From w2agz at pacbell.net Tue Jul 1 06:41:36 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 30 Jun 2008 21:41:36 -0700
Subject: [Pw_forum] Visualizing MP Meshes, etc.
Message-ID: <001301c8db34$bf7a6130$3e6f2390$@net>
To All:
Is there a tool to both compute Monkhorst-Pack meshes and visualize the
result (perhaps through XCrysDen?). I remember the generation source code
could be obtained from the authors, but maybe somebody complied a binary.
Also, is there an "XCrysDen look-alike" that can plot paths in k- or
r-space, a la k-paths in XCrysDen? E.g., the 19 point path in matdyn.freq
in Example O7?
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
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From vegalew at hotmail.com Tue Jul 1 07:23:26 2008
From: vegalew at hotmail.com (vega lew)
Date: Tue, 1 Jul 2008 13:23:26 +0800
Subject: [Pw_forum] server for PWgui and Xcrysden downloading is off,
please check it out
Message-ID:
dear administrator,
Your website for PWgui and Xcrysden downloading is no longer up to snuff. I can't connect it for a long time. please check it out.
The address I used to click is as follows,
PWgui: http://www-k3.ijs.si/kokalj/pwgui/
Xcrysden: http://www.xcrysden.org/
Am I clicked the right one?
Thank you
vega
_________________________________________________________________
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From giannozz at democritos.it Tue Jul 1 09:48:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 01 Jul 2008 09:48:16 +0200
Subject: [Pw_forum] server for PWgui and Xcrysden downloading is off,
please check it out
In-Reply-To:
References:
Message-ID: <4869E140.5040000@democritos.it>
vega lew wrote:
> Your website for PWgui and Xcrysden downloading is no longer up to
> snuff. I can't connect it for a long time. please check it out.
it looks like a network problem somewhere in Ljubljana (Slovenia),
where the servers are located. It should be a temporary problem.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From hushujun at mail.sdu.edu.cn Tue Jul 1 10:00:42 2008
From: hushujun at mail.sdu.edu.cn (=?gb2312?B?uvrK9778IFNodS1qdW4gSHU=?=)
Date: Tue, 01 Jul 2008 16:00:42 +0800
Subject: [Pw_forum] Small U for Co in ZnO for LDA+U
Message-ID: <414899242.31069@mail.sdu.edu.cn>
Dear All,
I would post my comments on the topic of LDA+U calculation of small U_Co.
(1) The self-consistently calculated U_Co is indeed sensitive to the oxidation
state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a very "small"
number. However, in Co-doped SnO2, we got a "reasonable" value of 3.7 eV.
U_projection_type is specified as the default (atomic) in both cases during the
calculation of U_Co.
(2) The calculated band structure is much sensitive to the value of U_Co and
U_Co=0.31 eV does have a significant effect with respect to U=0. U_Co=0.31 eV can
well fit the experimental results (APL 84 4233 (2004), and also J. Appl. Phys. 103
07D130 (2008)), where the occupied Co:3d majority state are deep in the valence
band rather than in the gap. If U_Co=2 to 5 eV is implemented, Nektarios is right:
a Co-d projected DOS far deep into the valence (completely non sense).
(3) The occupation is larger than 1 but not less than 1 in the "atomic" case. A
piece of output file is listed in the end.
Best wishes.
shu-jun
iteration # 1 ecut= 30.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 1.00E-06, avg # of iterations = 2.0
enter write_ns
U( 1) = 0.0000 U( 2) = 5.0000 U( 3) = 0.3100 U( 4) = 0.3100
alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = 0.0000 alpha(
4) = 0.0000
atom 1 Tr[ns(na)]= 20.2308353
atom 1 spin 1
eigenvalues: 2.6157258 2.6161606 2.6163747 2.6230370 2.6231626
eigenvectors
1 -0.1857398 0.4838857 -0.3108623 -0.4315218 0.6697081
2 0.7691240 -0.1376398 -0.3613721 -0.4813049 -0.1651042
3 -0.6107095 -0.2857263 -0.3371356 -0.4914774 -0.4361008
4 0.0275961 0.8118942 0.0830406 -0.0532713 -0.5747457
5 -0.0148797 0.0780907 -0.8076006 0.5811597 -0.0609523
occupations
2.616 0.000 0.000 0.000 0.000
0.000 2.621 0.000 0.000 -0.003
0.000 0.000 2.621 -0.003 0.000
0.000 0.000 -0.003 2.619 0.000
0.000 -0.003 0.000 0.000 2.618
atom 1 spin 2
eigenvalues: 0.6259172 0.6323802 0.6442143 2.6141658 2.6196970
eigenvectors
1 -0.1040632 -0.4885801 -0.2577671 -0.3860893 -0.7314038
2 -0.0078294 0.2638155 -0.4985241 -0.7299864 0.3859192
3 0.9945218 -0.0535680 -0.0330433 -0.0447136 -0.0704671
4 -0.0011093 -0.4865620 0.6672800 -0.4565376 0.3310092
5 -0.0058854 -0.6723680 -0.4885442 0.3280686 0.4489790
occupations
0.644 0.008 0.004 -0.004 -0.007
0.008 1.998 0.009 0.001 -0.921
0.004 0.009 1.989 -0.923 0.001
-0.004 0.001 -0.923 1.258 -0.009
-0.007 -0.921 0.001 -0.009 1.247
------------------------------
Shujun Hu e-mail: hushujun at 163.com
Shandong university Phone: +86/0531-88375097
Jinan, Shandong Province, China, 250100
From paulatto at sissa.it Tue Jul 1 10:26:58 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 1 Jul 2008 10:26:58 +0200 (CEST)
Subject: [Pw_forum] Visualizing MP Meshes, etc.
In-Reply-To: <001301c8db34$bf7a6130$3e6f2390$@net>
References: <001301c8db34$bf7a6130$3e6f2390$@net>
Message-ID: <3039.147.122.5.216.1214900818.squirrel@webmail.sissa.it>
On Mar, Luglio 1, 2008 06:41, Paul M. Grant wrote:
> To All:
>
> Is there a tool to both compute Monkhorst-Pack meshes
There is kpoint.x in pwtools/
> and visualize the result (perhaps through XCrysDen?).
Sometimes I use gnuplot: I take columns 2, 3 and 4 from kpoint.x output
and "splot with points". I know it's far from optimal, but it works.
> Also, is there an "XCrysDen look-alike" that can plot paths in k- or
> r-space, a la k-paths in XCrysDen?
I don't know.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
----------------------------------------------------------------
SISSA Webmail https://webmail.sissa.it/
Powered by SquirrelMail http://www.squirrelmail.org/
From vegalew at hotmail.com Tue Jul 1 10:31:58 2008
From: vegalew at hotmail.com (vega lew)
Date: Tue, 1 Jul 2008 16:31:58 +0800
Subject: [Pw_forum] server for PWgui and Xcrysden downloading is off,
please check it out
In-Reply-To: <4869E140.5040000@democritos.it>
References:
<4869E140.5040000@democritos.it>
Message-ID:
Dear sir,
Would you please send the xcrysden to me via mail or msn ?
Otherwise, you also can share it on net-disk for temporary use.
thank you.
Vega Lew
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
> Date: Tue, 1 Jul 2008 09:48:16 +0200
> From: giannozz at democritos.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] server for PWgui and Xcrysden downloading is off, please check it out
>
> vega lew wrote:
>
> > Your website for PWgui and Xcrysden downloading is no longer up to
> > snuff. I can't connect it for a long time. please check it out.
>
> it looks like a network problem somewhere in Ljubljana (Slovenia),
> where the servers are located. It should be a temporary problem.
>
> 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
_________________________________________________________________
Discover the new Windows Vista
http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
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From sathya_sheela1985001 at rediffmail.com Tue Jul 1 12:46:51 2008
From: sathya_sheela1985001 at rediffmail.com (sathya subramanyan)
Date: 1 Jul 2008 10:46:51 -0000
Subject: [Pw_forum] (no subject)
Message-ID: <20080701104651.28345.qmail@f4mail-235-243.rediffmail.com>
?
Dear Developers,
I am a new user of Espresso-4.0 and when I ran the example10 (polarizayion of cubic PbTiO3 via Berry phase calculation)I found that the total ionic phase is not the sum of the ionic phases of the individiual constituents i.e Pb ,Ti ,O but in the tetragonal PbTiO3 the total ionic phase is -0.22375 which is the individual sum of Pb ,Ti, O.
I am attaching the O/P files (only a section as the complete file is bulky)of cubic and tetra phase of PbTiO3 ( polarization calculation ) for comparison.
I would be really thankful for any explanations or reasoning in this context.
FOR CUBIC PHASE
IONIC POLARIZATION
~~~~~~~~~~~~~~~~~~
Note: (mod 1) means that the phases (angles ranging from
-pi to pi) have been mapped to the interval [-1/2,+1/2) by
dividing by 2*pi; (mod 2) refers to the interval [-1,+1)
============================================================================
Ion Species Charge Position Phase
----------------------------------------------------------------------------
1 Pb 14.000 0.0000 0.0000 0.0100 0.14000 (mod 2)
2 Ti 12.000 0.5000 0.5000 0.5000 0.00000 (mod 2)
3 O 6.000 0.0000 0.5000 0.5000 -1.00000 (mod 2)
4 O 6.000 0.5000 0.5000 0.0000 0.00000 (mod 2)
5 O 6.000 0.5000 0.0000 0.5000 -1.00000 (mod 2)
----------------------------------------------------------------------------
IONIC PHASE: 0.14000 (mod 2)
============================================================================
FOR TETRAGONAL PbTiO3
IONIC POLARIZATION
~~~~~~~~~~~~~~~~~~
Note: (mod 1) means that the phases (angles ranging from
-pi to pi) have been mapped to the interval [-1/2,+1/2) by
dividing by 2*pi; (mod 2) refers to the interval [-1,+1)
============================================================================
Ion Species Charge Position Phase
----------------------------------------------------------------------------
1 Pb 14.000 0.0000 0.0000 0.0100 0.13142 (mod 2)
2 Ti 12.000 0.5000 0.5000 0.5377 0.05689 (mod 2)
3 O 6.000 0.5000 0.5000 0.1118 0.62968 (mod 2)
4 O 6.000 0.0000 0.5000 0.6174 -0.52267 (mod 2)
5 O 6.000 0.5000 0.0000 0.6174 -0.52267 (mod 2)
----------------------------------------------------------------------------
IONIC PHASE: -0.22735 (mod 2)
============================================================================
Thanking You
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli - 620015
India
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From iphyboy at hotmail.com Tue Jul 1 13:50:53 2008
From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=)
Date: Tue, 1 Jul 2008 19:50:53 +0800
Subject: [Pw_forum] Cr with Perdew-Zunger (LDA) exch-corr
Message-ID:
Dear all,
Does anyone have the pseudopotential of Cr with Perdew-Zunger (LDA) exch-corr,
if any, please send me a copy of it,since I cannot find the LDA version pseudopential of Cr in PWSCF website.
Thanks in advance.
Wenmei
_________________________________________________________________
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From abdulrafiu.raji at uct.ac.za Tue Jul 1 14:00:03 2008
From: abdulrafiu.raji at uct.ac.za (ABDULRAFIU RAJI)
Date: Tue, 01 Jul 2008 14:00:03 +0200
Subject: [Pw_forum] How to handle the i/o error in davcio problem in
NEB calculations
Message-ID: <486A3863020000C500166A75@gwiasmtp.uct.ac.za>
Dear fellow Pwscf users,
I was using the QE vers.3.2.3 (parallel) to do NEB calculations. At the 11th iterations, and while relaxing the 4th image, it suddenly stopped with the following error message:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from davcio : error # 10
i/o error in davcio
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Also, "restart_mode = restart" in my input file, since the calculation had earlier stopped because the CPU time was over. I observed that similar problem was reported on this forum, and the response (by Carlo Sbraccia) was that the files in '$outdir' directory should be removed since the restart file for neb calculations is that with '.path' extension in the working directory. I implemented Carlo's suggestions and removed all the files in the scratch directory with prefixes of my calculations, and the program was then restarted. But on getting to 4th image, while carrying out the 12th iterations, it stopped again, displaying the similar error message as quoted above. Can anyone please advise on what I must do next?
Thank you very much.
Abdulrafiu Tunde Raji,
Dept. of Physics,
University of Cape Town,
Rondebosch 7701,
Cape Town,
South Africa.
Raji Abdulrafiu Tunde,
Department of Physics,
University of Cape Town (RW James Bld.),Private Bag X3,
Rondebosch 7701,
Cape Town. South Africa.
Office number : Rm. 522
Cell: +27722668228
Fax: +27216503342
From sathya_sheela1985001 at rediffmail.com Tue Jul 1 14:13:12 2008
From: sathya_sheela1985001 at rediffmail.com (sathya subramanyan)
Date: 1 Jul 2008 12:13:12 -0000
Subject: [Pw_forum] ionic phase calculation(for polarization) of cubic and
tetragonal PbTiO3
Message-ID: <20080701121312.19235.qmail@f4mail-235-241.rediffmail.com>
?
Dear Developers,
I am a new user of Espresso-4.0 and when I ran the example10 (polarizayion of cubic PbTiO3 via Berry phase calculation)I found that the total ionic phase is not the sum of the ionic phases of the individiual constituents i.e Pb ,Ti ,O but in the tetragonal PbTiO3 the total ionic phase is -0.22375 which is the individual sum of Pb ,Ti, O.
I am attaching the O/P files (only a section as the complete file is bulky)of cubic and tetra phase of PbTiO3 ( polarization calculation ) for comparison.
I would be really thankful for any explanations or reasoning in this context.
FOR CUBIC PHASE
IONIC POLARIZATION
~~~~~~~~~~~~~~~~~~
Note: (mod 1) means that the phases (angles ranging from
-pi to pi) have been mapped to the interval [-1/2,+1/2) by
dividing by 2*pi; (mod 2) refers to the interval [-1,+1)
============================================================================
Ion Species Charge Position Phase
----------------------------------------------------------------------------
1 Pb 14.000 0.0000 0.0000 0.0100 0.14000 (mod 2)
2 Ti 12.000 0.5000 0.5000 0.5000 0.00000 (mod 2)
3 O 6.000 0.0000 0.5000 0.5000 -1.00000 (mod 2)
4 O 6.000 0.5000 0.5000 0.0000 0.00000 (mod 2)
5 O 6.000 0.5000 0.0000 0.5000 -1.00000 (mod 2)
----------------------------------------------------------------------------
IONIC PHASE: 0.14000 (mod 2)
============================================================================
FOR TETRAGONAL PbTiO3
IONIC POLARIZATION
~~~~~~~~~~~~~~~~~~
Note: (mod 1) means that the phases (angles ranging from
-pi to pi) have been mapped to the interval [-1/2,+1/2) by
dividing by 2*pi; (mod 2) refers to the interval [-1,+1)
============================================================================
Ion Species Charge Position Phase
----------------------------------------------------------------------------
1 Pb 14.000 0.0000 0.0000 0.0100 0.13142 (mod 2)
2 Ti 12.000 0.5000 0.5000 0.5377 0.05689 (mod 2)
3 O 6.000 0.5000 0.5000 0.1118 0.62968 (mod 2)
4 O 6.000 0.0000 0.5000 0.6174 -0.52267 (mod 2)
5 O 6.000 0.5000 0.0000 0.6174 -0.52267 (mod 2)
----------------------------------------------------------------------------
IONIC PHASE: -0.22735 (mod 2)
============================================================================
Thanking You
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli - 620015
India
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From shhlv at 163.com Tue Jul 1 15:46:51 2008
From: shhlv at 163.com (shhlv)
Date: Tue, 1 Jul 2008 21:46:51 +0800 (CST)
Subject: [Pw_forum] pwo2xsf error when plot 3D charge density with xcrysden
Message-ID: <10699575.527661214920011341.JavaMail.coremail@bj163app39.163.com>
Dear pwscf users,
When I try to open a output file to see the 3D charge density plot with xcrysden, a error occurs:
Error:
while executing exec sh /opt/cluster/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor
/plate/shlv/study/pwscf/si/si_3D.rho.xsf > pwo2xsf.xsf.
(standard_in) 1: parse error
/opt/cluster/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh: line 88: test: -eq: unary operator expected
The script contained in pwo2xsf.sh is as follows:
pwoCheckPWSCFVersion() {
#
# Usage: $0 option file
#
# Purpose: if PWSCF version < 1.3 execute the old pwo2xsf_old.sh
# script and exit
version=`pwoGetVersion $input`
result=`echo "$version < 1.3"|bc -l`
if test $result -eq 1 ; then ---------line 88
if test -f $scriptdir/pwo2xsf_old.sh ; then
# execute pwo2xsf_old.sh
$scriptdir/pwo2xsf_old.sh $1 $2
pwoExit $?
else
echo "ERROR: PWscf output generated by version < 1.3 !!!"
pwoExit 1
fi
fi
}
And the pwscf version I used is 3.2.3, I don't know whether the script is right or not.
Can anyone help me to solve this problem? Any suggestion is appreciated. Thank you in advance.
With best regards.
Sincerely yours
lilyer
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From giannozz at democritos.it Tue Jul 1 16:13:05 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 01 Jul 2008 16:13:05 +0200
Subject: [Pw_forum] How to handle the i/o error in davcio problem in NEB
calculations
In-Reply-To: <486A3863020000C500166A75@gwiasmtp.uct.ac.za>
References: <486A3863020000C500166A75@gwiasmtp.uct.ac.za>
Message-ID: <486A3B71.6050704@democritos.it>
ABDULRAFIU RAJI wrote:
> At the 11th iterations, and while relaxing the 4th image,
> it suddenly stopped with the following error message:
> [...]from davcio : error # 10
> i/o error in davcio
is this reproducible? if it isn't, you either have flaky disks,
or you are writing via the network using nfs and a not-so-stable
network connection, in my opinion
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Tue Jul 1 16:16:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 01 Jul 2008 16:16:35 +0200
Subject: [Pw_forum] How to handle the i/o error in davcio problem in NEB
calculations
In-Reply-To: <486A3863020000C500166A75@gwiasmtp.uct.ac.za>
References: <486A3863020000C500166A75@gwiasmtp.uct.ac.za>
Message-ID: <486A3C43.5020103@democritos.it>
ABDULRAFIU RAJI wrote:
> [..] But on getting to 4th image, while carrying out the 12th
> iterations, it stopped again, displaying the similar error message
was it restarting from the 1st scf ityeration, or from the 11th?
in the latter case, it was looking for files that presumably were not
there. Check what the code has been writing when retsrting
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From w2agz at pacbell.net Tue Jul 1 17:24:05 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Tue, 1 Jul 2008 08:24:05 -0700
Subject: [Pw_forum] Visualizing MP Meshes, etc.
In-Reply-To: <3039.147.122.5.216.1214900818.squirrel@webmail.sissa.it>
References: <001301c8db34$bf7a6130$3e6f2390$@net>
<3039.147.122.5.216.1214900818.squirrel@webmail.sissa.it>
Message-ID: <006e01c8db8e$80389550$80a9bff0$@net>
Lorenzo, thanks for your response. I'll try what you suggest. -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 Lorenzo Paulatto
Sent: Tuesday, July 01, 2008 1:27 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Visualizing MP Meshes, etc.
On Mar, Luglio 1, 2008 06:41, Paul M. Grant wrote:
> To All:
>
> Is there a tool to both compute Monkhorst-Pack meshes
There is kpoint.x in pwtools/
> and visualize the result (perhaps through XCrysDen?).
Sometimes I use gnuplot: I take columns 2, 3 and 4 from kpoint.x output
and "splot with points". I know it's far from optimal, but it works.
> Also, is there an "XCrysDen look-alike" that can plot paths in k- or
> r-space, a la k-paths in XCrysDen?
I don't know.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
----------------------------------------------------------------
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From vranjan at ncsu.edu Tue Jul 1 17:08:34 2008
From: vranjan at ncsu.edu (Vivek Ranjan)
Date: Tue, 1 Jul 2008 11:08:34 -0400 (EDT)
Subject: [Pw_forum] self consistency does not converge
Message-ID: <46533.152.14.74.117.1214924914.squirrel@webmail.ncsu.edu>
Hello,
I am studying a system with elongated cell on one direction. I am using
"local-TF" for mixing_mode. However, the system does not converge. It does
4 dynamics step and then the self consistency error becomes fixed (does
not change for 100 steps). I am using "damp-pr" for dynamics.
I tried various things like dt = 20 - 100, damp-pr and damp-w, mixing beta
from 0.05 - 0.3. I get into the same condition everytime.
The system is not metallic.
Thanks,
Vivek Ranjan
NCSU
From giannozz at democritos.it Tue Jul 1 17:33:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 01 Jul 2008 17:33:48 +0200
Subject: [Pw_forum] self consistency does not converge
In-Reply-To: <46533.152.14.74.117.1214924914.squirrel@webmail.ncsu.edu>
References: <46533.152.14.74.117.1214924914.squirrel@webmail.ncsu.edu>
Message-ID: <486A4E5C.7060305@democritos.it>
Vivek Ranjan wrote:
> The system is not metallic.
sure? did you try a small broadening?
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From gbilalbegovic at gmail.com Tue Jul 1 20:05:30 2008
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Tue, 1 Jul 2008 20:05:30 +0200
Subject: [Pw_forum] condor grid script
Message-ID: <7332fead0807011105x4d4398e8i5a2106c854f25eaf@mail.gmail.com>
Hello,
I have just started to use a grid. It is not heterogeneous, consists of
similar linux clusters. I would like to submit a simple PWscf job
using the condor script, but I am not able to write a proper command
for the pseudopotential file. For example, the Condor-G submission
script is similar to:
--------------------------------------------
executable =/home/user/espresso-4.0/bin/pw.x
transfer_executable=true
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files =/home/user/espresso-4.0/pseudo/Si.vbc.UPF
universe=grid
grid_resource=gt2 .../jobmanager-sge
output = pw_condor.out
error = pw_condor.err
log = pw_condor.log
input = siscf.in
globusrsl=(jobType=mpi)(count=1)
queue
--------------------------------------------------
Job (the first part of example01) runs, but I do not know how to write
the lines "transfer_input_files", "arguments",..., and/or pseudo_dir=
in siscf.in to read the pseudopotential file. I was also trying by
writing getenv=true.
The error is always:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from readpp : error # 29
file ... Si.vbc.UPF not found
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Thank you for any advice about this problem and/or using the grid and Condor for
espresso jobs.
Best regards,
Goranka Bilalbegovic
Department of Physics, Faculty of Science
University of Zagreb, Croatia
From matteo at umn.edu Tue Jul 1 21:23:31 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Tue, 01 Jul 2008 14:23:31 -0500
Subject: [Pw_forum] Small U for Co in ZnO for LDA+U
In-Reply-To: <414899242.31069@mail.sdu.edu.cn>
References: <414899242.31069@mail.sdu.edu.cn>
Message-ID: <486A8433.8060208@umn.edu>
Dear Shu-jun
it's not totally clear to me whether the 0.31 eV U_Co was computed and
used with occupations of 2.6. If this is the case,
and it works as you say, this looks pretty amazing (and suspicious) to
me (although it is another demonstration that one should look at the
results produced with that U more than at the value of U itself). In
fact the LDA+U functional is designed for occupations between 0 and 1.
Using U_projection_type = 'norm-atomic' is a quick, temporary solution
to the problem but doesn't allow you to compute stresses. Hopefully
this will be fixed soon.
Matteo
??? Shu-jun Hu wrote:
> Dear All,
>
> I would post my comments on the topic of LDA+U calculation of small U_Co.
>
> (1) The self-consistently calculated U_Co is indeed sensitive to the oxidation
> state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a very "small"
> number. However, in Co-doped SnO2, we got a "reasonable" value of 3.7 eV.
> U_projection_type is specified as the default (atomic) in both cases during the
> calculation of U_Co.
>
> (2) The calculated band structure is much sensitive to the value of U_Co and
> U_Co=0.31 eV does have a significant effect with respect to U=0. U_Co=0.31 eV can
> well fit the experimental results (APL 84 4233 (2004), and also J. Appl. Phys. 103
> 07D130 (2008)), where the occupied Co:3d majority state are deep in the valence
> band rather than in the gap. If U_Co=2 to 5 eV is implemented, Nektarios is right:
> a Co-d projected DOS far deep into the valence (completely non sense).
>
> (3) The occupation is larger than 1 but not less than 1 in the "atomic" case. A
> piece of output file is listed in the end.
>
> Best wishes.
>
> shu-jun
>
>
>
> iteration # 1 ecut= 30.00 Ry beta=0.30
> Davidson diagonalization with overlap
> ethr = 1.00E-06, avg # of iterations = 2.0
> enter write_ns
> U( 1) = 0.0000 U( 2) = 5.0000 U( 3) = 0.3100 U( 4) = 0.3100
> alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = 0.0000 alpha(
> 4) = 0.0000
> atom 1 Tr[ns(na)]= 20.2308353
> atom 1 spin 1
> eigenvalues: 2.6157258 2.6161606 2.6163747 2.6230370 2.6231626
> eigenvectors
> 1 -0.1857398 0.4838857 -0.3108623 -0.4315218 0.6697081
> 2 0.7691240 -0.1376398 -0.3613721 -0.4813049 -0.1651042
> 3 -0.6107095 -0.2857263 -0.3371356 -0.4914774 -0.4361008
> 4 0.0275961 0.8118942 0.0830406 -0.0532713 -0.5747457
> 5 -0.0148797 0.0780907 -0.8076006 0.5811597 -0.0609523
> occupations
> 2.616 0.000 0.000 0.000 0.000
> 0.000 2.621 0.000 0.000 -0.003
> 0.000 0.000 2.621 -0.003 0.000
> 0.000 0.000 -0.003 2.619 0.000
> 0.000 -0.003 0.000 0.000 2.618
> atom 1 spin 2
> eigenvalues: 0.6259172 0.6323802 0.6442143 2.6141658 2.6196970
> eigenvectors
> 1 -0.1040632 -0.4885801 -0.2577671 -0.3860893 -0.7314038
> 2 -0.0078294 0.2638155 -0.4985241 -0.7299864 0.3859192
> 3 0.9945218 -0.0535680 -0.0330433 -0.0447136 -0.0704671
> 4 -0.0011093 -0.4865620 0.6672800 -0.4565376 0.3310092
> 5 -0.0058854 -0.6723680 -0.4885442 0.3280686 0.4489790
> occupations
> 0.644 0.008 0.004 -0.004 -0.007
> 0.008 1.998 0.009 0.001 -0.921
> 0.004 0.009 1.989 -0.923 0.001
> -0.004 0.001 -0.923 1.258 -0.009
> -0.007 -0.921 0.001 -0.009 1.247
>
>
>
>
>
>
>
>
>
>
> ------------------------------
> Shujun Hu e-mail: hushujun at 163.com
> Shandong university Phone: +86/0531-88375097
> Jinan, Shandong Province, China, 250100
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From manoj at phys.ufl.edu Tue Jul 1 21:31:48 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Tue, 1 Jul 2008 15:31:48 -0400 (EDT)
Subject: [Pw_forum] complex band of Cu
Message-ID:
Dear PWSCF users,
I have been trying to calculate the band structure of bulk Cu. I tried
two different kind of unit cells, 2 atoms tetragonal and 1 atom
rhombohedron. In case of tetragonal cell, i get the right band structure,
but in the case of rhombohedron, d bands of Cu are not at the right place.
I believe that these calculations should not depend on the choice of unit
cell. I would appreiate if someone could tell me what am I doing wrong?
Attached is the band-structure file I get for rhombohedron unit cell and
my input file is as follows-
&system
ibrav=0
celldm(1)=6.73
nat= 1,
ntyp= 1,
ecutwfc =50.0,
occupations= 'smearing',
smearing='gaussian',
degauss=0.01
/
&electrons
conv_thr = 1.0e-8
mixing_beta=0.7
/
ATOMIC_SPECIES
Cu 63.55 Cu.pbe-paw_kj.UPF
ATOMIC_POSITIONS
Cu 0.0 0.0 0.0
K_POINTS (automatic)
4 4 4 0 0 0
CELL_PARAMETERS
0.5 -0.5 0.0
0.5 0.5 0.0
0.5 0.0 0.5
# complex bands of cu along the 001 direction K_perp=0
cat > cu.cond.in << EOF
&inputcond
outdir='$TMP_DIR/'
prefixl='cu'
band_file ='bands.cu'
ikind=0
energy0=10.d0
denergy=-0.04d0
ewind=3.d0
epsproj=1.d-6
/
1
0.0 0.0 1.0
500
EOF
Regards,
Manoj Srivastava
Graduate Student
University of Florida
Gainesville, USA.
From vegalew at hotmail.com Wed Jul 2 08:56:32 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 2 Jul 2008 14:56:32 +0800
Subject: [Pw_forum] "from pzpotrf : error # 1 problems computing cholesky
decomposition"
Message-ID:
Dear all,
After several iterations of self-consistent calculation, there is an error encountered. And Information is
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from pzpotrf : error # 1
problems computing cholesky decomposition
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
more detail also attached at the bottom.
How does this happen? How to cope with this?
thank you for reading.
Vega Lew
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
Self-consistent Calculation
iteration # 1 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 1.00E-02, avg # of iterations = 3.0
negative rho (up, down): 0.621E-01 0.000E+00
total cpu time spent up to now is 755.25 secs
total energy = -7247.96686204 Ry
Harris-Foulkes estimate = -7258.07931507 Ry
estimated scf accuracy < 22.98796274 Ry
iteration # 2 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 2.39E-03, avg # of iterations = 3.0
negative rho (up, down): 0.619E-01 0.000E+00
total cpu time spent up to now is 1311.84 secs
total energy = -7252.71923993 Ry
Harris-Foulkes estimate = -7254.10096935 Ry
estimated scf accuracy < 4.63104492 Ry
iteration # 3 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 4.82E-04, avg # of iterations = 3.0
negative rho (up, down): 0.623E-01 0.000E+00
total cpu time spent up to now is 1824.24 secs
total energy = -7253.30999271 Ry
Harris-Foulkes estimate = -7253.45932341 Ry
estimated scf accuracy < 0.71665018 Ry
iteration # 4 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 7.47E-05, avg # of iterations = 2.8
negative rho (up, down): 0.651E-01 0.000E+00
total cpu time spent up to now is 2335.96 secs
total energy = -7253.35733981 Ry
Harris-Foulkes estimate = -7253.39732099 Ry
estimated scf accuracy < 0.25146001 Ry
iteration # 5 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 2.62E-05, avg # of iterations = 2.0
negative rho (up, down): 0.642E-01 0.000E+00
total cpu time spent up to now is 2852.68 secs
total energy = -7253.38499360 Ry
Harris-Foulkes estimate = -7253.39168977 Ry
estimated scf accuracy < 0.04134125 Ry
iteration # 6 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 4.31E-06, avg # of iterations = 14.0
negative rho (up, down): 0.646E-01 0.000E+00
total cpu time spent up to now is 3654.50 secs
total energy = -7253.38599588 Ry
Harris-Foulkes estimate = -7253.38854981 Ry
estimated scf accuracy < 0.01379492 Ry
iteration # 7 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from pzpotrf : error # 1
problems computing cholesky decomposition
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
_________________________________________________________________
Explore the seven wonders of the world
http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
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From smogunov at sissa.it Wed Jul 2 08:01:19 2008
From: smogunov at sissa.it (Alexander)
Date: Wed, 2 Jul 2008 08:01:19 +0200
Subject: [Pw_forum] complex band of Cu
In-Reply-To:
References:
Message-ID: <200807020801.19808.smogunov@sissa.it>
Dear Manoj
The PWCOND code works only for monoclinic cells
where the a3 vector of the unit cell (defining the transport direction) is
ORTHOGONAL to both a1 and a2. You SHOULD therefore use the tetragonal unit
cell with two atoms per cell.
Regards,
Alexander
On Tuesday 01 July 2008 21:31, Manoj Srivastava wrote:
> Dear PWSCF users,
> I have been trying to calculate the band structure of bulk Cu. I tried
> two different kind of unit cells, 2 atoms tetragonal and 1 atom
> rhombohedron. In case of tetragonal cell, i get the right band structure,
> but in the case of rhombohedron, d bands of Cu are not at the right place.
> I believe that these calculations should not depend on the choice of unit
> cell. I would appreiate if someone could tell me what am I doing wrong?
> Attached is the band-structure file I get for rhombohedron unit cell and
> my input file is as follows-
>
> &system
> ibrav=0
> celldm(1)=6.73
> nat= 1,
> ntyp= 1,
> ecutwfc =50.0,
> occupations= 'smearing',
> smearing='gaussian',
> degauss=0.01
> /
> &electrons
> conv_thr = 1.0e-8
> mixing_beta=0.7
> /
> ATOMIC_SPECIES
> Cu 63.55 Cu.pbe-paw_kj.UPF
> ATOMIC_POSITIONS
> Cu 0.0 0.0 0.0
> K_POINTS (automatic)
> 4 4 4 0 0 0
> CELL_PARAMETERS
> 0.5 -0.5 0.0
> 0.5 0.5 0.0
> 0.5 0.0 0.5
>
> # complex bands of cu along the 001 direction K_perp=0
> cat > cu.cond.in << EOF
> &inputcond
> outdir='$TMP_DIR/'
> prefixl='cu'
> band_file ='bands.cu'
> ikind=0
> energy0=10.d0
> denergy=-0.04d0
> ewind=3.d0
> epsproj=1.d-6
> /
> 1
> 0.0 0.0 1.0
> 500
> EOF
>
> Regards,
> Manoj Srivastava
> Graduate Student
> University of Florida
> Gainesville, USA.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From paulatto at sissa.it Wed Jul 2 10:40:26 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 2 Jul 2008 10:40:26 +0200 (CEST)
Subject: [Pw_forum] "from pzpotrf : error # 1 problems computing
cholesky decomposition"
In-Reply-To:
References:
Message-ID: <21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
On Mer, Luglio 2, 2008 08:56, vega lew wrote:
> After several iterations of self-consistent calculation, there is an
> error encountered.
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> from pzpotrf : error # 1
> problems computing cholesky decomposition
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The subroutine is called during parallel diagonalization, so it may be a
problem in you mpi setup as much as a problem of QE.
If the former is true, you can try to restart the calculation and see what
happens.
If it fails, you can also try to restart from scratch and see if it stops
at the same point.
If it stops at the same point, it is probably a bug in the parallel
implementation, you can try setting diagonalization='david-serial', which
should work around it but is slower for large systems.
