your
input file

On Sat, Nov 1, 2008 at 1:00 AM, David Tompsett <dat36 at cam.ac.uk> wrote:

> Dear All,
>             I have recently compiled the parallel version of Quantum
> Espresso without errors.
>
> But when I try to run some of the post-installation test examples I find
> that each fails with:
> Abort on node localhost due to MPI_Abort (Type 2)
> So the program is calling abort.
>
> It looks like there is some error from:  read_namelists  : error
> #         1
> The output files have:
>
>     Program PWSCF     v.4.0.3  starts ...
>     Today is 31Oct2008 at 13:25:44
>
>     Parallel version (MPI)
>
>     Number of processors in use:       2
>     K-points division:     npool     =    2
>
>     For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
>
>     Current dimensions of program pwscf are:
>     Max number of different atomic species (ntypx) = 10
>     Max number of k-points (npk) =  40000
>     Max angular momentum in pseudopotentials (lmaxx) =  3
>
>     from  read_namelists  : error #         1
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%     from
> read_namelists  : error #         1
>      reading namelist control
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
> bindloe04:0.MPID_Abort: bindloe04:0.MPI Abort by user Aborting program !
> bindloe04:0.MPID_CH_Abort: bindloe04:0.Aborting program!
> bindloe04:1.MPID_Abort: bindloe04:1.MPI Abort by user Aborting program !
> bindloe04:1.MPID_CH_Abort: bindloe04:1.Aborting program!
>
>
>
> What could cause this?
>
> Thanks for your help,
> David Tompsett.
>
> --
> David A. Tompsett
> Quantum Matter Group
> Cavendish Laboratory
> J. J. Thomson Avenue
> Cambridge CB3 0HE
> U.K.
> Tel: +44 7907 566351 (mobile)
> Fax: +44 1223 337351
> http://www-qm.phy.cam.ac.uk/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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