Please let us know the result of your tests.
bye
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
----------------------------------------------------------------
SISSA Webmail https://webmail.sissa.it/
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From vegalew at hotmail.com Wed Jul 2 13:06:16 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 2 Jul 2008 19:06:16 +0800
Subject: [Pw_forum] "from pzpotrf : error # 1 problems computing
cholesky decomposition"
In-Reply-To: <21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
References:
<21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
Message-ID:
Dear sir
I have tested a scecond run the error occurred at the same point.
but the error message seems to be a little different. This time is
" from pzpotrf : error # 841" not the "error # 1"
vega
Initial potential from superposition of free atoms
Check: negative starting charge= -0.059468
starting charge 919.99822, renormalised to 960.00000
negative rho (up, down): 0.621E-01 0.000E+00
Starting wfc are 720 atomic wfcs
total cpu time spent up to now is 193.35 secs
per-process dynamical memory: 440.5 Mb
Self-consistent Calculation
iteration # 1 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 1.00E-02, avg # of iterations = 3.0
negative rho (up, down): 0.621E-01 0.000E+00
total cpu time spent up to now is 751.23 secs
total energy = -7247.96686204 Ry
Harris-Foulkes estimate = -7258.07931507 Ry
estimated scf accuracy < 22.98796274 Ry
iteration # 2 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 2.39E-03, avg # of iterations = 3.0
negative rho (up, down): 0.619E-01 0.000E+00
total cpu time spent up to now is 1305.89 secs
total energy = -7252.71923993 Ry
Harris-Foulkes estimate = -7254.10096935 Ry
estimated scf accuracy < 4.63104492 Ry
iteration # 3 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 4.82E-04, avg # of iterations = 3.0
negative rho (up, down): 0.623E-01 0.000E+00
total cpu time spent up to now is 1815.69 secs
total energy = -7253.30999271 Ry
Harris-Foulkes estimate = -7253.45932341 Ry
estimated scf accuracy < 0.71665018 Ry
iteration # 4 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 7.47E-05, avg # of iterations = 2.8
negative rho (up, down): 0.651E-01 0.000E+00
total cpu time spent up to now is 2328.29 secs
total energy = -7253.35733982 Ry
Harris-Foulkes estimate = -7253.39732100 Ry
estimated scf accuracy < 0.25146000 Ry
iteration # 5 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 2.62E-05, avg # of iterations = 2.0
negative rho (up, down): 0.642E-01 0.000E+00
total cpu time spent up to now is 2844.30 secs
total energy = -7253.38499361 Ry
Harris-Foulkes estimate = -7253.39168977 Ry
estimated scf accuracy < 0.04134125 Ry
iteration # 6 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
ethr = 4.31E-06, avg # of iterations = 14.0
negative rho (up, down): 0.646E-01 0.000E+00
total cpu time spent up to now is 3646.59 secs
total energy = -7253.38599587 Ry
Harris-Foulkes estimate = -7253.38854982 Ry
estimated scf accuracy < 0.01379492 Ry
iteration # 7 ecut= 25.00 Ry beta=0.30
Davidson diagonalization with overlap
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from pzpotrf : error # 841
problems computing cholesky decomposition
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
[node5:16759] MPI_ABORT invoked on rank 18 in communicator MPI_COMM_WORLD with errorcode 0
forrtl: error (78): process killed (SIGTERM)
Vega Lew
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
_________________________________________________________________
Discover the new Windows Vista
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From wangqj1 at 126.com Thu Jul 3 04:45:05 2008
From: wangqj1 at 126.com (wangqj1)
Date: Thu, 3 Jul 2008 10:45:05 +0800 (CST)
Subject: [Pw_forum] How to compute surface energy and adsorbed energy ?
Message-ID: <7139883.84421215053105723.JavaMail.coremail@bj126app27.126.com>
Dear pwscf users;
Could someone tell me 'how to compute surface energy and adsorbed energy '?
whether the surface energy is the whole energy or not ?
I am looking forward to your advice .
Thanks!
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From manoj at phys.ufl.edu Thu Jul 3 05:32:03 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Wed, 2 Jul 2008 23:32:03 -0400 (EDT)
Subject: [Pw_forum] complex band of Cu
In-Reply-To: <200807020801.19808.smogunov@sissa.it>
Message-ID:
Dear Alexander and PWSCF users,
Thank you very much for your quick response. I am still wondering the
reason behind it. Is it beacause of that when we have different cell than
tetragonal, we loose the inversion symmetry in z direction?
I wish to calculate the complex band for an arbitrary monoclinic cell and
willing to modify to code, would it be lot of work? also what needs to be
modified? It would be great if you could suggest me something.
Regards,
Manoj
On Wed, 2
Jul 2008, Alexander wrote:
> Dear Manoj
> The PWCOND code works only for monoclinic cells
> where the a3 vector of the unit cell (defining the transport direction) is
> ORTHOGONAL to both a1 and a2. You SHOULD therefore use the tetragonal unit
> cell with two atoms per cell.
> Regards,
> Alexander
>
>
> On Tuesday 01 July 2008 21:31, Manoj Srivastava wrote:
> > Dear PWSCF users,
> > I have been trying to calculate the band structure of bulk Cu. I tried
> > two different kind of unit cells, 2 atoms tetragonal and 1 atom
> > rhombohedron. In case of tetragonal cell, i get the right band structure,
> > but in the case of rhombohedron, d bands of Cu are not at the right place.
> > I believe that these calculations should not depend on the choice of unit
> > cell. I would appreiate if someone could tell me what am I doing wrong?
> > Attached is the band-structure file I get for rhombohedron unit cell and
> > my input file is as follows-
> >
> > &system
> > ibrav=0
> > celldm(1)=6.73
> > nat= 1,
> > ntyp= 1,
> > ecutwfc =50.0,
> > occupations= 'smearing',
> > smearing='gaussian',
> > degauss=0.01
> > /
> > &electrons
> > conv_thr = 1.0e-8
> > mixing_beta=0.7
> > /
> > ATOMIC_SPECIES
> > Cu 63.55 Cu.pbe-paw_kj.UPF
> > ATOMIC_POSITIONS
> > Cu 0.0 0.0 0.0
> > K_POINTS (automatic)
> > 4 4 4 0 0 0
> > CELL_PARAMETERS
> > 0.5 -0.5 0.0
> > 0.5 0.5 0.0
> > 0.5 0.0 0.5
> >
> > # complex bands of cu along the 001 direction K_perp=0
> > cat > cu.cond.in << EOF
> > &inputcond
> > outdir='$TMP_DIR/'
> > prefixl='cu'
> > band_file ='bands.cu'
> > ikind=0
> > energy0=10.d0
> > denergy=-0.04d0
> > ewind=3.d0
> > epsproj=1.d-6
> > /
> > 1
> > 0.0 0.0 1.0
> > 500
> > EOF
> >
> > Regards,
> > Manoj Srivastava
> > Graduate Student
> > University of Florida
> > Gainesville, 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
>
From baroni at sissa.it Thu Jul 3 08:36:34 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 3 Jul 2008 08:36:34 +0200
Subject: [Pw_forum] How to compute surface energy and adsorbed energy ?
In-Reply-To: <7139883.84421215053105723.JavaMail.coremail@bj126app27.126.com>
References: <7139883.84421215053105723.JavaMail.coremail@bj126app27.126.com>
Message-ID:
On Jul 3, 2008, at 4:45 AM, wangqj1 wrote:
> Dear pwscf users;
Dear Mr. Unknown
> Could someone tell me 'how to compute surface energy and adsorbed
> energy '?
I am afraid, this question would be more appropriate for your
supervisor than for this forum.
in any event, think of the definition of surface energy:
"surface energy" = energy necessary to cut an infinite solid into two
semi-infinite parts (or in many slabs, for that matter, provided you
count properly the number of slabs). right? now you can calculate the
energy of bulk system (the result is infiite: what you get is an
energy per unit volume, or an energy per atom). you can also calculate
the energy of a system made of many (infinite, because of periodic
boundary conditions) slabs. The enrgy per atom will be different. the
difference will be proprortional to the surface area ... can you see
now how the calculation would proceed?
The same would apply to "adsorption" (NOT "adsorbed") energy = energy
of a surface (or a slam, for that matter) with an adsorbed molecule,
minus the sum of energy of an isolated (clean) surface and of an
isolated molecule.
> whether the surface energy is the whole energy or not ?
do not undesrtand what you mean. think of the definitiion above
> I am looking forward to your advice .
> Thanks!
would be so kind as to provide your name and full affiliation, the
next time you write to this forum?
Thanks - SB
>
>
>
>
>
> ??????????Qosmio??????
> ??????_______________________________________________
> 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
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Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From marzari at MIT.EDU Thu Jul 3 09:10:33 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 03 Jul 2008 09:10:33 +0200
Subject: [Pw_forum] How to compute surface energy and adsorbed energy ?
In-Reply-To: <7139883.84421215053105723.JavaMail.coremail@bj126app27.126.com>
References: <7139883.84421215053105723.JavaMail.coremail@bj126app27.126.com>
Message-ID: <486C7B69.5030102@mit.edu>
wangqj1 wrote:
> Dear pwscf users;
> Could someone tell me 'how to compute surface energy and adsorbed energy '?
> whether the surface energy is the whole energy or not ?
> I am looking forward to your advice .
> Thanks!
>
>
To follow-up on Stefano Baroni's suggestions, you could also look
at the first lectures of:
http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-320Spring-2005/CourseHome/index.htm
Both Lab 1 (classical potentials) and Lab 2 (quantum, using
Quantum-ESPRESSO) deal with surface energies.
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 marzari at MIT.EDU Thu Jul 3 09:16:40 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 03 Jul 2008 09:16:40 +0200
Subject: [Pw_forum] Small U for Co in ZnO for LDA+U
In-Reply-To: <414899242.31069@mail.sdu.edu.cn>
References: <414899242.31069@mail.sdu.edu.cn>
Message-ID: <486C7CD8.5050802@mit.edu>
Dear Shu-jun, All,
I get very nervous about using U with non-normalized occupations. Even
if U can have some amount of pseudopotential dependency, using it
with unnormalized projectors really messes up any meaningful discussion
of occupation values and U values.
And of course referees would go nuts at seeing that a U=0.3eV is
relevant - the reason is that that number doesn't really make sense.
To me, it's an option ("atomic") that should be removed altogether from
the code - others might have other opinions, but if we leave it as it
stands, we risk creating an enormous amount of headaches down the line.
nicola
??? Shu-jun Hu wrote:
> Dear All,
>
> I would post my comments on the topic of LDA+U calculation of small U_Co.
>
> (1) The self-consistently calculated U_Co is indeed sensitive to the oxidation
> state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a very "small"
> number. However, in Co-doped SnO2, we got a "reasonable" value of 3.7 eV.
> U_projection_type is specified as the default (atomic) in both cases during the
> calculation of U_Co.
>
> (2) The calculated band structure is much sensitive to the value of U_Co and
> U_Co=0.31 eV does have a significant effect with respect to U=0. U_Co=0.31 eV can
> well fit the experimental results (APL 84 4233 (2004), and also J. Appl. Phys. 103
> 07D130 (2008)), where the occupied Co:3d majority state are deep in the valence
> band rather than in the gap. If U_Co=2 to 5 eV is implemented, Nektarios is right:
> a Co-d projected DOS far deep into the valence (completely non sense).
>
> (3) The occupation is larger than 1 but not less than 1 in the "atomic" case. A
> piece of output file is listed in the end.
>
> Best wishes.
--
---------------------------------------------------------------------
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 paulatto at sissa.it Thu Jul 3 10:28:53 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 3 Jul 2008 10:28:53 +0200 (CEST)
Subject: [Pw_forum] "from pzpotrf : error # 1 problems computing
cholesky decomposition"
In-Reply-To:
References:
<21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
Message-ID: <20590.147.122.5.216.1215073733.squirrel@webmail.sissa.it>
On Mer, Luglio 2, 2008 13:06, vega lew wrote:
> I have tested a scecond run the error occurred at the same point.
> but the error message seems to be a little different. This time is
> " from pzpotrf : error # 841" not the "error # 1"
Thank you, unluckily the two errors are probably equivalent.
I'm not really in that part of code, anyway in order to find out any more
I should know if pw was using the distributed algorithm: just paste the
full output as it is printed in the first lines.
It may be that during a vc-relax step the cell shrunk a lot so that the
atoms got very close (you can check this). It happened to me a few times,
but it is rather uncommon. You can try changing the vc-relax parameters to
take smaller steps.
Anyway I'm going to ask C. Cavazzoni, who implemented that algorithm, to
see if he can provide some insight.
bye
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
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From lathiot at googlemail.com Thu Jul 3 13:22:58 2008
From: lathiot at googlemail.com (Nektarios Lathiotakis)
Date: Thu, 3 Jul 2008 14:22:58 +0300
Subject: [Pw_forum] Small U for Co in ZnO for LDA+U
In-Reply-To: <486C7CD8.5050802@mit.edu>
References: <414899242.31069@mail.sdu.edu.cn> <486C7CD8.5050802@mit.edu>
Message-ID: <65c086de0807030422h78aea2a2qca3dd83493bf6ce4@mail.gmail.com>
Hi all,
the option 'atomic' is the default and maybe that should change? I dont
know. It created
me a lot of trouble however. I confirm Shu-jun numbers (2.6 occupations)...
I get the same.
I think we used the same functional and consequently potentials for
Zn, O, Co (PBE functional).
Shu-jun, did you use the same pseudo for Co in ZnO and SnO2?
With the 'atomic' option in this case , U_Co=0.5 is enough to push all
Co-d states into the valence. The rule I found is that the U_Co with option
'atomic' has the same effect as 8*U with option 'ortho-atomic' on the Co-d
projected DOS.
So the self consistent value of Shu-jun correspond to U=2.5eV with
ortho-atomic. Of course this applies to
the position of Co-d occupied bands. Dont know about other properties. I
will have to
repeat calculations with 'ortho-atomic' or 'norm-atomic' option.
Thanks for the discussion
Nektarios
On Thu, Jul 3, 2008 at 10:16 AM, Nicola Marzari wrote:
>
>
>
> Dear Shu-jun, All,
>
>
> I get very nervous about using U with non-normalized occupations. Even
> if U can have some amount of pseudopotential dependency, using it
> with unnormalized projectors really messes up any meaningful discussion
> of occupation values and U values.
>
> And of course referees would go nuts at seeing that a U=0.3eV is
> relevant - the reason is that that number doesn't really make sense.
>
> To me, it's an option ("atomic") that should be removed altogether from
> the code - others might have other opinions, but if we leave it as it
> stands, we risk creating an enormous amount of headaches down the line.
>
> nicola
>
>
>
>
> ??? Shu-jun Hu wrote:
> > Dear All,
> >
> > I would post my comments on the topic of LDA+U calculation of small U_Co.
> >
> > (1) The self-consistently calculated U_Co is indeed sensitive to the
> oxidation
> > state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a very
> "small"
> > number. However, in Co-doped SnO2, we got a "reasonable" value of 3.7 eV.
> > U_projection_type is specified as the default (atomic) in both cases
> during the
> > calculation of U_Co.
> >
> > (2) The calculated band structure is much sensitive to the value of U_Co
> and
> > U_Co=0.31 eV does have a significant effect with respect to U=0.
> U_Co=0.31 eV can
> > well fit the experimental results (APL 84 4233 (2004), and also J. Appl.
> Phys. 103
> > 07D130 (2008)), where the occupied Co:3d majority state are deep in the
> valence
> > band rather than in the gap. If U_Co=2 to 5 eV is implemented, Nektarios
> is right:
> > a Co-d projected DOS far deep into the valence (completely non sense).
> >
> > (3) The occupation is larger than 1 but not less than 1 in the "atomic"
> case. A
> > piece of output file is listed in the end.
> >
> > Best wishes.
>
>
>
>
> --
> ---------------------------------------------------------------------
> 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
>
--
--------------------------------------------------------------------
Dr. Nektarios N. Lathiotakis
--------------------------------------------------------------------
Theoretical and Physical Chemistry Institute
National Hellenic Research Foundation
Vass. Constantinou 48, GR-11635,
Athens, Greece
--------------------------------------------------------------------
Tel: +30 210 7273805 FAX: +30 210 7273794
Inst. secretary: +30 210 7273792, +30 210 7273795
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From meisam_a84 at yahoo.com Thu Jul 3 13:46:51 2008
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Thu, 3 Jul 2008 04:46:51 -0700 (PDT)
Subject: [Pw_forum] the wave function after scf calculation
Message-ID: <878424.96651.qm@web30608.mail.mud.yahoo.com>
Dear all
?how can i get the converged wave function?in a?scf calculation?
M.Aghtar
the?Msc student
physics?department of Kashan university?
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From paulatto at sissa.it Thu Jul 3 14:14:15 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 3 Jul 2008 14:14:15 +0200 (CEST)
Subject: [Pw_forum] the wave function after scf calculation
In-Reply-To: <878424.96651.qm@web30608.mail.mud.yahoo.com>
References: <878424.96651.qm@web30608.mail.mud.yahoo.com>
Message-ID: <29054.147.122.5.216.1215087255.squirrel@webmail.sissa.it>
On Gio, Luglio 3, 2008 13:46, meisam aghtar wrote:
> Dear all
> ?how can i get the converged wave function?in a?scf calculation?
Dear Meisam,
you don't have one wavefunction, but one Kohn-Sham single-particle
wavefunction per kpoint per band. You can use pp.x to extract them after
the calculation is finished.
Please see the pp.x documentation for details (espresso/Doc/INPUT_PP for
Q.E 3.x, espresso/Doc/INPUT_PP.html for qe 4.0)
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
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From vegalew at hotmail.com Thu Jul 3 16:00:27 2008
From: vegalew at hotmail.com (vega lew)
Date: Thu, 3 Jul 2008 22:00:27 +0800
Subject: [Pw_forum] FW: cell optimization results seems to be a little
strange
Message-ID:
Dear all,
Thank to all your help, I could run a Q-E calculation on my cluster more correctly. Now I can learn to do some
simple calculations.
My first job is to calculate the Anatase-TiO2 lattice cell parameter using Q-E and compare it with literature.
I have tested the BFGS for vc-relax, but the cell parameters changed so much that an error was occured with
the information 'non orthogonal operation'. Then I used a symmetry-conserving algorithm as the QE manual
said. The input file as following,
&CONTROL
title = 'Anatase lattice' ,
calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
outdir = '/home/vega/espresso-4.0/tmp/' ,
wfcdir = '/tmp/' ,
pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
prefix = 'Anatase lattice default' ,
disk_io = 'none' ,
etot_conv_thr = 0.000000735 ,
forc_conv_thr = 0.0011668141375 ,
nstep = 1000 ,
/
&SYSTEM
ibrav = 6,
celldm(1) = 7.135605333,
celldm(3) = 2.5121822033898305084745762711864,
nat = 12,
ntyp = 2,
ecutwfc = 25 ,
ecutrho = 200 ,
/
&ELECTRONS
conv_thr = 7.3D-8 ,
/
&IONS
ion_dynamics = 'damp' ,
/
&CELL
cell_dynamics = 'damp-w' ,
/
ATOMIC_SPECIES
Ti 47.86700 Ti.pw91-sp-van_ak.UPF
O 15.99940 O.pw91-van_ak.UPF
ATOMIC_POSITIONS angstrom
Ti 0.000000000 0.000000000 0.000000000
Ti 1.888000000 1.888000000 4.743000000
Ti 0.000000000 1.888000000 2.372000000
Ti 1.888000000 0.000000000 7.115000000
O 0.000000000 0.000000000 1.973000000
O 1.888000000 1.888000000 6.716000000
O 0.000000000 1.888000000 4.345000000
O 1.888000000 0.000000000 9.088000000
O 1.888000000 0.000000000 5.141000000
O 0.000000000 1.888000000 0.398000000
O 1.888000000 1.888000000 2.770000000
O 0.000000000 0.000000000 7.513000000
K_POINTS automatic
7 7 3 1 1 1
The calculation can be done nearly 600 fs. The last few lines of results file is shown at the bottom.
But the cell parameters for Anatase lattice seems to be not perfectly match the results in literature.
In the literature, Journal of Physical Chemistry B, 2006, 110, 7464, the author used a conjugate-gradient
or quasi-Newton scheme as implemented in VASP to optimaize the geometries. And the cell parameters
are a = b = 3.803 A c = 9.603 A c/a = 2.525. But my Q-E result, a= 3.7546166A b= 3.75461729A c= 9.3911A
seems to be much smaller than his. I tried times times again, even, the starting geometry is from the
exprimental data for Journal of the American Society, 1987,109, 3639, which was also cited by him, the
result was still that small.
I also have tested it in CASTEP, using BFGS and same precision. The CASTEP results were a = b =3.798668A
c = 9.693431A c/a = 2.5518, which seemed to be more close to the literature results. The starting geometry
was also from Journal of the American Society, 1987,109, 3639.
I think maybe some parameter in my Q-E input file was wrong. Could you please point it to me?
thank you for reading. I am waiting for your responding.
Vega Lew
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 paulatto at sissa.it Thu Jul 3 16:31:02 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 3 Jul 2008 16:31:02 +0200 (CEST)
Subject: [Pw_forum] FW: cell optimization results seems to be a little
strange
In-Reply-To:
References:
Message-ID: <18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
On Gio, Luglio 3, 2008 16:00, vega lew wrote:
> I have tested the BFGS for vc-relax, but the cell parameters changed so
> much that an error was occured with the information 'non orthogonal
> operation'.
This error should be fixed in CVS version of QE, if you wish to use bfgs
you can wait for QE 4.0.1 (which should be out soon) or overwrite the file
PW/stress.f90 with the one I've attached (and recompile pw.x).
Hope this helps.
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
+39 040 3787 511
http://people.sissa.it/~paulatto/
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From vegalew at hotmail.com Thu Jul 3 17:17:24 2008
From: vegalew at hotmail.com (vega lew)
Date: Thu, 3 Jul 2008 23:17:24 +0800
Subject: [Pw_forum] FW: cell optimization results seems to be a little
strange
In-Reply-To: <18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
References:
<18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
Message-ID:
Dear sir,
It's so kind of you to send me the file. I'll try it immediately.
I'll show my results as soon as possible.
regards,
vega
Vega Lew
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
> Date: Thu, 3 Jul 2008 16:31:02 +0200
> From: paulatto at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] FW: cell optimization results seems to be a little strange
>
> On Gio, Luglio 3, 2008 16:00, vega lew wrote:
> > I have tested the BFGS for vc-relax, but the cell parameters changed so
> > much that an error was occured with the information 'non orthogonal
> > operation'.
>
> This error should be fixed in CVS version of QE, if you wish to use bfgs
> you can wait for QE 4.0.1 (which should be out soon) or overwrite the file
> PW/stress.f90 with the one I've attached (and recompile pw.x).
>
> Hope this helps.
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> +39 040 3787 511
> http://people.sissa.it/~paulatto/
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
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From holger.hesske at chem.ethz.ch Thu Jul 3 17:00:40 2008
From: holger.hesske at chem.ethz.ch (Holger Hesske)
Date: Thu, 3 Jul 2008 17:00:40 +0200
Subject: [Pw_forum] FW: cell optimization results seems to be a little
strange
In-Reply-To:
References:
Message-ID: <200807031700.40555.holger.hesske@chem.ethz.ch>
Dear vega,
next to the suggestion of Lorenzo to use the bfgs algorithm, the point in
your input is the missing timestep for the cell dynamics with the
Wentzcovitch algorithm. (see quantum-wiki) It looks like you got a
non-evolving (or almost non-evolving) dynamics.
A second, more general remark on you input: Set up only the variables you
really need (as Axel pointet out in several mails before: every non-written
line is per definition a correct one).
It doesn't make any sense to set numbers with more than 14 digits (the code
does not handle this) and in most cases 8 digits is more than enough,
Think about, why you set etot_conv_thr so tight (don't mix it up with
conv_thr, which seemed to be sloppy for this calculation ), while you set
forc_conv_thr to be really sloppy? (Btw, is there any reason to set the
cutoffs/thresholds to such precision?)
Hope this helps,
Holger
--
Dr. Holger Hesske
Inst.f.Chemie-/Bioingenieurwissenschaft.
Wolfgang-Pauli-Str. 10
ETH H?nggerberg, HCI E 133
CH-8093 Z?rich
Tel: +41 44 633 66 19
Fax: +41 44 632 11 63
E-Mail: holger.hesske at chem.ethz.ch
From vegalew at hotmail.com Thu Jul 3 18:51:38 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 4 Jul 2008 00:51:38 +0800
Subject: [Pw_forum] FW: cell optimization results seems to be a
little strange
In-Reply-To: <200807031700.40555.holger.hesske@chem.ethz.ch>
References:
<200807031700.40555.holger.hesske@chem.ethz.ch>
Message-ID:
Dear Holger,
Thank your for responding.
> next to the suggestion of Lorenzo to use the bfgs algorithm, the point in
> your input is the missing timestep for the cell dynamics with the
> Wentzcovitch algorithm. (see quantum-wiki) It looks like you got a
> non-evolving (or almost non-evolving) dynamics.
I have done the BFGS. And get the similar results. Both of Wentzcovitch and BFGS of QE
undervalue the cell parameters of anatase from my test. I'll show you my BFGS results soon.
Thank you for your point out that timestep is missing. But I don't know how to choose a proper
value for it. I'll google it later but not now. I think BFGS maybe handle the cell parametter calculation.
> A second, more general remark on you input: Set up only the variables you
> really need (as Axel pointet out in several mails before: every non-written
> line is per definition a correct one).
> It doesn't make any sense to set numbers with more than 14 digits (the code
> does not handle this) and in most cases 8 digits is more than enough,
I see. Thank you
> Think about, why you set etot_conv_thr so tight (don't mix it up with
> conv_thr, which seemed to be sloppy for this calculation ), while you set
> forc_conv_thr to be really sloppy? (Btw, is there any reason to set the
> cutoffs/thresholds to such precision?)
Many litterature doing so. The force threshold is usually set as 0.03eV and 0.05eV
for larger system. the cutoff in literature can be 380 or 400eV sometimes.
I'm only doing repeat work and learning how to do a perfect calculation.
Also the conv_thr and etot_conv_thr is taken from CASTEP calculation directly. Others
doing so of the same system is the only reason. I'm a beginner of PWscf and DFT
calculation. So I think doing repeat work of others and discuss with skilled people may be the
best way for me. What I'm doing now is something more like a homework rather than
the research work. I'm learning to using PWscf. Thank you for your help.
Vega Lew
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 vegalew at hotmail.com Thu Jul 3 19:12:26 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 4 Jul 2008 01:12:26 +0800
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
In-Reply-To:
References:
<18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
Message-ID:
Dear all,
Paulatto gave me the new file for BFGS calculation. I have recompiled my QE and finished the same calculation
for Anatase cell parameters. The results is my calculation can be finished without stop at errors. But the parameters
is still smaller than literature both majority DFT calculation and experimental data. The parameters are, a=3.7559
b=3.75561 c=9.3978, respectively.
My input file as follows,
&CONTROL
title = 'Anatase lattice' ,
calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
outdir = '/home/vega/espresso-4.0/tmp/' ,
wfcdir = '/tmp/' ,
pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
prefix = 'Anatase lattice default' ,
disk_io = 'none' ,
etot_conv_thr = 0.000000735 ,
forc_conv_thr = 0.0011668141375 ,
nstep = 1000 ,
/
&SYSTEM
ibrav = 6,
celldm(1) = 7.1469,
celldm(3) = 2.5124,
nat = 12,
ntyp = 2,
ecutwfc = 25 ,
ecutrho = 200 ,
/
&ELECTRONS
conv_thr = 7.3D-8 ,
/
&IONS
ion_dynamics = 'bfgs' ,
/
&CELL
cell_dynamics = 'bfgs' ,
/
ATOMIC_SPECIES
Ti 47.86700 Ti.pw91-sp-van_ak.UPF
O 15.99940 O.pw91-van_ak.UPF
ATOMIC_POSITIONS angstrom
Ti 0.000000000 0.000000000 0.000000000
Ti 1.888000000 1.888000000 4.743000000
Ti 0.000000000 1.888000000 2.372000000
Ti 1.888000000 0.000000000 7.115000000
O 0.000000000 0.000000000 1.973000000
O 1.888000000 1.888000000 6.716000000
O 0.000000000 1.888000000 4.345000000
O 1.888000000 0.000000000 9.088000000
O 1.888000000 0.000000000 5.141000000
O 0.000000000 1.888000000 0.398000000
O 1.888000000 1.888000000 2.770000000
O 0.000000000 0.000000000 7.513000000
K_POINTS automatic
4 4 2 1 1 1
I think there must be something wrong with my input file. Could you please do me a
favor tell me what's wrong and why the cell parameters so small I'm thinking about it
day and night.
By the way, I note that CASTEP has find 32 symmetry operations of my cell. My cell is
a standard anatase crystall. But Q-E only can find 4 at most since I adjust parameters of
~/espresso-4.0/PW/eqvect.f90. Do this matter effect my results significantly?
I'm look forwar for your advice.
Vega Lew
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 marzari at MIT.EDU Thu Jul 3 19:18:20 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 03 Jul 2008 19:18:20 +0200
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
In-Reply-To:
References: <18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
Message-ID: <486D09DC.9080508@mit.edu>
>
> I'm look forwar for your advice.
Try rutile. Try Ti metal. Try an oxygen molecule. Do they all work ?
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 manoj at phys.ufl.edu Thu Jul 3 19:22:21 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Thu, 3 Jul 2008 13:22:21 -0400 (EDT)
Subject: [Pw_forum] complex band of Cu (fwd)
Message-ID:
Dear PWSCF users,
my advisor is interested in the following question. Any suggestions?
-manoj
---------- Forwarded message ----------
Date: Thu, 03 Jul 2008 11:38:14 -0400
From: Xiaoguang Zhang
Reply-To: zhangx at ornl.gov
To: Manoj Srivastava , pw_forum at pwscf.org
Cc: zhangx at ornl.gov
Subject: Re: [Pw_forum] complex band of Cu (fwd)
Thanks for the reply. Even though we're experimenting with the (100)
direction which does allow a 2 atom/cell tetragonal unit which yields
the correct band structure, we are really interested in the (111)
complex bands. Why is it necessary to use a3 to define the transport
direction? Wouldn't it be simpler and conceptually clearer to define the
transport direction to be the norm of the base plane?
Thanks,
Xiaoguang
Manoj Srivastava wrote:
>
> ---------- Forwarded message ----------
> Date: Wed, 2 Jul 2008 08:01:19 +0200
> From: Alexander
> Reply-To: PWSCF Forum
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] complex band of Cu
>
> Dear Manoj
> The PWCOND code works only for monoclinic cells
> where the a3 vector of the unit cell (defining the transport direction) is
> ORTHOGONAL to both a1 and a2. You SHOULD therefore use the tetragonal unit
> cell with two atoms per cell.
> Regards,
> Alexander
>
>
> On Tuesday 01 July 2008 21:31, Manoj Srivastava wrote:
>
>>Dear PWSCF users,
>> I have been trying to calculate the band structure of bulk Cu. I tried
>>two different kind of unit cells, 2 atoms tetragonal and 1 atom
>>rhombohedron. In case of tetragonal cell, i get the right band structure,
>>but in the case of rhombohedron, d bands of Cu are not at the right place.
>>I believe that these calculations should not depend on the choice of unit
>>cell. I would appreiate if someone could tell me what am I doing wrong?
>>Attached is the band-structure file I get for rhombohedron unit cell and
>>my input file is as follows-
>>
>>&system
>> ibrav=0
>> celldm(1)=6.73
>> nat= 1,
>> ntyp= 1,
>> ecutwfc =50.0,
>> occupations= 'smearing',
>> smearing='gaussian',
>> degauss=0.01
>> /
>> &electrons
>> conv_thr = 1.0e-8
>> mixing_beta=0.7
>> /
>> ATOMIC_SPECIES
>> Cu 63.55 Cu.pbe-paw_kj.UPF
>> ATOMIC_POSITIONS
>> Cu 0.0 0.0 0.0
>>K_POINTS (automatic)
>>4 4 4 0 0 0
>>CELL_PARAMETERS
>> 0.5 -0.5 0.0
>> 0.5 0.5 0.0
>> 0.5 0.0 0.5
>>
>># complex bands of cu along the 001 direction K_perp=0
>>cat > cu.cond.in << EOF
>> &inputcond
>> outdir='$TMP_DIR/'
>> prefixl='cu'
>> band_file ='bands.cu'
>> ikind=0
>> energy0=10.d0
>> denergy=-0.04d0
>> ewind=3.d0
>> epsproj=1.d-6
>> /
>> 1
>> 0.0 0.0 1.0
>> 500
>>EOF
>>
>>Regards,
>>Manoj Srivastava
>>Graduate Student
>>University of Florida
>>Gainesville, 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
>
From akohlmey at cmm.chem.upenn.edu Thu Jul 3 19:21:07 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 3 Jul 2008 13:21:07 -0400 (EDT)
Subject: [Pw_forum] FW: cell optimization results seems to be a little
strange
In-Reply-To:
References:
<200807031700.40555.holger.hesske@chem.ethz.ch>
Message-ID:
On Fri, 4 Jul 2008, vega lew wrote:
VL> > Think about, why you set etot_conv_thr so tight (don't mix it up with
VL> > conv_thr, which seemed to be sloppy for this calculation ), while you set
VL> > forc_conv_thr to be really sloppy? (Btw, is there any reason to set the
VL> > cutoffs/thresholds to such precision?)
VL>
VL> Many litterature doing so. The force threshold is usually set as 0.03eV and 0.05eV
VL> for larger system. the cutoff in literature can be 380 or 400eV sometimes.
VL> I'm only doing repeat work and learning how to do a perfect calculation.
VL> Also the conv_thr and etot_conv_thr is taken from CASTEP calculation directly. Others
please note that convergence parameters can be _very_ arbitrary
between different codes and they can be in very strange units.
VL> doing so of the same system is the only reason. I'm a beginner of
VL> PWscf and DFT calculation. So I think doing repeat work of others
VL> and discuss with skilled people may be the best way for me. What I'm
VL> doing now is something more like a homework rather than the research
VL> work. I'm learning to using PWscf. Thank you for your help.
before going any further with running big calculations. try
smaller ones. and have you checked the requirements for each
pseudopotential? is your stress tensor converged wrt. wavefunction
_and_ density cutoff? ...and k-points? you are using vanderbilt
ultrasoft pseudopotentials and they can require unexpectedly high
density cutoffs. if i remember correctly. you are also not mentioning
whether the reference you are comparing to is using the _same_
functional that you are using. different functionals
tend to over/underestimate lattice parameters differently.
cheers,
axel.
VL>
VL>
VL> Vega Lew
VL> PH.D Candidate in Chemical Engineering
VL>
VL> State Key Laboratory of Materials-oriented Chemical Engineering
VL> College of Chemistry and Chemical Engineering
VL> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
VL>
VL>
VL>
VL> _________________________________________________________________
VL> Connect to the next generation of MSN Messenger?
VL> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
--
=======================================================================
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 vegalew at hotmail.com Thu Jul 3 20:10:42 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 4 Jul 2008 02:10:42 +0800
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
In-Reply-To:
References:
<18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
Message-ID:
Dear sir,
Thank you for responding
> please note that convergence parameters can be _very_ arbitrary
> between different codes and they can be in very strange units.
sure, I think I have convert the units properly. I want to use 1.0e-5 eV/atom as the CASTEP do
for my Energy convergence. Do you think I should multiple 12 for my cell has 12 atoms? Maybe
I did it wrong...
> before going any further with running big calculations. try
> smaller ones.
I think it's small enough. It can be finished within an hour.
> and have you checked the requirements for each
> pseudopotential? is your stress tensor converged wrt. wavefunction
> _and_ density cutoff? ...and k-points? you are using vanderbilt
> ultrasoft pseudopotentials and they can require unexpectedly high
> density cutoffs.
Many piece of works published on journals said 25 and 200 Ryd is enough.
I'll test a 400 eV ( 30 Ryd ) later.
> if i remember correctly. you are also not mentioning
> whether the reference you are comparing to is using the _same_
> functional that you are using. different functionals
> tend to over/underestimate lattice parameters differently.
Here is part of the reference: J. Phys. Chem. B 2006, 110, 7463-7472
Calculations were carried out in the framework of density functional theory by using
the Vienna ab-initio simulation package (VASP). Ultrasoft pseudopotentials were used to
describe the ionic cores, and a plane-wave basis set with a cutoff energy of 400 eV
was used to expand the valence electrons. The nonlocal exchange and correlation
energies were calculated with the Perdew-Wang (PW91) functional of the generalized
gradient approximation (GGA). Calculations including spinpolarization have been performed
for all structures presented here. The results were compared with those from non-spinpolarized
calculations in the case of a zero magnetic moment. The consistence of the results from
both calculations ensures that the system is in a true nonmagnetic state. The geometries
were relaxed using a conjugate-gradient or quasi-Newton scheme as implemented in VASP.
The atomic structures were relaxed until the forces on all unconstrained atoms were less
than 0.03 eV/?. Similar setups have been employed in the study of a wide range of systems
including metal and metal-oxide surfaces by the authors and many others.
The calculated bulk anatase TiO2 lattice parameters a = b = 3.803 A, c = 9.603 A, c/a = 2.525,
which agree well with the experiments, were used to construct the periodic slabs for
the (101) surface calculations. .............
Also other literatures, such as Journal of Molecular Structure (Theochem) 709 (2004) 73?78.
As the above paragraph in literature said, what kind of pseudopotentials should be used?Ti.pw91-nsp-van.UPF ?
Or Ti.pw91-sp-van_ak.UPF? Or Ti.pbe-sp-van_ak.UPF ?
I note that in castep the corresponding name of pseudopotentials are O_00PBE.usp, Ti_00PBE.usp.
But there is another option for us to choose x-c functional. While QE 4.0 doesn't has, QE read from
pseudopotential files. So Ti.pbe-xxxxx.UPF and O.pbe-xxx.UPF maybe not suitable. What do you think
witch is more suitable for calculation described by the reference?
By the way, I note that CASTEP has find 32 symmetry operations of my cell. My cell is
a standard anatase crystall. But Q-E only can find 4 at most since I adjust parameters of
~/espresso-4.0/PW/eqvect.f90. Do this matter effect my results significantly?
Vega Lew
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 padmaja_patnaik at yahoo.co.uk Fri Jul 4 07:29:53 2008
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Fri, 4 Jul 2008 05:29:53 +0000 (GMT)
Subject: [Pw_forum] Formation energy
Message-ID: <332904.81130.qm@web25404.mail.ukl.yahoo.com>
Dear all
I am doing calculations for a semiconductor with impurity. Can i find
out the formation energy by using PWSCF. If yes, can anybody please let
me know how to do?
Thanking in advance,
Regards
Padmaja
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From padmaja_patnaik at yahoo.co.uk Fri Jul 4 07:42:58 2008
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Fri, 4 Jul 2008 05:42:58 +0000 (GMT)
Subject: [Pw_forum] Doubt in gamma point calculations
Message-ID: <682999.79788.qm@web25402.mail.ukl.yahoo.com>
Dear all
I am doing calculations for semiconductors and plotting the density of
states(DOS) . The DOS plot obtained with K-points in scf calculation as
'Gamma'? found to have shifted towards the lower energy values in
comparision to the DOS curve? with K-points as given in the
example08 (fixed K-points). This is why i cant use K-point= Gamma for
supercell calculations.
Please advise.
Regards
Padmaja
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From andrea.vittadini at unipd.it Fri Jul 4 09:47:30 2008
From: andrea.vittadini at unipd.it (Andrea Vittadini)
Date: Fri, 04 Jul 2008 09:47:30 +0200
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
Message-ID: <486DD592.3090705@unipd.it>
Dear Vega,
A 25 Ry cutoff is too small for variable cell calculations on TiO2. It
is OK for static calculations only. You have to either increase the
cutoff to 40-50 Ry, or try to use the trick implemented by Bernasconi
(see the documentation). To retrieve all the symmetry operations you
should work with crystal coordinates (or increase the decimal figures of
angstrom coordinates).
Andrea
----
Dr. Andrea Vittadini - Istituto di Scienze e Tecnologie Molecolari
del CNR
Dip. Scienze Chimiche - Universita' di Padova, via Marzolo 1 I-35131
Padova, Italy
From vegalew at hotmail.com Fri Jul 4 12:22:00 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 4 Jul 2008 18:22:00 +0800
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
In-Reply-To: <486DD592.3090705@unipd.it>
References: <486DD592.3090705@unipd.it>
Message-ID:
Dear Andrea,
Thank you so much for your advice.
> A 25 Ry cutoff is too small for variable cell calculations on TiO2. It
> is OK for static calculations only. You have to either increase the
> cutoff to 40-50 Ry, or try to use the trick implemented by Bernasconi
I have increased my cutoff to 30 Ry. And the results seems to be more satisfied than before.
Now I see you mail, and I'll increase my cutoff to 40 Ry or more, later.
> (see the documentation). To retrieve all the symmetry operations you
> should work with crystal coordinates (or increase the decimal figures of
> angstrom coordinates).
I have converted my coordinates to coordinates in alat. 8 symmetry operations
could be found. And I found the k-point reduced to 3 evenif I set it to 4X4X2. Do you
think this is up to snuff?
As you adviced I'll try crystal coordinates later.
May you a happy weekend.
THANK YOU SO MUCH.
Vega Lew
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
>
> Andrea
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From vegalew at hotmail.com Fri Jul 4 12:27:31 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 4 Jul 2008 18:27:31 +0800
Subject: [Pw_forum] New BFGS file updated and the results is coming up.
In-Reply-To: <486D09DC.9080508@mit.edu>
References:
<18791.147.122.5.216.1215095462.squirrel@webmail.sissa.it>
<486D09DC.9080508@mit.edu>
Message-ID:
Dear nic,
After may friends here pointed out that the cutoff may be the reason for my small cell parameters.
So I increase the cutoff to 30 Ry and try again. The results seems to be more satisfied. And I'll
increase it to 40 Ry or more. I'll show my results later.
Thank you for your advise. I'll check it later.
Vega Lew
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
m
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From szs_naghavi at yahoo.com Sat Jul 5 13:21:06 2008
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Sat, 5 Jul 2008 04:21:06 -0700 (PDT)
Subject: [Pw_forum] nanotubes symmetry
Message-ID: <984344.53549.qm@web63015.mail.re1.yahoo.com>
Dear all !
Armchairs??and Zigzags? nanotubes have? 24 symmetry oprerations.of course it is important that in which latticce they are located but in Hexagonal we expected 24 symmetrys for?(6,6) but pw.x does not distinguish horizental mirror planes and talk about only 12.
can anybody help??
?
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From szs_naghavi at yahoo.com Sat Jul 5 13:28:13 2008
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Sat, 5 Jul 2008 04:28:13 -0700 (PDT)
Subject: [Pw_forum] nanotubes bandstructure
Message-ID: <6832.15282.qm@web63010.mail.re1.yahoo.com>
Dear all!
Dose any body know? why tetrahehra method yields in?strange results for (6,6) DOS?
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From szs_naghavi at yahoo.com Sat Jul 5 13:40:37 2008
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Sat, 5 Jul 2008 04:40:37 -0700 (PDT)
Subject: [Pw_forum] symmetry
Message-ID: <572336.66358.qm@web63002.mail.re1.yahoo.com>
Dear all!
Dose pwscf recognize symmetry oprations either in the whole lattice or only in one primittive cell?
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From sagarambavale at yahoo.co.in Sat Jul 5 14:03:59 2008
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Sat, 5 Jul 2008 17:33:59 +0530 (IST)
Subject: [Pw_forum] segmentation fault -stack -gfortran
Message-ID: <341402.71709.qm@web94613.mail.in2.yahoo.com>
hi all,
I am running conduction calculations of linear chain comprising of '3 carbons and 2 silicons placed alternate' using pwcond.x of espresso-4.0 compiled with LAM-MPI, ifort10.1 on double cpu Quad-core xeon machine which gives me "forrtl: severe (174): SIGSEGV, segmentation fault occurred". {For chain of 3 Carbons and 1 Si it didn't gave error. } Manual of ifort says "This message indicates that the program attempted an invalid memory reference. Check the program for possible errors." Is this related to stack limit? But for that ifort should write error message like:" severe (174): SIGSEGV, possible program stack overflow occurred"
?
Moreover i read in ../Doc/changelog-4.0 that C subroutine named 'stack.c' is called in the starting of program to remove(?) the stack limit imposed by ifort. Where should i make change to increase the stack limit to 4gb? Moreover, i think there is one '}' is missing... if i uncomment the portion that defines Axel's version (1 gb).
?
?P.S.: In ifort manual i found one variable called "KMP_STACKSIZE".{Sets the number of bytes to allocate for each OpenMP* thread to use as the private stack for the thread.
Recommended size is 16m.??? Use the optional suffixes: b (bytes), k (kilobytes), m (megabytes), g (gigabytes), or t (terabytes) to specify the units.?? This variable does not affect the native operating system threads created by the user program nor the thread executing the sequential part of an OpenMP* program or parallel programs created using -parallel (Linux and Mac OS X) or /Qparallel (Windows).}
?How to set this variable?
One more question:
?
When i configured espresso with gfortran (version 4.1)giving:
../configure --disable-parallel F90=gfortran CC=gcc LAPACK_LIBS="~/espresso-4.0/flib/lapack.a" BLAS_LIBS=" ~/espresso-4.0/flib/blas.a" DFLAGS=-D__USE_INTERNAL_FFTW
It gave the error at the time of compilation :
?REAL(DP),?? allocatable :: of_r(:,:)? ! the charge density in R-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:49
?
???? COMPLEX(DP),allocatable :: of_g(:,:)? ! the charge density in G-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:50
............
..........
........
make[1]: *** [scf_mod.o] Error 1
make[1]: Leaving directory `/home/sagar/espresso-4.0/PW'
make: *** [pw] Error 2
[sagar at localhost espresso-4.0]$
?
?
Sagar Ambavale
Phd student
The M.S. University of Baroda
India
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From sagarambavale at yahoo.co.in Sat Jul 5 14:04:37 2008
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Sat, 5 Jul 2008 17:34:37 +0530 (IST)
Subject: [Pw_forum] segmentation fault -stack -gfortran
Message-ID: <233418.16134.qm@web94607.mail.in2.yahoo.com>
hi all,
I am running conduction calculations of linear chain comprising of '3 carbons and 2 silicons placed alternate' using pwcond.x of espresso-4.0 compiled with LAM-MPI, ifort10.1 on double cpu Quad-core xeon machine which gives me "forrtl: severe (174): SIGSEGV, segmentation fault occurred". {For chain of 3 Carbons and 1 Si it didn't gave error. } Manual of ifort says "This message indicates that the program attempted an invalid memory reference. Check the program for possible errors." Is this related to stack limit? But for that ifort should write error message like:" severe (174): SIGSEGV, possible program stack overflow occurred"
?
Moreover i read in ../Doc/changelog-4.0 that C subroutine named 'stack.c' is called in the starting of program to remove(?) the stack limit imposed by ifort. Where should i make change to increase the stack limit to 4gb? Moreover, i think there is one '}' is missing... if i uncomment the portion that defines Axel's version (1 gb).
?
?P.S.: In ifort manual i found one variable called "KMP_STACKSIZE".{Sets the number of bytes to allocate for each OpenMP* thread to use as the private stack for the thread.
Recommended size is 16m.??? Use the optional suffixes: b (bytes), k (kilobytes), m (megabytes), g (gigabytes), or t (terabytes) to specify the units.?? This variable does not affect the native operating system threads created by the user program nor the thread executing the sequential part of an OpenMP* program or parallel programs created using -parallel (Linux and Mac OS X) or /Qparallel (Windows).}
?How to set this variable?
One more question:
?
When i configured espresso with gfortran (version 4.1)giving:
../configure --disable-parallel F90=gfortran CC=gcc LAPACK_LIBS="~/espresso-4.0/flib/lapack.a" BLAS_LIBS=" ~/espresso-4.0/flib/blas.a" DFLAGS=-D__USE_INTERNAL_FFTW
It gave the error at the time of compilation :
?REAL(DP),?? allocatable :: of_r(:,:)? ! the charge density in R-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:49
?
???? COMPLEX(DP),allocatable :: of_g(:,:)? ! the charge density in G-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:50
............
..........
........
make[1]: *** [scf_mod.o] Error 1
make[1]: Leaving directory `/home/sagar/espresso-4.0/PW'
make: *** [pw] Error 2
[sagar at localhost espresso-4.0]$
?
?
Sagar Ambavale
Phd student
The M.S. University of Baroda
India
Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/
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From sagarambavale at yahoo.co.in Sat Jul 5 14:04:56 2008
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Sat, 5 Jul 2008 17:34:56 +0530 (IST)
Subject: [Pw_forum] segmentation fault -stack -gfortran
Message-ID: <281206.39546.qm@web94602.mail.in2.yahoo.com>
hi all,
I am running conduction calculations of linear chain comprising of '3 carbons and 2 silicons placed alternate' using pwcond.x of espresso-4.0 compiled with LAM-MPI, ifort10.1 on double cpu Quad-core xeon machine which gives me "forrtl: severe (174): SIGSEGV, segmentation fault occurred". {For chain of 3 Carbons and 1 Si it didn't gave error. } Manual of ifort says "This message indicates that the program attempted an invalid memory reference. Check the program for possible errors." Is this related to stack limit? But for that ifort should write error message like:" severe (174): SIGSEGV, possible program stack overflow occurred"
?
Moreover i read in ../Doc/changelog-4.0 that C subroutine named 'stack.c' is called in the starting of program to remove(?) the stack limit imposed by ifort. Where should i make change to increase the stack limit to 4gb? Moreover, i think there is one '}' is missing... if i uncomment the portion that defines Axel's version (1 gb).
?
?P.S.: In ifort manual i found one variable called "KMP_STACKSIZE".{Sets the number of bytes to allocate for each OpenMP* thread to use as the private stack for the thread.
Recommended size is 16m.??? Use the optional suffixes: b (bytes), k (kilobytes), m (megabytes), g (gigabytes), or t (terabytes) to specify the units.?? This variable does not affect the native operating system threads created by the user program nor the thread executing the sequential part of an OpenMP* program or parallel programs created using -parallel (Linux and Mac OS X) or /Qparallel (Windows).}
?How to set this variable?
One more question:
?
When i configured espresso with gfortran (version 4.1)giving:
../configure --disable-parallel F90=gfortran CC=gcc LAPACK_LIBS="~/espresso-4.0/flib/lapack.a" BLAS_LIBS=" ~/espresso-4.0/flib/blas.a" DFLAGS=-D__USE_INTERNAL_FFTW
It gave the error at the time of compilation :
?REAL(DP),?? allocatable :: of_r(:,:)? ! the charge density in R-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:49
?
???? COMPLEX(DP),allocatable :: of_g(:,:)? ! the charge density in G-space
?????????????????????????? 1
Error: Attribute at (1) is not allowed in a TYPE definition
?In file scf_mod.f90:50
............
..........
........
make[1]: *** [scf_mod.o] Error 1
make[1]: Leaving directory `/home/sagar/espresso-4.0/PW'
make: *** [pw] Error 2
[sagar at localhost espresso-4.0]$
?
?
Sagar Ambavale
Phd student
The M.S. University of Baroda
India
Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
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From lanhaiping at gmail.com Sat Jul 5 16:49:50 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 5 Jul 2008 22:49:50 +0800
Subject: [Pw_forum] nanotubes symmetry
In-Reply-To: <984344.53549.qm@web63015.mail.re1.yahoo.com>
References: <984344.53549.qm@web63015.mail.re1.yahoo.com>
Message-ID:
Hi,
how do you come to this conclusion ? The symmetry operation of nanotubes
should depend on their chiral indexs..
On Sat, Jul 5, 2008 at 7:21 PM, zahra sadat naghavi
wrote:
> Dear all !
>
> Armchairs and Zigzags nanotubes have 24 symmetry oprerations.*of course
> it is important that in which latticce they are located *but in Hexagonal
> we expected 24 symmetrys for (6,6) but pw.x does not distinguish horizental
> mirror planes and talk about only 12.
>
> can anybody help?
>
>
>
>
> _______________________________________________
> 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 zhaohscas at yahoo.com.cn Sat Jul 5 16:58:18 2008
From: zhaohscas at yahoo.com.cn (zhaohscas)
Date: Sat, 5 Jul 2008 22:58:18 +0800
Subject: [Pw_forum] Balance the efficiency and veracity of PWscf vs. other
DFT codes.
Message-ID: <200807052258184221498@yahoo.com.cn>
Hi all,
When the system under study is large, i.e., including hundreds of atoms or more, in this case, form the point of balancing the efficiency and veracity, whether the PWscf is suitable for such computation or not? Furthermore, in this case, which will be more promising DFT code(s)?
Any help or hints would be appreciated.
Sincerely yours,
--------------
Hongsheng Zhao
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences
GnuPG DSA: 0xD10849
2008-07-05
From akohlmey at cmm.chem.upenn.edu Sat Jul 5 20:20:55 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 5 Jul 2008 14:20:55 -0400 (EDT)
Subject: [Pw_forum] Balance the efficiency and veracity of PWscf vs.
other DFT codes.
In-Reply-To: <200807052258184221498@yahoo.com.cn>
References: <200807052258184221498@yahoo.com.cn>
Message-ID:
On Sat, 5 Jul 2008, zhaohscas wrote:
HZ> Hi all,
hi!
HZ> When the system under study is large, i.e., including hundreds of
HZ> atoms or more, in this case, form the point of balancing the
HZ> efficiency and veracity, whether the PWscf is suitable for such
HZ> computation or not? Furthermore, in this case, which will be more
HZ> promising DFT code(s)?
this is a strange kind of question to ask to a mailing list that
supports a specific code. what do you expect people to answer?
QE is complete crap and does not run correctly on anything and
does not scale to boot?? you are better off using code X???
i hope not.
of course, QE does run as accurate as possible within the confines
of using DFT with plane waves and pseudopotentials, modulo the
occasional bug that every large, versatile and thus complex software
package contains. of course we would like you to use it and not
something else. of course, that are weaknesses, but the code offers
a lot of possiblilities for good performance and scaling and people
are continuously trying to improve it. it cannot beat the scaling
of the underlying physics, though, and one always has to make a tradeoff
between the flexibility, capabilities, and maintainability of a code
and its absolute performance.
since there is no "one-size fits all" kind of solution, the best
choice of approach (and thus code) always depends on the specific
problem at hand.
HZ> Any help or hints would be appreciated.
my suggestion: try it and see for yourself.
cheers,
axel.
HZ> Sincerely yours,
HZ> --------------
HZ> Hongsheng Zhao
HZ> Xinjiang Technical Institute of Physics and Chemistry
HZ> Chinese Academy of Sciences
HZ> GnuPG DSA: 0xD10849
HZ> 2008-07-05
HZ>
HZ> _______________________________________________
HZ> Pw_forum mailing list
HZ> Pw_forum at pwscf.org
HZ> http://www.democritos.it/mailman/listinfo/pw_forum
HZ>
--
=======================================================================
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 cesards at msi.umn.edu Sun Jul 6 00:37:40 2008
From: cesards at msi.umn.edu (Cesar R.S. da Silva)
Date: Sat, 5 Jul 2008 17:37:40 -0500 (CDT)
Subject: [Pw_forum] segmentation fault -stack -gfortran (ambavale sagar)
Message-ID:
Dear Ambavale,
Some time ago I posted a suggestion for a small improvement in stack.c that
would prevent the segmentation fault error in many situations.
At the time, my suggestion was dismissed as irrelevant as the only effect
of the sloppy code should be the generation of an annoying message. For
the record, the only thing I agree is that the message is really annoying.
The code in v4.x tries to set the stack as unlimited, if it fails it tries
to set to 1.0 GB. However, some systems have a maximum limit for the
stack. 1.0 GB is a lot of stack, and is also very likely to exceed the
maximum limit. So, the code is still as sloppy as it was before the last
revisions.
My fix is to set the stack to the maximum allowed by the system, if
unlimited fails. It is eventually still insufficient but, as far as I
know, there is nothing better to do within user level programming to
further increase the stack. If setting to the maximum allowed is not
enough, You can, at compile time, make espresso to allocate local vars in
the heap. This can cause the heap to become fragmented, but is not as bad
as not running at all.
If there is a lesson to be taken, it is: Never use a sloppy code unless
the fix us unfeasible, no matter how inconsequential it seems to be.
Well, I am using the following code for stack.c and it is working so far.
Yours,
Cesar R.S. da Silva.
***************************************************************************
/*
Copyright (C) 2007 Quantum-Espresso group
This file is distributed under the terms of the
GNU General Public License. See the file `License'
in the root directory of the present distribution,
or http://www.gnu.org/copyleft/gpl.txt .
*/
#include
#include
#include
#include "c_defs.h"
void F77_FUNC(remove_stack_limit,REMOVE_STACK_LIMIT) (void) {
struct rlimit rlim = { RLIM_INFINITY, RLIM_INFINITY };
if ( setrlimit(RLIMIT_STACK, &rlim) == -1 ) {
if ( getrlimit(RLIMIT_STACK, &rlim) == 0 ) {
rlim.rlim_cur = rlim.rlim_max;
if ( setrlimit(RLIMIT_STACK, &rlim) == 0 ) {
getrlimit(RLIMIT_STACK, &rlim);
} else {
perror(" Cannot set stack size to new value");
}
}
}
}
***************************************************************************
> ------------------------------
>
> Message: 5
> Date: Sat, 5 Jul 2008 17:34:37 +0530 (IST)
> From: ambavale sagar
> Subject: [Pw_forum] segmentation fault -stack -gfortran
> To: pwforum que-ans
> Message-ID: <233418.16134.qm at web94607.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> hi all,
> I am running conduction calculations of linear chain comprising of '3
> carbons and 2 silicons placed alternate' using pwcond.x of espresso-4.0
> compiled with LAM-MPI, ifort10.1 on double cpu Quad-core xeon machine
> which gives me "forrtl: severe (174): SIGSEGV, segmentation fault
> occurred". {For chain of 3 Carbons and 1 Si it didn't gave error. } Manual
> of ifort says "This message indicates that the program attempted an
> invalid memory reference. Check the program for possible errors." Is this
> related to stack limit? But for that ifort should write error message
> like:" severe (174): SIGSEGV, possible program stack overflow occurred"
> ?
> Moreover i read in ../Doc/changelog-4.0 that C subroutine named 'stack.c'
> is called in the starting of program to remove(?) the stack limit imposed
> by ifort. Where should i make change to increase the stack limit to 4gb?
> Moreover, i think there is one '}' is missing... if i uncomment the
> portion that defines Axel's version (1 gb).
> ?
> ?P.S.: In ifort manual i found one variable called "KMP_STACKSIZE".{Sets
> the number of bytes to allocate for each OpenMP* thread to use as the
> private stack for the thread.
> Recommended size is 16m.??? Use the optional suffixes: b (bytes), k
> (kilobytes), m (megabytes), g (gigabytes), or t (terabytes) to specify the
> units.?? This variable does not affect the native operating system threads
> created by the user program nor the thread executing the sequential part
> of an OpenMP* program or parallel programs created using -parallel (Linux
> and Mac OS X) or /Qparallel (Windows).}
> ?How to set this variable?
> One more question:
> ?
> When i configured espresso with gfortran (version 4.1)giving:
> ../configure --disable-parallel F90=gfortran CC=gcc
> LAPACK_LIBS="~/espresso-4.0/flib/lapack.a" BLAS_LIBS="
> ~/espresso-4.0/flib/blas.a" DFLAGS=-D__USE_INTERNAL_FFTW
> It gave the error at the time of compilation :
> ?REAL(DP),?? allocatable :: of_r(:,:)? ! the charge density in R-space
> ?????????????????????????? 1
> Error: Attribute at (1) is not allowed in a TYPE definition
> ?In file scf_mod.f90:49
> ?
> ???? COMPLEX(DP),allocatable :: of_g(:,:)? ! the charge density in G-space
> ?????????????????????????? 1
> Error: Attribute at (1) is not allowed in a TYPE definition
> ?In file scf_mod.f90:50
> ............
> ..........
> ........
> make[1]: *** [scf_mod.o] Error 1
> make[1]: Leaving directory `/home/sagar/espresso-4.0/PW'
> make: *** [pw] Error 2
> [sagar at localhost espresso-4.0]$
> ?
> ?
> Sagar Ambavale
> Phd student
> The M.S. University of Baroda
> India
>
>
> Explore your hobbies and interests. Go to
> http://in.promos.yahoo.com/groups/
> -------------- next part --------------
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> http://www.democritos.it/pipermail/pw_forum/attachments/20080705/54437581/attachment.htm
>
> ------------------------------
>
From flitimein at yahoo.fr Sun Jul 6 01:59:35 2008
From: flitimein at yahoo.fr (Fatma Litimein)
Date: Sun, 6 Jul 2008 01:59:35 +0200 (CEST)
Subject: [Pw_forum] how to optimize the lattice parameters of monoclinic
structure ?
Message-ID: <342448.80375.qm@web23104.mail.ird.yahoo.com>
Dear PWscf users,
first, I would like to thank prof baroni for it reply .
second, I have a question about optimization of an monoclinic structure, so to do that have I to optimize c/a, V, b/a, V, ...., c/a, V, in SCF manner until convergence of the structure or can I perform just one c/a, b/a, V optimization ? How can I to optimize i.e. beta angel? Any comments are welcome.
Thank you in advance
=======================================================
Fatma Litimein
Computational Materials Science Laboratory,
Physics Department, University of Sidi Bel Abbes
Sidi Bel Abbes, 22000 - Algeria
Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
=======================================================
---------------------------------
Envoy? avec Yahoo! Mail.
Une boite mail plus intelligente.
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From mansourehp at gmail.com Sun Jul 6 07:24:55 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Sun, 6 Jul 2008 08:54:55 +0330
Subject: [Pw_forum] molecular dynamics for metallic system
Message-ID:
Dear All
I am a PhD. student.I am interested in molecular dynamics for metallic
systems with external
pressure,but at first I began learning Car-Parrinello molecular dynamics
and then I used it
for my system with small dt (I am sending its plots for you).Do using CP
with small dtinstead
of BO for metallic systems obtain correct result or not?
How can I find the best dt ,emass.emass_cutoff for my system in BOMD and
CPMD()?
I want to find affect of external pressure on ions in my system and I must
consider many ions
in a big cell.can I use a smaller cell with fewer ions to find dt
,emass,...?
I look forward to hearing from you as soon as possible.
Thanks,
Mansoureh
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From marzari at MIT.EDU Sun Jul 6 07:57:36 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 06 Jul 2008 07:57:36 +0200
Subject: [Pw_forum] Balance the efficiency and veracity of PWscf vs.
other DFT codes.
In-Reply-To:
References: <200807052258184221498@yahoo.com.cn>
Message-ID: <48705ED0.2070403@mit.edu>
> On Sat, 5 Jul 2008, zhaohscas wrote:
>
> HZ> When the system under study is large, i.e., including hundreds of
> HZ> atoms or more, in this case, form the point of balancing the
> HZ> efficiency and veracity, whether the PWscf is suitable for such
> HZ> computation or not? Furthermore, in this case, which will be more
> HZ> promising DFT code(s)?
Besides PWscf, you might consider CP, as well - this is also part of
the QE distribution, and, albeit more finnicky to use, has been built
and optimized for large calculations - it can only do Gamma sampling
(hence it can impose to the k-s orbitals to be real, halving the
memory cost).
Traditionally, it would do static calculations (and ionic relaxations)
using damped dynamics on electrons (or electrons and ions); in this
mode, it is very efficient and worth considering for large scale
calculations. Recently, a conjugate-gradient strategy on electrons has
been added, as the possibility of doing metals (using ensemble-dft).
Neither of these are extensively tested, but are being polished off -
for ensemble-dft there is one last bug that used to affect parallel
calculations, that has just been found (and not yet corrected, even in
the CVS).
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 marzari at MIT.EDU Sun Jul 6 08:00:05 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 06 Jul 2008 08:00:05 +0200
Subject: [Pw_forum] molecular dynamics for metallic system
In-Reply-To:
References:
Message-ID: <48705F65.8050806@mit.edu>
If your system is a true metal, it will be tough to have a meaningful
dynamics with CP. You need to use PWSCF B-O simulations, and/or start
experimenting with CP in ensemble-dft mode.
If the system has a few states around the Fermi energy, and run in CP
mode would show a mild but steady increase of the fictitious electronic
kinetic energy, then you might succeed, by applying a thermostat on
electrons and one on ions.
In all these cases, you need experience, a lot of testing in small
systems to get a feeling of things, etc... . It would be safe to start
with reference calculations using PWSCF B-O.
nicola
Mansoureh Pashangpour wrote:
> Dear All
> I am a PhD. student.I am interested in molecular dynamics for metallic
> systems with external
> pressure,but at first I began learning Car-Parrinello molecular
> dynamics and then I used it
> for my system with small dt (I am sending its plots for you).Do using
> CP with small dtinstead
> of BO for metallic systems obtain correct result or not?
> How can I find the best dt ,emass.emass_cutoff for my system in BOMD and
> CPMD()?
> I want to find affect of external pressure on ions in my system and I
> must consider many ions
> in a big cell.can I use a smaller cell with fewer ions to find dt
> ,emass,...?
> I look forward to hearing from you as soon as possible.
> Thanks,
> Mansoureh
--
---------------------------------------------------------------------
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 wangqj1 at 126.com Sun Jul 6 10:28:58 2008
From: wangqj1 at 126.com (wangqj1)
Date: Sun, 6 Jul 2008 16:28:58 +0800 (CST)
Subject: [Pw_forum] How to set the parameter of U in LDA+U
Message-ID: <19631776.671241215332938760.JavaMail.coremail@bj126app28.126.com>
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 mansourehp at gmail.com Sun Jul 6 11:03:56 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Sun, 6 Jul 2008 12:33:56 +0330
Subject: [Pw_forum] How to set the parameter of U in LDA+U
In-Reply-To: <19631776.671241215332938760.JavaMail.coremail@bj126app28.126.com>
References: <19631776.671241215332938760.JavaMail.coremail@bj126app28.126.com>
Message-ID:
Dear Wang
have you got U for this system?or do you want to calculate it?
Mansoureh
2008/7/6 wangqj1 :
>
> 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
> **
>
>
>
> ------------------------------
> ??????3D??"??2"?6?6?????
> _______________________________________________
> 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 Jul 6 11:16:16 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Sun, 6 Jul 2008 12:46:16 +0330
Subject: [Pw_forum] my plots with CP for a small cell
Message-ID:
Dea all
I am sending one of my plots from CP molecular dynamics run.
could you help me find the best dt and emass?
thanks
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From vegalew at hotmail.com Sun Jul 6 19:59:56 2008
From: vegalew at hotmail.com (vega lew)
Date: Mon, 7 Jul 2008 01:59:56 +0800
Subject: [Pw_forum] (no subject)
Message-ID:
Dear all,
Now I have tested Anatase lattice parameters using new BFGS file of PWscf. The new BFGS files
seem to be perfect. The data in following table is calculated by PWscf except for the first two lines.
The first line is the experimental data at 15K of J. Am. Chem. SOC. 1987, 109, 3639-3646.
The second line is the average value calculated by CASTEP. But the value is not stable, it's
would be changed a bit of different run.
From vegalew at hotmail.com Sun Jul 6 20:58:27 2008
From: vegalew at hotmail.com (vega lew)
Date: Mon, 7 Jul 2008 02:58:27 +0800
Subject: [Pw_forum] Anatase lattice parameters testing results
Message-ID:
Dear all,
There is someting wrong with last mail, so I send it again.
Now I have tested Anatase lattice parameters using new BFGS file of PWscf. The new BFGS filesseem to be perfect. The data in following table is calculated by PWscf except for the first two lines.The first line is the experimental data at 15K of J. Am. Chem. SOC. 1987, 109, 3639-3646.The second line is the average value calculated by CASTEP. But the value is not stable, it'swould be changed a bit of different run.From the third line to the bottom is the data calculated by PWscf. The value is quite stable.The value remain the same when calculate by same number of CPUs and pools. There would be only a little different for different number of CPUs and pools, less than 0.01% in energy.
K-point mesh Pseudopotentials Cutoff / Ry Anatase lattice parameters time
a=b c Energy / Ry CPU Wall
experiment* x 3.78216 9.50465 x x x
CASTEP 400 eV 3.7987 9.6934 -730.11745
gamma (1X1X1) 30,240 3.39021 11.77804 -725.08174 4m18.70s 18m 9.12s
2X2X1 30?240 3.8683 9.0275 -725.48834 8m 4.25s 32m33.56s
4X4X2 25,200 3.7500 9.3829 -725.41398 9m58.82s 17m46.87s
30,240 3.7899 9.6203 -725.49520 3m41.55s 7m50.32s
40,320 3.7850 9.5716 -725.54336 8m54.73s 34m 1.43s
50,400 3.7926 9.6366 -725.59434 10m14.46s 41m 3.22s
7X7X3 30,240 3.7919 9.6058 -725.49443 31m59.60s 46m37.77s
10X10X4 30,240 3.7916 9.6067 -725.49451 31m32.94s 44m 4.11s
The input file as follows, &CONTROL title = 'Anatase lattice' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/vega/espresso-4.0/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , prefix = 'Anatase lattice default' , disk_io = 'none' , etot_conv_thr = 0.0005 , forc_conv_thr = 0.0011668141375 , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 7.1356, celldm(3) = 2.5122, nat = 12, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , / &ELECTRONS conv_thr = 7.3D-8 , / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , /ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPFATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.500000000 0.250000000 Ti 0.500000000 0.000000000 0.750000000 O 0.000000000 0.500000000 0.042000000 O 0.000000000 0.000000000 0.208000000 O 0.500000000 0.500000000 0.292000000 O 0.000000000 0.500000000 0.458000000 O 0.500000000 0.000000000 0.542000000 O 0.500000000 0.500000000 0.708000000 O 0.000000000 0.000000000 0.792000000 O 0.500000000 1.000000000 0.958000000K_POINTS automatic2 2 1 1 1 1 But it is especially strange that the total energy was -730.11745 Ry, rather different than the PWscf's results. Also PWscf's results seems to be a litter lager than experimental data. Is it because the pseudopotential Ti.pw91-sp-van_ak.UPF underbinding for TiO2? Vega LewPH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, ChinaVega LewPH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China
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From giannozz at democritos.it Sun Jul 6 21:24:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 6 Jul 2008 21:24:33 +0200
Subject: [Pw_forum] Anatase lattice parameters testing results
In-Reply-To:
References:
Message-ID:
On Jul 6, 2008, at 20:58 , vega lew wrote:
> But it is especially strange that the total energy was -730.11745 Ry,
> rather different than the PWscf's results.
absolute energies depend on the pseudopotential used
---
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 Sun Jul 6 21:34:02 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 6 Jul 2008 21:34:02 +0200
Subject: [Pw_forum] nanotubes symmetry
In-Reply-To: <984344.53549.qm@web63015.mail.re1.yahoo.com>
References: <984344.53549.qm@web63015.mail.re1.yahoo.com>
Message-ID: <295F9129-E62B-422F-81D5-9F791E837315@democritos.it>
On Jul 5, 2008, at 13:21 , zahra sadat naghavi wrote:
> Armchairs and Zigzags nanotubes have 24 symmetry oprerations.of
> course it is important that in which latticce they are located but
> in Hexagonal we expected 24 symmetrys for (6,6) but pw.x does not
> distinguish horizental mirror planes and talk about only 12.
>
pw.x finds only symmetry operations that i) are compatible with the
lattice,
ii) are there, as explained in detail in the user guide.
---
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 Sun Jul 6 21:40:54 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 6 Jul 2008 21:40:54 +0200
Subject: [Pw_forum] segmentation fault -stack -gfortran
In-Reply-To: <281206.39546.qm@web94602.mail.in2.yahoo.com>
References: <281206.39546.qm@web94602.mail.in2.yahoo.com>
Message-ID:
On Jul 5, 2008, at 14:04 , ambavale sagar wrote:
> "forrtl: severe (174): SIGSEGV, segmentation fault occurred" [...]
> Is this related to stack limit?
not necessarily. It may also mean that you are using too much memory,
or 1001 other things (as explained no less than 1001 times in this list)
> When i configured espresso with gfortran (version 4.1)giving:
> ./configure --disable-parallel F90=gfortran CC=gcc LAPACK_LIBS="~/
> espresso-4.0/flib/lapack.a" BLAS_LIBS=" ~/espresso-4.0/flib/blas.a"
> DFLAGS=-D__USE_INTERNAL_FFTW
who told you to use all these options? stick to the default
unless you know what you are doing
---
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 Sun Jul 6 21:55:00 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 6 Jul 2008 21:55:00 +0200
Subject: [Pw_forum] "from pzpotrf : error # 1 problems computing
cholesky decomposition"
In-Reply-To: <21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
References:
<21708.147.122.27.135.1214988026.squirrel@webmail.sissa.it>
Message-ID: <68EBC110-785B-47AA-9253-D8F83179F04F@democritos.it>
On Jul 2, 2008, at 10:40 , Lorenzo Paulatto wrote:
>
> On Mer, Luglio 2, 2008 08:56, vega lew wrote:
>> from pzpotrf : error # 1
>> problems computing cholesky decomposition
> [...] it is probably a bug in the parallel implementation,
> you can try setting diagonalization='david-serial'
the correct way to disable paralled distributed diagonalization
is " .. pw.x -ndiag 1"
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 Sun Jul 6 22:07:14 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 6 Jul 2008 22:07:14 +0200
Subject: [Pw_forum] segmentation fault -stack -gfortran (ambavale sagar)
In-Reply-To:
References:
Message-ID: <1291F5F7-E00D-4E15-A281-119C72659AE7@democritos.it>
On Jul 6, 2008, at 24:37 , Cesar R.S. da Silva wrote:
> Some time ago I posted a suggestion for a small improvement in
> stack.c that
> would prevent the segmentation fault error in many situations.
>
> At the time, my suggestion was dismissed as irrelevant as the only
> effect
> of the sloppy code should be the generation of an annoying message.
> For
> the record, the only thing I agree is that the message is really
> annoying.
>
> The code in v4.x tries to set the stack as unlimited, if it fails
> it tries
> to set to 1.0 GB. However, some systems have a maximum limit for the
> stack. 1.0 GB is a lot of stack, and is also very likely to exceed the
> maximum limit. So, the code is still as sloppy as it was before the
> last
> revisions.
>
> My fix is to set the stack to the maximum allowed by the system, if
> unlimited fails. It is eventually still insufficient but, as far as I
> know, there is nothing better to do within user level programming to
> further increase the stack. If setting to the maximum allowed is not
> enough, You can, at compile time, make espresso to allocate local
> vars in
> the heap. This can cause the heap to become fragmented, but is not
> as bad
> as not running at all.
>
> If there is a lesson to be taken, it is: Never use a sloppy code
> unless
> the fix us unfeasible, no matter how inconsequential it seems to be.
I have no evidence that the "sloppy code", as you call it, causes
any trouble on any machine.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From polynmr at physics.unc.edu Sun Jul 6 22:44:30 2008
From: polynmr at physics.unc.edu (Charles Chen)
Date: Sun, 06 Jul 2008 16:44:30 -0400
Subject: [Pw_forum] Anatase lattice parameters testing results
In-Reply-To:
References:
Message-ID: <48712EAE.40707@physics.unc.edu>
vega lew wrote:
> Dear all,
>
> There is someting wrong with last mail, so I send it again.
>
> Now I have tested Anatase lattice parameters using new BFGS file of
> PWscf. The new BFGS files
> seem to be perfect. The data in following table is calculated by PWscf
> except for the first two lines.
> The first line is the experimental data at 15K of J. Am. Chem. SOC.
> 1987, 109, 3639-3646.
> The second line is the average value calculated by CASTEP. But the
> value is not stable, it's
> would be changed a bit of different run.
> From the third line to the bottom is the data calculated by PWscf. The
> value is quite stable.
> The value remain the same when calculate by same number of CPUs and
> pools. There would
> be only a little different for different number of CPUs and pools,
> less than 0.01% in energy.
>
> K-point mesh Pseudopotentials Cutoff / Ry Anatase lattice parameters time
> a=b c Energy / Ry CPU Wall
> experiment* x 3.78216 9.50465 x x x
> CASTEP 400 eV 3.7987 9.6934 -730.11745
> gamma (1X1X1) 30,240 3.39021 11.77804 -725.08174 4m18.70s 18m 9.12s
> 2X2X1 30?240 3.8683 9.0275 -725.48834 8m 4.25s 32m33.56s
> 4X4X2 25,200 3.7500 9.3829 -725.41398 9m58.82s 17m46.87s
> 30,240 3.7899 9.6203 -725.49520 3m41.55s 7m50.32s
> 40,320 3.7850 9.5716 -725.54336 8m54.73s 34m 1.43s
> 50,400 3.7926 9.6366 -725.59434 10m14.46s 41m 3.22s
> 7X7X3 30,240 3.7919 9.6058 -725.49443 31m59.60s 46m37.77s
> 10X10X4 30,240 3.7916 9.6067 -725.49451 31m32.94s 44m 4.11s
I bet you did not check force convergence wrt ecutwfc, ecutrho, and MP
grid. I would rather have a more systematic convergence test.
Another point is, anatase is in space group I41/amd or ibrav=7. Of
course this will not make much difference as you use ibrav=6
>
> The input file as follows,
>
> &CONTROL
> title = 'Anatase lattice' ,
> calculation = 'vc-relax' ,
> restart_mode = 'from_scratch' ,
> outdir = '/home/vega/espresso-4.0/tmp/' ,
> wfcdir = '/tmp/' ,
> pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
> &n! bsp; prefix = 'Anatase lattice default' ,
> disk_io = 'none' ,
> etot_conv_thr = 0.0005 ,
> forc_conv_thr = 0.0011668141375 ,
> nstep = 1000 ,
> /
> &SYSTEM
> ibrav = 6,
> celldm(1) = 7.1356,
> ! ; &nb sp; celldm(3) = 2.5122,
> nat = 12,
> ntyp = 2,
> ecutwfc = 30 ,
> ecutrho = 240 ,
> /
> &ELECTRONS
> conv_thr = 7.3D-8 ,
> /
> &IONS
> ion_dynamics = 'bfgs' ,
> /
> &CELL
> &nbs! p; cell_dynamics = 'bfgs' ,
> /
> ATOMIC_SPECIES
> Ti 47.86700 Ti.pw91-sp-van_ak.UPF
> O 15.99940 O.pw91-van_ak.UPF
> ATOMIC_POSITIONS crystal
> Ti 0.000000000 0.000000000 0.000000000
> Ti 0.500000000 0.500000000 0.500000000
> Ti 0.000000000 0.500000000 0.250000000
> Ti 0.500000000 0.000000000 0.750000000
> O 0.000000000 0.500000000 0.042000000
> O 0.000000000 0.000000000 0.208000000
> &n! bsp; O 0.500000000 &nbs p; 0.500000000 0.292000000
> O 0.000000000 0.500000000 0.458000000
> O 0.500000000 0.000000000 0.542000000
> O 0.500000000 0.500000000 0.708000000
> O 0.000000000 0.000000000 0.792000000
> O 0.500000000 1.000000000 0.958000000
> K_POINTS automatic
> 2 2 1 1 1 1
>
> But it is especially strange that the total energy was -730.11745 Ry,
> rather different than the PWscf's results.
> Also PWscf's results seems to be a litter lager than experimental
> data. Is it because the pseudopotential Ti.pw91-sp-van_ak.UPF
> underbinding! for TiO2?
>
>
> Vega Lew
> 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
> Vega Lew
> 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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>
>
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>
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>
> Not spam
>
> Forget previous vote
>
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From mansourehp at gmail.com Mon Jul 7 05:36:23 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Mon, 7 Jul 2008 07:06:23 +0330
Subject: [Pw_forum] molecular dynamics
Message-ID:
Dear all
I performed CP molecular dynamics for a system that is metal with LDA and
insulator with LDA+U.It contains Fe ions so I must use LDA+U for it .Now I
want to obtain external pressure affect on it.These are my plan to BO MD:
(dt=6)
1.electron minimization
&electrons
emass = 200.d0,
emass_cutoff = 3.0d0,
orthogonalization = 'ortho',
electron_dynamics = 'damp',
/
&ions
ion_dynamics = 'none',
/
&cell
cell_dynamics = 'none',
press = 0.0d0,
-----------------------------------------
&electrons
emass = 200.d0,
emass_cutoff = 3.0d0,
orthogonalization = 'ortho',
electron_dynamics = 'damp',
/
&ions
ion_dynamics = 'none',
/
&cell
cell_dynamics = 'none',
press = 0.0d0,
-----------------------------------------
2.randomization
&electrons
emass = 200.d0,
ortho_max=40
emass_cutoff = 3.0d0,
orthogonalization = 'ortho',
electron_dynamics = 'sd',
/
&ions
ion_dynamics = 'none',
tranp(2) = .TRUE.
amprp(2) = 0.05
/
&cell
cell_dynamics = 'none',
press = 0.0d0,
------------------------------------------
3. dynamics
&electrons
emass = 200.d0,
emass_cutoff = 3.0d0,
orthogonalization = 'ortho',
electron_dynamics = 'cg',
electron_temperature = 'nose',
ekincw=0.0001,
fnosee=0.5,
/
&ions
ion_dynamics = 'verlet',
ion_temperature = 'nose',
tempw = 300.0,
fnosep = 70
/
&cell
cell_dynamics = 'pr',
press = 0.0d0,
Is this way correct ?
I look forward to hearing from you?
Thanks
Mansoureh
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From mansourehp at gmail.com Mon Jul 7 10:25:31 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Mon, 7 Jul 2008 11:55:31 +0330
Subject: [Pw_forum] CRASH
Message-ID:
Dear all
I ound this error when I run CP MD(in QE code)
what dose it mean?
from newnlinit : error # 1
interpolation tables recalculation, not implemented yet
thanks
Mansoureh
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From giannozz at democritos.it Mon Jul 7 14:34:19 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 7 Jul 2008 14:34:19 +0200
Subject: [Pw_forum] CRASH
In-Reply-To:
References:
Message-ID:
On Jul 7, 2008, at 10:25 , Mansoureh Pashangpour wrote:
> what does it mean?
> from newnlinit : error # 1
> interpolation tables recalculation, not implemented yet
it means that your cell has either contracted or expanded
too much wrt the starting cell in a variable-cell dynamics
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 tone.kokalj at ijs.si Mon Jul 7 16:40:33 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 07 Jul 2008 16:40:33 +0200
Subject: [Pw_forum] pwo2xsf error when plot 3D charge density
with xcrysden
In-Reply-To: <10699575.527661214920011341.JavaMail.coremail@bj163app39.163.com>
References: <10699575.527661214920011341.JavaMail.coremail@bj163app39.163.com>
Message-ID: <1215441633.5008.65.camel@walk.ijs.si>
On Tue, 2008-07-01 at 21:46 +0800, shhlv wrote:
> Dear pwscf users,
> When I try to open a output file to see the 3D charge density plot
> with xcrysden, a error occurs:
> Error:
> while executing exec
> sh /opt/cluster/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor
> /plate/shlv/study/pwscf/si/si_3D.rho.xsf > pwo2xsf.xsf.
>From this message, I presume you are trying to open an XSF file as pw.x
output file (which is wrong). Try the following instead:
xcrysden --xsf si_3D.rho.xsf
Regards, Tone
--
Tone Kokalj
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 Jul 7 16:47:48 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 07 Jul 2008 16:47:48 +0200
Subject: [Pw_forum] server for PWgui and Xcrysden downloading is off,
please check it out
In-Reply-To: <4869E140.5040000@democritos.it>
References:
<4869E140.5040000@democritos.it>
Message-ID: <1215442068.5008.73.camel@walk.ijs.si>
On Tue, 2008-07-01 at 09:48 +0200, Paolo Giannozzi wrote:
> vega lew wrote:
>
> > Your website for PWgui and Xcrysden downloading is no longer up to
> > snuff. I can't connect it for a long time. please check it out.
>
> it looks like a network problem somewhere in Ljubljana (Slovenia),
> where the servers are located. It should be a temporary problem.
Actually, it was a paranoid firewall problem
(caused by a new firewall installation by the IT people at my institute).
The server is (should be) reachable again. I apologise for the inconvinience.
Regards, Tone
--
Tone Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)
From flitimein at yahoo.fr Mon Jul 7 21:21:40 2008
From: flitimein at yahoo.fr (Fatma Litimein)
Date: Mon, 7 Jul 2008 21:21:40 +0200 (CEST)
Subject: [Pw_forum] how to optimize the lattice parameters of monoclinic
structure ?
Message-ID: <831524.25484.qm@web23101.mail.ird.yahoo.com>
Dear PWscf users, I have a question about optimization of an monoclinic structure, so to do that have I to optimize c/a, V, b/a, V, ...., beta, V, in SCF manner until convergence of the structure or can I perform just one c/a, b/a, V optimization ? How can I to optimize i.e. beta angel? Any comments are welcome.
Thank you in advance
=======================================================
Fatma Litimein
Computational Materials Science Laboratory,
Physics Department, University of Sidi Bel Abbes
Sidi Bel Abbes, 22000 - Algeria
Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
=======================================================
---------------------------------
Envoy? avec Yahoo! Mail.
Une boite mail plus intelligente.
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From flitimein at yahoo.fr Mon Jul 7 21:22:02 2008
From: flitimein at yahoo.fr (Fatma Litimein)
Date: Mon, 7 Jul 2008 21:22:02 +0200 (CEST)
Subject: [Pw_forum] how to optimize the lattice parameters of monoclinic
structure ?
Message-ID: <352568.37260.qm@web23107.mail.ird.yahoo.com>
Dear PWscf users, I have a question about optimization of an monoclinic structure, so to do that have I to optimize c/a, V, b/a, V, ...., beta, V, in SCF manner until convergence of the structure or can I perform just one c/a, b/a, V optimization ? How can I to optimize i.e. beta angel? Any comments are welcome.
Thank you in advance
=======================================================
Fatma Litimein
Computational Materials Science Laboratory,
Physics Department, University of Sidi Bel Abbes
Sidi Bel Abbes, 22000 - Algeria
Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
=======================================================
---------------------------------
Envoy? avec Yahoo! Mail.
Une boite mail plus intelligente.
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From jhashemifar at gmail.com Tue Jul 8 04:02:06 2008
From: jhashemifar at gmail.com (Javad hashemifar)
Date: Tue, 8 Jul 2008 05:32:06 +0330
Subject: [Pw_forum] how to optimize the lattice parameters of monoclinic
structure ?
In-Reply-To: <352568.37260.qm@web23107.mail.ird.yahoo.com>
References: <352568.37260.qm@web23107.mail.ird.yahoo.com>
Message-ID: <2fb18d9f0807071902p43153cev1d29b63f63c9c39b@mail.gmail.com>
Dear Fatma
I think the best option for you is the vc (volume-cell) relaxation. In this
kind of calculations all lattice parameters and atomic positions are relaxed
simultaneously. Please see the INPUT_PW file for adjusting the required
input parameters.
another option is to relax lattice parameters one by one. In each step you
should vary one lattice parameter and fix others. After finding the
optimized value of this lattice parameter, it should be fixed and another
lattice parameter should be optimized. The following sequence of relaxation
may be useful:
1. betha (a, b/a, and c/a are fixed to experimental or any other reported
value)
2. Volume (betha, b/a, and c/a should be fixed)
3. b/a (betha, Volume, and c/a are fixed)
4. c/a (bethe, Volume, and b/a are fixed)
it is better to repeat the above sequence more than one time.
It should be noted that vc relaxation seems to be more appropriate for you.
Javad
On Mon, Jul 7, 2008 at 10:52 PM, Fatma Litimein wrote:
> *Dear PWscf users, * *I have a question about optimization of an
> monoclinic structure, so to do that have I to optimize c/a, V, b/a, V,
> ...., beta, V, in SCF manner until convergence of the structure or can I
> perform just one c/a, b/a, V optimization ? How can I to optimize i.e. beta
> angel? Any comments are welcome. *
> *Thank you in advance *
>
>
>
>
> =======================================================
> Fatma Litimein
> Computational Materials Science Laboratory,
> Physics Department, University of Sidi Bel Abbes
> Sidi Bel Abbes, 22000 - Algeria
> Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
> =======================================================
>
> ------------------------------
> Envoy? avec Yahoo! Mail
> .
> Une boite mail plus intelligente.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
======================================
Seyed Javad Hashemifar, Ph.D.
current address:
Physics Department, University of Duisburg-Essen,
47057 Duisburg, Germany
Tel:+49 203 379 4743 Fax:+49 203 379 4741
permanent address:
Physics Department, Isfahan University of Technology
84154 Isfahan, Iran
Tel: +98 311 391 2375 Fax:+98 311 3912376
---------------------------------------------------------------------------
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From chenhanghuipwscf at gmail.com Tue Jul 8 05:19:25 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Mon, 7 Jul 2008 23:19:25 -0400
Subject: [Pw_forum] external electric field
Message-ID: <22ae3ca40807072019i30eb7341w1694401506c94c4d@mail.gmail.com>
Dear PWSCF users,
I know this question might be too general but I just want to give a
try.
In PWSCF, there are two options for external field. One is 'tefield'
to simulate a sawlike potential, the other is 'lelfield' to simulate a
homogeneous electric field. Could you tell the difference between these two
options? Or can you link me to some useful references about how to use these
two types of external field?
Thank you very much.
Hanghui
Department of Physics,
Yale University
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From baroni at sissa.it Tue Jul 8 08:06:22 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 8 Jul 2008 14:06:22 +0800
Subject: [Pw_forum] external electric field
In-Reply-To: <22ae3ca40807072019i30eb7341w1694401506c94c4d@mail.gmail.com>
References: <22ae3ca40807072019i30eb7341w1694401506c94c4d@mail.gmail.com>
Message-ID: <29F63975-0DB5-4676-8BAC-CFFD7F2328FF@sissa.it>
a "sawlike" potential is not homegeneous! as simple as that ...
the first is implemented as a regular potential, the second using
Berry's phases and constrained optimization, following ideas from
Resta, Vanderbilt, Umari-Pasquarello among others
Cheers - SB
On Jul 8, 2008, at 11:19 AM, alan chen wrote:
> Dear PWSCF users,
> I know this question might be too general but I just want to
> give a try.
> In PWSCF, there are two options for external field. One is
> 'tefield' to simulate a sawlike potential, the other is 'lelfield'
> to simulate a homogeneous electric field. Could you tell the
> difference between these two options? Or can you link me to some
> useful references about how to use these two types of external field?
> Thank you very much.
>
> Hanghui
> Department of Physics,
> Yale University
> _______________________________________________
> 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 sathya_sheela1985001 at rediffmail.com Tue Jul 8 12:44:44 2008
From: sathya_sheela1985001 at rediffmail.com (sathya subramanyan)
Date: 8 Jul 2008 10:44:44 -0000
Subject: [Pw_forum] negative value of polarization and Z* for Pb in
Tetragonal PbTiO3 and discrepancy
Message-ID: <20080708104444.23353.qmail@f4mail-234-223.rediffmail.com>
?Dear Sir,
I have checked the k -point sampling for the tetragonal PbTiO3 and I hope that the k-point sampling is alright. I am giving below the input file for your reference. Pl, let me know if anything is wrong in the input.:
THE I/P FILE FOR TETRAGONAL PbTiO3
&CONTROL
calculation = 'nscf'
pseudo_dir = '/home/nbaski/espresso-4.0/pseudo/'
outdir = '/home/nbaski/tmp/'
lberry = .true.
gdir = 3
nppstr = 7
/
&SYSTEM
ibrav = 6
celldm(1) = 7.3415
celldm(3) = 1.0653
nat = 5
ntyp = 3
nbnd = 22
ecutwfc = 30.0
occupations = 'fixed'
degauss = 0.00
/
&ELECTRONS
conv_thr = 1e-5
mixing_beta = 0.3
/
ATOMIC_SPECIES
Pb 207.2 Pb.vdb.UPF
Ti 47.867 Ti.vdb.UPF
O 15.9994 O.vdb.UPF
ATOMIC_POSITIONS
Pb 0.00000 0.00000 0.01000
Ti 0.50000 0.50000 0.53770
O 0.50000 0.50000 0.11180
O 0.00000 0.50000 0.61740
O 0.50000 0.00000 0.61740
K_POINTS {automatic}
4 4 7 1 1 1
Thank you in advance for any help
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli
On Fri, 27 Jun 2008 Stefano Baroni wrote :
>the sum of the all the effective charges should be zero for any structure, due dynamical charge neutrality (or acoustic sum rule, or whatever you want to call the fact that a homogeneouse electric field will not exert a net (and infinite!) force on a crystal. Vioation of this charge neutrality/acoustic sum rule are often due to numerical inaccuracy, often inaccurate k-point sampling. you may want to check the convergence of your calculations with respect to the number of k points and/or try to calculate the effective charges using linear- response theory. SB
>
>On Jun 27, 2008, at 11:51 AM, sathya subramanyan wrote:
>
>>
>>Dear Developers,
>> I am trying to calculate the Berry Phaze Polarization and effective charge on Pb(with the displacement of . 01*ao) for PbTiO3(tetragonal) but am getting a negative value, using quantum espresso ver 4.0.
>>
>> When I run the example 10 for cubic phase the polarization and the Z* comes out to be alright. But, when I try for tetragonal phase, I am getting negative ionic phase leading to negative polarization for Pb.
>> If I compare the out put file for both cubic and tertragonal phase, to my surprise in the cubic phase the total ionic phase comes out to be positive (actually, if you sum it is negative), where as in the case of tetragonal phase the ionic phase comes out to be negative (but, it is positive if you sum the same way as for the cubic).
>> I do not understand this differrent summing rule for different phases. I am attaching both the input and out files for cubic and tetragonal phases. I would appreciate any useful suggestions to clear this point.
>>I am very sorry for the long mail and data files.
>>
>>- 620015
>>India
>>
>>_______________________________________________
>>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 giannozz at democritos.it Tue Jul 8 14:59:20 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 8 Jul 2008 14:59:20 +0200
Subject: [Pw_forum] condor grid script
In-Reply-To: <7332fead0807011105x4d4398e8i5a2106c854f25eaf@mail.gmail.com>
References: <7332fead0807011105x4d4398e8i5a2106c854f25eaf@mail.gmail.com>
Message-ID: <404C0736-EF51-4668-9F6A-3BA8DFD939EE@democritos.it>
On Jul 1, 2008, at 20:05 , Goranka Bilalbegovic wrote:
> [...] the Condor-G submission script is similar to:
>
> --------------------------------------------
> executable =/home/user/espresso-4.0/bin/pw.x
> transfer_executable=true
> should_transfer_files = yes
> when_to_transfer_output = ON_EXIT
> transfer_input_files =/home/user/espresso-4.0/pseudo/Si.vbc.UPF
> universe=grid
> grid_resource=gt2 .../jobmanager-sge
> output = pw_condor.out
> error = pw_condor.err
> log = pw_condor.log
> input = siscf.in
> globusrsl=(jobType=mpi)(count=1)
> queue
> --------------------------------------------------
>
> Job (the first part of example01) runs, but I do not know how to write
> the lines "transfer_input_files", "arguments",..., and/or pseudo_dir=
> in siscf.in to read the pseudopotential file [...] The error is
> always:
>
> from readpp : error # 29
> file ... Si.vbc.UPF not found
this is very funny: three dots and a space? Anyway: I would try first
to set
pseudo_dir='./' in siscf.in . This will search for file Si.vbc.UPF in
the
current directory (whatever it is).
Disclaimer: I know close to nothing about the grid.
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 Daniele.Passerone at empa.ch Tue Jul 8 17:58:10 2008
From: Daniele.Passerone at empa.ch (Daniele Passerone)
Date: Tue, 08 Jul 2008 17:58:10 +0200
Subject: [Pw_forum] STS spectra
Message-ID: <4873AAB2.11F0.001D.0@empa.ch>
Dear Pwscf users and developers,
The postprocessing facilities of espresso allow to extract stm images,
that correspond in Tersoff-Hamann approximation to the
localized density of states integrated between Efermi and a given
(positive or negative) bias. The more convenient way to analyze this
quantity is in my opinion by generating a 3d grid and visualizing it
with xcrysden, which incidentally can also show planes parallel to the
cell
sides.
The ILDOS option of pp.x (plot_num=10) somewhat extends this, allowing
to compute the LDOS integrated between emin and emax.
STS (scanning tunneling spectroscopy) experiments sample the local
density of states at a surface: one obtains a profile of dI/dV
at a certain point on the surface, and this gives valuable information
about the local conductivity and presence of peaks in the DOS etc.
The question is: what is the more convenient and fast way to get the
LDOS profile from Emin to Emax, on a certain plane (let us say, 2
Angstrom above the surface)? I thought one could make several jobs of
pp.x : from Emin to Emin+DeltaE, from Emin + Delta E to
Emin + 2*Delta E.... and so on... but maybe there are much better ways
to do that.
Thank you in advance for any advice,
Daniele
*************************************************************
Dr. Daniele Passerone
Abteilung nanotech at surfaces
Theory and atomistic simulation of materials
Empa - Materials Science & Technology
Ueberlandstrasse 129
CH-8600 D?bendorf
Tel +41 44 823 4877
Fax +41 44 823 4031
daniele.passerone at empa.ch
www.empa.ch
E-mail from non-academic servers:
daniele at passerone.net
************************************************************
From gbilalbegovic at gmail.com Tue Jul 8 21:03:11 2008
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Tue, 8 Jul 2008 21:03:11 +0200
Subject: [Pw_forum] condor grid script
In-Reply-To: <404C0736-EF51-4668-9F6A-3BA8DFD939EE@democritos.it>
References: <7332fead0807011105x4d4398e8i5a2106c854f25eaf@mail.gmail.com>
<404C0736-EF51-4668-9F6A-3BA8DFD939EE@democritos.it>
Message-ID: <7332fead0807081203q69902e00u13ef7750767a94@mail.gmail.com>
On 7/8/08, Paolo Giannozzi wrote:
> > from readpp : error # 29
> > file ... Si.vbc.UPF not found
> this is very funny: three dots and a space? Anyway: I would try first
> to set
> pseudo_dir='./' in siscf.in . This will search for file Si.vbc.UPF in
> the
> current directory (whatever it is).
Of course it is funny because I have replaced the name of my dir by
three dots (sorry !). The error message is:
file /home/user/espresso/pseudo/Si.vbc.UPF not found
> Disclaimer: I know close to nothing about the grid.
Me too, but I have to learn to use the grid because the University
computing center have decided to support the grid computing only.
Perhaps, it is interesting for this list that people on TeraGrid work for some
time on the espresso implementation:
http://sangpall.blogspot.com/2008/01/compiling-espresso-in-tg-machines.html
and
http://sangpall.blogspot.com/2008_01_01_archive.html
Dr Pallikara have told me that he actually did not do anything special to
implement pwscf on his grid. Of course, he manages TeraGrid an they
have installed the program on the grid. I was doing everything from my
own directory.
Programs with a simple input-executable-output line work without any
problems, but as for now I am not able to run espresso jobs using all
these Condor/GridWay/GRAM/WS-GRAM grid related scripts. However, I
have just learn how to use uberftp to transfer all my directories
directly to the grid and hope that soon everything is going to be OK
on the grid.
Best regards,
Goranka Bilalbegovic
Department of Physics,
Faculty of Science,
University of Zagreb, Croatia
From giannozz at democritos.it Tue Jul 8 22:43:10 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 8 Jul 2008 22:43:10 +0200
Subject: [Pw_forum] condor grid script
In-Reply-To: <7332fead0807081203q69902e00u13ef7750767a94@mail.gmail.com>
References: <7332fead0807011105x4d4398e8i5a2106c854f25eaf@mail.gmail.com>
<404C0736-EF51-4668-9F6A-3BA8DFD939EE@democritos.it>
<7332fead0807081203q69902e00u13ef7750767a94@mail.gmail.com>
Message-ID: <54AAD73C-F85E-4A7F-B615-109956BA1311@democritos.it>
On Jul 8, 2008, at 21:03 , Goranka Bilalbegovic wrote:
> The error message is:
> file /home/user/espresso/pseudo/Si.vbc.UPF not found
$HOME/espresso/pseudo is the default place where pseudopotential
files are looked for, so apparently you haven't set "pseudo_dir" to
anything. Try to set it in the input file to the current directory,
'./'
(it is also possible to use the environment variable ESPRESSO_PSEUDO,
but then you have to know how to set it in a grid environment). The
pseudopotential files are copied somewhere (I think into a temporary
storage called "sandbox" or something like this), and so is the
executable.
My guess is that they are copied in the same place.
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 chenhanghuipwscf at gmail.com Tue Jul 8 23:27:00 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Tue, 8 Jul 2008 17:27:00 -0400
Subject: [Pw_forum] startingwfc='file' ?
Message-ID: <22ae3ca40807081427p67c51406v17d52c0ec7a7fcca@mail.gmail.com>
Dear PWSCF users,
I am now running a calculation of insulators in an external electric
field. From the example31, I need to first run a self-consistent calculation
and then run another self-consistent calculation with 'lelfield' option
turning on. In the README file, it says that 'startingwfc' should be 'file'
because 'a copy of the wavefunctions is read from the disk'.
However, whenever I set 'startingwfc' to 'file', I got the CRASH which
reads: 'error in zgefa'. I believe that is because the wavefuction is NOT
properly read in. And if I set 'startingwfc' to 'atomic', the code runs
smoothly.
I want to ask: 1) whether it is necessary to set 'startingwfc' to
'file'? 2) if it is necesary, how to collect the wave functions corrrectly
in the previous run?
Thank you very much.
Hanghui
Department of Physics,
Yale University
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From baroni at sissa.it Wed Jul 9 01:53:26 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 9 Jul 2008 07:53:26 +0800
Subject: [Pw_forum] negative value of polarization and Z* for Pb in
Tetragonal PbTiO3 and discrepancy
In-Reply-To: <20080708104444.23353.qmail@f4mail-234-223.rediffmail.com>
References: <20080708104444.23353.qmail@f4mail-234-223.rediffmail.com>
Message-ID:
what I was suggesting is that YOU perform a convergence test and ley
us know ...
SB
On Jul 8, 2008, at 6:44 PM, sathya subramanyan wrote:
> Dear Sir,
> I have checked the k -point sampling for the tetragonal
> PbTiO3 and I hope that the k-point sampling is alright. I am giving
> below the input file for your reference. Pl, let me know if anything
> is wrong in the input.:
>
> THE I/P FILE FOR TETRAGONAL PbTiO3
>
> &CONTROL
> calculation = 'nscf'
> pseudo_dir = '/home/nbaski/espresso-4.0/pseudo/'
> outdir = '/home/nbaski/tmp/'
> lberry = .true.
> gdir = 3
> nppstr = 7
> /
> &SYSTEM
> ibrav = 6
> celldm(1) = 7.3415
> celldm(3) = 1.0653
> nat = 5
> ntyp = 3
> nbnd = 22
> ecutwfc = 30.0
> occupations = 'fixed'
> degauss = 0.00
> /
> &ELECTRONS
> conv_thr = 1e-5
> mixing_beta = 0.3
> /
> ATOMIC_SPECIES
> Pb 207.2 Pb.vdb.UPF
> Ti 47.867 Ti.vdb.UPF
> O 15.9994 O.vdb.UPF
> ATOMIC_POSITIONS
> Pb 0.00000 0.00000 0.01000
> Ti 0.50000 0.50000 0.53770
> O 0.50000 0.50000 0.11180
> O 0.00000 0.50000 0.61740
> O 0.50000 0.00000 0.61740
> K_POINTS {automatic}
> 4 4 7 1 1 1
>
>
>
>
>
> Thank you in advance for any help
> SATHYA SHEELA.S
> Grad. Student
> Department of Physics
> National Institute of Technology
> Tiruchirapalli
>
>
> On Fri, 27 Jun 2008 Stefano Baroni wrote :
> >the sum of the all the effective charges should be zero for any
> structure, due dynamical charge neutrality (or acoustic sum rule,
> or whatever you want to call the fact that a homogeneouse electric
> field will not exert a net (and infinite!) force on a crystal.
> Vioation of this charge neutrality/acoustic sum rule are often due
> to numerical inaccuracy, often inaccurate k-point sampling. you may
> want to check the convergence of your calculations with respect to
> the number of k points and/or try to calculate the effective
> charges using linear- response theory. SB
> >
> >On Jun 27, 2008, at 11:51 AM, sathya subramanyan wrote:
> >
> >>
> >>Dear Developers,
> >> I am trying to calculate the Berry Phaze
> Polarization and effective charge on Pb(with the displacement of .
> 01*ao) for PbTiO3(tetragonal) but am getting a negative value,
> using quantum espresso ver 4.0.
> >>
> >> When I run the example 10 for cubic phase the
> polarization and the Z* comes out to be alright. But, when I try
> for tetragonal phase, I am getting negative ionic phase leading to
> negative polarization for Pb.
> >> If I compare the out put file for both cubic and
> tertragonal phase, to my surprise in the cubic phase the total
> ionic phase comes out to be positive (actually, if you sum it is
> negative), where as in the case of tetragonal phase the ionic phase
> comes out to be negative (but, it is positive if you sum the same
> way as for the cubic).
> >> I do not understand this differrent summing rule
> for different phases. I am attaching both the input and out files
> for cubic and tetragonal phases. I would appreciate any useful
> suggestions to clear this point.
> >>I am very sorry for the long mail and data files.
> >>
> >>- 620015
> >>India
> >>
> >>_______________________________________________
> >>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
> >
> >
> >
> >
> >
> >
>
>
>
> _______________________________________________
> 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 chenhanghuipwscf at gmail.com Wed Jul 9 04:48:04 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Tue, 8 Jul 2008 22:48:04 -0400
Subject: [Pw_forum] high-frequency dielectric constant of SrTiO3
Message-ID: <22ae3ca40807081948h62264e94gb7d002034970a64d@mail.gmail.com>
Dear PWSCF users,
I am calculating the high-frequency dielectric constant of SrTiO3.
Using the method given in the example31, I calculate D[E=0.001a.u.] and
D[E=0] and eps_inf=4*pi*(D[E=0.001a.u.]-D[E=0])/(0.001a.u.*Omega) + 1 where
Omega is the volume of the unit cell.
I sample the Brillouin zone by 4x4x8 (uniformly distributed) and
obtain: D[E=0.001 a.u.] = 0.155 and D[E=0] is almost zero, therefore
eps_inf=6.0 which is much smaller than experimental values.
Did I do the calculation correctly? Does anyone have experience about
calculating high-frequency dielectric constant of SrTiO3?
Thank you very much.
Hanghui
Department of Physics,
Yale University
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From giannozz at democritos.it Wed Jul 9 14:26:32 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 9 Jul 2008 14:26:32 +0200
Subject: [Pw_forum] startingwfc='file' ?
In-Reply-To: <22ae3ca40807081427p67c51406v17d52c0ec7a7fcca@mail.gmail.com>
References: <22ae3ca40807081427p67c51406v17d52c0ec7a7fcca@mail.gmail.com>
Message-ID: <76AC3B8E-7C68-45E8-B719-729959A84085@democritos.it>
On Jul 8, 2008, at 23:27 , alan chen wrote:
> However, whenever I set 'startingwfc' to 'file'
whenever when? always? in a specific case?
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From iphyboy at hotmail.com Wed Jul 9 15:00:22 2008
From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=)
Date: Wed, 9 Jul 2008 21:00:22 +0800
Subject: [Pw_forum] parallel phonon code ????
Message-ID:
Dear users:
I am a very confused question: Is the phonon code (ph.x) really implemented in parallel version?
since the phonon computational time usually is intolerable,for example, the task was not completed
when I calculated the phonon dispersion of superconducting material LaOFeAs. Furthermore, the speed of computation shows
no difference when I used 32 CPUs from that when I only 8 CPUs. Also, the dynamic matrix files *.dyn(1-n)
are generated one by one, totally different from SCF wavefunctin files which are generated parallelly(like
*.wavfc1,*.wavfc2, ......, *.wavfc8 in case of 8 CPUs parallelization sheme)
thanks a lot
Wenmei Ming
www.iphy.ac.cn
_________________________________________________________________
MSN ????????????????????
http://cn.msn.com
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From baroni at sissa.it Wed Jul 9 16:51:02 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 9 Jul 2008 22:51:02 +0800
Subject: [Pw_forum] high-frequency dielectric constant of SrTiO3
In-Reply-To: <22ae3ca40807081948h62264e94gb7d002034970a64d@mail.gmail.com>
References: <22ae3ca40807081948h62264e94gb7d002034970a64d@mail.gmail.com>
Message-ID:
Have you tried linear response? have you performed any convergence
test 9especially wrt the number of k points)? SB
On Jul 9, 2008, at 10:48 AM, alan chen wrote:
> Dear PWSCF users,
> I am calculating the high-frequency dielectric constant of
> SrTiO3. Using the method given in the example31, I calculate
> D[E=0.001a.u.] and D[E=0] and eps_inf=4*pi*(D[E=0.001a.u.]-D[E=0])/
> (0.001a.u.*Omega) + 1 where Omega is the volume of the unit cell.
> I sample the Brillouin zone by 4x4x8 (uniformly distributed)
> and obtain: D[E=0.001 a.u.] = 0.155 and D[E=0] is almost zero,
> therefore eps_inf=6.0 which is much smaller than experimental values.
> Did I do the calculation correctly? Does anyone have
> experience about calculating high-frequency dielectric constant of
> SrTiO3?
> Thank you very much.
>
> Hanghui
> Department of Physics,
> Yale University
> _______________________________________________
> 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 sunyang198498 at gmail.com Wed Jul 9 17:52:25 2008
From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=)
Date: Wed, 9 Jul 2008 10:52:25 -0500
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
Message-ID: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Hi!
how could I relax the atoms position without changing the cell parameters
say, if i have a simple cubic cell with each point having a benzene
structure. How could I relax the benzene's atoms, say, hydrogen and
carbon with the fixed edge size within the simple cubic cell.
Thank you,
Yang
From polynmr at physics.unc.edu Wed Jul 9 17:54:46 2008
From: polynmr at physics.unc.edu (Charles Chen)
Date: Wed, 09 Jul 2008 11:54:46 -0400
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
In-Reply-To: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
References: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Message-ID: <4874DF46.5020903@physics.unc.edu>
use relax instead vc-relax?
?? wrote:
> Hi!
> how could I relax the atoms position without changing the cell parameters
> say, if i have a simple cubic cell with each point having a benzene
> structure. How could I relax the benzene's atoms, say, hydrogen and
> carbon with the fixed edge size within the simple cubic cell.
>
> Thank you,
>
> Yang
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
--
NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR
NMR Dr. Qiang "Charles" Chen NMR
NMR Department of Physics and Astronomy NMR
NMR University of North Carolina NMR
NMR Phillips Hall, CB#3255 NMR
NMR Chapel Hill, NC 27599-3255 NMR
NMR Tel: 919-962-1571 (O) NMR
NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR
From kondor.jess at gmail.com Wed Jul 9 18:13:32 2008
From: kondor.jess at gmail.com (Jess Kondor)
Date: Wed, 9 Jul 2008 11:13:32 -0500
Subject: [Pw_forum] a problem with polarization
Message-ID: <1d9d5d9d0807090913x16c7645bm54e33aa2a1c4084@mail.gmail.com>
Dear all,
I am working on bulk multiferroic, BiFeO3. It is suppose to have a
spontaneous polarization around 100 mC/cm^2 along [111] direction .
However, I got ~2.5 mC/cm^2 using LSDA+U approximation and Berry Phase
method:
along x: P = 0.0143864 (mod 0.7250294) C/m^2
along y: P = 0.0143881 (mod 0.7250294) C/m^2
along z: P = 0.0139124 (mod 0.7250294) C/m^2
P_[111]=sqrt(Px*Px + Py*Py + Pz*Pz) = 2.47 mC/cm^2 . The funny part is
that using the same structure and ABINIT code I was able to get a
value of polarization that is closed to 100 mC/cm^2. I am sure that I
did something wrong and there is a simple explanation to this. All
other parameters (lattice parameters, wyckoff positions) obtained by
PWscf and ABINIT are almost equivalent.
Does anybody have any hints?
Best regards,
--
=====================================
Jess Kondor,
PhD student
PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
From lanhaiping at gmail.com Wed Jul 9 18:15:44 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 10 Jul 2008 00:15:44 +0800
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
In-Reply-To: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
References: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Message-ID:
Why not to read the Document and related INPUT ?
If you just want to do a simple relaxation for a molecule , two points
should be
taken into attention :
1, The cell should be large enough to avoid image intetactions.
2, gamma sampling for BZ
P.S , please supply your affiliation
On Wed, Jul 9, 2008 at 11:52 PM, ?? wrote:
> Hi!
> how could I relax the atoms position without changing the cell parameters
> say, if i have a simple cubic cell with each point having a benzene
> structure. How could I relax the benzene's atoms, say, hydrogen and
> carbon with the fixed edge size within the simple cubic cell.
>
> Thank you,
>
> Yang
> _______________________________________________
> 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 flitimein at yahoo.fr Wed Jul 9 19:00:48 2008
From: flitimein at yahoo.fr (Fatma Litimein)
Date: Wed, 9 Jul 2008 19:00:48 +0200 (CEST)
Subject: [Pw_forum] RE : Re: how to optimize the lattice parameters of
monoclinic structure ?
In-Reply-To: <2fb18d9f0807071902p43153cev1d29b63f63c9c39b@mail.gmail.com>
Message-ID: <513020.93655.qm@web23104.mail.ird.yahoo.com>
Dear Javad,
Thank you very much for your help, and for your time.
I have already done the vc relaxation. The problem is in my output file.The crystal axes seems to be not similar to that in INPUT_PW file.
Any comments are highly appreciated.
Regards,
Fatma
monoclinic (p)
====================== INPUT_PW ======================
v1 = (a,0,0), v2= (b*cos(gamma), b*sin(gamma), 0), v3 = (0, 0, c)
where gamma is the angle between axis a and b
============here is my output file=================
bravais-lattice index = 12
lattice parameter (a_0) = 23.1113 a.u.
unit-cell volume = 1413.2148 (a.u.)^3
number of atoms/cell = 20
number of atomic types = 5
number of electrons = 176.00
number of Kohn-Sham states= 88
kinetic-energy cutoff = 25.0000 Ry
charge density cutoff = 100.0000 Ry
convergence threshold = 1.0E-08
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = SLA PW GGX GGC (1422)
nstep = 55
celldm(1)= 23.111300 celldm(2)= 0.248500 celldm(3)= 0.474200
celldm(4)= -0.237000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of a_0)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( -0.058895 0.241420 0.000000 )
a(3) = ( 0.000000 0.000000 0.474200 )
reciprocal axes: (cart. coord. in units 2 pi/a_0)
b(1) = ( 1.000000 0.243950 -0.000000 )
b(2) = ( 0.000000 4.142156 0.000000 )
b(3) = ( 0.000000 -0.000000 2.108815 )
:
.
:
No symmetry!
.
.
.
==========================================================
Javad hashemifar a ?crit :
Dear Fatma
I think the best option for you is the vc (volume-cell) relaxation. In this kind of calculations all lattice parameters and atomic positions are relaxed simultaneously. Please see the INPUT_PW file for adjusting the required input parameters.
another option is to relax lattice parameters one by one. In each step you should vary one lattice parameter and fix others. After finding the optimized value of this lattice parameter, it should be fixed and another lattice parameter should be optimized. The following sequence of relaxation may be useful:
1. betha (a, b/a, and c/a are fixed to experimental or any other reported value)
2. Volume (betha, b/a, and c/a should be fixed)
3. b/a (betha, Volume, and c/a are fixed)
4. c/a (bethe, Volume, and b/a are fixed)
it is better to repeat the above sequence more than one time.
It should be noted that vc relaxation seems to be more appropriate for you.
Javad
On Mon, Jul 7, 2008 at 10:52 PM, Fatma Litimein wrote:
Dear PWscf users, I have a question about optimization of an monoclinic structure, so to do that have I to optimize c/a, V, b/a, V, ...., beta, V, in SCF manner until convergence of the structure or can I perform just one c/a, b/a, V optimization ? How can I to optimize i.e. beta angel? Any comments are welcome.
Thank you in advance
=======================================================
Fatma Litimein
Computational Materials Science Laboratory,
Physics Department, University of Sidi Bel Abbes
Sidi Bel Abbes, 22000 - Algeria
Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
=======================================================
---------------------------------
Envoy? avec Yahoo! Mail.
Une boite mail plus intelligente.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
--
======================================
Seyed Javad Hashemifar, Ph.D.
current address:
Physics Department, University of Duisburg-Essen,
47057 Duisburg, Germany
Tel:+49 203 379 4743 Fax:+49 203 379 4741
permanent address:
Physics Department, Isfahan University of Technology
84154 Isfahan, Iran
Tel: +98 311 391 2375 Fax:+98 311 3912376
--------------------------------------------------------------------------- _______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
=======================================================
Fatma Litimein
Computational Materials Science Laboratory,
Physics Department, University of Sidi Bel Abbes
Sidi Bel Abbes, 22000 - Algeria
Tel:+213 48-54-95-46 Fax:+213 48-54-19-28 flitimein at yahoo.fr
=======================================================
---------------------------------
Envoy? avec Yahoo! Mail.
Une boite mail plus intelligente.
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From eyvaz_isaev at yahoo.com Wed Jul 9 22:03:24 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 9 Jul 2008 13:03:24 -0700 (PDT)
Subject: [Pw_forum] negative value of polarization and Z* for Pb in
Tetragonal PbTiO3 and discrepancy
In-Reply-To:
Message-ID: <717949.97771.qm@web65706.mail.ac4.yahoo.com>
Hi,
In addition to Stefano's comment I would recommend check your input file by means of XCrysDen? in order to see whether you have correct structure. At this time it seems to be incorrect.
Besides, use lower convergence threshold, conv_thr=1d-8, 1e-6 looks quite high.
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 Wed, 7/9/08, Stefano Baroni wrote:
From: Stefano Baroni
Subject: Re: [Pw_forum] negative value of polarization and Z* for Pb in Tetragonal PbTiO3 and discrepancy
To: "sathya subramanyan" , "PWSCF Forum"
Date: Wednesday, July 9, 2008, 3:53 AM
what I was suggesting is that YOU perform a convergence test and ley us know ...SB
On Jul 8, 2008, at 6:44 PM, sathya subramanyan wrote:
? Dear Sir,
? ? ? ? ? ? I have checked the k -point sampling for the tetragonal PbTiO3 and I hope that the k-point sampling is alright. I am giving below the input file for your reference. Pl, let me know if anything is wrong in the input.:
? THE I/P FILE FOR TETRAGONAL PbTiO3
&CONTROL
? ? calculation? = 'nscf'
? ? pseudo_dir? ? = '/home/nbaski/espresso-4.0/pseudo/'
? ? outdir? ? ? ? = '/home/nbaski/tmp/'
? ? lberry? ? ? ? = .true.
? ? gdir? ? ? ? ? = 3
? ? nppstr? ? ? ? = 7
/
&SYSTEM
? ? ibrav? ? ? ? = 6
? ? ? celldm(1)? ? = 7.3415
? ? celldm(3)? ? = 1.0653
? ? nat? ? ? ? ? = 5
? ? ntyp? ? ? ? ? = 3
? ? nbnd? ? ? ? ? = 22
? ? ecutwfc? ? ? = 30.0
? ? occupations? = 'fixed'
? ? degauss? ? ? = 0.00
/
&ELECTRONS
? conv_thr? ? ? = 1e-5
? ? mixing_beta? = 0.3
/
ATOMIC_SPECIES
? Pb? 207.2? ? ? Pb.vdb.UPF
? Ti? ? 47.867? ? Ti.vdb.UPF
? O? ? 15.9994? O.vdb.UPF
ATOMIC_POSITIONS
? Pb? ? 0.00000? ? 0.00000? ? 0.01000
? Ti? ? 0.50000? ? 0.50000? ? 0.53770
? O? ? 0.50000? ? 0.50000? ? 0.11180
? O? ? 0.00000? ? 0.50000? ? 0.61740
? O? ? 0.50000? ? 0.00000? ? 0.61740
K_POINTS {automatic}
? 4 4 7? 1 1 1
Thank you in advance for any help
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli
On Fri, 27 Jun 2008 Stefano Baroni wrote :
>the sum of the all the effective charges should be zero for any? structure, due dynamical charge neutrality (or acoustic sum rule, or? whatever you want to call the fact that a homogeneouse electric field? will not exert a net (and infinite!) force on a crystal. Vioation of? this charge neutrality/acoustic sum rule are often due to numerical? inaccuracy, often inaccurate k-point sampling. you may want to check? the convergence of your calculations with respect to the number of k? points and/or try to calculate the effective charges using linear- response theory. SB
>
>On Jun 27, 2008, at 11:51 AM, sathya subramanyan wrote:
>
>>
>>Dear Developers,
>>? ? ? ? ? ? ? ? I am trying to calculate the Berry Phaze? Polarization and effective charge on Pb(with the displacement of . 01*ao) for PbTiO3(tetragonal) but am getting a negative value, using? quantum espresso ver 4.0.
>>
>>? ? ? ? ? ? ? ? When I run the example 10 for cubic phase the? polarization and the Z* comes out to be alright. But, when I try for? tetragonal phase, I am getting negative ionic phase leading to? negative polarization for Pb.
>>? ? ? ? ? ? ? ? If I compare the out put file for both cubic and? tertragonal phase, to my surprise in the cubic phase the total ionic? phase comes out to be positive (actually, if you sum it is? negative), where as in the case of tetragonal phase the ionic phase? comes out to be negative (but, it is positive if you sum the same? way as for the cubic).
>>? ? ? ? ? ? ? ? I do not understand this differrent summing rule for? different phases. I am attaching both the input and out files for? cubic and tetragonal phases. I would appreciate any useful? suggestions to clear this point.
>>I am very sorry for the long mail and data files.
>>
>>- 620015
>>India
>>
>>_______________________________________________
>>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
>
>
>
>
>
>
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
---Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Triestehttp://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 attachmentsWhy? See:??http://www.gnu.org/philosophy/no-word-attachments.html
_______________________________________________
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From royanin at gmail.com Wed Jul 9 22:05:59 2008
From: royanin at gmail.com (Anindya Roy)
Date: Wed, 9 Jul 2008 16:05:59 -0400
Subject: [Pw_forum] a problem with polarization
Message-ID: <1f47ca5f0807091305u4b799524y3886bc14e0c05413@mail.gmail.com>
Hi Jess,
I'm not sure if your conversion from C -> mC and m^2 -> cm^2 is correct. But
there is still another issue that I'd like to point out:
To best of my knowledge there is some mismatch with the ionic contribution
of polarization between ABINIT and PWscf. Please check (and let us know) if
the electronic part is the same between both these codes.
Best,
Anindya
PhD student
Rutgers University
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From sunyang198498 at gmail.com Wed Jul 9 23:49:22 2008
From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=)
Date: Wed, 9 Jul 2008 16:49:22 -0500
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
In-Reply-To:
References: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Message-ID: <98e7a0810807091449h75231982u54de6f2daa6b5401@mail.gmail.com>
Thanks for Haiping's reply.
Simple relaxation requests a tolerance uplimit for the atomic force.
I look it up in the INPUT file and find nothing to get control of that
quantity. I could only that under the default set. Any one would like to
answer it?
Thanks!
Yang
2008/7/9 lan haiping :
> Why not to read the Document and related INPUT ?
> If you just want to do a simple relaxation for a molecule , two points
> should be
> taken into attention :
> 1, The cell should be large enough to avoid image intetactions.
> 2, gamma sampling for BZ
>
> P.S , please supply your affiliation
>
> On Wed, Jul 9, 2008 at 11:52 PM, ?? wrote:
>>
>> Hi!
>> how could I relax the atoms position without changing the cell parameters
>> say, if i have a simple cubic cell with each point having a benzene
>> structure. How could I relax the benzene's atoms, say, hydrogen and
>> carbon with the fixed edge size within the simple cubic cell.
>>
>> Thank you,
>>
>> Yang
>> _______________________________________________
>> 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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
From akohlmey at cmm.chem.upenn.edu Wed Jul 9 23:57:46 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 9 Jul 2008 17:57:46 -0400 (EDT)
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
In-Reply-To:
References: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Message-ID:
On Thu, 10 Jul 2008, lan haiping wrote:
LH> Why not to read the Document and related INPUT ?
please read e-mails a little bit more carefully
before responding and giving potentially incorrect
advice. it mentions a simple cubic crystal with
a benzene molecule on each position, so it is
not about a simple molecule optimization.
the problem for these systems is actually, that
with DFT you get too _little_ interaction between
the benzene molecules (except at high pressure,
of course) due to the incomplete description of
dispersion interactions...
cheers,
axel.
LH> If you just want to do a simple relaxation for a molecule , two
LH> points
LH> should be
LH> taken into attention :
LH> 1, The cell should be large enough to avoid image intetactions.
LH> 2, gamma sampling for BZ
LH> P.S , please supply your affiliation
On Wed, Jul 9, 2008 at 11:52 PM, ???? wrote:
> Hi!
> how could I relax the atoms position without changing the cell parameters
> say, if i have a simple cubic cell with each point having a benzene
> structure. How could I relax the benzene's atoms, say, hydrogen and
> carbon with the fixed edge size within the simple cubic cell.
>
> Thank you,
>
> Yang
> _______________________________________________
> 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
--
=======================================================================
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 mansourehp at gmail.com Thu Jul 10 07:18:33 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 08:48:33 +0330
Subject: [Pw_forum] how to relax the atoms position without changing the
cell parameters
In-Reply-To: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
References: <98e7a0810807090852s1a3dd659s1afdc24f473a9195@mail.gmail.com>
Message-ID:
Dear Yang
you can do relaxation with calculation = "relax", and
&electrons
conv_thr = 1.d-6,
startingwfc = 'atomic',
mixing_beta = 0.3,
diagonalization = 'david_overlap',
/
&ions
ion_dynamics = 'damp',
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
and also you can fix positions with '0' after any ATOMIC_POSITIONS
bye Mansoureh
On Wed, Jul 9, 2008 at 7:22 PM, ?? wrote:
> Hi!
> how could I relax the atoms position without changing the cell parameters
> say, if i have a simple cubic cell with each point having a benzene
> structure. How could I relax the benzene's atoms, say, hydrogen and
> carbon with the fixed edge size within the simple cubic cell.
>
> Thank you,
>
> Yang
> _______________________________________________
> 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 Thu Jul 10 07:33:24 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 09:03:24 +0330
Subject: [Pw_forum] minimization in CP molecular dynamics
Message-ID:
Dear Sir/Madam
I am learning CP molecular dynamics with QE.
I built one of pseudopotentials that I need for my system with ld1.x.
Its energys are near all electron.I think it's correct.and then I started CP
with relaxed cell.but durning minmization for Cp I found high stress and
pressure.
what is its fault?and how can I correct it?
here is end of its output
Total stress (GPa)
-506.53802028 0.05576883 -0.10526666
0.05576883 -506.41419672 -0.28220620
-0.10526666 -0.28220622 -542.53815723
pressure : -472.77946 -472.77946 (Gpa)
temperature : 127.39515 127.39515 (K )
Forces acting on atoms (au) ~1.0E-03
and also I have got another question :why total energy with scf run and CP
run are different?
I look forward to hearing from you as soon as possible.
Thanks
bye
Mansoureh
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From giannozz at democritos.it Thu Jul 10 09:15:07 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 10 Jul 2008 09:15:07 +0200
Subject: [Pw_forum] parallel phonon code ????
In-Reply-To:
References:
Message-ID: <10BFCD84-170F-4FC7-9E02-22AD12251C38@democritos.it>
On Jul 9, 2008, at 15:00 , ??? wrote:
> Is the phonon code (ph.x) really implemented in parallel version?
it is. Parallelization on plane waves and on k-points is implemented.
Other kinds of parallelization aren't.
> Furthermore, the speed of computation shows no difference when
> I used 32 CPUs from that when I only 8 CPUs.
the efficiency of parallelization for each phonon calculation is
similar to that for the self-consistent solution. The optimal number
of cpus depend upon a number of factors: cell size and type, kind
of parallelization, speed of communications in your machine.
This is more or less explained in the documentation
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 Thu Jul 10 09:20:07 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 10 Jul 2008 09:20:07 +0200
Subject: [Pw_forum] RE : Re: how to optimize the lattice parameters of
monoclinic structure ?
In-Reply-To: <513020.93655.qm@web23104.mail.ird.yahoo.com>
References: <513020.93655.qm@web23104.mail.ird.yahoo.com>
Message-ID: <06B30D56-28E1-4D5F-880C-E258C069F16D@democritos.it>
On Jul 9, 2008, at 19:00 , Fatma Litimein wrote:
> The problem is in my output file.The crystal axes seems to be not
> similar
> to that in INPUT_PW file.
> [...]
> ====================== INPUT_PW ======================
> v1 = (a,0,0), v2= (b*cos(gamma), b*sin(gamma), 0), v3 = (0, 0, c)
> where gamma is the angle between axis a and b
> ============here is my output file=================
> [...]
> celldm(1)= 23.111300 celldm(2)= 0.248500 celldm(3)= 0.474200
> celldm(4)= -0.237000 celldm(5)= 0.000000 celldm(6)= 0.000000
>
> crystal axes: (cart. coord. in units of a_0)
> a(1) = ( 1.000000 0.000000 0.000000 )
> a(2) = ( -0.058895 0.241420 0.000000 )
> a(3) = ( 0.000000 0.000000 0.474200 )
I don't see anything wrong here
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 giannozz at democritos.it Thu Jul 10 09:20:50 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 10 Jul 2008 09:20:50 +0200
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To:
References:
Message-ID: <8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
On Jul 10, 2008, at 7:33 , Mansoureh Pashangpour wrote:
> why total energy with scf run and CP run are different?
because one is in Ry and one in Ha?
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From mansourehp at gmail.com Thu Jul 10 09:42:53 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 11:12:53 +0330
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To: <8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
References:
<8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
Message-ID:
Dear Paolo
I know one of them is in Ry and another one in Ha,but when I compare them
they are different
scf: total energy = -243.33284101 Ry
CP: ekinc : 10.67409 10.67409 (AU)
ekin : 153.58930 153.58930 (AU)
epot : -458.58466 -458.58466 (AU)
totel energy : -258.18270 -258.18270 (AU)
temperature : 0.00000 0.00000 (K )
enthalpy : -258.18270 -258.18270 (AU)
econs : -258.18270 -258.18270 (AU)
pressure : -3.47982 -3.47982 (Gpa)
volume : 488.11442 488.11442 (AU)
Thanks
On Thu, Jul 10, 2008 at 10:50 AM, Paolo Giannozzi
wrote:
>
> On Jul 10, 2008, at 7:33 , Mansoureh Pashangpour wrote:
>
> > why total energy with scf run and CP run are different?
>
> because one is in Ry and one in Ha?
> ---
> 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 marzari at MIT.EDU Thu Jul 10 10:20:06 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 10 Jul 2008 10:20:06 +0200
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To:
References: <8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
Message-ID: <4875C636.3020007@mit.edu>
Shouldn't ekinc be zero ? I forgot the name used, but in a properly
executed CP calculation, in which you do damped dynamics on the
electrons to reach the ground state at fixed ions, the kinetic energy
of the electrons (as opposed to the quantum kinetic energy of your
system, ekin) should be zero.
I suggest to anyone learning CP calculations (a very worthy
endeavour, and one that would be extremely useful in the long
run) to study carefully the review paper on the topic by Marx and
Hutter,
http://www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf
CP in Q-E now can also do conjugate gradients minimization on
the electrons (more efficient than damped dynamics) and, for
metals, ensemble-dft (i.e. born-oppenheimer dynamics).
For cg/edft, there was one bug (memmory misallocation)
for parallel execution, just found by by Brandon Wood. It'll
be fixed in the cvs in the next few days.
nicola
Mansoureh Pashangpour wrote:
> Dear Paolo
> I know one of them is in Ry and another one in Ha,but when I compare
> them they are different
> scf: total energy = -243.33284101 Ry
>
> CP: ekinc : 10.67409 10.67409 (AU)
> ekin : 153.58930 153.58930 (AU)
> epot : -458.58466 -458.58466 (AU)
> totel energy : -258.18270 -258.18270 (AU)
> temperature : 0.00000 0.00000 (K )
> enthalpy : -258.18270 -258.18270 (AU)
> econs : -258.18270 -258.18270 (AU)
> pressure : -3.47982 -3.47982 (Gpa)
> volume : 488.11442 488.11442 (AU)
> Thanks
--
---------------------------------------------------------------------
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 mansourehp at gmail.com Thu Jul 10 10:48:17 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 12:18:17 +0330
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To: <4875C636.3020007@mit.edu>
References:
<8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
<4875C636.3020007@mit.edu>
Message-ID:
dear Nicola
this is ekinc for end of minimization I found it small after verlet dynamics
ekinc : 0.10064 0.10064 (AU)
ekin : 144.72166 144.72166 (AU)
epot : -473.07863 -473.07863 (AU)
totel energy : -280.01088 -280.01088 (AU)
why they are different with
> scf: total energy = -243.33284101 Ry
Thanks
On Thu, Jul 10, 2008 at 11:50 AM, Nicola Marzari wrote:
>
>
> Shouldn't ekinc be zero ? I forgot the name used, but in a properly
> executed CP calculation, in which you do damped dynamics on the
> electrons to reach the ground state at fixed ions, the kinetic energy
> of the electrons (as opposed to the quantum kinetic energy of your
> system, ekin) should be zero.
>
> I suggest to anyone learning CP calculations (a very worthy
> endeavour, and one that would be extremely useful in the long
> run) to study carefully the review paper on the topic by Marx and
> Hutter,
>
> http://www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf
>
> CP in Q-E now can also do conjugate gradients minimization on
> the electrons (more efficient than damped dynamics) and, for
> metals, ensemble-dft (i.e. born-oppenheimer dynamics).
>
> For cg/edft, there was one bug (memmory misallocation)
> for parallel execution, just found by by Brandon Wood. It'll
> be fixed in the cvs in the next few days.
>
>
> nicola
>
> Mansoureh Pashangpour wrote:
> > Dear Paolo
> > I know one of them is in Ry and another one in Ha,but when I compare
> > them they are different
> > scf: total energy = -243.33284101 Ry
> >
> > CP: ekinc : 10.67409 10.67409 (AU)
> > ekin : 153.58930 153.58930 (AU)
> > epot : -458.58466 -458.58466 (AU)
> > totel energy : -258.18270 -258.18270 (AU)
> > temperature : 0.00000 0.00000 (K )
> > enthalpy : -258.18270 -258.18270 (AU)
> > econs : -258.18270 -258.18270 (AU)
> > pressure : -3.47982 -3.47982 (Gpa)
> > volume : 488.11442 488.11442 (AU)
> > Thanks
>
> --
> ---------------------------------------------------------------------
> 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 marzari at MIT.EDU Thu Jul 10 10:51:48 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 10 Jul 2008 10:51:48 +0200
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To:
References: <8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it> <4875C636.3020007@mit.edu>
Message-ID: <4875CDA4.30308@mit.edu>
Mansoureh Pashangpour wrote:
> dear Nicola
> this is ekinc for end of minimization I found it small after verlet dynamics
> ekinc : 0.10064 0.10064 (AU)
> ekin : 144.72166 144.72166 (AU)
> epot : -473.07863 -473.07863 (AU)
> totel energy : -280.01088 -280.01088 (AU)
>
> why they are different with
> > scf: total energy = -243.33284101 Ry
It is actually (very) large, and it needs to be well below 10-5 au.
If after that it's still different, try something easy - a hydrogen
molecule, and go from there.
In any case, the fact that the cp calculation has a much lower energy
than pwscf means that probably something incorrect is going on. As
mentioned, try very simple things, and move up from there.
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 mansourehp at gmail.com Thu Jul 10 10:58:08 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 12:28:08 +0330
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To: <4875CDA4.30308@mit.edu>
References:
<8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
<4875C636.3020007@mit.edu>
<4875CDA4.30308@mit.edu>
Message-ID:
Dear Nicola
Is it related to nstep
I chose nstep = 5000,
should it be more or less ?
On Thu, Jul 10, 2008 at 12:21 PM, Nicola Marzari wrote:
> Mansoureh Pashangpour wrote:
> > dear Nicola
> > this is ekinc for end of minimization I found it small after verlet
> dynamics
> > ekinc : 0.10064 0.10064 (AU)
> > ekin : 144.72166 144.72166 (AU)
> > epot : -473.07863 -473.07863 (AU)
> > totel energy : -280.01088 -280.01088 (AU)
> >
> > why they are different with
> > > scf: total energy = -243.33284101 Ry
>
>
> It is actually (very) large, and it needs to be well below 10-5 au.
>
> If after that it's still different, try something easy - a hydrogen
> molecule, and go from there.
>
> In any case, the fact that the cp calculation has a much lower energy
> than pwscf means that probably something incorrect is going on. As
> mentioned, try very simple things, and move up from there.
>
>
> 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
> _______________________________________________
> 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 Thu Jul 10 11:02:43 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 10 Jul 2008 12:32:43 +0330
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To:
References:
<8ADF7C51-3FC5-494C-AC70-47C99D80388B@democritos.it>
<4875C636.3020007@mit.edu>
<4875CDA4.30308@mit.edu>
Message-ID:
Dear Nicola
I've got experience with CP for H2O.
It is simple but I couden't
find the best way to run CP for my system
On Thu, Jul 10, 2008 at 12:28 PM, Mansoureh Pashangpour <
mansourehp at gmail.com> wrote:
> Dear Nicola
> Is it related to nstep
> I chose nstep = 5000,
> should it be more or less ?
>
>
> On Thu, Jul 10, 2008 at 12:21 PM, Nicola Marzari wrote:
>
>> Mansoureh Pashangpour wrote:
>> > dear Nicola
>> > this is ekinc for end of minimization I found it small after verlet
>> dynamics
>> > ekinc : 0.10064 0.10064 (AU)
>> > ekin : 144.72166 144.72166 (AU)
>> > epot : -473.07863 -473.07863 (AU)
>> > totel energy : -280.01088 -280.01088 (AU)
>> >
>> > why they are different with
>> > > scf: total energy = -243.33284101 Ry
>>
>>
>> It is actually (very) large, and it needs to be well below 10-5 au.
>>
>> If after that it's still different, try something easy - a hydrogen
>> molecule, and go from there.
>>
>> In any case, the fact that the cp calculation has a much lower energy
>> than pwscf means that probably something incorrect is going on. As
>> mentioned, try very simple things, and move up from there.
>>
>>
>> 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
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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From bsnebiha at yahoo.fr Thu Jul 10 11:49:39 2008
From: bsnebiha at yahoo.fr (nebiha ben sedrine)
Date: Thu, 10 Jul 2008 02:49:39 -0700 (PDT)
Subject: [Pw_forum] no access to the K-point mesh and shift
Message-ID: <19428.44125.qm@web52907.mail.re2.yahoo.com>
Dear PWscf users,
when entering the k-point data, I have no access to the K-point mesh and shift (either by typing the numbers or by using the arrows up and down) , whatever the k-point input option. What can be the solution?
Thank you in advance.
nebiha ben sedrine (PhD)
_____________________________________________________________________________
Envoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.yahoo.fr
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From tone.kokalj at ijs.si Thu Jul 10 13:25:59 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 10 Jul 2008 13:25:59 +0200
Subject: [Pw_forum] no access to the K-point mesh and shift
In-Reply-To: <19428.44125.qm@web52907.mail.re2.yahoo.com>
References: <19428.44125.qm@web52907.mail.re2.yahoo.com>
Message-ID: <1215689159.9818.8.camel@walk.ijs.si>
On Thu, 2008-07-10 at 02:49 -0700, nebiha ben sedrine wrote:
> Dear PWscf users,
> when entering the k-point data, I have no access to the K-point mesh
> and shift (either by typing the numbers or by using the arrows up and
> down) , whatever the k-point input option. What can be the solution?
I presume you are referring to pwgui; right? This is due to a bug in
4.0, that has been corrected in 4.0.1. You may download 4.0.1 from
either of these places:
http://www.pwscf.org/download.php
http://www.quantum-espresso.org/download.php
http://www-k3.ijs.si/kokalj/pwgui/download.html
(the last link also contains the pre-compiled binary executable)
Regards, Tone
--
Tone Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)
From bsnebiha at yahoo.fr Thu Jul 10 17:02:10 2008
From: bsnebiha at yahoo.fr (nebiha ben sedrine)
Date: Thu, 10 Jul 2008 08:02:10 -0700 (PDT)
Subject: [Pw_forum] load atom coordinates from file
Message-ID: <480022.50227.qm@web52909.mail.re2.yahoo.com>
Dear PWscf users,
I would like to know more about the file format to load for atom coordinates in the Lattice and Atomic data menu, especially the file extension.
Thank you in advance.
nebiha ben sedrine (PhD)
_____________________________________________________________________________
Envoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.yahoo.fr
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From brandonw at MIT.EDU Fri Jul 11 03:56:27 2008
From: brandonw at MIT.EDU (Brandon Wood)
Date: Fri, 11 Jul 2008 07:26:27 +0530
Subject: [Pw_forum] minimization in CP molecular dynamics
In-Reply-To:
References:
Message-ID: <4876BDCB.2080000@mit.edu>
Dear Mansoureh and Nicola,
If memory serves, the values printed at the end of the file represent
averages throughout the course of the simulation rather than final
values. So ekinc <> 0 is actually expected, unless you start from an
already converged electronic configuration (although your value is still
surprisingly high). It also means the total energy doesn't accurately
represent your final configuration.
A better thing to do is to take a look at the data output for the
_final_ CP timestep in your run. If ekinc is still nonzero at that
timestep, increase nstep. In any case, it is much more efficient to use
CG minimization.
Brandon
----------------------------------------------------------
Dr. Brandon C. Wood
NSF Postdoctoral Fellow, Theoretical Sciences Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Bangalore, India
----------------------------------------------------------
Nicola Marzari wrote:
>
> Shouldn't ekinc be zero ? I forgot the name used, but in a properly
> executed CP calculation, in which you do damped dynamics on the
> electrons to reach the ground state at fixed ions, the kinetic energy
> of the electrons (as opposed to the quantum kinetic energy of your
> system, ekin) should be zero.
>
> I suggest to anyone learning CP calculations (a very worthy
> endeavour, and one that would be extremely useful in the long
> run) to study carefully the review paper on the topic by Marx and
> Hutter,
>
> http://www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf
>
> CP in Q-E now can also do conjugate gradients minimization on
> the electrons (more efficient than damped dynamics) and, for
> metals, ensemble-dft (i.e. born-oppenheimer dynamics).
>
> For cg/edft, there was one bug (memmory misallocation)
> for parallel execution, just found by by Brandon Wood. It'll
> be fixed in the cvs in the next few days.
>
>
> nicola
>
> Mansoureh Pashangpour wrote:
>> Dear Paolo
>> I know one of them is in Ry and another one in Ha,but when I compare
>> them they are different
>> scf: total energy = -243.33284101 Ry
>>
>> CP: ekinc : 10.67409 10.67409 (AU)
>> ekin : 153.58930 153.58930 (AU)
>> epot : -458.58466 -458.58466 (AU)
>> totel energy : -258.18270 -258.18270 (AU)
>> temperature : 0.00000 0.00000 (K )
>> enthalpy : -258.18270 -258.18270 (AU)
>> econs : -258.18270 -258.18270 (AU)
>> pressure : -3.47982 -3.47982 (Gpa)
>> volume : 488.11442 488.11442 (AU)
>> Thanks
>
From sathya_sheela1985001 at rediffmail.com Fri Jul 11 06:10:23 2008
From: sathya_sheela1985001 at rediffmail.com (sathya subramanyan)
Date: 11 Jul 2008 04:10:23 -0000
Subject: [Pw_forum] negative value of polarization and Z* for Pb in
Tetragonal PbTiO3 and discrepancy
Message-ID: <20080711041023.8305.qmail@f4mail-235-143.rediffmail.com>
?
?
?
Dear Prof. Eyvaz,
Thank you very much for your reply In response to your advice regarding the inaccuracy in structure input for tetragonal PbTiO3, I checked the literature and thus have taken the structural input parameteres(lattice constant,c/a and atomic positions)from PRL 80,1998,4321 and done the convergence test. conv_threshold used now is 1e-12
The result is as follows.Could you please let me know whether the convergence is good or not.
THE INPUT FILE FOR TETRAGONAL PbTiO3
&control
calculation = 'scf'
restart_mode = 'from_scratch'
pseudo_dir = '/home/nbaski/espresso-4.0.1/pseudo/'
outdir = '/home/nbaski/tmp/'
/
&system
ibrav=6
celldm(1)=7.373,
celldm(3)=1.065
nat=5
ntyp=3
nbnd=25
ecutwfc=30.0
occupations = 'fixed'
degauss=0.00
/
&electrons
conv_thr = 1e-12,
mixing_beta=0.3,
/
ATOMIC_SPECIES
Pb 207.2 Pb.vdb.UPF
Ti 47.867 Ti.vdb.UPF
O 15.9994 O.vdb.UPF
ATOMIC_POSITIONS
Pb 0.000 0.000 0.000
Ti 0.500 0.500 0.538
O 0.500 0.000 0.612
O 0.000 0.500 0.612
O 0.500 0.500 0.117
K_POINTS {automatic}
4 4 4 1 1 1
**************
THE OUTPUT FILE(a part only as it is a heavy file)
highest occupied, lowest unoccupied level (ev): 9.6746 12.5554
! total energy = -333.71409381 Ry
Harris-Foulkes estimate = -333.71409381 Ry
estimated scf accuracy < 5.8E-13 Ry
The total energy is the sum of the following terms:
one-electron contribution = -94.69940998 Ry
hartree contribution = 73.25826560 Ry
xc contribution = -49.63383021 Ry
ewald contribution = -262.63911922 Ry
convergence has been achieved in 19 iterations
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli - 620015
India
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From prasenjit.jnc at gmail.com Fri Jul 11 18:29:17 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 11 Jul 2008 18:29:17 +0200
Subject: [Pw_forum] negative value of polarization and Z* for Pb in
Tetragonal PbTiO3 and discrepancy
In-Reply-To: <20080711041023.8305.qmail@f4mail-235-143.rediffmail.com>
References: <20080711041023.8305.qmail@f4mail-235-143.rediffmail.com>
Message-ID: <627e0ffa0807110929o9936e28q20701ec335fab8d5@mail.gmail.com>
Dear Sathya,
First of all I would like you to note that the method used in the PRL is
different from that used in QE, while the former is based on LAPW method,
Pwscf is a plane wave code. So the structural parameters given in the PRL is
a good guess to start your calculation. However, you should first obtain the
optimized values of cell parameters and atomic positions using pwscf and
then proceed to do other calculations. These values should be comparable to
those mentioned in the PRL, provided you use same level of theory (eg. same
exchange correlation, same pseudopotential, same k-points, etc.) and you do
the things correctly.
As mentioned by others, you should test your pseudopotentials and also
perform convergence tests for k-point mesh used, ecutwfc, etc. Moreover,
since you are using ultrasoft pseudo potential, I would suggest you to use
ecutrho=8-10*ecutwfc, presently u r using ecutrho=4.0*ecutwfc, which is
often not sufficient for US psps. At least for structural relaxations,
"conv_thr=1e-08" is sufficient, although you may need to use a more strict
condition when you calculate the effective charges.
Hope this helps.
Prasenjit.
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)
2008/7/11 sathya subramanyan :
>
>
>
> Dear Prof. Eyvaz,
> Thank you very much for your reply In response to your
> advice regarding the inaccuracy in structure input for tetragonal PbTiO3, I
> checked the literature and thus have taken the structural input
> parameteres(lattice constant,c/a and atomic positions)from PRL 80,1998,4321
> and done the convergence test. conv_threshold used now is 1e-12
> The result is as follows.Could you please let me know whether the
> convergence is good or not.
>
> THE INPUT FILE FOR TETRAGONAL PbTiO3
>
> &control
> calculation = 'scf'
> restart_mode = 'from_scratch'
> pseudo_dir = '/home/nbaski/espresso-4.0.1/pseudo/'
> outdir = '/home/nbaski/tmp/'
> /
> &system
> ibrav=6
> celldm(1)=7.373,
> celldm(3)=1.065
> nat=5
> ntyp=3
> nbnd=25
> ecutwfc=30.0
> occupations = 'fixed'
> degauss=0.00
> /
> &electrons
> conv_thr = 1e-12,
> mixing_beta=0.3,
> /
> ATOMIC_SPECIES
> Pb 207.2 Pb.vdb.UPF
> Ti 47.867 Ti.vdb.UPF
> O 15.9994 O.vdb.UPF
> ATOMIC_POSITIONS
> Pb 0.000 0.000 0.000
> Ti 0.500 0.500 0.538
> O 0.500 0.000 0.612
> O 0.000 0.500 0.612
> O 0.500 0.500 0.117
> K_POINTS {automatic}
> 4 4 4 1 1 1
>
> **************
> THE OUTPUT FILE(a part only as it is a heavy file)
>
> highest occupied, lowest unoccupied level (ev): 9.6746 12.5554
>
> ! total energy = -333.71409381 Ry
> Harris-Foulkes estimate = -333.71409381 Ry
> estimated scf accuracy < 5.8E-13 Ry
>
> The total energy is the sum of the following terms:
>
> one-electron contribution = -94.69940998 Ry
> hartree contribution = 73.25826560 Ry
> xc contribution = -49.63383021 Ry
> ewald contribution = -262.63911922 Ry
>
> convergence has been achieved in 19 iterations
>
>
> SATHYA SHEELA.S
> Grad. Student
> Department of Physics
> National Institute of Technology
> Tiruchirapalli - 620015
> India
>
> [image: Rediff Shopping]
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
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From chenhanghuipwscf at gmail.com Fri Jul 11 22:59:58 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Fri, 11 Jul 2008 16:59:58 -0400
Subject: [Pw_forum] cholesky decomposition
Message-ID: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
Dear PWSCF users,
When I calculate a large system (320 atoms in the super cell), I get
the following error message:
from pzpotrf : error # 452
problems computing cholesky decomposition
I calculate the same system with fewer atoms, there is no such
problem. Is it because the system becomes too large? What is the maxmium
number of atoms in the super cell PWSCF can calculate stably?
Thank you very much.
Hanghui
Department of Physics
Yale University
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From akohlmey at cmm.chem.upenn.edu Fri Jul 11 23:03:15 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 11 Jul 2008 17:03:15 -0400 (EDT)
Subject: [Pw_forum] cholesky decomposition
In-Reply-To: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
References: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
Message-ID:
On Fri, 11 Jul 2008, alan chen wrote:
AC> Dear PWSCF users,
AC> When I calculate a large system (320 atoms in the super cell), I get
AC> the following error message:
AC> from pzpotrf : error # 452
AC> problems computing cholesky decomposition
AC> I calculate the same system with fewer atoms, there is no such
AC> problem. Is it because the system becomes too large? What is the maxmium
AC> number of atoms in the super cell PWSCF can calculate stably?
the same or very similar problem has been reported very recently
and the suggestion was to turn off the parallel diagonalization, IIRC.
please check the mailing list archives for details.
cheers,
axel.
AC> Thank you very much.
AC>
AC> Hanghui
AC> Department of Physics
AC> Yale University
AC>
--
=======================================================================
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 min0220 at postech.ac.kr Sat Jul 12 09:46:16 2008
From: min0220 at postech.ac.kr (Min Seung Kyu)
Date: Sat, 12 Jul 2008 16:46:16 +0900 (KST)
Subject: [Pw_forum] Calculating atoms
Message-ID:
Dear users,
Can I calculate the electronic structure of any atoms?
When I calculating a sodium atom, I got the error message about charge
difference.
Thank you in advance.
Sincerely, Min.
-------------------------------Sig.---------------------------
Center for Superfunctional Materials, Department of Chemistry,
Pohang University of Science and Technology (POSTECH), S. Korea
Mr. Seung Kyu, Min
Ph.D. Candidate
E-Mail: min0220 at postech.ac.kr
Tel. : 82-54-279-5858
----------------------------------------------
From meisam_a84 at yahoo.com Sat Jul 12 11:25:06 2008
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Sat, 12 Jul 2008 02:25:06 -0700 (PDT)
Subject: [Pw_forum] DOS of graphene
Message-ID: <959737.47307.qm@web30604.mail.mud.yahoo.com>
Dear all
?I want to calculate the density of state of graphene but there is a problem that it is?extremely variant by changing the parameters.?the best plot of?DOS?that I could find is?linear?at fermi energy but there is a gap there.
what is the reason of these variation? and which parameters should be?adjusted? would you give me an input?which you know it gives a good resault. the potential that?I use is in LDA approximation.
thank you.
M. Aghtar
Msc student
physics department of Kashan university??
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From miguel.martinez at ehu.es Sat Jul 12 11:46:07 2008
From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=)
Date: Sat, 12 Jul 2008 11:46:07 +0200
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <959737.47307.qm@web30604.mail.mud.yahoo.com>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
Message-ID: <20080712114607.7270d215@ehu.es>
Dear Meisam,
What parametres have you used to calculate the electronic DOS? In case
you haven't tried, you may be interested to use Blochl's tetrahedron
method as occupation. Whenever I tried, using a "normal" smearing
method (m-p, gaussian or m-v) requires a pretty dense k-point mesh in
order to get a decent DOS, while tetrahedra can work fine (but as far
as I know it requires a regular automatically generated K-point mesh).
Regards,
Miguel
PS: Note that, at least in espresso 3.2.3, partial DOS doesn't work
with tetrahedra. I can't comment on 4.0.1, since I haven't done any
pDOS calculations with it yet.
El Sat, 12 Jul 2008 02:25:06 -0700 (PDT)
meisam aghtar escribi?:
> Dear all
> ?I want to calculate the density of state of graphene but there is a
> problem that it is?extremely variant by changing the parameters.?the
> best plot of?DOS?that I could find is?linear?at fermi energy but
> there is a gap there. what is the reason of these variation? and
> which parameters should be?adjusted? would you give me an input?which
> you know it gives a good resault. the potential that?I use is in LDA
> approximation. thank you. M. Aghtar Msc student physics department of
> Kashan university??
>
>
>
From paulatto at sissa.it Sat Jul 12 12:29:25 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 12 Jul 2008 12:29:25 +0200 (CEST)
Subject: [Pw_forum] Calculating atoms
In-Reply-To:
References:
Message-ID: <12397.218.80.242.169.1215858565.squirrel@webmail.sissa.it>
On Sab, Luglio 12, 2008 09:46, Min Seung Kyu wrote:
> Can I calculate the electronic structure of any atoms?
Yes, which code are you using?
> When I calculating a sodium atom, I got the error message about charge
> difference.
How are you computing it? Which error do you get?
> Thank you in advance.
You have to provide much more informations for someone to reply.
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 Sat Jul 12 12:41:13 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Jul 2008 12:41:13 +0200
Subject: [Pw_forum] cholesky decomposition
In-Reply-To:
References: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
Message-ID: <89377430-E9D8-44E3-B0FC-227F8C7DD112@democritos.it>
On Jul 11, 2008, at 23:03 , Axel Kohlmeyer wrote:
> AC> from pzpotrf : error # 452
> AC> problems computing cholesky decomposition
>
> the same or very similar problem has been reported very recently
but nobody has ever provided a test job, and not even details on
code version, hardware/software. It might be a real bug; it might
be a numerical problem, or a problem with mathematical libraries,
or some other weirdness, like this one, fixed in v.4 for real
diagonalization (Gamma case):
http://www.democritos.it:8888/O-sesame/chngview?cn=5777
and in v.4.0.1 for complex diagonalization (generic k-point):
http://www.democritos.it:8888/O-sesame/chngview?cn=5932
The subspace diagonalization algorithm is the same used in CP
for iterative orthonormalization, and has been tested on O(1000)
atoms.
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 Sat Jul 12 12:46:44 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Jul 2008 12:46:44 +0200
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <959737.47307.qm@web30604.mail.mud.yahoo.com>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
Message-ID: <92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
On Jul 12, 2008, at 11:25 , meisam aghtar wrote
> I want to calculate the density of state of graphene
> but there is a problem that it is extremely variant by
> changing the parameters. the best plot of DOS that
> I could find is linear at fermi energy but there is a gap there.
2-d graphene has zero gap only at isolated points of the
Brillouin Zone. Reproducing the exact behavior around
those points with numerical calculations and algorithms
devised to work in 3-d is impractical to say the least.
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 Sat Jul 12 12:49:08 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 12 Jul 2008 12:49:08 +0200
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <20080712114607.7270d215@ehu.es>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<20080712114607.7270d215@ehu.es>
Message-ID:
On Jul 12, 2008, at 11:46 , Miguel Mart?nez wrote:
> PS: Note that, at least in espresso 3.2.3, partial DOS doesn't work
more exactly, "it is not implemented"
> with tetrahedra. I can't comment on 4.0.1, since I haven't done any
> pDOS calculations with it yet.
it is still not implemented. I vaguely remember that somebody
in this list had implemented it, but I don't remember who
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 zhaohscas at yahoo.com.cn Sat Jul 12 17:09:34 2008
From: zhaohscas at yahoo.com.cn (zhaohscas)
Date: Sat, 12 Jul 2008 23:09:34 +0800
Subject: [Pw_forum]
=?gb2312?B?Q29tcHV0ZSBidWxrIG1vZHVsdXMgYnkgdXNpbmcgdGhlIGZvcm11bGFlIG9mICBQLVYgYW5kIEUtViBCaXJjaKhDTXVybmFnaGFuIGVxdWF0aW9uIG9mIHN0YXRlLg==?=
Message-ID: <200807122309342654362@yahoo.com.cn>
Hi forks,
I use the pwscf to compute bulk modulus of BaHfO_3, I obtaibed the the volume and energy under zero pressure first, then I compute the several volume and energy dataset of BaHfO_3 under 2.5GPa, 5.0GPa, 7.5GPa, 10GPa, 20GPa, and 30GPa respectively.
Then, I use the dataset to compute bulk modulus. Due to the formulae of P-V and E-V Birch?CMurnaghan equation of state are all can be used to do this, in order to comparison, both the P-V and E-V Birch?CMurnaghan equation of state are used. But, I found that there're great difference between the result obtained from fitting P-V Birch?CMurnaghan equation of state and that of the E-V Birch?CMurnaghan equation of state. I also found that the result from P-V fitting is more close to the reports value in the literatures.
Furthermore, I also have a puzzle about the form of the formulae of P-V and E-V Birch?CMurnaghan equation of state, in detail, I've read from the different literatures that there are two forms of the P-V Birch?CMurnaghan equation of state:
a) P(V) = \frac{{3B_0 }}{2}\left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{7}{3}} - \left( {\frac{{V_0 }}{V}} \right)^{\frac{5}{3}} } \right]\left\{ {1 + \frac{3}{4}\left( {B_0^' - 4} \right)\left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{2}{3}} - 1} \right]} \right\}
b) P(V) = \frac{{3B_0 }}{2}\left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{7}{3}} - \left( {\frac{{V_0 }}{V}} \right)^{\frac{5}{3}} } \right]\left\{ {1 + \frac{3}{4}\left( {4 - B_0^'} \right)\left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{2}{3}} - 1} \right]} \right\}
Where, the B_0 and the B_0^' are the bulk modulus and its pressure derivative respectively.
Which of the above is correct?
As for the E-V Birch?CMurnaghan equation of state, I read the following form:
E(V) = E_0 + \frac{{9V_0 B_0 }}{{16}}\left\{ {\left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{2}{3}} - 1} \right]^3 B_0^' + \left[ {\left( {\frac{{V_0 }}{V}} \right)^{\frac{2}{3}} - 1} \right]^2 \left[ {6 - 4\left( {\frac{{V_0 }}{V}} \right)^{\frac{2}{3}} } \right]} \right\}
Is this right or not?
Who can give me some hints?
Sincerely yours,
--------------
Hongsheng Zhao
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences
GnuPG DSA: 0xD10849
2008-07-12
From meisam_a84 at yahoo.com Sun Jul 13 15:14:00 2008
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Sun, 13 Jul 2008 06:14:00 -0700 (PDT)
Subject: [Pw_forum] DOS of graphene
Message-ID: <585561.30992.qm@web30606.mail.mud.yahoo.com>
Dear Miguel & Paolo
?
This time I used the smearing occupation instead of tetrahedral method using a dense meshed BZ. The result is better , for example there is not any gap but that still does not seem to be the exact DOS. Blow are my scf and nscf inputs.
Of course according to Paolo?s response I have not tested the 4.0.1 version. I don?t know if that one makes a better result.
?
/
?&SYSTEM
?????????????????????? ibrav = 4,
?????????????????? celldm(1) = 4.647779861,
?????????????????? celldm(3) = 8,
???????????????????????? nat = 2,
??????????????????????? ntyp = 1,
???????????????????? ecutwfc = 40 ,
?/
?&ELECTRONS
?/
ATOMIC_SPECIES
??? C?? 12.01070? C.pz-vbc.UPF
ATOMIC_POSITIONS angstrom
??? C????? 0.000000000??? 1.420000000??? 0.000000000???
??? C????? 1.229756073??? 0.710000000??? 0.000000000???
K_POINTS automatic
? 10 10 1?? 1 1 1
?
Nscf :
?
/
?&SYSTEM
?????????????????????? ibrav = 4,
?????????????????? celldm(1) = 4.647779861,
?????????????????? celldm(3) = 8,
???????????????????????? nat = 2,
??????????????????????? ntyp = 1,
???????????????????? ecutwfc = 40 ,
???????????????????? ??nosym = .true. ,
???????????????? occupations = 'smearing' ,
???????????????????? degauss = 0.05 ,
??????????????????? smearing = 'methfessel-paxton' ,
?/
?&ELECTRONS
?/
ATOMIC_SPECIES
??? C?? 12.01070? C.pz-vbc.UPF
ATOMIC_POSITIONS crystal
??? C????? 0.000000000??? 1.420000000??? 0.000000000???
??? C????? 1.229756073??? 0.710000000??? 0.000000000???
K_POINTS tpiba
301
M. Aghtar
M.sc student
Physics department of Kashan university
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From chenhanghuipwscf at gmail.com Sun Jul 13 19:29:32 2008
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Sun, 13 Jul 2008 13:29:32 -0400
Subject: [Pw_forum] igk files
Message-ID: <22ae3ca40807131029n7316e833s6c310e2dae4cd169@mail.gmail.com>
Dear PWSCF users,
In my calculation, I set wfcdir to be '/scratch' in order to save disk
space. I have found some xxx.igk files are dumped in the scratch direction.
I have two questions.
1) I have a few jobs running at the same time. Unfortunately they have the
same 'prefix' so that these xxx.igk files may overwrite each other. Does
that matter? Does the code read in these files?
2) Recently when I calculate large jobs, I got the following error message:
'input statement requires too much data, unit 16, file
/home1/hc336/scratch/IF-relax.igk19'. Does that mean the xxx.igk19 file is
too large for the code to read in?
Thank you very much.
Hanghui
Department of Physics
Yale University
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From akohlmey at cmm.chem.upenn.edu Sun Jul 13 22:21:49 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 13 Jul 2008 16:21:49 -0400 (EDT)
Subject: [Pw_forum] igk files
In-Reply-To: <22ae3ca40807131029n7316e833s6c310e2dae4cd169@mail.gmail.com>
References: <22ae3ca40807131029n7316e833s6c310e2dae4cd169@mail.gmail.com>
Message-ID:
On Sun, 13 Jul 2008, alan chen wrote:
AC> Dear PWSCF users,
AC> In my calculation, I set wfcdir to be '/scratch' in order to save disk
AC> space. I have found some xxx.igk files are dumped in the scratch direction.
AC> I have two questions.
AC> 1) I have a few jobs running at the same time. Unfortunately they have the
AC> same 'prefix' so that these xxx.igk files may overwrite each other. Does
AC> that matter? Does the code read in these files?
yes, it matters. that is the reason for 'prefix' in the first place.
i'm usually too paranoid for just using 'prefix' and alway create
separate directories for each job in the scratch using the jobid
string from the batch system (which is guaranteed to be unique in
the cluster and i don't have to worry about somebody else accidentally
having created a file that would have the same name as mine).
AC> 2) Recently when I calculate large jobs, I got the following error message:
AC> 'input statement requires too much data, unit 16, file
AC> /home1/hc336/scratch/IF-relax.igk19'. Does that mean the xxx.igk19 file is
AC> too large for the code to read in?
how should we know? nobody here can read the mind of your computer(s).
what is the exact sequence of actions/inputs to reproduce this?
cheers,
axel.
AC>
AC> Thank you very much.
AC>
AC> Hanghui
AC> Department of Physics
AC> Yale University
AC>
--
=======================================================================
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 Mon Jul 14 10:12:51 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 14 Jul 2008 10:12:51 +0200
Subject: [Pw_forum] igk files
In-Reply-To: <22ae3ca40807131029n7316e833s6c310e2dae4cd169@mail.gmail.com>
References: <22ae3ca40807131029n7316e833s6c310e2dae4cd169@mail.gmail.com>
Message-ID: <487B0A83.5060209@democritos.it>
alan chen wrote:
> 1) I have a few jobs running at the same time. Unfortunately they have
> the same 'prefix' so that these xxx.igk files may overwrite each other.
> Does that matter? Does the code read in these files?
if you have more than one k-point, it reads them during
self-consistency. Otherwise, at the end, but only when
collecting wavefunctions, IIRC. In any case, you should
never run two jobs in the same scratch directory with the
same file names.
> 2) Recently when I calculate large jobs, I got the following error
> message: 'input statement requires too much data, unit 16, file
> /home1/hc336/scratch/IF-relax.igk19'.
it looks like one process is trying to read data overwritten by
another process. Not good.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Mon Jul 14 10:16:14 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 14 Jul 2008 10:16:14 +0200
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <585561.30992.qm@web30606.mail.mud.yahoo.com>
References: <585561.30992.qm@web30606.mail.mud.yahoo.com>
Message-ID: <487B0B4E.2090907@democritos.it>
meisam aghtar wrote:
> This time I used the smearing occupation instead of tetrahedral method
> using a dense meshed BZ. The result is better , for example there is not
> any gap but that still does not seem to be the exact DOS. Blow are my
> scf and nscf inputs.
>
> Of course according to Paolo?s response I have not tested the 4.0.1
> version. I don?t know if that one makes a better result.
no, it will yield the same result, or ratrher, lack of it: there is no
way to get the exact DOS around the K points in graphene using
broadening, except for an unpractically large number of k-points
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From yukihiro_okuno at fujifilm.co.jp Mon Jul 14 11:54:34 2008
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Mon, 14 Jul 2008 18:54:34 +0900
Subject: [Pw_forum] Use of SIC in PWSCF
Message-ID:
Dear PWSCF users and developers.
I want to know the Self Interaction Correction is available in PWscf ?
I found the sorce code sic.f90 in /espresso-4.0/Modules.
But is seems this sic formula have a limit that the system must be
electron up = electron down + 1,
and further, I can't found the place this modules called in the program.
I want to correct the band gap for III-V semiconductor system. without
empirical parameter.
Is there plan to implement the more general SIC schema in PWSCF?
(like pseudo SIC formula , for example PRB vol 67 125109 (2003) )
Sincerely.
Yukihiro Okuno.
From glevita at units.it Mon Jul 14 14:09:17 2008
From: glevita at units.it (glevita at units.it)
Date: Mon, 14 Jul 2008 14:09:17 +0200
Subject: [Pw_forum] file .workf
In-Reply-To: <92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
Message-ID: <20080714140917.qyukn9becv8kgow4@webmail.units.it>
Dear All,
I have some doubts about the file .workf produced in post-processing
operations.
First of all, it is not clear to me from which main the subroutine is
called: if I am not wrong, the file is generated when I perform STM
simulation.
Then, it is not clear to me the format of such file. If it is a grid
of values of the calculated workfunction, I have some problems in
uderstanding what they are referring to (different directions?).
I am therefore asking you if someone can suggest me some link or
example where I can have some delucidations about the whole file; I
searched a bit through the forum and the PWScf website, but didn't
manage to get my mind clear....
Thank you very much,
Giacomo Levita
(UniTrieste)
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
From aisma073 at uottawa.ca Mon Jul 14 16:49:49 2008
From: aisma073 at uottawa.ca (Arif Ismail)
Date: Mon, 14 Jul 2008 10:49:49 -0400 (EDT)
Subject: [Pw_forum] all electron calculation problem
Message-ID: <36265.137.122.14.20.1216046989.squirrel@webmail01.uottawa.ca>
Hi,
I'm trying to generate a US-PP for Ce using Vanderbilt's package, and the
first step is to run the AE calculation. This is my input file:
1 0 0 0 4 ifae,ifpsp,ifprt,ifplw,ilogd (5i5)
1.80 -2.4 1.6 600 rlogd,emin,emax,nnt (3f10.5,i5)
1.0d-10 1.0d-09 0.10 600 thresh,tol.damp (2e10.1,f10.5)
Cerium
58 0.0 5.0
200.0 4.0 39.0 rmax,aasf,bbsf (3f10.5)
15 2 ncspvs,irel (2i5)
100 2. -10660.8
200 2. -3450.2
210 6. -219.9
300 2. -430.0
310 6. -350.4
320 10. -220.1
400 2. -60.0
410 6. -30.7
420 10. -20.0
430 1. -15.0
500 2. -10.0
510 6. -5.0
520 1. -4.0
600 2. -3.0
610 0. -2.0
I get this error message:
pseudopotential program version 7.3.6 date: 7 - 14 - 2008
========================================================================
ifae = 1 ifpsp = 0 ifprt = 0 ifplw = 0 ilogd = 4
rlogd= 1.80000 emin= -2.40000 emax= 1.60000 nnt= 60
thresh, tol = 1.000E-10 1.000E-09 damp = 0.100 maxit = 600
*************************************************************
Cerium PBE - GGA exchange-correlation
*************************************************************
z = 58.00 xion = 0.00 exfact = 5.00000 irel= 2
ncspvs = 15
rmax = 200.00000 aasf = 4.00000 bbsf = 39.00000
value of mesh generated in rinit is 523
irel = 2 so all electron calculations use koelling-harmon equations
***error in koesol
ninf 524 too big for this mesh 523
I tried changing aasf, bbsf, and rmax, and it changes the value of mesh
generated in rinit ... but still I get the same error - ninf is always 1
greater than the mesh. Does anyone know how to solve this problem?
I think it may have to do with the fact that it's a lanthanide atom.
Thanks.
From fabris at democritos.it Mon Jul 14 17:39:58 2008
From: fabris at democritos.it (Stefano Fabris)
Date: Mon, 14 Jul 2008 17:39:58 +0200
Subject: [Pw_forum] all electron calculation problem
In-Reply-To: <36265.137.122.14.20.1216046989.squirrel@webmail01.uottawa.ca>
References: <36265.137.122.14.20.1216046989.squirrel@webmail01.uottawa.ca>
Message-ID: <35135CB5-CD90-4562-9001-65AE4392A0EE@democritos.it>
Dear Arif,
I remember having a similar problem some years ago when trying to
generate a US-PP for Ce using Vanderbilt's package. Although at the
moment I do not remember the solution, I will go back into my old data
and be back to you with some advice.
Yours,
Stefano Fabris
PS: remember to include your affiliation when posting to the forum
On 14 Jul 2008, at 16:49, Arif Ismail wrote:
> Hi,
> I'm trying to generate a US-PP for Ce using Vanderbilt's package,
> and the
> first step is to run the AE calculation. This is my input file:
>
> 1 0 0 0 4 ifae,ifpsp,ifprt,ifplw,ilogd
> (5i5)
> 1.80 -2.4 1.6 600 rlogd,emin,emax,nnt (3f10.5,i5)
> 1.0d-10 1.0d-09 0.10 600 thresh,tol.damp (2e10.1,f10.5)
> Cerium
> 58 0.0 5.0
> 200.0 4.0 39.0 rmax,aasf,bbsf (3f10.5)
> 15 2 ncspvs,irel (2i5)
> 100 2. -10660.8
> 200 2. -3450.2
> 210 6. -219.9
> 300 2. -430.0
> 310 6. -350.4
> 320 10. -220.1
> 400 2. -60.0
> 410 6. -30.7
> 420 10. -20.0
> 430 1. -15.0
> 500 2. -10.0
> 510 6. -5.0
> 520 1. -4.0
> 600 2. -3.0
> 610 0. -2.0
>
>
> I get this error message:
>
> pseudopotential program version 7.3.6 date: 7 - 14 - 2008
> =
> =
> ======================================================================
>
> ifae = 1 ifpsp = 0 ifprt = 0 ifplw = 0 ilogd = 4
> rlogd= 1.80000 emin= -2.40000 emax= 1.60000 nnt= 60
> thresh, tol = 1.000E-10 1.000E-09 damp = 0.100 maxit = 600
>
> *************************************************************
> Cerium PBE - GGA exchange-correlation
> *************************************************************
>
> z = 58.00 xion = 0.00 exfact = 5.00000 irel= 2
> ncspvs = 15
> rmax = 200.00000 aasf = 4.00000 bbsf = 39.00000
>
> value of mesh generated in rinit is 523
> irel = 2 so all electron calculations use koelling-harmon equations
> ***error in koesol
> ninf 524 too big for this mesh 523
>
>
> I tried changing aasf, bbsf, and rmax, and it changes the value of
> mesh
> generated in rinit ... but still I get the same error - ninf is
> always 1
> greater than the mesh. Does anyone know how to solve this problem?
> I think it may have to do with the fact that it's a lanthanide atom.
> Thanks.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Fabris
Theory at Elettra Group
CNR-INFM DEMOCRITOS National Simulation Center
c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE
website: www.democritos.it/the-group
email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776
---
From eyvaz_isaev at yahoo.com Mon Jul 14 17:42:35 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 14 Jul 2008 08:42:35 -0700 (PDT)
Subject: [Pw_forum] all electron calculation problem
In-Reply-To: <36265.137.122.14.20.1216046989.squirrel@webmail01.uottawa.ca>
Message-ID: <293425.22133.qm@web65701.mail.ac4.yahoo.com>
Dear Arif,
Change your atomic configuration, and it will work.
Besides, please provide your affiliation.
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, 7/14/08, Arif Ismail wrote:
> From: Arif Ismail
> Subject: [Pw_forum] all electron calculation problem
> To: pw_forum at pwscf.org
> Date: Monday, July 14, 2008, 6:49 PM
> Hi,
> I'm trying to generate a US-PP for Ce using
> Vanderbilt's package, and the
> first step is to run the AE calculation. This is my input
> file:
>
> 1 0 0 0 4
> ifae,ifpsp,ifprt,ifplw,ilogd (5i5)
> 1.80 -2.4 1.6 600 rlogd,emin,emax,nnt
> (3f10.5,i5)
> 1.0d-10 1.0d-09 0.10 600 thresh,tol.damp
> (2e10.1,f10.5)
> Cerium
> 58 0.0 5.0
> 200.0 4.0 39.0 rmax,aasf,bbsf
> (3f10.5)
> 15 2 ncspvs,irel (2i5)
> 100 2. -10660.8
> 200 2. -3450.2
> 210 6. -219.9
> 300 2. -430.0
> 310 6. -350.4
> 320 10. -220.1
> 400 2. -60.0
> 410 6. -30.7
> 420 10. -20.0
> 430 1. -15.0
> 500 2. -10.0
> 510 6. -5.0
> 520 1. -4.0
> 600 2. -3.0
> 610 0. -2.0
>
>
> I get this error message:
>
> pseudopotential program version 7.3.6 date: 7 - 14 -
> 2008
> ========================================================================
>
> ifae = 1 ifpsp = 0 ifprt = 0 ifplw = 0
> ilogd = 4
> rlogd= 1.80000 emin= -2.40000 emax= 1.60000
> nnt= 60
> thresh, tol = 1.000E-10 1.000E-09 damp = 0.100
> maxit = 600
>
>
> *************************************************************
> Cerium PBE - GGA
> exchange-correlation
>
> *************************************************************
>
> z = 58.00 xion = 0.00 exfact = 5.00000 irel=
> 2
> ncspvs = 15
> rmax = 200.00000 aasf = 4.00000 bbsf = 39.00000
>
> value of mesh generated in rinit is 523
> irel = 2 so all electron calculations use koelling-harmon
> equations
> ***error in koesol
> ninf 524 too big for this mesh 523
>
>
> I tried changing aasf, bbsf, and rmax, and it changes the
> value of mesh
> generated in rinit ... but still I get the same error -
> ninf is always 1
> greater than the mesh. Does anyone know how to solve this
> problem?
> I think it may have to do with the fact that it's a
> lanthanide atom.
> Thanks.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From lyu7 at ncsu.edu Mon Jul 14 18:26:40 2008
From: lyu7 at ncsu.edu (Liping Yu)
Date: Mon, 14 Jul 2008 12:26:40 -0400
Subject: [Pw_forum] cholesky decomposition
In-Reply-To: <89377430-E9D8-44E3-B0FC-227F8C7DD112@democritos.it>
References: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
<89377430-E9D8-44E3-B0FC-227F8C7DD112@democritos.it>
Message-ID: <487B7E40.4060607@ncsu.edu>
Hi, Paolo,
I have been met this kind of error messages many times when doing
structure relaxation with 'bfgs' using espresso-4.0. This error ever
occurred on IMB sp4/5 and Sun cluster comprised of Opteron processors.
There is no such error message if I change 'bfgs' to 'damp', or use the
older code version (< 4.0). I didn't check it in v.4.0.1.
Liping
Paolo Giannozzi wrote:
> On Jul 11, 2008, at 23:03 , Axel Kohlmeyer wrote:
>
>
>> AC> from pzpotrf : error # 452
>> AC> problems computing cholesky decomposition
>>
>> the same or very similar problem has been reported very recently
>>
>
> but nobody has ever provided a test job, and not even details on
> code version, hardware/software. It might be a real bug; it might
> be a numerical problem, or a problem with mathematical libraries,
> or some other weirdness, like this one, fixed in v.4 for real
> diagonalization (Gamma case):
> http://www.democritos.it:8888/O-sesame/chngview?cn=5777
> and in v.4.0.1 for complex diagonalization (generic k-point):
> http://www.democritos.it:8888/O-sesame/chngview?cn=5932
> The subspace diagonalization algorithm is the same used in CP
> for iterative orthonormalization, and has been tested on O(1000)
> atoms.
>
> 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
>
--
Liping YU, PhD Candidate
Department of Physics & Center for High Performance Simulation
North Carolina State University, Raleigh, NC 27695, USA
tel: 1-919-5157228
From amosleffler at sbcglobal.net Mon Jul 14 20:59:16 2008
From: amosleffler at sbcglobal.net (Amos Leffler)
Date: Mon, 14 Jul 2008 11:59:16 -0700
Subject: [Pw_forum] Problems with espresso-4.0 running example01
Message-ID:
Dear Forum,
On June 13 Todd Beaudet reported trying to run example01 in espresso-4.0 using intel compiler 10.1.011, mkl 10.0.1.014 and reported the output file that stopped with the K_POINTS for Si even though a number of other materials were to be calculated. Some suggestions were made including the compiler being at fault.
I ran the sample example using the g95 compiler and got the exact same results showing it is not the compiler. On June 17 Paolo G. suggested modifying the ./configure command to disable the parallel. I tried this, modifying the compiler, but it didn't work either. Since then I have seen nothing in the Forum on this problem.
If the espresso-4.0 example01 is replaced with the espresso-3.2 example 01 the output shown below results. Note particularly the lines 82 and 128 where the location of the si.scf.in files was changed but permission was denied. Below that the original file location was used and si.band.david.out was used and it failed also. In the espresso-4.0 version the diagonalization is set to "david" but I don't know if the example was set up to run in parallel but I could not find "david" anywhere and reset the location of si.scf.in to the locations shown below in the output.
One further note. If the original example01 is run libguide.so is mentioned and cant seem to share libraries. Also the setup did not include any MPI files.
Hopefully there is a simple resolution to this problem.
Amos Leffler
unaffiliated
Script started on Mon 14 Jul 2008 11:11:39 AM PDT
]2;amos at leffler2:...examples/example01]1;leffler2amos at leffler2:~/Desktop/espresso-4.0/examples/example01> ./run_example
/home/amos/Desktop/espresso-4.0/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: /home/amos/Desktop/espresso-4.0/bin
pseudo directory: /home/amos/Desktop/espresso-4.0/pseudo
temporary directory: /home/amos/tmp
checking that needed directories and files exist... done
running pw.x as: /home/amos/Desktop/espresso-4.0/bin/pw.x
running bands.x as: /home/amos/Desktop/espresso-4.0/bin/bands.x
cleaning /home/amos/tmp... done
./run_example: line 82: /home/amos/Desktop/espresso-4.0/GUI/PWgui/examples/pw/si.scf.in: Permission denied
running the scf calculation for Si..../run_example: line 122: /home/amos/Desktop/espresso-4.0/GUI/PWgui/examples/pw/si.scf.out: Permission denied
done
./run_example: line 128: si.band.david.in: Permission denied
running the band-structure calculation for Si..../run_example: line 179: si.band.david.out: Permission denied
done
./run_example: line 183: si.bands.in: Permission denied
running the symmetry analysis for Si bands..../run_example: line 194: si.bands.out: Permission denied
done
cleaning /home/amos/tmp... done
./run_example: line 204: al.scf.david.in: Permission denied
running the scf calculation for Al..../run_example: line 290: al.scf.david.out: Permission denied
done
./run_example: line 294: al.band.david.in: Permission denied
running the band-structure calculation for Al..../run_example: line 344: al.band.david.out: Permission denied
done
cleaning /home/amos/tmp... done
./run_example: line 353: cu.scf.david.in: Permission denied
running the scf calculation for Cu..../run_example: line 381: cu.scf.david.out: Permission denied
done
./run_example: line 385: cu.band.david.in: Permission denied
running the band-structure calculation for Cu..../run_example: line 435: cu.band.david.out: Permission denied
done
./run_example: line 438: cu.bands.in: Permission denied
running the symmetry analysis for Cu bands..../run_example: line 449: cu.bands.out: Permission denied
done
cleaning /home/amos/tmp... done
./run_example: line 460: ni.scf.david.in: Permission denied
running the scf calculation for Ni..../run_example: line 549: ni.scf.david.out: Permission denied
done
./run_example: line 553: ni.band.david.in: Permission denied
running the band-structure calculation for Ni..../run_example: line 604: ni.band.david.out: Permission denied
done
cleaning /home/amos/tmp... done
./run_example: line 82: /home/amos/Desktop/espresso-4.0/GUI/PWgui/examples/pw/si.scf.in: Permission denied
running the scf calculation for Si..../run_example: line 122: /home/amos/Desktop/espresso-4.0/GUI/PWgui/examples/pw/si.scf.out: Permission denied
done
./run_example: line 128: si.band.cg.in: Permission denied
running the band-structure calculation for Si..../run_example: line 179: si.band.cg.out: Permission denied
done
./run_example: line 183: si.bands.in: Permission denied
cleaning /home/amos/tmp... done
./run_example: line 204: al.scf.cg.in: Permission denied
running the scf calculation for Al..../run_example: line 290: al.scf.cg.out: Permission denied
done
./run_example: line 294: al.band.cg.in: Permission denied
running the band-structure calculation for Al..../run_example: line 344: al.band.cg.out: Permission denied
done
cleaning /home/amos/tmp... done
./run_example: line 353: cu.scf.cg.in: Permission denied
running the band-structure calculation for Cu..../run_example: line 435: cu.band.cg.out: Permission denied
done
./run_example: line 438: cu.bands.in: Permission denied
cleaning /home/amos/tmp... done
./run_example: line 460: ni.scf.cg.in: Permission denied
running the scf calculation for Ni..../run_example: line 549: ni.scf.cg.out: Permission denied
done
./run_example: line 553: ni.band.cg.in: Permission denied
running the band-structure calculation for Ni..../run_example: line 604: ni.band.cg.out: Permission denied
done
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From akohlmey at cmm.chem.upenn.edu Mon Jul 14 22:26:44 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 14 Jul 2008 16:26:44 -0400 (EDT)
Subject: [Pw_forum] Problems with espresso-4.0 running example01
In-Reply-To:
References:
Message-ID:
On Mon, 14 Jul 2008, Amos Leffler wrote:
AL> Dear Forum,
dear amos,
i don't use QE much for production run, so i tend to compile and
test mostly the cvs version, but to prove that this is a PEBCAC-type
of problem, i just downloaded the current 4.0.1 version, ran ./configure
(QE picks up intel 9.1.040 as default fortran 90 compiler, with
OpenMPI, and MKL 10.0.1.014. on an x86_64 machine running fedora 6)
and compiled fine without futher modifications of make.sys.
i then changed the directory to examples/example01 and did a
./run_example and it worked without a flaw. please note, that the
compiled executable is a parallel one, but with OpenMPI, starting
a parallel executable without mpirun is the same as 'mpirun -np 1'.
not all MPI libraries allow this and for those the file
examples/environment_variables must be modified (see below).
as a next step i told OpenMPI and QE to use g95 instead of ifort
(export OMPI_FC=g95; export OMPI_F77=g95 ; export F77=g95 ; export
F90=g95) and ran configure again and compiled. the configure
again picked up MKL as BLAS/LAPACK and the compiled went through.
now, i am getting a:
"error while loading shared libraries: libguide.so: cannot open shared
object files"
but this is _deservedly_ so, since i have a _non-standard_ mkl
installation, since i want to be able to use multiple versions of
it at the same time without much hassle (for benchmarks and tests),
and thus i don't set the LD_LIBRARY_PATH environment, but usually
modify my makefiles to encode the search path explicitly into the
executable upon linking. since here i didn't do this, i get this
failure, but running with:
env LD_LIBRARY_PATH=/path/to/mkl/lib/dir ./run_example
example01 completes just fine.
as a final test i reset my environment to replace intel 9.1 with intel
10.1.015. fresh compilation and again example01 runs just fine without
any modification.
AL> On June 13 Todd Beaudet reported trying to run example01 in
AL> espresso-4.0 using intel compiler 10.1.011, mkl 10.0.1.014 and
AL> reported the output file that stopped with the K_POINTS for Si even
AL> though a number of other materials were to be calculated. Some
AL> suggestions were made including the compiler being at fault.
i noticed two issues: intel 10.1 with patchlevels lower than 014
miscompiles parts of all plane wave codes that i've tested recently.
i also saw that for a while in the cvs there was a bug with the
parallel davidson that would crash pw.x after initialization when
you were running the parallel executable with only one mpi task.
the latter has since been resolved and for the former that are
newer patchlevels.
AL> I ran the sample example using the g95 compiler and got the exact
AL> same results showing it is not the compiler. On June 17 Paolo G.
AL> suggested modifying the ./configure command to disable the parallel.
AL> I tried this, modifying the compiler, but it didn't work either.
AL> Since then I have seen nothing in the Forum on this problem.
AL> If the espresso-4.0 example01 is replaced with the
AL> espresso-3.2 example 01 the output shown below results. Note
the run_example scripts depend on scripts in upper level.
you have to use the full tree.
if you want to test a parallel compile you usually also
_have_ to edit the PARA_PREFIX part (and PARA_POSTFIX in
a few cases. it is important to use quotation marks here.
AL> particularly the lines 82 and 128 where the location of the
AL> si.scf.in files was changed but permission was denied. Below that
AL> the original file location was used and si.band.david.out was used
AL> and it failed also. In the espresso-4.0 version the diagonalization
AL> is set to "david" but I don't know if the example was set up to run
AL> in parallel but I could not find "david" anywhere and reset the
AL> location of si.scf.in to the locations shown below in the output.
what about: the line "for diago in david cg; do" ?
this input tests two different diagonalizers from the
the same section of the shell script.
AL> One further note. If the original example01 is run
AL> libguide.so is mentioned and cant seem to share libraries. Also the
come again? do you mean the error i mentioned above? that is
an indication of an incorrect installation or usage of MKL.
there are several ways to alleviate this. setting LD_LIBRARY_PATH
accordingly is one, passing an appropriate -rpath flag
to the linker a second and linking MKL statically a third.
this is not the fault of QE. QE _has_ to depend on a correct
setup of a machine. ...and even then an occasional tweak to
make.sys is needed to correct where configure guesses wrong
(there are far too many combinations of
linux/intel/mkl/g95/pgi/atlas/whatever installations around
to get it right all the time).
AL> setup did not include any MPI files.
???
AL> Hopefully there is a simple resolution to this problem.
the (simple) resolution is, that there is no problem
that has to be resolved on the side of QE. if you have
a machine that is properly installed, it should work
just fine.
AL> Amos Leffler
AL> unaffiliated
AL> Script started on Mon 14 Jul 2008 11:11:39 AM PDT
AL> ]2;amos at leffler2:...examples/example01]1;leffler2amos at leffler2:~/Desktop/espresso-4.0/examples/example01> AL> ]./run_example
where do the escape sequences come from? do you have some sort
of "prompt hack" going (e.g. to update the xterminal title text
or colorized prompt) that produces output in a script environment
(i.e. it is set regardless of whether you are using /bin/sh or
/bin/bash) ?
AL> /home/amos/Desktop/espresso-4.0/examples/example01 : starting
AL>
AL> This example shows how to use pw.x to calculate the total energy and
AL> the band structure of four simple systems: Si, Al, Cu, Ni.
AL>
AL> executables directory: /home/amos/Desktop/espresso-4.0/bin
AL> pseudo directory: /home/amos/Desktop/espresso-4.0/pseudo
AL> temporary directory: /home/amos/tmp
AL> checking that needed directories and files exist... done
AL>
AL> running pw.x as: /home/amos/Desktop/espresso-4.0/bin/pw.x
AL> running bands.x as: /home/amos/Desktop/espresso-4.0/bin/bands.x
AL>
AL> cleaning /home/amos/tmp... done
AL> ./run_example: line 82: /home/amos/Desktop/espresso-4.0/GUI/PWgui/examples/pw/si.scf.in: Permission denied
where does this path come from? something is messed up that irritates
the shell script. it could be related to your shell prompt setup.
please try editing examples/environment_variables to give the value
of PREFIX explicitly. the current code changes the directory in a
subshell and if you have a "prompt hack" active, the value of PREFIX
could be messed up. of course, i'm assuming that you are running the
./run_example from 4.0.1 without any modifications...
[...]
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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From mansourehp at gmail.com Tue Jul 15 07:03:24 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Tue, 15 Jul 2008 08:33:24 +0330
Subject: [Pw_forum] BO molecular dynamics
Message-ID:
Deal PWscf users
I want to do minimization for Born-Oppenhiemer molecular dynamics.
which of these way is correct?
dt =6.0d0,
.
.
.
&electrons
emass = 500.d0,
emass_cutoff = 2.25d0,
orthogonalization = 'ortho',
electron_dynamics = 'damp',
/
&ions
ion_dynamics = 'none',
/
---------------------------------
dt =20.0d0,
.
.
.
&electrons
emass = 500.d0,
emass_cutoff = 2.25d0,
orthogonalization = 'ortho',
electron_dynamics = 'cg',
/
&ions
ion_dynamics = 'none',
/
----------------------------------
I look forward to hearing from you.
Thanks
Mansoureh
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From mansourehp at gmail.com Tue Jul 15 07:48:01 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Tue, 15 Jul 2008 09:18:01 +0330
Subject: [Pw_forum] BO molecular dynamics
Message-ID:
Dear all
I did a cg minmization for BO molecular dynamics its result is:
Total stress (GPa)
-502.29556521 -0.00085909 0.00005914
-0.00085909 -502.29637140 -0.00006054
0.00005914 -0.00006054 -548.75663133
.
.
.
nfi tempp E -T.S-mu.nbsp +K_p #Iter
Step 35 0 -280.06247 -280.06247 -280.06247 6
Step 36 0 -280.06247 -280.06247 -280.06247 6
Step 37 0 -280.06247 -280.06247 -280.06247 6
Step 38 0 -280.06247 -280.06247 -280.06247 6
Step 39 0 -280.06247 -280.06247 -280.06247 6
.
.
.
.
Averaged Physical Quantities
accumulated this run
ekinc : 0.00000 0.00000 (AU)
ekin : 145.33184 145.33184 (AU)
epot : -473.58591 -473.58591 (AU)
totel energy : -280.03728 -280.03728 (AU)
temperature : 0.00000 0.00000 (K )
enthalpy : 0.00000 0.00000 (AU)
econs : -280.03728 -280.03728 (AU)
pressure : -517.83659 -517.83659 (Gpa)
volume : 488.11442 488.11442 (AU)
I think Total stress and pressure are very high but they are equal .
Dose it cause any problem?
Still energy from scf run is different with BO run.why?
total energy = -243.33284101 Ry
good luck
bye
Mansoureh
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From vegalew at hotmail.com Tue Jul 15 10:36:01 2008
From: vegalew at hotmail.com (vega lew)
Date: Tue, 15 Jul 2008 16:36:01 +0800
Subject: [Pw_forum] something extremly strange for anatase 001 structure
prediction
Message-ID:
Dear all,
I'm doing anatase 001 surface relaxation using different pseudo cutoff. But the surface structure depending
strongly on pseudo cutoff.
For example, when I set ecutwfc=30 Ry and ecutrho=240 Ry for the calculation, the relaxed structure is
ATOMIC_POSITIONS (angstrom)
Ti 0.000019234 0.000016929 5.241338958
Ti 1.896866310 1.894973881 0.424606117
Ti -0.002611826 1.894973568 7.609344136
Ti 1.894935792 0.000016645 2.794368221
O -0.000497095 1.894979291 5.668409409
O 0.000892662 0.000020764 7.220228726
O 1.897822837 1.894975309 8.112610082
O -0.002069692 1.894975762 -0.077265872
O 1.894316864 0.000021111 0.814634124
O 1.895351386 1.894979829 2.365218854
O 0.000036842 0.000033726 3.235875667
O 1.894936685 0.000033184 4.800631577
when I set ecutwfc=50 Ry and ecutrho=400 Ry for the same calculation, the relaxed structure is
ATOMIC_POSITIONS (angstrom)
Ti 0.022799298 0.000081081 5.241509392
Ti 1.936096642 1.894995998 0.443063583
Ti -0.037388794 1.894978067 7.592310260
Ti 1.868524560 -0.000008072 2.794849232
O -0.102420723 1.894969978 5.654104817
O 0.193587382 0.000011079 7.215460406
O 2.107237211 1.894969616 8.171152812
O -0.209955519 1.895019689 -0.141004735
O 1.700007345 0.000017676 0.820240249
O 1.998867848 1.894956901 2.381473163
O 0.007469691 0.000019075 3.237525157
O 1.885175059 -0.000011088 4.799315665
unfortunately this forum is not support pictures or pdf files, I can't display it in photos. I'll illustrate
the big difference in structure of the calculations only by word.
In the case of ecutwfc=30 Ry and ecutrho=240 Ry, there is a the mirror plane symmetry along
the [100] direction. The two Ti-O bonds on surface is about 1.964 Angstrom and the angle of
surface O-Ti-O atoms is about 150.269 degrees. The structure is consistent well with the literature
(figure SI in supporting information of J. Phys. Chem. B 2006, 110, 2804-2811). But the my calculated s
urface energy is 1.06049 J/m^2, which is about 8% higher than the literature.
I think the surface energy difference may be because of the ecutwfc and ecutrho. So I increased it to
higher value, ecutwfc=50 Ry and ecutrho=400 Ry. But the calculated structure with this cutoff is so surprising.
As shown above, the mirror plane symmetry along the [100] direction is broken: the two O-Ti bonds on
the surface become strongly inequivalent, with bond lengths of 1.74 and 2.22 angstrom. And the angle of
surface O-Ti-O atoms is about 145.508 degrees. Even from the coordinate of each atom is quite different in
the two cases. I also find this kind of structure reported by literature Physical Review letters, 2001, 87, 266105.
But my calculated structure parameters is about 1% errors, and energetic parameters is about 6% errors with
respect to the literature.
For my two tested case the structure is so greatly depending on the cutoff. I think the higher cutoff must be more accurate.
So there may be something inaccurate with the former case and the literature J. Phys. Chem. B 2006, 110, 2804-2811,
because of the smaller cutoff.
How do you think about it?
And Why my calculated energy is ~6-8% different than the literature.
Here is my input file
&CONTROL
title = 'Anatase 001' ,
calculation = 'relax' ,
restart_mode = 'from_scratch' ,
outdir = '/home/vega/TiO2/Anatase/001/relaxtest/tmp/' ,
wfcdir = '/tmp/' ,
pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
prefix = 'Anatase 001 1X1' ,
disk_io = 'none' ,
etot_conv_thr = 0.0005 ,
forc_conv_thr = 0.0011668141375 ,
nstep = 1000 ,
/
&SYSTEM
ibrav = 6,
celldm(1) = 7.1619,
celldm(3) = 4.7591,
nat = 12,
ntyp = 2,
ecutwfc = 30 , #ecutwfc=50 for later case
ecutrho = 240 , #ecutrho=400 for later case
/
&ELECTRONS
conv_thr = 1.0D-8 ,
/
&IONS
ion_dynamics = 'bfgs' ,
/
ATOMIC_SPECIES
Ti 47.86700 Ti.pw91-sp-van_ak.UPF
O 15.99940 O.pw91-van_ak.UPF
ATOMIC_POSITIONS angstrom
Ti 0.000000000 0.000000000 5.220000000
Ti 1.895000000 1.895000000 0.410000000
Ti 0.000000000 1.895000000 7.625000000
Ti 1.895000000 0.000000000 2.815000000
O 0.000000000 1.895000000 5.630000000
O 0.000000000 0.000000000 7.214000000
O 1.895000000 1.895000000 8.036000000
O 0.000000000 1.895000000 0.000000000
O 1.895000000 0.000000000 0.820000000
O 1.895000000 1.895000000 2.404000000
O 0.000000000 0.000000000 3.226000000
O 1.895000000 0.000000000 4.810000000
K_POINTS automatic
4 4 1 1 1 1
Thank you for reading. looking forward to your reply.
Vega Lew
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
_________________________________________________________________
Discover the new Windows Vista
http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
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From vegalew at hotmail.com Tue Jul 15 12:11:56 2008
From: vegalew at hotmail.com (vega lew)
Date: Tue, 15 Jul 2008 18:11:56 +0800
Subject: [Pw_forum] How to simulate cation H+ without electron or Li+ with
only two electrons
Message-ID:
Dear all,
I want to simulate H+ without electron and Li+ with only two electrons. How could I do
this?
The system I want to simulate is composed of ~100 nomoral atoms and ~1-3 cations.
The nomoral atoms has ordinary electrons such as C with 6 electrons and Si with 14 electrons.
Cations lose some electrons such as H+ without any electrons and Li with only 2 electrons.
Do you think pseudopotential with plane wave basis sets DFT calculation is suitable for this mater?
If so, which parameter I should control in Q-E to separate the cation H+/Li+ from the atom
H with 1 electron/ Li with 3 electrons?
best wishes,
vega
Vega Lew
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
_________________________________________________________________
Connect to the next generation of MSN Messenger?
http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
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From paulatto at sissa.it Tue Jul 15 14:44:38 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 15 Jul 2008 14:44:38 +0200 (CEST)
Subject: [Pw_forum] How to simulate cation H+ without electron or Li+
with only two electrons
In-Reply-To:
References:
Message-ID: <52646.147.122.5.216.1216125878.squirrel@webmail.sissa.it>
On Mar, Luglio 15, 2008 12:11, vega lew wrote:
> Si with 14 electrons.
> Cations lose some electrons such as H+ without any electrons and Li with
> only 2 electrons.
You cannot force it: you can remove one electron from the system, than if
the ground state (in the adopted theoretical frame) has a ionized H or Li
it shall be found at convergence.
Actually Sit, Cococcioni and Marzari (PRL97, 028303) use some sort of
trick to force a certain ionization state. I don't know if the code is
available (but you can certainly ask them).
> Do you think pseudopotential with plane wave basis sets DFT calculation
> is suitable for this mater?
I have no idea, certainly it may take a bit of effort to converge an
isolated charged system wrt the size of the unit cell.
bye
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
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From mahkameh_va at yahoo.com Tue Jul 15 15:24:23 2008
From: mahkameh_va at yahoo.com (raheleh vaziri)
Date: Tue, 15 Jul 2008 06:24:23 -0700 (PDT)
Subject: [Pw_forum] (no subject)
Message-ID: <905721.65852.qm@web32903.mail.mud.yahoo.com>
hello.
I?wanna relaxation calculations with constrains some angle and di hedral.please guide me.thanks.
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From akohlmey at cmm.chem.upenn.edu Tue Jul 15 15:54:22 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 Jul 2008 09:54:22 -0400 (EDT)
Subject: [Pw_forum] BO molecular dynamics
In-Reply-To:
References:
Message-ID:
On Tue, 15 Jul 2008, Mansoureh Pashangpour wrote:
MP> Deal PWscf users
MP>
MP> I want to do minimization for Born-Oppenhiemer molecular dynamics.
MP> which of these way is correct?
please explain. what is "minimization for BO dynamics"?
both your input fragments don't make much sense as they
contain too little information...
cheers,
axel.
MP>
MP> dt =6.0d0,
MP> .
MP> .
MP> .
MP> &electrons
MP> emass = 500.d0,
MP> emass_cutoff = 2.25d0,
MP> orthogonalization = 'ortho',
MP> electron_dynamics = 'damp',
MP> /
MP> &ions
MP> ion_dynamics = 'none',
MP> /
MP> ---------------------------------
MP> dt =20.0d0,
MP> .
MP> .
MP> .
MP> &electrons
MP> emass = 500.d0,
MP> emass_cutoff = 2.25d0,
MP> orthogonalization = 'ortho',
MP> electron_dynamics = 'cg',
MP> /
MP> &ions
MP> ion_dynamics = 'none',
MP> /
MP> ----------------------------------
MP> I look forward to hearing from you.
MP> Thanks
MP> Mansoureh
MP>
--
=======================================================================
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 polynmr at physics.unc.edu Tue Jul 15 15:52:05 2008
From: polynmr at physics.unc.edu (Charles)
Date: Tue, 15 Jul 2008 09:52:05 -0400
Subject: [Pw_forum] (no subject)
In-Reply-To: <905721.65852.qm@web32903.mail.mud.yahoo.com>
References: <905721.65852.qm@web32903.mail.mud.yahoo.com>
Message-ID: <487CAB85.1030305@physics.unc.edu>
raheleh vaziri wrote:
> hello.
>
> I wanna relaxation calculations with constrains some angle and di
> hedral.please guide me.thanks.
>
I Think this is well documented already in INPUT_PW
>
> ------------------------------------------------------------------------
>
> Not spam
> Forget previous vote
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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 Jul 15 16:06:26 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 Jul 2008 10:06:26 -0400 (EDT)
Subject: [Pw_forum] How to simulate cation H+ without electron or Li+
with only two electrons
In-Reply-To:
References:
Message-ID:
On Tue, 15 Jul 2008, vega lew wrote:
VL>
VL> Dear all,
VL>
VL> I want to simulate H+ without electron and Li+ with only two
VL> electrons. How could I do this?
VL> The system I want to simulate is composed of ~100 nomoral atoms and
VL> ~1-3 cations. The nomoral atoms has ordinary electrons such as C
VL> with 6 electrons and Si with 14 electrons. Cations lose some
VL> electrons such as H+ without any electrons and Li with only 2
VL> electrons.
please pick up your elmentary quantum chemistry text book,
read it again and realize that your question doesn't make
much sense. what do you compute in quantum chemistry?
the electronic structure in the field of the atom cores.
one fundamental outcome of quantum mechanics is that you
cannot distinguish electrons. they have no labels and they
don't belong to an atom or ion (even people try _very_ hard
to put them back on in postprocessing). so all you have to
do is to determine the total number of electrons and the
electrostatic field of the atoms (which is approximated by
pseudopotentials, i.e. you have to sum up the valence
electrons) and let the physics of the problem work its magic.
VL> Do you think pseudopotential with plane wave basis sets DFT
VL> calculation is suitable for this mater?
VL> If so, which parameter I should control in Q-E to separate the
VL> cation H+/Li+ from the atom
none. if you want to force ions to be like this, you are doing
classical mechanics. QE does not do that. depending on how
much your substrate attracts or provides electrons, you may
need to use a semi-core li potential (i.e. one with 3 valence
electrons).
cheers,
axel.
VL>
VL> H with 1 electron/ Li with 3 electrons?
VL>
VL> best wishes,
VL>
VL> vega
VL>
VL> Vega Lew
VL> PH.D Candidate in Chemical Engineering
VL> State Key Laboratory of Materials-oriented Chemical Engineering
VL> College of Chemistry and Chemical Engineering
VL> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
VL> _________________________________________________________________
VL> Connect to the next generation of MSN Messenger?
VL> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
--
=======================================================================
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
=======================================================================
Q: what are quantum mechanics? A: people who repair quantums, i guess.
From akohlmey at cmm.chem.upenn.edu Tue Jul 15 16:13:09 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 Jul 2008 10:13:09 -0400 (EDT)
Subject: [Pw_forum] (no subject)
In-Reply-To: <905721.65852.qm@web32903.mail.mud.yahoo.com>
References: <905721.65852.qm@web32903.mail.mud.yahoo.com>
Message-ID:
On Tue, 15 Jul 2008, raheleh vaziri wrote:
RV> hello.
RV> I?wanna relaxation calculations with constrains some angle and di
RV> hedral.please guide me.thanks.
how about reading the documentation? particularly
the discription of the input?
look for (hint, hint!) "constraints".
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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From mahkameh_va at yahoo.com Tue Jul 15 16:44:08 2008
From: mahkameh_va at yahoo.com (raheleh vaziri)
Date: Tue, 15 Jul 2008 07:44:08 -0700 (PDT)
Subject: [Pw_forum] constraints
Message-ID: <763368.92762.qm@web32908.mail.mud.yahoo.com>
Dear users
I wanna relaxation calculations with some angle and dihedral fixed and performed "constrains" in INPUT_PW but it didnt work and not fixed.please guide me.
thanks
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From paulatto at sissa.it Tue Jul 15 17:09:16 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 15 Jul 2008 17:09:16 +0200 (CEST)
Subject: [Pw_forum] constraints
In-Reply-To: <763368.92762.qm@web32908.mail.mud.yahoo.com>
References: <763368.92762.qm@web32908.mail.mud.yahoo.com>
Message-ID: <45051.147.122.5.216.1216134556.squirrel@webmail.sissa.it>
On Mar, Luglio 15, 2008 16:44, raheleh vaziri wrote:
> Dear users
> I wanna relaxation calculations with some angle and dihedral fixed and
> performed "constrains" in INPUT_PW but it didnt work and not fixed.please
> guide me.
Dear Mahkmeh,
please, take some time to reread your emails before sending them to the
list; your request is so cryptic that anybody trying to help you will have
to spend much more time on *your* problem than *you* actually did. You can
see that it does not make much sense.
You may also benefit from reading this short essay:
, it will
give you some useful hints on how to have your questions answered.
Kind regards.
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
----------------------------------------------------------------
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From mansourehp at gmail.com Tue Jul 15 17:48:48 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Tue, 15 Jul 2008 19:18:48 +0330
Subject: [Pw_forum] BO molecular dynamics
In-Reply-To:
References:
Message-ID:
Dear Axle
At first I wanted to use CP molecular dynamics for my system but after that
I found I couden't use it for metalic systems.so I must use born-oppenhiemer
molecular dynamics.I think it needs to minmization like CP MD.do you think
different?
good luck
Mansoureh
On 7/15/08, Axel Kohlmeyer wrote:
>
> On Tue, 15 Jul 2008, Mansoureh Pashangpour wrote:
>
> MP> Deal PWscf users
> MP>
> MP> I want to do minimization for Born-Oppenhiemer molecular dynamics.
> MP> which of these way is correct?
>
> please explain. what is "minimization for BO dynamics"?
>
>
> both your input fragments don't make much sense as they
> contain too little information...
>
> cheers,
> axel.
>
> MP>
> MP> dt =6.0d0,
> MP> .
> MP> .
> MP> .
> MP> &electrons
> MP> emass = 500.d0,
> MP> emass_cutoff = 2.25d0,
> MP> orthogonalization = 'ortho',
> MP> electron_dynamics = 'damp',
> MP> /
> MP> &ions
> MP> ion_dynamics = 'none',
> MP> /
> MP> ---------------------------------
> MP> dt =20.0d0,
> MP> .
> MP> .
> MP> .
> MP> &electrons
> MP> emass = 500.d0,
> MP> emass_cutoff = 2.25d0,
> MP> orthogonalization = 'ortho',
> MP> electron_dynamics = 'cg',
> MP> /
> MP> &ions
> MP> ion_dynamics = 'none',
> MP> /
> MP> ----------------------------------
> MP> I look forward to hearing from you.
> MP> Thanks
> MP> Mansoureh
> MP>
>
> --
> =======================================================================
> 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 akohlmey at cmm.chem.upenn.edu Tue Jul 15 18:04:11 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 Jul 2008 12:04:11 -0400 (EDT)
Subject: [Pw_forum] BO molecular dynamics
In-Reply-To:
References:
Message-ID:
On Tue, 15 Jul 2008, Mansoureh Pashangpour wrote:
MP> Dear Axle
MP> At first I wanted to use CP molecular dynamics for my system but after that
MP> I found I couden't use it for metalic systems.so I must use born-oppenhiemer
MP> molecular dynamics.I think it needs to minmization like CP MD.do you think
MP> different?
what you have to do or not is not a matter of my opinion,
but of the requirements of the physics of your system (which is ?),
the accuracy of the results you want to achieve and the
effort you want to invest.
please have a look at what is done to the wavefunction in CP
dynamics and what is done in BO dynamics instead then you
can answer this for yourself. this something you should know
_before_ starting _any_ of those calculations. for example
the review by dominik marx and juerg hutter (listed on the QE
homepage somewhere under "learn") gives a good overview (it is
a bit dated by now, there have been significant improvements,
particularly in BO-dynamics since).
cheers,
axel.
MP> good luck
MP> Mansoureh
MP>
MP> On 7/15/08, Axel Kohlmeyer wrote:
MP> >
MP> > On Tue, 15 Jul 2008, Mansoureh Pashangpour wrote:
MP> >
MP> > MP> Deal PWscf users
MP> > MP>
MP> > MP> I want to do minimization for Born-Oppenhiemer molecular dynamics.
MP> > MP> which of these way is correct?
MP> >
MP> > please explain. what is "minimization for BO dynamics"?
MP> >
MP> >
MP> > both your input fragments don't make much sense as they
MP> > contain too little information...
MP> >
MP> > cheers,
MP> > axel.
MP> >
MP> > MP>
MP> > MP> dt =6.0d0,
MP> > MP> .
MP> > MP> .
MP> > MP> .
MP> > MP> &electrons
MP> > MP> emass = 500.d0,
MP> > MP> emass_cutoff = 2.25d0,
MP> > MP> orthogonalization = 'ortho',
MP> > MP> electron_dynamics = 'damp',
MP> > MP> /
MP> > MP> &ions
MP> > MP> ion_dynamics = 'none',
MP> > MP> /
MP> > MP> ---------------------------------
MP> > MP> dt =20.0d0,
MP> > MP> .
MP> > MP> .
MP> > MP> .
MP> > MP> &electrons
MP> > MP> emass = 500.d0,
MP> > MP> emass_cutoff = 2.25d0,
MP> > MP> orthogonalization = 'ortho',
MP> > MP> electron_dynamics = 'cg',
MP> > MP> /
MP> > MP> &ions
MP> > MP> ion_dynamics = 'none',
MP> > MP> /
MP> > MP> ----------------------------------
MP> > MP> I look forward to hearing from you.
MP> > MP> Thanks
MP> > MP> Mansoureh
MP> > MP>
MP> >
MP> > --
MP> > =======================================================================
MP> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
MP> > Center for Molecular Modeling -- University of Pennsylvania
MP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
MP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
MP> > =======================================================================
MP> > If you make something idiot-proof, the universe creates a better idiot.
MP> > _______________________________________________
MP> > Pw_forum mailing list
MP> > Pw_forum at pwscf.org
MP> > http://www.democritos.it/mailman/listinfo/pw_forum
MP> >
MP>
--
=======================================================================
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 sit at sas.upenn.edu Tue Jul 15 18:47:58 2008
From: sit at sas.upenn.edu (Hoi-land Sit)
Date: Tue, 15 Jul 2008 12:47:58 -0400 (EDT)
Subject: [Pw_forum] How to simulate cation H+ without electron or Li+
with only two electrons
In-Reply-To: <52646.147.122.5.216.1216125878.squirrel@webmail.sissa.it>
References:
<52646.147.122.5.216.1216125878.squirrel@webmail.sissa.it>
Message-ID:
Dear Vega,
I am not sure if i understand well your question. But in the work
mentioned by Lorenzo, we introduced a penalty functional to control the
ionization state of an ion. It is done by forcing a desired occupation
number on the ion when the K-S orbitals are projected on the atomic
orbitals. This technique was used to study electron transfer reactions, in
particular to calculate the energy gap between diabatic states. In such
calculations, the system is forced out of its DFT ground state. at this
moment, we are working to incorporate this part of the code to be
available for download.
Best,
Patrick Sit
Postdoctoral Associate
Center for Molecular Modeling
University of Pennsylvania
On Tue, 15 Jul 2008, Lorenzo Paulatto wrote:
>
> On Mar, Luglio 15, 2008 12:11, vega lew wrote:
>> Si with 14 electrons.
>> Cations lose some electrons such as H+ without any electrons and Li with
>> only 2 electrons.
>
> You cannot force it: you can remove one electron from the system, than if
> the ground state (in the adopted theoretical frame) has a ionized H or Li
> it shall be found at convergence.
>
> Actually Sit, Cococcioni and Marzari (PRL97, 028303) use some sort of
> trick to force a certain ionization state. I don't know if the code is
> available (but you can certainly ask them).
>
>
>> Do you think pseudopotential with plane wave basis sets DFT calculation
>> is suitable for this mater?
>
> I have no idea, certainly it may take a bit of effort to converge an
> isolated charged system wrt the size of the unit cell.
>
> bye
>
>
From vegalew at hotmail.com Wed Jul 16 06:18:49 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 16 Jul 2008 12:18:49 +0800
Subject: [Pw_forum] [update]How to simulate cation H+ without electron or
Li+ with only two electrons
In-Reply-To:
References:
<52646.147.122.5.216.1216125878.squirrel@webmail.sissa.it>
Message-ID:
Dear all,
thanks for the reply of
Lorenzo Paulatto, Axel Kohlmeyer and Hoi-land Sit.
I think I didn't introduce the background of the problem very clearly.
We want to design a kind of materials for Li+/H+ cation storage. So the cations
are injected to the materials by voltage during the charge process and it will
also can be driven out of the materials during the discharge process. Therefore
I think what I should concern is the ionization state of Li+ and H+. We want to
know the behavior of the _cation_ in the different positions of the materials, such
as binding energy, transfer energy barrier from position to position in the material.
We can simplely imagine that the materials is a porous materials which can confine
small cations by a force between chemical bond and physical force.
Of course the cations may be accept some electrons from the storage materials.
As Axel Kohlmeyer said the electrons of the system is not distinguishable, if I simplely
remove a electrons from the whole system, and do the calculation by Q-E to investigate
the cations binding energy @ different site, or transfer energy barrier from site to site, do
you think the calculation can represent the real problem approximately?
thank you for reading.
Vega Lew
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
_________________________________________________________________
Explore the seven wonders of the world
http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
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From vegalew at hotmail.com Wed Jul 16 06:39:46 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 16 Jul 2008 12:39:46 +0800
Subject: [Pw_forum] How to calculate the Mulliken Charges of a relaxed
structure
Message-ID:
Dear all,
Now, I have relaxed a structure. After calculation fininshed, there was a dictionary named
prefix.save createde by pw.x. I think the Mulliken Charges of atoms in the system were stored in it.
Could you tell me how to extract the Mulliken Charges information from it? using pp.x?
best wishes,
vega
Vega Lew
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
_________________________________________________________________
Discover the new Windows Vista
http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
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From baroni at sissa.it Wed Jul 16 08:11:36 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 16 Jul 2008 08:11:36 +0200
Subject: [Pw_forum] How to calculate the Mulliken Charges of a relaxed
structure
In-Reply-To:
References:
Message-ID: <2BEFA524-E3BD-4688-9F08-9C8DA7275295@sissa.it>
Dear Vega Lew: did you know that QE comes with some documentation?
Ever thought to take a glance at it before posting a question here? If
anything else fails, try to google, e.g. "mulliken, site: pwscf.org"
and/or to search the archive of this mailing list Also consider that
learning is a slow and steep process that requires efforts and
dedication. Haste does not help much here. Best wishes. SB
On Jul 16, 2008, at 6:39 AM, vega lew wrote:
> Dear all,
>
> Now, I have relaxed a structure. After calculation fininshed, there
> was a dictionary named
> prefix.save createde by pw.x. I think the Mulliken Charges of atoms
> in the system were stored in it.
> Could you tell me how to extract the Mulliken Charges information
> from it? using pp.x?
>
> best wishes,
>
> vega
>
> Vega Lew
> 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
> Discover the new Windows Vista Learn more!
> _______________________________________________
> 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 Wed Jul 16 10:38:30 2008
From: lfhuang at theory.issp.ac.cn (lfhuang at theory.issp.ac.cn)
Date: Wed, 16 Jul 2008 16:38:30 +0800 (CST)
Subject: [Pw_forum] about convergence criterion in supercell
Message-ID: <36167.210.73.17.131.1216197510.squirrel@210.73.16.4>
Dear all friends:
I have a question on convergence criterion in supercell, which is:
For unit cell, I define "conv_thr" and "tr2_ph" to be 1*d-12 and
1*d-14,respectively. Then I take a 4*4*4 supercell, and is it
precise enough to define 4*4*4*d-12 and 4*4*4d-14 for "conv_thr"
and "tr2_ph" respectively? If it is not, what is the reason?
Thanks a lot for your time to read my letter!
And I would like greatly appreciate the one who can give me some resonable
rationale!
Best Wishes!
From giannozz at democritos.it Wed Jul 16 15:27:20 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 16 Jul 2008 15:27:20 +0200
Subject: [Pw_forum] cholesky decomposition
In-Reply-To: <487B7E40.4060607@ncsu.edu>
References: <22ae3ca40807111359ld41091fmbe663edbc4e48579@mail.gmail.com>
<89377430-E9D8-44E3-B0FC-227F8C7DD112@democritos.it>
<487B7E40.4060607@ncsu.edu>
Message-ID:
On Jul 14, 2008, at 18:26 , Liping Yu wrote:
> I have been met this kind of error messages many times when doing
> structure relaxation with 'bfgs' using espresso-4.0. This error ever
> occurred on IMB sp4/5 and Sun cluster comprised of Opteron processors.
> There is no such error message if I change 'bfgs' to 'damp', or use
> the
> older code version (< 4.0). I didn't check it in v.4.0.1.
> Liping
>
> Paolo Giannozzi wrote:
>> but nobody has ever provided a test job
and you didn't either
---
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 Jul 16 15:30:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 16 Jul 2008 15:30:40 +0200
Subject: [Pw_forum] file .workf
In-Reply-To: <20080714140917.qyukn9becv8kgow4@webmail.units.it>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
<20080714140917.qyukn9becv8kgow4@webmail.units.it>
Message-ID:
On Jul 14, 2008, at 14:09 , glevita at units.it wrote:
> I have some doubts about the file .workf produced in post-processing
> operations.
please look into file PP/work_function.f90 (file .workf is unit 17),
clarify
your doubts, and most important: report what you discover
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 glevita at units.it Wed Jul 16 15:45:54 2008
From: glevita at units.it (glevita at units.it)
Date: Wed, 16 Jul 2008 15:45:54 +0200
Subject: [Pw_forum] file .workf
In-Reply-To:
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
<20080714140917.qyukn9becv8kgow4@webmail.units.it>
Message-ID: <20080716154554.7xn21ty2v2g4084w@webmail.units.it>
Dear Paolo, in fact you're right. Yesterday I searched through the
subroutine, and got (roughly) what I needed to know. The row incuding
the "slice number" should be the calculated wrkf (using the total
electrostatic potential) and its variance, the following row are the
workf without XC and its variance.
A bit uneasy format to plot, maybe. I also struggled a bit to plot
along an axis other than z (I preferred to rotate the cell...).
Then there will be further questions about the reliability of the
workfunction of a metal slab+organic adsorbate... but for the moment I
prefer get the basics going.
Sorry for the thread: sometimes you feel it's easier to ask the forum
rather than investigating subroutines! :-)
Thanks,
Giacomo
Quoting Paolo Giannozzi :
>
> On Jul 14, 2008, at 14:09 , glevita at units.it wrote:
>
>> I have some doubts about the file .workf produced in post-processing
>> operations.
>
> please look into file PP/work_function.f90 (file .workf is unit 17),
> clarify
> your doubts, and most important: report what you discover
>
> 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 akohlmey at cmm.chem.upenn.edu Wed Jul 16 16:18:10 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 16 Jul 2008 10:18:10 -0400 (EDT)
Subject: [Pw_forum] about convergence criterion in supercell
In-Reply-To: <36167.210.73.17.131.1216197510.squirrel@210.73.16.4>
References: <36167.210.73.17.131.1216197510.squirrel@210.73.16.4>
Message-ID:
On Wed, 16 Jul 2008, lfhuang at theory.issp.ac.cn wrote:
LFH> Dear all friends:
dear ,
LFH> I have a question on convergence criterion in supercell, which is:
LFH>
LFH> For unit cell, I define "conv_thr" and "tr2_ph" to be 1*d-12 and
LFH> 1*d-14,respectively. Then I take a 4*4*4 supercell, and is it
LFH> precise enough to define 4*4*4*d-12 and 4*4*4d-14 for "conv_thr"
LFH> and "tr2_ph" respectively? If it is not, what is the reason?
perhaps you should first explain _your_ rationale for lowering
the convergence threshold when increasing the system size.
a convergence parameter that would depend this much on
the system size would not be a good choice.
in any case, the rationale to choose a specific convergence criterion
should be based on the convergence of the property that you are
interested in. i.e. if you want to do a geometry optimization, the
forces have to be converged accurately enough, not only with respect
to wavefunction/density-cutoffs, k-point sampling but also relative
to the wavefunction convergence. similarly, for other calculation types.
cheers,
axel.
LFH>
LFH> Thanks a lot for your time to read my letter!
LFH> And I would like greatly appreciate the one who can give me some resonable
LFH> rationale!
LFH>
LFH> Best Wishes!
LFH>
LFH>
LFH> _______________________________________________
LFH> Pw_forum mailing list
LFH> Pw_forum at pwscf.org
LFH> http://www.democritos.it/mailman/listinfo/pw_forum
LFH>
--
=======================================================================
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 baroni at sissa.it Wed Jul 16 18:07:35 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 16 Jul 2008 18:07:35 +0200
Subject: [Pw_forum] file .workf
In-Reply-To: <20080716154554.7xn21ty2v2g4084w@webmail.units.it>
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
<20080714140917.qyukn9becv8kgow4@webmail.units.it>
<20080716154554.7xn21ty2v2g4084w@webmail.units.it>
Message-ID:
On Jul 16, 2008, at 3:45 PM, glevita at units.it wrote:
> Sorry for the thread: sometimes you feel it's easier to ask the forum
> rather than investigating subroutines! :-)
if you had not told us, we would have never guessed! ;-)
cheers - 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 glevita at units.it Wed Jul 16 19:01:46 2008
From: glevita at units.it (glevita at units.it)
Date: Wed, 16 Jul 2008 19:01:46 +0200
Subject: [Pw_forum] file .workf
In-Reply-To:
References: <959737.47307.qm@web30604.mail.mud.yahoo.com>
<92987CD3-CC31-4DEC-BDEC-6EC9B0D09FF2@democritos.it>
<20080714140917.qyukn9becv8kgow4@webmail.units.it>
<20080716154554.7xn21ty2v2g4084w@webmail.units.it>
Message-ID: <20080716190146.4mdjrtgb7pwscwgk@webmail.units.it>
Important concepts are always worthwhile repeating... ;-)
Cheers,
Giacomo
Quoting Stefano Baroni :
>
> On Jul 16, 2008, at 3:45 PM, glevita at units.it wrote:
>> Sorry for the thread: sometimes you feel it's easier to ask the forum
>> rather than investigating subroutines! :-)
>
> if you had not told us, we would have never guessed! ;-)
>
> cheers - 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 hkiee3 at snu.ac.kr Thu Jul 17 03:28:34 2008
From: hkiee3 at snu.ac.kr (Hoonkyung Lee)
Date: Thu, 17 Jul 2008 10:28:34 +0900 (KST)
Subject: [Pw_forum] posting for gamma phonon
Message-ID: <15008187.1216258114417.JavaMail.root@auk1>
When I am calculating gamma phonon,
error message is as follows
Program PHONON v.3.2.3 starts ...
Today is 16Jul2008 at 18:14: 3
Parallel version (MPI)
Number of processors in use: 2
R & G space division: proc/pool = 2
Ultrasoft (Vanderbilt) Pseudopotentials
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from phq_readin : error # 1
reading inputph namelist
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
What is the problem?
I have tried many times as inputph changes,
I can not succeed.
Please help me out!!!
Input files are as follows
#This is relaxing PW file
&control
prefix='H2'
calculation='relax'
restart_mode='from_scratch'
pseudo_dir='$PSEUDO'
outdir='./OUT'
nstep=130
/
&system
ibrav= 0, celldm(1) =1.889726878, nat=2, ntyp=1, nspin=1
ecutwfc=35, occupations='smearing', degauss=0.0007353,
starting_magnetization(1)=0.001
/
&electrons
electron_maxstep=250
mixing_mode = 'plain'
mixing_beta = 0.01
conv_thr = 1.0e-6
/
&ions
/
ATOMIC_SPECIES
H 1.008 H.pbe-van_bm.UPF
ATOMIC_POSITIONS {angstrom}
H 0.0 0.0 0.0
H 0.75 0.0 0.0
K_POINTS {automatic}
1 1 1 0 0 0
CELL_PARAMETERS { cubic }
11.00000 0.00000 0.00000
0.00000 10.00000 0.00000
0.00000 0.00000 10.00000
#This is gamma phonon file
&inputph
tr2_ph=1.0d-14,
prefix='H2',
epsil=.true.,
amass(1)=1.008,
outdir='$OUT/',
fildyn='H2.dynG',
/
0.0 0.0 0.0
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From akohlmey at cmm.chem.upenn.edu Thu Jul 17 05:34:42 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 16 Jul 2008 23:34:42 -0400 (EDT)
Subject: [Pw_forum] posting for gamma phonon
In-Reply-To: <15008187.1216258114417.JavaMail.root@auk1>
References: <15008187.1216258114417.JavaMail.root@auk1>
Message-ID:
On Thu, 17 Jul 2008, Hoonkyung Lee wrote:
please configure your mail program to send
plain ascii text. writing base64 encoded text
_and_ html formatted mails is creating a big
mess for people using plain text mail programs.
please keep in mind that mailing list processors
modify mails and on top of that encoded mails
get a high spam rating, i.e. less people will
see it. thanks
HL> When I am calculating gamma phonon,
error message is as follows
Program PHONON v.3.2.3 starts ...
version 3.2. is outdated. please use 4.0.1.
Today is 16Jul2008 at 18:14: 3
Parallel version (MPI)
Number of processors in use: 2
R & G space division: proc/pool = 2
Ultrasoft (Vanderbilt) Pseudopotentials
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from phq_readin : error # 1
reading inputph namelist
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
What is the problem?
I have tried many times as inputph changes,
I can not succeed.
Please help me out!!!
please help yourself. the error message indicates that the
error is in the inputph section. remove the lines one by
one and the one where the error message goes away is the
culprit. my guess is the one containing $OUT.
axel
Input files are as follows
#This is relaxing PW file
&control
prefix='H2'
calculation='relax'
restart_mode='from_scratch'
pseudo_dir='$PSEUDO'
outdir='./OUT'
nstep=130
/
&system
ibrav= 0, celldm(1) =1.889726878, nat=2, ntyp=1, nspin=1
ecutwfc=35, occupations='smearing', degauss=0.0007353,
starting_magnetization(1)=0.001
/
&electrons
electron_maxstep=250
mixing_mode = 'plain'
mixing_beta = 0.01
conv_thr = 1.0e-6
/
&ions
/
ATOMIC_SPECIES
H 1.008 H.pbe-van_bm.UPF
ATOMIC_POSITIONS {angstrom}
H 0.0 0.0 0.0
H 0.75 0.0 0.0
K_POINTS {automatic}
1 1 1 0 0 0
CELL_PARAMETERS { cubic }
11.00000 0.00000 0.00000
0.00000 10.00000 0.00000
0.00000 0.00000 10.00000
#This is gamma phonon file
&inputph
tr2_ph=1.0d-14,
prefix='H2',
epsil=.true.,
amass(1)=1.008,
outdir='$OUT/',
fildyn='H2.dynG',
/
0.0 0.0 0.0
--
=======================================================================
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 vegalew at hotmail.com Thu Jul 17 06:11:56 2008
From: vegalew at hotmail.com (vega lew)
Date: Thu, 17 Jul 2008 12:11:56 +0800
Subject: [Pw_forum] something strange with my nscf and projwfc calculations
Message-ID:
Dear all
I have done the relax calculation for my system. Then I downloaded the results
file with all the file at $outdir fold from the computer center. And put the last
coordinate in the output file to the scf inputfile to carry out the scf calculation in my
own cluster in the office. Whe the scf calculation was done, the calculated energy
was exactly the same as output file of the relaxed results. The I chage the 'scf' command
in &control section directly to 'nscf'. But the 'nscf' output file said,
Band Structure Calculation
Davidson diagonalization with overlap
WARNING: 14 eigenvalues not converged
And There was also an error occured during the projwfc calculations. the error information
was,
Calling projwave ....
gamma-point specific algorithms are used
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from davcio : error # 10
error while reading from file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
There is also another thing I should mentioned that when I doing the relax and scf calculation
I set disk_io to 'none' to save communication and disk space. Does these cause the error in the
post-processing?
thank you for reading
vega
Vega Lew
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
_________________________________________________________________
Explore the seven wonders of the world
http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
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From paulatto at sissa.it Thu Jul 17 08:54:08 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 17 Jul 2008 08:54:08 +0200 (CEST)
Subject: [Pw_forum] something strange with my nscf and projwfc
calculations
In-Reply-To:
References:
Message-ID: <42927.147.122.5.32.1216277648.squirrel@webmail.sissa.it>
On Gio, Luglio 17, 2008 06:11, vega lew wrote:
> I set disk_io to 'none' to save communication and disk space. Does these
> cause the error in the
> post-processing?
Indeed.
You must leave disk-io to its default to do postprocesing; setting it to
high should make pp faster in some circumstances, but is not necessary.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
----------------------------------------------------------------
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Powered by SquirrelMail http://www.squirrelmail.org/
From benjalalyouness3 at yahoo.fr Thu Jul 17 10:31:38 2008
From: benjalalyouness3 at yahoo.fr (youness benjalal)
Date: Thu, 17 Jul 2008 08:31:38 +0000 (GMT)
Subject: [Pw_forum] pseudopotentials_H.US;
RRKJ3.UPF_C.US_PBE.RRKJ3.UPF_N.US_PBE.RRKJ3.UPF
Message-ID: <208633.86288.qm@web26206.mail.ukl.yahoo.com>
Hi all,
?????
????? Can you send me the pseudopotentials ? :
H.US_PBE.RRKJ3.UPF
C.US_PBE.RRKJ3.UPF
N.US_PBE.RRKJ3.UPF
thamk you for help.
------------------------------------------------------------------------
Youness BENJALAL
Laboratoire de Chimie Physique g?n?rale des Mat?riaux.
D?partement de Chimie,
Facult? des Sciences, Ben M'sik BP 7955,
Casablanca, Maroc.
T?l. : +212 64 82 63 60
benjalalyouness3 at yahoo.fr
_____________________________________________________________________________
Envoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.yahoo.fr
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From archx at 163.com Thu Jul 17 12:03:44 2008
From: archx at 163.com (pem)
Date: Thu, 17 Jul 2008 18:03:44 +0800
Subject: [Pw_forum] A FORMAT error in example
In-Reply-To:
References:
Message-ID: <200807171803.53983.archx@163.com>
Dear all,
I've just compiled espresso.4.0 on my desktop with ifort10. When run rhe
example in "espresso.4.0/examples/autopilot-example", I found some errors in
the formatted outputs win the generated file titled water.autopilot.out .
It's like fellow:
0.0000 0.0000 -0.0121 -9.9528
1071 0.00023 0.0 827.2 -17.20243 -17.20243 -17.19850 -17.20624
0.0000 0.0000 -0.0119 -9.9887
1072 0.00024 0.0 849.0 -17.20240 -17.20240 -17.19837 -17.20638
0.0000 0.0000 -0.0116 *******
1073 0.00025 0.0 870.1 -17.20237 -17.20237 -17.19824 -17.20652
0.0000 0.0000 -0.0114 *******
the "*"s appear from line 4762.
I checked the source and found the line 267 of espresso.4.0/CPV/print_out.f90
is causing this error:
Line266: WRITE( stdout, 1948 ) nfi, ekinc, temphc, tempp, etot,
enthal, econs, &
econt, vnhh(3,3), xnhh0(3,3), vnhp(1), xnhp0(1)
Line297: 1948 FORMAT( I5,1X,F8.5,1X,F6.1,1X,F6.1,4(1X,F11.5),4(1X,F7.4) ),
better if 4(1X,F7.4) be changed into 4(2X,F8.4) here.
Does this problem occur when your run this example? I am not sure it's caused
by my installation failure, or it's a bug in the code.
Regards,
pem
07/17/2008
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From sathya_sheela1985001 at rediffmail.com Thu Jul 17 12:31:08 2008
From: sathya_sheela1985001 at rediffmail.com (sathya subramanyan)
Date: 17 Jul 2008 10:31:08 -0000
Subject: [Pw_forum] Pw_forum] negative value of polarization and Z* for Pb
in Tetragonal PbTiO3 and discrepancy
Message-ID: <20080717103108.43795.qmail@f4mail-235-149.rediffmail.com>
?Dear Dr.Prasenjit,
Thank you so very much for your detailed reply and advice.Using your advice I performed the convergence tests and I think it has worked. I will use the converged values and check for further calculations and let you know about the results.Thank you once again as this has helped me to proceed in my work
Regards
SATHYA SHEELA.S
Grad. Student
Department of Physics
National Institute of Technology
Tiruchirapalli - 620015
India
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From giannozz at democritos.it Thu Jul 17 15:35:14 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 17 Jul 2008 15:35:14 +0200
Subject: [Pw_forum] posting for gamma phonon
In-Reply-To: <15008187.1216258114417.JavaMail.root@auk1>
References: <15008187.1216258114417.JavaMail.root@auk1>
Message-ID: <065EDDE8-494D-4F87-99D6-ECD268788DEF@democritos.it>
On Jul 17, 2008, at 3:28 , Hoonkyung Lee wrote:
> from phq_readin : error # 1
> reading inputph namelist
From the FAQ:
----
The code stops with an "error reading namelist xxxx"
A: Most likely there is a misspelled variable in namelist xxxx. If
there isn't any (have you looked carefully? really?? REALLY???),
beware control characters like DOS ^M (control-M): they can confuse
the namelist-reading code.
If this message concerns the first namelist to be read (usually
"&control"), and if you are running in parallel: try "code -inp
input_file" instead of "code < input_file". Some MPI libraries do not
properly handle input redirection.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From baroni at sissa.it Thu Jul 17 15:45:58 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 17 Jul 2008 15:45:58 +0200
Subject: [Pw_forum] pseudopotentials_H.US;
RRKJ3.UPF_C.US_PBE.RRKJ3.UPF_N.US_PBE.RRKJ3.UPF
In-Reply-To: <208633.86288.qm@web26206.mail.ukl.yahoo.com>
References: <208633.86288.qm@web26206.mail.ukl.yahoo.com>
Message-ID: <75EE0C30-870D-4202-BEFA-A4FAE402CC21@sissa.it>
How about downloading them yourself from the QE PP table:
http://www.quantum-espresso.org/pseudo.php
??? regards - SB
On Jul 17, 2008, at 10:31 AM, youness benjalal wrote:
> Hi all,
>
> Can you send me the pseudopotentials ? :
> H.US_PBE.RRKJ3.UPF
> C.US_PBE.RRKJ3.UPF
> N.US_PBE.RRKJ3.UPF
> thamk you for help.
>
>
> ------------------------------------------------------------------------
> Youness BENJALAL
> Laboratoire de Chimie Physique g?n?rale des Mat?riaux.
> D?partement de Chimie,
> Facult? des Sciences, Ben M'sik BP 7955,
> Casablanca, Maroc.
> T?l. : +212 64 82 63 60
> benjalalyouness3 at yahoo.fr
>
> Envoy? avec Yahoo! Mail.
> Une boite mail plus intelligente.
> _______________________________________________
> 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 baroni at sissa.it Thu Jul 17 15:50:14 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 17 Jul 2008 15:50:14 +0200
Subject: [Pw_forum] A FORMAT error in example
In-Reply-To: <200807171803.53983.archx@163.com>
References:
<200807171803.53983.archx@163.com>
Message-ID:
Dear Pem (???): you are on the right track. Just change the FORMAT
statement as indicated, and try again. SB
OOh, yes: would you be so kind as to sign your correspondence with
name-family name-affiliations?
Cheers - SB
On Jul 17, 2008, at 12:03 PM, pem wrote:
> Dear all,
>
> I've just compiled espresso.4.0 on my desktop with ifort10. When run
> rhe
> example in "espresso.4.0/examples/autopilot-example", I found some
> errors in
> the formatted outputs win the generated file titled
> water.autopilot.out .
> It's like fellow:
>
> 0.0000 0.0000 -0.0121 -9.9528
> 1071 0.00023 0.0 827.2 -17.20243 -17.20243 -17.19850
> -17.20624
> 0.0000 0.0000 -0.0119 -9.9887
> 1072 0.00024 0.0 849.0 -17.20240 -17.20240 -17.19837
> -17.20638
> 0.0000 0.0000 -0.0116 *******
> 1073 0.00025 0.0 870.1 -17.20237 -17.20237 -17.19824
> -17.20652
> 0.0000 0.0000 -0.0114 *******
>
>
> the "*"s appear from line 4762.
>
> I checked the source and found the line 267 of espresso.4.0/CPV/
> print_out.f90
> is causing this error:
>
> Line266: WRITE( stdout, 1948 ) nfi, ekinc, temphc, tempp,
> etot,
> enthal, econs, &
> econt, vnhh(3,3), xnhh0(3,3), vnhp(1),
> xnhp0(1)
>
> Line297: 1948 FORMAT( I5,1X,F8.5,1X,F6.1,1X,F6.1,4(1X,F11.5),
> 4(1X,F7.4) ),
> better if 4(1X,F7.4) be changed into 4(2X,F8.4) here.
>
> Does this problem occur when your run this example? I am not sure
> it's caused
> by my installation failure, or it's a bug in the code.
>
> Regards,
>
>
> pem
> 07/17/2008
>
> _______________________________________________
> 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 giannozz at democritos.it Thu Jul 17 15:49:49 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 17 Jul 2008 15:49:49 +0200
Subject: [Pw_forum] Use of SIC in PWSCF
In-Reply-To:
References:
Message-ID: <165C513F-F1C1-41F5-93A9-DC03B6E20E2C@democritos.it>
On Jul 14, 2008, at 11:54 , yukihiro_okuno at fujifilm.co.jp wrote:
> I want to know the Self Interaction Correction is available in PWscf ?
short answer: no
> I found the sorce code sic.f90 in /espresso-4.0/Modules.
> But is seems this sic formula have a limit that the system must be
> electron up = electron down + 1, and further, I can't found the place
> this modules called in the program.
it is called in CP, not in PWscf, and it is designed to work only for
the
case you mentioned
> Is there plan to implement the more general SIC schema in PWSCF?
> (like pseudo SIC formula , for example PRB vol 67 125109 (2003) )
some years ago somebody started, but never finished, to implement
the algorithm of the above-mentioned paper. I would be personally
curious to try it. At least it looks numerically safe and well-defined,
unlike straightforward SIC whose usage in extended systems is
rather questionable. Note however that some authors have found
that even carefully performed SIC calculations in finite systems
don't give such a big improvement.
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 archx at 163.com Thu Jul 17 17:43:26 2008
From: archx at 163.com (pem)
Date: Thu, 17 Jul 2008 23:43:26 +0800
Subject: [Pw_forum] A FORMAT error in example
In-Reply-To:
References:
Message-ID: <200807172343.36312.archx@163.com>
Dear Stefano,
I changed the FORMAT and rebuilt it. It works well now.
Thank you.
Regards,
pem
07/17/2008
-------------------------------------------------------------------
Yan Ren, Ph.D candidate archx at 163.com
Institute of Physics, Chinese Academy of Sciences
P. O. Box 603, Beijing, 100190, China
Tel: +86-10-8264-8102 Fax: +86-10-6256-1422
-------------------------------------------------------------------
On Thursday 17 July 2008 Stefano Baroni wrote:
> Date: Thu, 17 Jul 2008 15:50:14 +0200
> From: Stefano Baroni
> Subject: Re: [Pw_forum] A FORMAT error in example
> To: PWSCF Forum
> Message-ID:
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Pem:
> you are on the right track. Just change the FORMAT ?
> statement as indicated, and try again.
>
> OOh, yes: would you be so kind as to sign your correspondence with ?
> name-family name-affiliations?
>
> Cheers - SB
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From Matthias.Timmer at uni-due.de Thu Jul 17 18:54:26 2008
From: Matthias.Timmer at uni-due.de (Matthias Timmer)
Date: Thu, 17 Jul 2008 18:54:26 +0200
Subject: [Pw_forum] Relation between the magnetic field and the Fermi
energies
In-Reply-To:
References:
Message-ID: <487F7942.9090008@uni-due.de>
Dear Madams and Sirs,
I am a PhD student from Germany, and at the moment I treat spin
relaxation effects.
I am trying to figure out how the relation between the magnetic field
(bfield(3) in weights, was in sum_band before) and the Fermi energies
(in a constrained calculation) is justified, which is given there. The
given relation is bfield(3) = 0.5D0*( ef_up - ef_dw ), which I
understand is just a simple model, i.e. twice the Zeeman energy is equal
to the difference in the Fermi energies.
However, the Bohr magneton should be present, if I assume that the
magnetic field is given in Rydberg atomic units. The Bohr magneton is
sqrt(2) in Rydberg a.u. (Bohr magneton = e \hbar / (2 m_electron) =
sqrt(2) *1 / (2 * 0.5)). That means I expect the formula bfield(3) =
0.5D0*( ef_up - ef_dw )/sqrt(2) should be there. When I take a look at
"electrons.f90", however, the output for bfield(3) says that it is
already in Rydberg atomic units (format 9071).
Now I ask myself: Am I missing something (a line of code, or a line of
thought, or a factor somewhere), or is there something wrong with the
output (should it say "bohr" instead of "Rydberg" for bfield(3))?
I am sorry if this has been answered before, but at least I did not find
this in the archive.
Thank you in advance for your answers!
Best regards,
Matthias Timmer
Universitaet Duisburg-Essen
Fachbereich Physik
Lotharstrasse 1
47057 Duisburg
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From vegalew at hotmail.com Thu Jul 17 19:11:36 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 18 Jul 2008 01:11:36 +0800
Subject: [Pw_forum] something strange with my nscf and projwfc
calculations
In-Reply-To:
References:
Message-ID:
Dear all,
Thank you for Lorenzo Paulatto's reply. I have done the 'scf' calculation with the default
disk_io. And the projwf.x calculation could be done smoothly. But the nscf calculation was
still something wrong. The nscf output file still with a warning that
Band Structure Calculation Davidson diagonalization with overlap WARNING: 14 eigenvalues not converged
Than I thought this may because of the gamma point calculation. So I changed the k-point
mesh to 2X2X1. But the cholesky decomposition problem occurred during the nscf calculation.
To better understand the problem, I'll give my input file for nscf calculation. the coordinate is
from the previous relax calculation.
&CONTROL title = 'Anatase_101_1X3_50_500' , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = '/home/vega/espresso-4.0/TiO2/Anatase/101/' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , prefix = 'Anatase_101_1X3_50_500' , etot_conv_thr = 0.0005 , forc_conv_thr = 0.0011668141375 , nstep = 1000 , / &SYSTEM ibrav = 8, celldm(1) = 19.5395, celldm(2) = 1.09960, celldm(3) = 1.72824, nat = 72, ntyp = 2, ecutwfc = 50 , ecutrho = 500 , / &ELECTRONS electron_maxstep = 1000, conv_thr = 1d-8 , /ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS angstrom Ti 2.705000000 1.895000000 0.731000000 0 0 0Ti 4.088029892 1.895099246 4.442701913Ti 7.875000000 0.000000000 0.731000000 0 0 0Ti 9.258126398 0.000112350 4.442537339Ti 0.467000000 0.000000000 1.612000000 0 0 0Ti 1.722094411 0.000128162 5.084441577Ti 5.637000000 1.895000000 1.612000000 0 0 0Ti 6.891944371 1.895169000 5.084434718O 2.323000000 0.000000000 0.881000000 0 0 0O 3.688596839 0.000131731 4.459388032O 0.850000000 1.895000000 1.462000000 0 0 0O 2.255763183 1.895180831 5.291602661O 9.730000000 0.000000000 0.000000000 0 0 0O 0.810046420 0.000140092 3.553838348O 8.951000000 0.000000000 2.344000000 0 0 0O 0.086181034 0.000117179 5.897424380O 7.493000000 1.895000000 0.881000000 0 0 0O 8.858544520 1.895007861 4.459227191O 6.020000000 0.000000000 1.462000000 0 0 0O 7.425660950 0.000122473 5.291647079O 4.560000000 1.895000000 0.000000000 0 0 0O 5.979795208 1.895048385 3.553757785O 3.781000000 1.895000000 2.344000000 0 0 0O 5.255954630 1.895416907 5.897410181Ti 2.705000000 5.685000000 0.731000000 0 0 0Ti 4.088163820 5.684976660 4.442456424Ti 7.875000000 3.790000000 0.731000000 0 0 0Ti 9.257986672 3.789993347 4.442741191Ti 0.467000000 3.790000000 1.612000000 0 0 0Ti 1.722025586 3.789919332 5.084452567Ti 5.637000000 5.685000000 1.612000000 0 0 0Ti 6.892007257 5.684967660 5.084409356O 2.323000000 3.790000000 0.881000000 0 0 0O 3.688611476 3.790077951 4.459218356O 0.850000000 5.685000000 1.462000000 0 0 0O 2.255751964 5.684979863 5.291624584O 9.730000000 3.790000000 0.000000000 0 0 0O 0.809880177 3.789997972 3.553798474O 8.951000000 3.790000000 2.344000000 0 0 0O 0.086020093 3.789707926 5.897442616O 7.493000000 5.685000000 0.881000000 0 0 0O 8.858536904 5.684975329 4.459341712O 6.020000000 3.790000000 1.462000000 0 0 0O 7.425685241 3.789923135 5.291562160O 4.560000000 5.685000000 0.000000000 0 0 0O 5.979963647 5.684980051 3.553775805O 3.781000000 5.685000000 2.344000000 0 0 0O 5.256105682 5.684967206 5.897363232Ti 2.705000000 9.475000000 0.731000000 0 0 0Ti 4.088030765 9.474858391 4.442666625Ti 7.875000000 7.580000000 0.731000000 0 0 0Ti 9.257989986 7.579955980 4.442781034Ti 0.467000000 7.580000000 1.612000000 0 0 0Ti 1.722038923 7.580052383 5.084443898Ti 5.637000000 9.475000000 1.612000000 0 0 0Ti 6.891925555 9.474759050 5.084464803O 2.323000000 7.580000000 0.881000000 0 0 0O 3.688606225 7.579882807 4.459214611O 0.850000000 9.475000000 1.462000000 0 0 0O 2.255761915 9.474781120 5.291594612O 9.730000000 7.580000000 0.000000000 0 0 0O 0.809874524 7.579996236 3.553797216O 8.951000000 7.580000000 2.344000000 0 0 0O 0.086036275 7.580229348 5.897454520O 7.493000000 9.475000000 0.881000000 0 0 0O 8.858544796 9.474921534 4.459289341O 6.020000000 7.580000000 1.462000000 0 0 0O 7.425679676 7.580009180 5.291598539O 4.560000000 9.475000000 0.000000000 0 0 0O 5.979803382 9.474838611 3.553782132O 3.781000000 9.475000000 2.344000000 0 0 0O 5.255933180 9.474558506 5.897415287K_POINTS gamma # if I set it to gamma the output file said the warning I mentioned above
# if I set it to 2X2X1 the cholesky decomposition problem occurred
#end of the input file
By the way, I use the 5 CPUs with 20 cores for the calculation.
The job is big, I can't test it with serial instead of parallel.
How could I handle this. Thank you for reading.
vega
Vega LewPH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China
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From giannozz at democritos.it Thu Jul 17 21:23:42 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 17 Jul 2008 21:23:42 +0200
Subject: [Pw_forum] something strange with my nscf and projwfc
calculations
In-Reply-To:
References:
Message-ID: <8F69C04C-67F1-420F-BF9B-CCA537B1E0E9@democritos.it>
On Jul 17, 2008, at 19:11 , vega lew wrote:
> Band Structure Calculation
> Davidson diagonalization with overlap
> WARNING: 14 eigenvalues not converged
http://www.democritos.it/pipermail/pw_forum/2007-November/007832.html
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From vegalew at hotmail.com Fri Jul 18 03:25:01 2008
From: vegalew at hotmail.com (vega lew)
Date: Fri, 18 Jul 2008 09:25:01 +0800
Subject: [Pw_forum] something strange with my nscf and
projwfc calculations
In-Reply-To: <8F69C04C-67F1-420F-BF9B-CCA537B1E0E9@democritos.it>
References:
<8F69C04C-67F1-420F-BF9B-CCA537B1E0E9@democritos.it>
Message-ID:
Dear Paolo Giannozzi,
Thank you for your reply
But Why the cholesky decomposition problem of the nscf calculation occurred using 2X2X1 K point mesh
instead of gamma? Have you test it my input file with 2X2X1 mesh?
How could I get rid of it?
vega
Vega Lew
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: giannozz at democritos.it
> Date: Thu, 17 Jul 2008 21:23:42 +0200
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] something strange with my nscf and projwfc calculations
>
>
> On Jul 17, 2008, at 19:11 , vega lew wrote:
>
> > Band Structure Calculation
> > Davidson diagonalization with overlap
> > WARNING: 14 eigenvalues not converged
>
> http://www.democritos.it/pipermail/pw_forum/2007-November/007832.html
> ---
> 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 lfhuang at theory.issp.ac.cn Fri Jul 18 03:16:43 2008
From: lfhuang at theory.issp.ac.cn (lfhuang at theory.issp.ac.cn)
Date: Fri, 18 Jul 2008 09:16:43 +0800 (CST)
Subject: [Pw_forum] one error in pw.x when calculating graphene supercell
Message-ID: <36976.210.73.17.131.1216343803.squirrel@210.73.16.4>
Hellow everyone:
When I calcute a 6*6*1 supercell of graphene with a Hydrogen atom adsorbed
on it. the key parameters are set below:
pseudopotentials: C.pz-vbc.UPF H.pz-vbc.UPF
ecutwfc = 70.0 Ry
'mp' 0.02
kgrid 6*6*1
nbnd = 240
conv_thr = 1*d-12
but at the start of calculation, one error message appears in the outputfile,
and the task was stpped:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task # 0
from read_rho_xml : error # 1
dimensions do not match
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Who could tell me where it come from?
Thanks!
From baroni at sissa.it Fri Jul 18 08:02:05 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 18 Jul 2008 08:02:05 +0200
Subject: [Pw_forum] something strange with my nscf and
projwfc calculations
In-Reply-To: