Dear all, I wish to look at the? electron localization function for Au and Pt clusters. The obtained values are between 0-0.5 for? normconserving psp from Rappe group and abinit.?I have read the comments in ?forum but the result is between 0.-0.5. Would you please let me know if there exists any solution. regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110612/de110c0e/attachment.htm From degironc at sissa.it Sun Jun 12 18:00:32 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 12 Jun 2011 18:00:32 +0200 Subject: [Pw_forum] Wrong value for elf In-Reply-To: <27214.85.185.211.90.1307868157.squirrel@mail.iasbs.ac.ir> References: <20110609121210.20253dyi05b3ic1m@webmail.epfl.ch> <27214.85.185.211.90.1307868157.squirrel@mail.iasbs.ac.ir> Message-ID: <4DF4E2A0.10402@sissa.it> why do you think that values between 0 and 0.5 are wrong ? stefano On 06/12/2011 10:42 AM, nazari at iasbs.ac.ir wrote: >

> > Dear all, > I wish to look at the? electron localization > function for Au and Pt clusters. The obtained values are between 0-0.5 > for? normconserving psp from Rappe group and abinit.?I have read > the comments in ?forum but the result is between 0.-0.5. Would you > please let me know if there exists any solution. > regards > Fariba > Nazari > IASBS > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110612/679f3593/attachment.htm From syuva2987 at gmail.com Mon Jun 13 08:14:43 2011 From: syuva2987 at gmail.com (yuva rani) Date: Mon, 13 Jun 2011 11:44:43 +0530 Subject: [Pw_forum] Constraints Message-ID: Thanks for your suggestion about ecutwfc and ecutrho. I had another doubt to share with you. I had relaxed two layers of aluminium atoms consisting of 112 atoms. Now, I want to stack a molecule on its surface. Inorder to relax this, I need to use constraints. So please give me the suggestion of using Constraint_cards and how to fix the parameters. Also give me the example input file using constraints. Thanks in advance. From m.g.p.krishna at chem.leidenuniv.nl Mon Jun 13 08:42:23 2011 From: m.g.p.krishna at chem.leidenuniv.nl (m.g.p.krishna at chem.leidenuniv.nl) Date: Mon, 13 Jun 2011 08:42:23 +0200 Subject: [Pw_forum] Constraints Message-ID: <20110613084223.12439bllg1135bnz@webmail.chem.leidenuniv.nl> Hi Yuva, If you look at the previous post, you can see a small example script, where a CONSTRAINT card is used. Also to use CONSTRAINT card you SHOULD use 'damp' rather than 'bfgs'. It is easy to use 'distance' constraint. But I failed to fix the coordination number for selected atoms (using 'atom_coord' and 'type_coord') as It described in the previous mail. Moreover some strange things are there, for example from the previous input, it do a relaxation if you use: CONSTRAINTS 1 0.5 'atom_coord' 5 1 3.5 0.5 and you will get an ERROR message if you swap the atom index (VERY STRANGE): ie. CONSTRAINTS 1 0.5 'atom_coord' 1 5 3.5 0.5 So someone can help us to give a working/reliable example script on 'atom_coord' and 'type_coord' constraints. It will be very useful, since the default examples dont include this... otherwise I am going to do a Quantum-Espresso plugin for ASE/CamD just for a reliable geometry optimization. :-( With best regards Krishna Mohan GP Center for Superfunctional Materials POSTECH Sotuh Korea. From mayankaditya at gmail.com Mon Jun 13 11:41:45 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 13 Jun 2011 15:11:45 +0530 Subject: [Pw_forum] Phonon calculation of magnetic system Message-ID: Dear Users Is it necessary to include magnetic interaction (spin) and Hubbard term for phonon calculation of a magnetic system. Thanks Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: ?022-25595606 Home: 9920397437 / 9869834437 From zafartariq2003 at yahoo.com Mon Jun 13 14:44:09 2011 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Mon, 13 Jun 2011 05:44:09 -0700 (PDT) Subject: [Pw_forum] How we can create Supercell from atomic positions of unit cell? Message-ID: <776616.48310.qm@web65411.mail.ac4.yahoo.com> Hi ? ?? I am PhD scholar and using Quantum Espresso Software. I do not know how to create supercell from unit cell. I do not know how to?set?CELL PARAMETERS option when we set ibrav=0. We actually want to create nanotube. I hope that you will guide me about this. ? Best Regards ? Muhammad zafar ? PhD scholar ? The Islamia University of Bahawalpur, Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110613/3a0e64f3/attachment.htm From flux_ray12 at 163.com Mon Jun 13 15:06:20 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 13 Jun 2011 21:06:20 +0800 (CST) Subject: [Pw_forum] How we can create Supercell from atomic positions of unit cell? In-Reply-To: <776616.48310.qm@web65411.mail.ac4.yahoo.com> References: <776616.48310.qm@web65411.mail.ac4.yahoo.com> Message-ID: <65c329db.fd68.130891c2477.Coremail.flux_ray12@163.com> There are two choices. First, you'd better learn crystallography well, and calculate the CELL_PARAMTERS and atoms positions by yourself. Second, you can use the program spacegroup in ELK FP-LAPW code to find them. At 2011-06-13 20:44:09?"zafar rasheed" wrote: Hi I am PhD scholar and using Quantum Espresso Software. I do not know how to create supercell from unit cell. I do not know how to set CELL PARAMETERS option when we set ibrav=0. We actually want to create nanotube. I hope that you will guide me about this. Best Regards Muhammad zafar PhD scholar TheIslamia University of Bahawalpur, Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110613/71d61275/attachment.htm From swapnil.chandratre at gmail.com Mon Jun 13 16:31:05 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 13 Jun 2011 09:31:05 -0500 Subject: [Pw_forum] Dimensions dont match Message-ID: Hi, I am trying to run berry phase calculation, the 'scf' calculation works fine and the results converge, but the nscf calculations gives me the following result though I dont change the ecutwfc and the cell parameters. What could be the error ?? *from read_rho_xml : error # 1* * dimensions do not match* -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110613/fff6eae5/attachment.htm From samolyuk at gmail.com Mon Jun 13 21:39:12 2011 From: samolyuk at gmail.com (German Samolyuk) Date: Mon, 13 Jun 2011 15:39:12 -0400 Subject: [Pw_forum] Fwd: pwscf: energy convergence of noncollinear with spin-orbit calculations, withdraw question In-Reply-To: References:

Message-ID: Hello Gabriele, Thank you for your response and advices. I used version 4.2.1 the actual (final) input contains instructions: for magnetization along z-direction starting_magnetization(1) = 0.1, starting_magnetization(2) = 0.4, noncolin = .true. , angle1(1) = 0, angle1(2) = 0, angle2(1) = 0, angle2(2) = 0, lspinorb = .true. , constrained_magnetization = 'atomic direction' , lambda = 0.3, nosym = .true., and magnetization perpendicular to z-direction starting_magnetization(1) = 0.1, starting_magnetization(2) = 0.4, noncolin = .true. , angle1(1) = 90, angle1(2) = 90, angle2(1) = 0, angle2(2) = 0, lspinorb = .true. , constrained_magnetization = 'atomic direction' , lambda = 0.3, nosym = .true., the resulting energies looks reasonable and convergence is really fast. Thank you for advice with degauss value. I'll check dependence from it. Best, German On Wed, Jun 8, 2011 at 3:55 AM, Gabriele Sclauzero wrote: > Hello German, > Il giorno 01/giu/2011, alle ore 23.02, German Samolyuk ha scritto: > > I withdraw my question. It works with nosym=true. > German > > > ---------- Forwarded message ---------- > From: German Samolyuk > Date: Wed, May 18, 2011 at 10:25 AM > Subject: pwscf: energy convergence of noncollinear with spin-orbit > calculations > To: PWSCF Forum > > > Dear qe users, > > I'm trying to calculate total energy of artificial FCC PtFe compound > with magnetic moment (MM) along z- and x-directionsi (MAE). > > In order to supress oscillation of moment direction I used for MM||z > calculation > input instructions > > ?constrained_magnetization = 'total direction' , > ? fixed_magnetization(1) = 0.0, > ? fixed_magnetization(2) = 0.0, > ? fixed_magnetization(3) = 1.0, > > > If it is v.>4.2, then a > Are you sure that this is what you want? > From the Doc/INPUT_PW: > ?? ? ? ? ? ? ? ? ? 'total direction': > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? the angle theta of the total magnetization > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? with the z axis (theta = > fixed_magnetization(3)) > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? is constrained: > > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? LAMBDA * ( arccos(magnetization(3)/mag_tot) - > theta )**2 > > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? where mag_tot is the modulus of the total > magnetization. > Then?fixed_magnetization(3) = 1.0 does not correspond to the magnetization > along the z axis (but you should reach the corresponding constrained > solution anyway, even if different from what you actually want). > Can you please specify which version of the code you've been using? > Could you try to compare v.4.1.1 with v.4.3.1 (using the correct value for > theta=fixed_magnetization(3)) > The constraining potential implemented is different: in the most recent > version it should work also for theta=90? (magnetization along x), while in > the previous you could get into troubles, since it was defined as: > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? LAMBDA * ( magnetization(1) - > magnetization(3)*tan(theta) )**2 > > Also convergency should be better in the 4.3.1, though I'm not sure of that. > You should try to start with local magnetizations on Pt and Fe close to the > desired target direction. It would be nice if you perform this test. > Also, reporting only the total energy oscillations is not that useful. You > should at least report the magnitude and angles of the total magnetization > while the calculation is going. > Further advice: from your input, perhaps degauss=0.02 is not enough to get > accurate magnetizations. I would use at least 0.01, better 0.005. > > HTH > > GS > > However I can not reach total energy convergence and it looks like I > still have direction oscillation of MM. > > What can be done to resolve this problem? > > Thank you in advance. > > The complete input file for MM||z is and energy accuracy output file > are attached. > > German Samolyuk, > ORNL, USA > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From syuva2987 at gmail.com Tue Jun 14 03:26:10 2011 From: syuva2987 at gmail.com (yuva rani) Date: Tue, 14 Jun 2011 06:56:10 +0530 Subject: [Pw_forum] Dimensions dont match In-Reply-To: References: Message-ID: On 6/13/11, swapnil chandratre wrote: > Hi, > > I am trying to run berry phase calculation, the 'scf' calculation works fine > and the results converge, but the nscf calculations gives me the following > result though I dont change the ecutwfc and the cell parameters. What could > be the error ?? > > *from read_rho_xml : error # 1* > * dimensions do not match* > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > From syuva2987 at gmail.com Tue Jun 14 03:56:45 2011 From: syuva2987 at gmail.com (yuva rani) Date: Tue, 14 Jun 2011 07:26:45 +0530 Subject: [Pw_forum] Constraints Message-ID: Hi, thank for your suggestion. But still I am not clear for constraining the parameters. I have attached the input file for aluminium pentacene stack with 148 atoms. I need to constraint the interplanar distance between the top layer of aluminium and pentacene stack during relaxaton. So please give me the conditions used for such constraints. I also have another question about K_points. Give me the suggestion of how to set the k_points for the system we contructed. Thanks in advance. -------------- next part -------------- #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/$.*$\/.*/\1/'` # extract pathname EXAMPLE_DIR=`pwd` # check whether ECHO has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi # function to test the exit status of a job . ../check_failure.sh $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x to compute the equilibrium geometry" $ECHO "of a simple molecule, alpen." $ECHO "In the latter case the relaxation is performed in two ways:" $ECHO "1) using the quasi-Newton BFGS algorithm" $ECHO "2) using a damped dynamics algorithm." # set the needed environment variables #. ../environment_variables # required executables and pseudopotentials BIN_LIST="pw.x" PSEUDO_LIST=" Al.pz-vbc.UPF H.pz-vbc.UPF C.pz-vbc.UPF " $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # for parallel calculation PARA_PREFIX="mpiexec -np 8" PARA_POSTFIX="-npool 4" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # self-consistent calculation cat > alpen148.rx.in << EOF &CONTROL calculation = "relax", nstep = 200, pseudo_dir = "$PSEUDO_DIR", outdir = "$TMP_DIR", / &SYSTEM ibrav = 8, celldm(1) = 16, celldm(2) = 0.5, celldm(3) = 1.77, nat = 148, ntyp = 3, ecutwfc = 12.D0, occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.05D0, / &ELECTRONS electron_maxstep = 700 conv_thr = 1.D-6, mixing_beta = 0.3D0, / &IONS bfgs_ndim = 3, / ATOMIC_SPECIES Al 1.00 Al.pz-vbc.UPF H 1.00 H.pz-vbc.UPF C 1.00 C.pz-vbc.UPF ATOMIC_POSITIONS {bohr} Al 11.039040 5.580000 24.296861 Al 15.088000 5.580000 24.296861 Al 2.940000 5.580000 24.296861 Al 6.988960 5.580000 24.296861 Al 11.039040 5.580000 0.000000 Al 15.088000 5.580000 0.000000 Al 2.940000 5.580000 0.000000 Al 6.988960 5.580000 0.000000 Al 11.039040 5.580000 4.050043 Al 15.088000 5.580000 4.050043 Al 2.940000 5.580000 4.050043 Al 6.988960 5.580000 4.050043 Al 11.039040 5.580000 8.098954 Al 15.088000 5.580000 8.098954 Al 2.940000 5.580000 8.098954 Al 6.988960 5.580000 8.098954 Al 11.039040 5.580000 12.148997 Al 15.088000 5.580000 12.148997 Al 2.940000 5.580000 12.148997 Al 6.988960 5.580000 12.148997 Al 11.039040 5.580000 16.197907 Al 15.088000 5.580000 16.197907 Al 2.940000 5.580000 16.197907 Al 6.988960 5.580000 16.197907 Al 11.039040 5.580000 20.247101 Al 15.088000 5.580000 20.247101 Al 2.940000 5.580000 20.247101 Al 6.988960 5.580000 20.247101 Al 13.063040 3.555040 24.296861 Al 0.915040 3.555040 24.296861 Al 4.964000 3.555040 24.296861 Al 9.013920 3.555040 24.296861 Al 13.063040 3.555040 0.000000 Al 0.915040 3.555040 0.000000 Al 4.964000 3.555040 0.000000 Al 9.013920 3.555040 0.000000 Al 13.063040 3.555040 4.050043 Al 0.915040 3.555040 4.050043 Al 4.964000 3.555040 4.050043 Al 9.013920 3.555040 4.050043 Al 13.063040 3.555040 8.098954 Al 0.915040 3.555040 8.098954 Al 4.964000 3.555040 8.098954 Al 9.013920 3.555040 8.098954 Al 13.063040 3.555040 12.148997 Al 0.915040 3.555040 12.148997 Al 4.964000 3.555040 12.148997 Al 9.013920 3.555040 12.148997 Al 13.063040 3.555040 16.197907 Al 0.915040 3.555040 16.197907 Al 4.964000 3.555040 16.197907 Al 9.013920 3.555040 16.197907 Al 13.063040 3.555040 20.247101 Al 0.915040 3.555040 20.247101 Al 4.964000 3.555040 20.247101 Al 9.013920 3.555040 20.247101 Al 11.039040 3.555040 26.297102 Al 15.088000 3.555040 26.297102 Al 2.940000 3.555040 26.297102 Al 6.988960 3.555040 26.297102 Al 11.039040 3.555040 2.024880 Al 15.088000 3.555040 2.024880 Al 2.940000 3.555040 2.024880 Al 6.988960 3.555040 2.024880 Al 11.039040 3.555040 6.074074 Al 15.088000 3.555040 6.074074 Al 2.940000 3.555040 6.074074 Al 6.988960 3.555040 6.074074 Al 11.039040 3.555040 10.124117 Al 15.088000 3.555040 10.124117 Al 2.940000 3.555040 10.124117 Al 6.988960 3.555040 10.124117 Al 11.039040 3.555040 14.173027 Al 15.088000 3.555040 14.173027 Al 2.940000 3.555040 14.173027 Al 6.988960 3.555040 14.173027 Al 11.039040 3.555040 18.223070 Al 15.088000 3.555040 18.223070 Al 2.940000 3.555040 18.223070 Al 6.988960 3.555040 18.223070 Al 11.039040 3.555040 22.271981 Al 15.088000 3.555040 22.271981 Al 2.940000 3.555040 22.271981 Al 6.988960 3.555040 22.271981 Al 13.063040 5.580000 26.297102 Al 0.915040 5.580000 26.297102 Al 4.964000 5.580000 26.297102 Al 9.013920 5.580000 26.297102 Al 13.063040 5.580000 2.024880 Al 0.915040 5.580000 2.024880 Al 4.964000 5.580000 2.024880 Al 9.013920 5.580000 2.024880 Al 13.063040 5.580000 6.074074 Al 0.915040 5.580000 6.074074 Al 4.964000 5.580000 6.074074 Al 9.013920 5.580000 6.074074 Al 13.063040 5.580000 10.124117 Al 0.915040 5.580000 10.124117 Al 4.964000 5.580000 10.124117 Al 9.013920 5.580000 10.124117 Al 13.063040 5.580000 14.173027 Al 0.915040 5.580000 14.173027 Al 4.964000 5.580000 14.173027 Al 9.013920 5.580000 14.173027 Al 13.063040 5.580000 18.223070 Al 0.915040 5.580000 18.223070 Al 4.964000 5.580000 18.223070 Al 9.013920 5.580000 18.223070 Al 13.063040 5.580000 22.271981 Al 0.915040 5.580000 22.271981 Al 4.964000 5.580000 22.271981 Al 9.013920 5.580000 22.271981 C 5.627040 0.000000 22.367986 C 4.193920 0.000000 22.362888 C 6.326080 0.000000 21.194971 C 5.647040 0.000000 19.929067 C 4.192000 0.000000 19.923970 C 3.504960 0.000000 21.183926 C 6.332000 0.000000 18.720936 C 5.657920 0.000000 17.477122 C 4.200960 0.000000 17.472024 C 3.516960 0.000000 18.709891 C 6.343040 0.000000 16.253131 C 5.667040 0.000000 15.024043 C 4.210080 0.000000 15.018946 C 3.524960 0.000000 16.242086 C 6.351040 0.000000 13.785043 C 5.676000 0.000000 12.572098 C 4.220000 0.000000 12.565867 C 3.535040 0.000000 13.775131 C 6.364000 0.000000 11.311008 C 5.675040 0.000000 10.132046 C 4.240960 0.000000 10.126949 C 3.542080 0.000000 11.299963 H 6.155040 0.000000 23.318971 H 3.660000 0.000000 23.309059 H 7.412960 0.000000 21.196104 H 2.416960 0.000000 21.177979 H 7.420960 0.000000 18.724901 H 2.428000 0.000000 18.705926 H 7.431040 0.000000 16.257096 H 2.436960 0.000000 16.238122 H 7.440000 0.000000 13.789008 H 2.447040 0.000000 13.770883 H 7.451040 0.000000 11.318088 H 6.208960 0.000000 9.185875 H 3.713920 0.000000 9.177096 H 2.455040 0.000000 11.297981 K_POINTS 3 0.125 0.125 0.0 1.0 0.125 0.375 0.0 2.0 0.375 0.375 0.0 1.0 EOF $ECHO " running the geometry relaxation for alpen...\c" $PW_COMMAND < alpen148.rx.in > alpen148.rx.out check_failure $? $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" From cwandtj at gmail.com Tue Jun 14 04:27:36 2011 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Mon, 13 Jun 2011 22:27:36 -0400 Subject: [Pw_forum] Required modifications for restarting NEB in QE V.4.3 Message-ID: <000301cc2a3a$a1ef5c30$e5ce1490$@gmail.com> Dear QE users, I need your help in figuring out how I can restart NEB calculations in new QE V.4.3. In particular, - As an initial step, based on advice from Dr. Lorenzo Paulatto (http://www.quantum-espresso.org/user_guide/node29.html), all atoms except moving (or problematic) atom are all fixed ( by adding 0 0 0 after coordination of each atom) and NEB calculation was performed. For running job, I used a single input file with command-line options "neb.x -inp ". Luckily, I got converged images. - For next step, I needed to let all atoms for each image be relaxed. To do so, a. I modified initial input file (which contains both neb.dat and pw_*.in files) as 0 0 0 --> 1 1 1 and added restart_mode = 'restart', line. This didn't work. What I mean by this didn't work is that 0 0 0 was not changed to 1 1 1. b. I modified *.path as 0 0 0 --> 1 1 1. This also didn't work. Same as case a. c. I modified pw_*.in as 0 0 0 --> 1 1 1. Now, it looks like working fine. What I did to check whether the job is working fine is to see whether coordinates in PW.out of each image directory are followed by 0 0 0 or not. My questions are: 1. "Exactly", what kind of files should be modified to restart NEB calculations in new QE? (especially, 0 0 0-->1 1 1) 2. If I made mistakes in my calculations, which parts do I need to modify? 3. Any additional suggestions? ++++++++++++++++++++++++++++++++++++++ Chan-Woo Lee, Ph. D. Department of Chemistry, University of Pennsylvania 231 South 34th Street, Philadelphia, PA 19104-6323 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110613/b5c081be/attachment.htm From m.g.p.krishna at chem.leidenuniv.nl Tue Jun 14 04:49:13 2011 From: m.g.p.krishna at chem.leidenuniv.nl (m.g.p.krishna at chem.leidenuniv.nl) Date: Tue, 14 Jun 2011 04:49:13 +0200 Subject: [Pw_forum] Constraints Message-ID: <20110614044913.23611ks90rig4rhl@webmail.chem.leidenuniv.nl> yuva: there are some quick answer... Relaxation: you can use FLAGS in atoms to relax/not relax in a particular Cartesian direction. example: Al 11.039040 5.580000 24.296861 0 0 1, means that Aluminium is fixed EXCEPT in the Z direction. So it will relax on Z direction. In your case I suggest to use this kind of relaxation for every atom with a fixed Constraint on bond lengths (see previous posts of mine). KPoints: I, generally, use 'automatic' K points which is a kind of Monkhorst-Pack grid (more genereic). Suppose you have orthorhombic cell (a,b,c) where the magnitudes are (a=b < c), then I will use more Kpoints in a and b direction and less kpoints in c direction. Since Kpoints are defined in the reciprocal space (say, a'b'c' where magnitudes are a'b' > c'), you should use more k points to span the necessery irrep. areas in that reciproal space of a'b'c'. simply You can start with (see manual) K_POINTS automatic nx ny nz shiftx shifty shifty It is a good idea to visualize your supercell prior to put some values in nx,... By the way why you are using a BASH script? It was in QE package just to make tests quite smoothly/interactively. So pls use a simple *.in file which contains the input-data BETWEEN cat > alpen148.rx.in << EOF to EOF (bottom, near to Kpoints...) good luck Krishna Mohan GP Center for Superfunctional Materials POSTECH Sotuh Korea. From sclauzer at sissa.it Tue Jun 14 09:41:10 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 14 Jun 2011 09:41:10 +0200 Subject: [Pw_forum] Fwd: pwscf: energy convergence of noncollinear with spin-orbit calculations, withdraw question In-Reply-To: References:

Message-ID: In the first message you were speaking about fixing the total magnetization, here you do something different. Anyway I'm happy for you that you could converge the calculations. It's a bit curious that you get converge only with nosym=true. What is the symmetry found by the code at the beginning of the run? Il giorno 13/giu/2011, alle ore 21.39, German Samolyuk ha scritto: > Hello Gabriele, > > Thank you for your response and advices. > > I used version 4.2.1 > > the actual (final) input contains instructions: > > for magnetization along z-direction > > starting_magnetization(1) = 0.1, > starting_magnetization(2) = 0.4, > noncolin = .true. , > angle1(1) = 0, > angle1(2) = 0, > angle2(1) = 0, > angle2(2) = 0, > lspinorb = .true. , > constrained_magnetization = 'atomic direction' , > lambda = 0.3, > nosym = .true., > > and magnetization perpendicular to z-direction > > starting_magnetization(1) = 0.1, > starting_magnetization(2) = 0.4, > noncolin = .true. , > angle1(1) = 90, > angle1(2) = 90, > angle2(1) = 0, > angle2(2) = 0, > lspinorb = .true. , > constrained_magnetization = 'atomic direction' , > lambda = 0.3, > nosym = .true., > > the resulting energies looks reasonable and convergence is really fast. The constraint (penalty) energy should be almost zero at convergence. Could you obtain that with such a small lambda? Regards, Gabriele > > Thank you for advice with degauss value. I'll check dependence from it. > > Best, > > German > > > On Wed, Jun 8, 2011 at 3:55 AM, Gabriele Sclauzero wrote: >> Hello German, >> Il giorno 01/giu/2011, alle ore 23.02, German Samolyuk ha scritto: >> >> I withdraw my question. It works with nosym=true. >> German >> >> >> ---------- Forwarded message ---------- >> From: German Samolyuk >> Date: Wed, May 18, 2011 at 10:25 AM >> Subject: pwscf: energy convergence of noncollinear with spin-orbit >> calculations >> To: PWSCF Forum >> >> >> Dear qe users, >> >> I'm trying to calculate total energy of artificial FCC PtFe compound >> with magnetic moment (MM) along z- and x-directionsi (MAE). >> >> In order to supress oscillation of moment direction I used for MM||z >> calculation >> input instructions >> >> constrained_magnetization = 'total direction' , >> fixed_magnetization(1) = 0.0, >> fixed_magnetization(2) = 0.0, >> fixed_magnetization(3) = 1.0, >> >> >> If it is v.>4.2, then a >> Are you sure that this is what you want? >> From the Doc/INPUT_PW: >> 'total direction': >> the angle theta of the total magnetization >> with the z axis (theta = >> fixed_magnetization(3)) >> is constrained: >> >> LAMBDA * ( arccos(magnetization(3)/mag_tot) - >> theta )**2 >> >> where mag_tot is the modulus of the total >> magnetization. >> Then fixed_magnetization(3) = 1.0 does not correspond to the magnetization >> along the z axis (but you should reach the corresponding constrained >> solution anyway, even if different from what you actually want). >> Can you please specify which version of the code you've been using? >> Could you try to compare v.4.1.1 with v.4.3.1 (using the correct value for >> theta=fixed_magnetization(3)) >> The constraining potential implemented is different: in the most recent >> version it should work also for theta=90? (magnetization along x), while in >> the previous you could get into troubles, since it was defined as: >> LAMBDA * ( magnetization(1) - >> magnetization(3)*tan(theta) )**2 >> >> Also convergency should be better in the 4.3.1, though I'm not sure of that. >> You should try to start with local magnetizations on Pt and Fe close to the >> desired target direction. It would be nice if you perform this test. >> Also, reporting only the total energy oscillations is not that useful. You >> should at least report the magnitude and angles of the total magnetization >> while the calculation is going. >> Further advice: from your input, perhaps degauss=0.02 is not enough to get >> accurate magnetizations. I would use at least 0.01, better 0.005. >> >> HTH >> >> GS >> >> However I can not reach total energy convergence and it looks like I >> still have direction oscillation of MM. >> >> What can be done to resolve this problem? >> >> Thank you in advance. >> >> The complete input file for MM||z is and energy accuracy output file >> are attached. >> >> German Samolyuk, >> ORNL, USA >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> _______________________________________________ >> 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 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/a3a56780/attachment-0001.htm From baroni at sissa.it Tue Jun 14 09:45:52 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 14 Jun 2011 09:45:52 +0200 Subject: [Pw_forum] Phonon calculation of magnetic system In-Reply-To: References: Message-ID: Sounds like a weird question: "is it necessary to be more accurate, rather than less?" DFPT in magnetic systems has been implemented by A. Dal Corso including standard LSDA/GGA and spin-orbit interactions. I've heard somebody has been working on DFPT+U, but I am not sure of the status of the project This being said, you better answer your question, when and where you can: just do a few sample calculations including and excluding magnetic interactions and judge by yourself what is best ... Stefano B On Jun 13, 2011, at 11:41 AM, mayank gupta wrote: > Dear Users > > Is it necessary to include magnetic interaction (spin) and Hubbard > term for phonon calculation of a magnetic system. > Thanks > > > > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: 022-25595606 > Home: 9920397437 / 9869834437 > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/5b0d4937/attachment.htm From baroni at sissa.it Tue Jun 14 09:47:09 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 14 Jun 2011 09:47:09 +0200 Subject: [Pw_forum] How to calculate the energy barrier for nanoribbon? In-Reply-To: <4DF41FE7.3090600@yahoo.com.cn> References: <4DF41FE7.3090600@yahoo.com.cn> Message-ID: Forgive my ignorance: what do you mean by "energy barrier"? Barriere between what and what? SB On Jun 12, 2011, at 4:09 AM, Hongsheng Zhao wrote: > Hi all, > > I've read many papers which calculate the energy barrier for > nanoribbon, but all of these papers don't give the formulae to do this > calculatation. Could someone please give me some hints on the formula > to calculate the energy barrier for our system? Thanks in advance. > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/5d382da0/attachment.htm From baroni at sissa.it Tue Jun 14 09:49:58 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 14 Jun 2011 09:49:58 +0200 Subject: [Pw_forum] Constraint optimization: how to fix coordination number? In-Reply-To: <20110612044111.34992seijmijq893@webmail.chem.leidenuniv.nl> References: <20110612044111.34992seijmijq893@webmail.chem.leidenuniv.nl> Message-ID: <9531D6B5-026C-4261-8E91-AA7A23349515@sissa.it> I would introduce a penalty function such as A(N-C)**2, where C is the constraining coordination, and N the effective number of neighbors, calculated using your favorite definition. Not sure this has ever been implemented in QE, but it should not be a difficult task ... SB On Jun 12, 2011, at 4:41 AM, m.g.p.krishna at chem.leidenuniv.nl wrote: > Dear List, > > In many situations, one need to constraint the .coordination. number > of atoms, so that, say, a chemically adsorbed molecule wont move away > from the reactant > surface (ie. to keep coordination number as a constant, bonds never > break w.r.t. a cutoff radius). > > In order to test that constraint optimization in Quantum Espresso > [4.3], I use an ethane molecule as test case. > > My doubt: > How can one constraint the .coordination number. of an atom (so that > the bonds of that particular atom, will remain the same before and > after the optimizatio > n, regardless of the ions displacements). > > Please note that in my test.in I used a shorter C-C bond length > (1.3Ang.) which is supposed to increase and it didn.t. I used > 'atom_coord' and 'type_coord' > and in all time it tried to keep the bond fixed! > > Can any one give an idea on how to fix the coordination number in a > geometry optimization? Hope some one can also explain why it always > fixes the bondlength > and not following the <0 0 0> and <0 0 1> flags? > > Please also see below for my test run, > > Thanks in advance, > > Krishna Mohan GP > Center for Superfunctional Materials > POSTECH > Sotuh Korea. > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = './' , > pseudo_dir = '/home01/a202kks/krishna/myPSP' , > prefix = 'Final_' , > verbosity = 'high' , > nstep = 50 , > tprnfor = .true., > / > &SYSTEM > ibrav = 0, > celldm(1)= 1., > nat = 8, > ntyp = 2, > ecutwfc = 20 , > nosym = .true. , > occupations = 'smearing', > smearing = 'gauss', > degauss = 0.002, > / > &ELECTRONS > / > &IONS > ion_dynamics='damp', > / > > CONSTRAINTS > 1 0.5 > 'atom_coord' 5 1 3.5 0.5 > > CELL_PARAMETERS Cubic > 12 0 0 > 0 12 0 > 0 0 12 > ATOMIC_SPECIES > C 12.0107 C.pbe-paw_kj.UPF > H 1.00674 H.pbe-paw_kj.UPF > K_POINTS automatic > 3 3 3 0 0 0 > ATOMIC_POSITIONS angstrom > C -0.00000000 -0.00000000 0.6500000 0 0 1 > H 0.00000000 1.00880567 1.0066666 0 0 0 > H 0.87365134 -0.50440284 1.0066666 0 0 0 > H -0.87365134 -0.50440284 1.0066666 0 0 0 > C -0.00000000 -0.00000000 -0.6500000 0 0 1 > H 0.87365134 0.50440284 -1.0066666 0 0 0 > H -0.87365134 0.50440284 -1.0066666 0 0 0 > H -0.00000000 -1.00880567 -1.0066666 0 0 0 > > ----------------------------------------------------------------------------- > After geometry optimization, I Got: > Damped Dynamics: convergence achieved in 11 steps > . . . . . . > Begin final coordinates > new unit-cell volume = 1728.00000 a.u.^3 ( 256.06318 Ang^3 ) > > CELL_PARAMETERS (alat= 1.00000000) > 12.000000000 0.000000000 0.000000000 > 0.000000000 12.000000000 0.000000000 > 0.000000000 0.000000000 12.000000000 > > ATOMIC_POSITIONS (angstrom) > C 0.000000000 -0.001564190 0.649998147 > H 0.000000000 1.058348951 1.147005976 > H 0.919069360 -0.531092625 1.145321656 > H -0.919069360 -0.531092625 1.145321656 > C 0.000000000 0.001564190 -0.649998147 > H 0.919069360 0.531092625 -1.145321656 > H -0.919069360 0.531092625 -1.145321656 > H 0.000000000 -1.058348951 -1.147005976 > End final coordinates > > > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/fc771ca2/attachment-0001.htm From baroni at sissa.it Tue Jun 14 09:50:55 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 14 Jun 2011 09:50:55 +0200 Subject: [Pw_forum] How we can create Supercell from atomic positions of unit cell? In-Reply-To: <776616.48310.qm@web65411.mail.ac4.yahoo.com> References: <776616.48310.qm@web65411.mail.ac4.yahoo.com> Message-ID: Give xcrysden a try SB On Jun 13, 2011, at 2:44 PM, zafar rasheed wrote: > > > Hi > > I am PhD scholar and using Quantum Espresso Software. I do not know how to create supercell from unit cell. I do not know how to set CELL PARAMETERS option when we set ibrav=0. We actually want to create nanotube. I hope that you will guide me about this. > > Best Regards > > Muhammad zafar > > PhD scholar > > The Islamia University of Bahawalpur, Pakistan > > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/e7857d63/attachment.htm From dalcorso at sissa.it Tue Jun 14 09:51:13 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 14 Jun 2011 09:51:13 +0200 Subject: [Pw_forum] Phonon calculation of magnetic system In-Reply-To: References:

Message-ID: <1308037873.3997.2.camel@ulisse.cm.sissa.it> The present status of the phonon code is written at the beginning of the PH/phonon.f90 file: ! ... Presently implemented: ! ... dynamical matrix (q/=0) NC [4], US [4], PAW [4] ! ... dynamical matrix (q=0) NC [5], US [5], PAW [4] ! ... dielectric constant NC [5], US [5], PAW [3] ! ... born effective charges NC [5], US [5], PAW [3] ! ... polarizability (iu) NC [2], US [2] ! ... electron-phonon NC [3], US [3] ! ... electro-optic NC [1] ! ... raman tensor NC [1] ! ! NC = norm conserving pseudopotentials ! US = ultrasoft pseudopotentials ! PAW = projector augmented-wave ! [1] LDA, ! [2] [1] + GGA, ! [3] [2] + LSDA/sGGA, ! [4] [3] + Spin-orbit/nonmagnetic, ! [5] [4] + Spin-orbit/magnetic (experimental when available) ! Not implemented in ph.x: ! [6] [5] + constraints on the magnetization ! [7] [6] + Hubbard U ! [8] [7] + Hybrid functionals ! [9] ? + External Electric field HTH, Andrea On Tue, 2011-06-14 at 09:45 +0200, Stefano Baroni wrote: > Sounds like a weird question: "is it necessary to be more accurate, > rather than less?" > DFPT in magnetic systems has been implemented by A. Dal Corso > including standard LSDA/GGA and spin-orbit interactions. > I've heard somebody has been working on DFPT+U, but I am not sure of > the status of the project > This being said, you better answer your question, when and where you > can: just do a few sample calculations including and excluding > magnetic interactions and judge by yourself what is best ... > Stefano B > > On Jun 13, 2011, at 11:41 AM, mayank gupta wrote: > > > Dear Users > > > > Is it necessary to include magnetic interaction (spin) and Hubbard > > term for phonon calculation of a magnetic system. > > Thanks > > > > > > > > Mayank > > > > BHABHA ATOMIC RESEARCH CENTER > > MUMBAI, INDIA > > Office: 022-25595606 > > Home: 9920397437 / 9869834437 > > _______________________________________________ > > 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://stefano.baroni.me [+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 -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From glapenna at iccom.cnr.it Tue Jun 14 15:15:09 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Tue, 14 Jun 2011 15:15:09 +0200 (CEST) Subject: [Pw_forum] Constraint optimization: how to fix coordination In-Reply-To: <20110613084223.12439bllg1135bnz@webmail.chem.leidenuniv.nl> References: <20110613084223.12439bllg1135bnz@webmail.chem.leidenuniv.nl> Message-ID: Even though be not the same thing, I would suggest to use a dynamical approach like metadynamics for restraining the coordination number (CN) close to a desired value, CN(reference). The current version of QE can use the PLUMED plugin: M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Parrinello. PLUMED: a portable plugin for free-energy calculations with molecular dynamics, Comp. Phys. Comm. 2009 vol. 180 (10) pp. 1961-1972. make plumed makes cp and pw with metadynamics. See the Plumed manual for its definition of coordination number. Using CN as a collective variable, given values of CN can be sampled according to an added given external weight. This latter can be constructed via metadynamics or, alternatively, can be assigned as a finite difference approximation to an external bias. In this latter case, the bias can be, for instance, harmonic and centered around the desired CN. Here below is the input for the Plumed plugin (plumed.dat): ## plumed.dat begins # Metadynamics with CV=coordination number of a Cu # ion (atom 1 in QE numbering) with O of water molecules # (atoms 2,3,4,..., n_wat+1=19+1=20) # d0=2 Ang, r0=0.5 Ang NOTE atomic order: QE output (pseudo-pot. order, then input) NOTE distance units: bohr NOTE energy units: Ha(CP); Ry(PW) #W_STRIDE must be larger than number of steps (no bias update) HILLS HEIGHT 0.0 W_STRIDE 1000000 COORD LIST NN 6 MM 12 D_0 3.779 R_0 0.945 SIGMA 0.35 solute-> 1 solute<- solvent-> LOOP 2 20 1 solvent<- PRINT W_STRIDE 10 GRID CV 1 MIN 0. MAX 10. NBIN 20 EXTERNAL NCV 1 CV 1 FILENAME uext.dat ENDMETA ##plumed.dat ends One can perform dynamics (both Born-Oppenheimer and Car-Parrinello) with the external harmonic bias uext.dat. #uext.dat begins #! FORCE 0 #! NVAR 1 #! TYPE 3 #! BIN 20 #! MIN 0.000000 #! MAX 10.000000 #! PBC 1 ... CN U=K/2(CN-CN(reference))^2 ... #uext.dat ends Choice of K and CN(reference) needs a careful calibration. Decreasing temperature provides a relaxed configuration. Due to the many possibilities for collective variables, I found the implementation quite useful in different fields. Giovanni La Penna ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From prayerz.omo at gmail.com Tue Jun 14 17:22:43 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Tue, 14 Jun 2011 11:22:43 -0400 Subject: [Pw_forum] Bug in v4.3.1's dos.x ? Message-ID: Hi, I got the following error when I used dos.x bundled with QE vs. 4.3.1 to try to obtain the dos for a nanowire. I don't think I am doing anything wrong since dos.x from QE vs. 4.2 works but you never can tell, so pls let me know if my input is in error. The scf was always performed with pw.x in QE vs. 4.3.1: ######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=-1) # ERROR IN: iotk_scan_dat (iotk_dat.spp:1002) # CVS Revision: 1.27 # Dat not found name=NON-PERIODIC_CELL_CORRECTION ######################################################################################################################## ERROR: 0031-250 task 0: Terminated ERROR: 0031-250 task 1: Terminated My input (dos.in): &INPUTPP prefix='nt12', outdir = './SCRATCH/', fildos='mydos.dat' Emin=-25.0, Emax=5.0, DeltaE=0.00350 degauss=0.0036764705882352945 / Grazie! o. Omololu AKIN-OJO Postdoctoral Fellow, International Centre for Theoretical Physics (ICTP) Trieste, Italy. -- ***************** Seek GOD! ************* From henod2001 at yahoo.com Tue Jun 14 18:33:51 2011 From: henod2001 at yahoo.com (henry odhiambo) Date: Tue, 14 Jun 2011 09:33:51 -0700 (PDT) Subject: [Pw_forum] commands Message-ID: <852446.31783.qm@web121013.mail.ne1.yahoo.com> I am a QUANTUM Espresso user. Please, can anyone tell me the commands for doing the following; 1. Making the charge density contour plot to be color (as opposed to a white and black plot). 2. Labelling the atoms in a charge density contour plot. Regards, Henry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/8ff0c5a8/attachment.htm From kucukben at sissa.it Tue Jun 14 19:41:23 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Tue, 14 Jun 2011 19:41:23 +0200 Subject: [Pw_forum] Bug in v4.3.1's dos.x ? In-Reply-To: References: Message-ID: <20110614194123.85xvg3j17o4kcwoo@webmail.sissa.it> Dear Omololu Akin-Ojo, It is a known bug and fixed. You can update the version of the code you are using. It is not supposed to appear if consistent versions of pw is used for reading(post processing) and writing(tha actual calculation) the data.. Thanks for reporting. emine kucukbenli, phd student, sissa, italy. Quoting Omololu Akin-Ojo : > Hi, > > I got the following error when I used dos.x bundled with QE vs. 4.3.1 > to try to obtain the dos for a nanowire. I don't think I am doing > anything wrong since dos.x from QE vs. 4.2 works but you never can > tell, so pls let me know if my input is in error. The scf was always > performed with pw.x in QE vs. 4.3.1: > > ######################################################################################################################## > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=-1) > # ERROR IN: iotk_scan_dat (iotk_dat.spp:1002) > # CVS Revision: 1.27 > # Dat not found > name=NON-PERIODIC_CELL_CORRECTION > ######################################################################################################################## > ERROR: 0031-250 task 0: Terminated > ERROR: 0031-250 task 1: Terminated > > My input (dos.in): > &INPUTPP > prefix='nt12', > outdir = './SCRATCH/', > fildos='mydos.dat' > Emin=-25.0, > Emax=5.0, > DeltaE=0.00350 > degauss=0.0036764705882352945 > / > > Grazie! > > o. > > Omololu AKIN-OJO > Postdoctoral Fellow, > International Centre for Theoretical Physics (ICTP) > Trieste, Italy. > > > > > > > -- > ***************** Seek GOD! ************* > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From amin.torabi at gmail.com Tue Jun 14 20:08:31 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Tue, 14 Jun 2011 14:08:31 -0400 Subject: [Pw_forum] ecut vs energy In-Reply-To: References: Message-ID: Dear experts! Could you please have a look at my input file, attached to this email. My main problem is that I expect the total energy to converge at lower ecutwfc energy. ( or I am expecting too much?) ecut energy 25 -38.36026321 30 -38.44145201 35 -38.49537648 40 -38.53312799 45 -38.55904483 50 -38.57650475 55 -38.58840904 60 -38.59670631 65 -38.60253103 70 -38.60653038 75 -38.60918176 80 -38.61090436 85 -38.61200805 90 -38.61269007 95 -38.61308582 100 -38.61329742 Notes: 1. Do I have to be at the minimum structure to check for convergence of ecut vs energy, or I can check the convergency from a non-optimized structure? 2. I used USPP for one of my atoms and NCPP for the other atom, and set ecutrho = 10*ecutwfc... Many thanks in advance! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/36da66e6/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: input.rtf Type: application/rtf Size: 1686 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110614/36da66e6/attachment.rtf From faccin.giovani at gmail.com Tue Jun 14 20:39:26 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 14 Jun 2011 14:39:26 -0400 Subject: [Pw_forum] ecut vs energy In-Reply-To: References: Message-ID: Dear Amin, 1 - Convergence should not depend on the structure. You can check it for any reasonable structure (obviously if you push two atoms inside each other you'll be forcing your pseudopotential reliability, but for normal, not optimized structures, with reasonably low forces, should work fine). 2 - Your energy convergence table looks normal to me. The question you should now ask is: for the purpose you are doing your calculation, how much precision do you need? Is it 10^-1, 10^-2, 10^-3 Ry? That answer will define the value of ecut you have to use. Best, Giovani M. Faccin UFMS/Unicamp - Brazil 2011/6/14 Amin Torabi > Dear experts! > > Could you please have a look at my input file, attached to this email. > > My main problem is that I expect the total energy to converge at lower > ecutwfc energy. ( or I am expecting too much?) > > ecut energy > 25 -38.36026321 > 30 -38.44145201 > 35 -38.49537648 > 40 -38.53312799 > 45 -38.55904483 > 50 -38.57650475 > 55 -38.58840904 > 60 -38.59670631 > 65 -38.60253103 > 70 -38.60653038 > 75 -38.60918176 > 80 -38.61090436 > 85 -38.61200805 > 90 -38.61269007 > 95 -38.61308582 > 100 -38.61329742 > > > > Notes: > > 1. Do I have to be at the minimum structure to check for convergence of > ecut vs energy, or I can check the convergency from a non-optimized > structure? > > 2. I used USPP for one of my atoms and NCPP for the other atom, and set > ecutrho = 10*ecutwfc... > > > > Many thanks in advance! > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/8bb3e186/attachment.htm From gbocan at gmail.com Tue Jun 14 21:00:50 2011 From: gbocan at gmail.com (Gisela Bocan) Date: Tue, 14 Jun 2011 16:00:50 -0300 Subject: [Pw_forum] ecut vs energy In-Reply-To: References: Message-ID: Hi Amin, Do not know the problem you are addressing but wise people say that energy differences converge much faster than absolute energies. If you are after sth like, say, adsorption energies, you might do with checking energy vs ecut for them instead. Bye! Gisela. On Tue, Jun 14, 2011 at 3:08 PM, Amin Torabi wrote: > Dear experts! > > Could you please have a look at my input file, attached to this email. > > My main problem is that I expect the total energy to converge at lower > ecutwfc energy. ( or I am expecting too much?) > > ecut energy > 25 -38.36026321 > 30 -38.44145201 > 35 -38.49537648 > 40 -38.53312799 > 45 -38.55904483 > 50 -38.57650475 > 55 -38.58840904 > 60 -38.59670631 > 65 -38.60253103 > 70 -38.60653038 > 75 -38.60918176 > 80 -38.61090436 > 85 -38.61200805 > 90 -38.61269007 > 95 -38.61308582 > 100 -38.61329742 > > > > Notes: > > 1. Do I have to be at the minimum structure to check for convergence of > ecut vs energy, or I can check the convergency from a non-optimized > structure? > > 2. I used USPP for one of my atoms and NCPP for the other atom, and set > ecutrho = 10*ecutwfc... > > > > Many thanks in advance! > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110614/0b9ce1aa/attachment.htm From giannozz at democritos.it Tue Jun 14 22:47:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 14 Jun 2011 22:47:19 +0200 Subject: [Pw_forum] Dimensions dont match In-Reply-To: References: Message-ID: <39F72B91-81A8-4905-B350-6B3C322D671A@democritos.it> On Jun 13, 2011, at 16:31 , swapnil chandratre wrote: > I am trying to run berry phase calculation, the 'scf' calculation > works > fine and the results converge, but the nscf calculations gives me the > following result though I dont change the ecutwfc and the cell > parameters. > What could be the error ?? > > from read_rho_xml : error # 1 > dimensions do not match hard to say if you do not explain in detail what you have done. The error means that the FFT dimensions of the nscf calculation do not match what is read from the data file prodiced by the scf calculation. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From m.g.p.krishna at chem.leidenuniv.nl Wed Jun 15 06:22:17 2011 From: m.g.p.krishna at chem.leidenuniv.nl (m.g.p.krishna at chem.leidenuniv.nl) Date: Wed, 15 Jun 2011 06:22:17 +0200 Subject: [Pw_forum] Constraint optimization: how to fix coordination number? In-Reply-To: <20110612044111.34992seijmijq893@webmail.chem.leidenuniv.nl> References: <20110612044111.34992seijmijq893@webmail.chem.leidenuniv.nl> Message-ID: <20110615062217.1640151ugqq9uqnt@webmail.chem.leidenuniv.nl> Dear GL Penna Thanks for your suggestion and help. I will try, Since I have a QE version with PLUMED. But can you give a simple working example (QE and PLUMED input files) to demonstrate a simple constraint optimization ?(because I am not very familiar with PLUMED). I am sure that it will be very useful for QE community. thanks in advance Krishna Mohan GP From prayerz.omo at gmail.com Wed Jun 15 08:12:22 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Wed, 15 Jun 2011 02:12:22 -0400 Subject: [Pw_forum] Bug in v4.3.1's dos.x ? In-Reply-To: <20110614194123.85xvg3j17o4kcwoo@webmail.sissa.it> References: <20110614194123.85xvg3j17o4kcwoo@webmail.sissa.it> Message-ID: Thank you so much, Emine. I appreciate your response. I found I was actually using 4.2 for the the scf (not 4.3.1 as I earlier wrote/thought) and 4.3.1 for the dos.x. I will make changes in order to be consistent. Thanks again! o. On Tue, Jun 14, 2011 at 1:41 PM, Emine Kucukbenli wrote: > Dear Omololu Akin-Ojo, > It is a known bug and fixed. You can update the version of the code > you are using. > It is not supposed to appear if consistent versions of pw is used for > reading(post processing) and writing(tha actual calculation) the data.. > Thanks for reporting. > emine kucukbenli, phd student, sissa, italy. > > Quoting Omololu Akin-Ojo : > >> Hi, >> >> I got the following error when I used dos.x bundled with QE vs. 4.3.1 >> to try to obtain the dos for a nanowire. I don't think I am doing >> anything wrong since dos.x from QE vs. 4.2 works but you never can >> tell, so pls let me know if my input is in error. The scf was always >> performed with pw.x in QE vs. 4.3.1: >> >> ######################################################################################################################## >> # FROM IOTK LIBRARY, VERSION 1.2.0 >> # UNRECOVERABLE ERROR (ierr=-1) >> # ERROR IN: iotk_scan_dat (iotk_dat.spp:1002) >> # CVS Revision: 1.27 >> # Dat not found >> name=NON-PERIODIC_CELL_CORRECTION >> ######################################################################################################################## >> ERROR: 0031-250 ?task 0: Terminated >> ERROR: 0031-250 ?task 1: Terminated >> >> My input (dos.in): >> &INPUTPP >> ? ? prefix='nt12', >> ? ? ? outdir = './SCRATCH/', >> ? ? ? fildos='mydos.dat' >> ? ? ? Emin=-25.0, >> ? ? ? Emax=5.0, >> ? ? ? DeltaE=0.00350 >> ? ? ? degauss=0.0036764705882352945 >> ? ?/ >> >> Grazie! >> >> o. >> >> Omololu AKIN-OJO >> Postdoctoral Fellow, >> International Centre for Theoretical Physics (ICTP) >> Trieste, Italy. >> >> >> >> >> >> >> -- >> ***************** Seek GOD! ************* >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ---------------------------------------------------------------- > ? SISSA Webmail https://webmail.sissa.it/ > ? Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ***************** Seek GOD! ************* From sclauzer at sissa.it Wed Jun 15 10:03:05 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 15 Jun 2011 10:03:05 +0200 Subject: [Pw_forum] ecut vs energy In-Reply-To: References: Message-ID: <4A0FD0F9-60ED-406D-965C-68C8E50CF5C4@sissa.it> Dear Amin, I think that your convergence looks "slow" to you because your PP for H is norm-conserving: you'll need about 85 Ry to get a 1mRy accuracy, but that's not much surprise with a hard NCPP. I believe that by replacing the H PP with a corresponding USPP you could get convergence at a much lower energy. If instead you want to keep the NC PP for H, I think there's no need to use ecutrho=10*ecutwfc, since this is required only for the PP of B, which should converge at much lower ecutwfc (you could check this). Let's suppose that you need 35 Ry for B (hence you need to take an ecutrho of about 350 Ry), while 85 Ry are needed for H (therefore ecutrho=4*85=340 ~ 350): I believe that you can keep the ecutrho as low as 350 Ry (or 4*ecutwfc for higher ecutwfc) without any problem. HTH GS Il giorno 14/giu/2011, alle ore 20.08, Amin Torabi ha scritto: > Dear experts! > > Could you please have a look at my input file, attached to this email. > > My main problem is that I expect the total energy to converge at lower ecutwfc energy. ( or I am expecting too much?) > > ecut energy > 25 -38.36026321 > 30 -38.44145201 > 35 -38.49537648 > 40 -38.53312799 > 45 -38.55904483 > 50 -38.57650475 > 55 -38.58840904 > 60 -38.59670631 > 65 -38.60253103 > 70 -38.60653038 > 75 -38.60918176 > 80 -38.61090436 > 85 -38.61200805 > 90 -38.61269007 > 95 -38.61308582 > 100 -38.61329742 > > > > Notes: > > 1. Do I have to be at the minimum structure to check for convergence of ecut vs energy, or I can check the convergency from a non-optimized structure? > > 2. I used USPP for one of my atoms and NCPP for the other atom, and set ecutrho = 10*ecutwfc... > > > > Many thanks in advance! > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/fa740df0/attachment.htm From yhho at pub.iams.sinica.edu.tw Wed Jun 15 11:28:03 2011 From: yhho at pub.iams.sinica.edu.tw (yhho) Date: Wed, 15 Jun 2011 17:28:03 +0800 Subject: [Pw_forum] graphene phonon dispersion Message-ID: <003601cc2b3e$8690b920$61706d8c@mychatd6d7d1f2> Dear all, I have tried many different way as I saw on pw_forum but I still can't get a good result which is similar to tthe figure from paper I found. In this figure, red line is what I got and gray line is from reference ref: Physics ReportsVolume 409, Issue 2, March 2005, Pages 47-99 http://imageshack.us/photo/my-images/853/c2phdosvc1.jpg/ I also found another paper shows a little different phonon dispersion figure of graphite: red line is my result and gray line is from reference ref: 10.1103/PhysRevLett.92.075501 http://imageshack.us/photo/my-images/851/c2phdosvc3.jpg/ I have no idea to improve this because I have tried vc-relax and relax and the structure didn't change a lot due to that. And I also tried increasing q-points, there's no much different from the fewer q-points results. Please give me some suggestion. Thanks very much. input file (scf.in) &control calculation ='scf' restart_mode ='from_scratch' pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' outdir ='./' prefix ='AuC' / &system ibrav =0 celldm(1)= 4.6514 nat = 2 , ntyp = 1 , ecutwfc = 24.0, ecutrho = 240.0, occupations ='smearing', degauss= 0.02 / &electrons diagonalization= 'david' conv_thr = 1.0d-12 mixing_beta = 0.7 / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF CELL_PARAMETERS (alat) 0.984533834 0.000000000 0.000000000 -0.492266917 0.852631311 0.000000000 0.000000000 0.000000000 5.328569075 ATOMIC_POSITIONS {crystal} C 0.481112321 1.128944752 0.517391300 C 0.814471461 0.795556146 0.517391309 K_POINTS 7 0.0000000 0.0000000 0.0000000 0.1250000 0.0000000 0.2932100 0.0000000 0.2500000 0.0000000 -0.5864199 0.0000000 0.1250000 0.2539273 0.1466050 0.0000000 0.5000000 0.2539273 0.4398150 0.0000000 0.5000000 -0.5078546 -0.2932100 0.0000000 0.2500000 -0.5078546 0.0000000 0.0000000 0.2500000 (ph.in) phonons of AuC &inputph tr2_ph=1.0d-12, ldisp=.true., nq1=4, nq2=4, nq3=1 amass(1)= 12.0107 prefix='AuC', outdir='./' fildyn='AuC.dyn', / -- Yu-Han Ho Research Assistant Institute of Atomic and Molecular Sciences(IAMS), lab503 No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan Tel: 886-2-2362-0212 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/2418f5b0/attachment.htm From yccheng.nju at gmail.com Wed Jun 15 13:11:42 2011 From: yccheng.nju at gmail.com (yccheng.nju) Date: Wed, 15 Jun 2011 14:11:42 +0300 Subject: [Pw_forum] graphene phonon dispersion In-Reply-To: <003601cc2b3e$8690b920$61706d8c@mychatd6d7d1f2> References: <003601cc2b3e$8690b920$61706d8c@mychatd6d7d1f2> Message-ID: <4DF8936E.7090107@gmail.com> Why dont you show us your input file for matdyn.x ? I think it is due to the wrong q-point setting. On 15/06/11 12:28, yhho wrote: > Dear all, > I have tried many different way as I saw on pw_forum > but I still can't get a good result which is similar to tthe figure > from paper I found. > In this figure, red line is what I got and gray line is from reference > ref: *Physics Reports* > *Volume 409, > Issue 2* > *, > March 2005, Pages 47-99* > http://imageshack.us/photo/my-images/853/c2phdosvc1.jpg/ > I also found another paper shows a little different phonon dispersion > figure of graphite: > red line is my result and gray line is from reference > ref: *10.1103/PhysRevLett.92.075501* > http://imageshack.us/photo/my-images/851/c2phdosvc3.jpg/ > I have no idea to improve this > because I have tried vc-relax and relax and the structure didn't > change a lot due to that. > And I also tried increasing q-points, there's no much different from > the fewer q-points results. > Please give me some suggestion. Thanks very much. > *input file* > *(scf.in)* > &control > calculation ='scf' > restart_mode ='from_scratch' > pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' > outdir ='./' > prefix ='AuC' > / > &system > ibrav =0 > celldm(1)= 4.6514 > nat = 2 , > ntyp = 1 , > ecutwfc = 24.0, > ecutrho = 240.0, > occupations ='smearing', > degauss= 0.02 > / > &electrons > diagonalization= 'david' > conv_thr = 1.0d-12 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF > CELL_PARAMETERS (alat) > 0.984533834 0.000000000 0.000000000 > -0.492266917 0.852631311 0.000000000 > 0.000000000 0.000000000 5.328569075 > ATOMIC_POSITIONS {crystal} > C 0.481112321 1.128944752 0.517391300 > C 0.814471461 0.795556146 0.517391309 > K_POINTS > 7 > 0.0000000 0.0000000 0.0000000 0.1250000 > 0.0000000 0.2932100 0.0000000 0.2500000 > 0.0000000 -0.5864199 0.0000000 0.1250000 > 0.2539273 0.1466050 0.0000000 0.5000000 > 0.2539273 0.4398150 0.0000000 0.5000000 > -0.5078546 -0.2932100 0.0000000 0.2500000 > -0.5078546 0.0000000 0.0000000 0.2500000 > (*ph.in*) > phonons of AuC > &inputph > tr2_ph=1.0d-12, > ldisp=.true., > nq1=4, nq2=4, nq3=1 > amass(1)= 12.0107 > prefix='AuC', > outdir='./' > fildyn='AuC.dyn', > / > -- > Yu-Han Ho > Research Assistant > Institute of Atomic and Molecular Sciences(IAMS), lab503 > No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan > Tel: 886-2-2362-0212 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/f927ed65/attachment-0001.htm From s.m.rezaeisani at gmail.com Wed Jun 15 14:31:23 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Wed, 15 Jun 2011 17:01:23 +0430 Subject: [Pw_forum] vc-relax runnig error Message-ID: Dear all When I try to run vc-relax calculation on a cluster scf doesn't start and I get this error: task # 126 from n_plane_waves : error # 1 No PWs ! While there is no error when I run it on my local machine. What's the problem? Best regards -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/a8580004/attachment.htm From lmartinsamos at gmail.com Wed Jun 15 14:38:57 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 15 Jun 2011 14:38:57 +0200 Subject: [Pw_forum] NEB error In-Reply-To: References: <5682E80C36D6D449B2D4552B5884AE57127801CB7B@UQEXMB03.soe.uq.edu.au> <3DB1BB68-5ED9-4F5F-BAB3-1E767FF82EC1@democritos.it>

Message-ID: Dear Jin, re-examining neb.f90 I found that a mp_bcast was missing. Can you please, try the attached neb.f90, and tell me if it is working now? thank you for helping us in improving the portability Layla 2011/6/14 Jin Qu > Dear Layla, it is correct that I run the calculation as "neb.x -inp input > > out" as you mentioned. > > Many thanks > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/43e5590e/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: neb.f90 Type: text/x-fortran Size: 5738 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110615/43e5590e/attachment.bin From syuva2987 at gmail.com Wed Jun 15 16:40:04 2011 From: syuva2987 at gmail.com (yuva rani) Date: Wed, 15 Jun 2011 20:10:04 +0530 Subject: [Pw_forum] Constraints In-Reply-To: <20110614044913.23611ks90rig4rhl@webmail.chem.leidenuniv.nl> References: <20110614044913.23611ks90rig4rhl@webmail.chem.leidenuniv.nl> Message-ID: Thank you sir. But I did not get clear idea about FLAGS. So please could you attach me the example file using constraints. Thanks in advance On 6/14/11, m.g.p.krishna at chem.leidenuniv.nl wrote: > yuva: there are some quick answer... > > Relaxation: > you can use FLAGS in atoms to relax/not relax in a particular > Cartesian direction. > example: > Al 11.039040 5.580000 24.296861 0 0 1, > means that Aluminium is fixed EXCEPT in the Z direction. So it will > relax on Z direction. In your case I suggest to use this kind of > relaxation for every atom with a fixed Constraint on bond lengths (see > previous posts of mine). > > KPoints: I, generally, use 'automatic' K points which is a kind of > Monkhorst-Pack grid (more genereic). Suppose you have orthorhombic > cell (a,b,c) where the magnitudes are (a=b < c), then I will use more > Kpoints in a and b direction and less kpoints in c direction. Since > Kpoints are defined in the reciprocal space (say, a'b'c' where > magnitudes are a'b' > c'), you should use more k points to span the > necessery irrep. areas in that reciproal space of a'b'c'. > simply You can start with (see manual) > K_POINTS automatic > nx ny nz shiftx shifty shifty > > It is a good idea to visualize your supercell prior to put some values > in nx,... > > > By the way why you are using a BASH script? It was in QE package just > to make tests quite smoothly/interactively. So pls use a simple *.in > file which contains the input-data BETWEEN cat > alpen148.rx.in << EOF > to EOF (bottom, near to Kpoints...) > > good luck > > Krishna Mohan GP > Center for Superfunctional Materials > POSTECH > Sotuh Korea. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From izaakw89 at yahoo.com Wed Jun 15 19:22:20 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Wed, 15 Jun 2011 10:22:20 -0700 (PDT) Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: References: Message-ID: <139345.24926.qm@web43410.mail.sp1.yahoo.com> Hello everyone, I use XCrySDen frequently to view my structures built with Quantum ESPRESSO. When I open old relax output files in XCrySDen that were produced with espresso-3.2.3, I can view "latest coordinates" or "all coordinates as animation" with no troubles. When I was using espresso-4.1.3, there must have been a certain line (or lack of a line) in the output files that made them not work in XCrySDen. Specifically, when I open these outputs in XCrySDen, only the "view initial coordinates" button works. By viewing "optimized coordinates" I get an error that reads: ERROR: while executing exec sh ../XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor ../relax.out > pwo2xsf.xsf. and when I click on "Error Info" it says: Child process exited abnormally The "view latest coordinates" option produces a blank window and the "view all coordinates as animation" option only shows one slide (the initial structure). I think these errors were caused by a change that was made in the wording of the output files with the update of espresso-4.1.3 because when I compiled espresso-4.2.1, I did not have any of these problems. Now I am using the most recent version, espresso-4.3.1, and I am getting the same errors that I did with 4.1.3. What, in the code, is causing these problems to arise? Should I try updating my version of XCrySDen (from 1.4.1)? Any incite on the matter would be much appreciated. Thanks in advance. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/6dca30da/attachment.htm From padmaja_patnaik at yahoo.co.uk Wed Jun 15 20:15:48 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 15 Jun 2011 19:15:48 +0100 (BST) Subject: [Pw_forum] Problem while generating pseudopotential Message-ID: <971969.856.qm@web28511.mail.ukl.yahoo.com> Hi All I am trying to generate fully relativistic pseudopotential for Cr. It runs gives the output, but following message is printed repeatedly. ?WARNING! Expected number of nodes:?? 0=???? 1-? 0-? 1, number of nodes found:? 4. ?????? Setting wfc to zero for this iteration. ?????? (This warning will only be printed once per wavefunction) ?????? Zero norm: self consistency problem; state:? 1 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 2 (l=? 1, j=0.5) ?????? Zero norm: self consistency problem; state:? 3 (l=? 1, j=1.5) ?????? Zero norm: self consistency problem; state:? 4 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 1 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 2 (l=? 1, j=0.5) ?????? Zero norm: self consistency problem; state:? 3 (l=? 1, j=1.5) ?????? Zero norm: self consistency problem; state:? 4 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 1 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 2 (l=? 1, j=0.5) ?????? Zero norm: self consistency problem; state:? 3 (l=? 1, j=1.5) ?????? Zero norm: self consistency problem; state:? 4 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 1 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 2 (l=? 1, j=0.5) ?????? Zero norm: self consistency problem; state:? 3 (l=? 1, j=1.5) ?????? Zero norm: self consistency problem; state:? 4 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 1 (l=? 0, j=0.5) ?????? Zero norm: self consistency problem; state:? 2 (l=? 1, j=0.5) While searching I learned? that even if this message is displayed and the self-consistency is achieved that means there is no problem. The pseudopotential plot is also found to be incorrect. What can I do now? Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110615/3ca2f1bb/attachment-0001.htm From germaneau at gucas.ac.cn Thu Jun 16 12:59:47 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 16 Jun 2011 06:59:47 -0400 Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: <508158501.27402@test1.gucas.ac.cn> References: <508158501.27402@test1.gucas.ac.cn> Message-ID: <4DF9E223.7030207@gucas.ac.cn> Dear Izaak, First of all this is not the right place to post such request. You's better make a post to XcrySDen mailing list. Then, the problem does not come from QE but rather the version of XcrySDen you use. I use the last release and I don't have any trouble. It makes sence to update XcrySDen when you update QE since it adapts according to QE features. Hope it help. Best, ?ric. On 06/15/2011 01:22 PM, Izaak Williamson wrote: > Hello everyone, > > I use XCrySDen frequently to view my structures built with Quantum > ESPRESSO. When I open old relax output files in XCrySDen that were > produced with espresso-3.2.3, I can view "latest coordinates" or "all > coordinates as animation" with no troubles. When I was using > espresso-4.1.3, there must have been a certain line (or lack of a > line) in the output files that made them not work in XCrySDen. > Specifically, when I open these outputs in XCrySDen, only the "view > initial coordinates" button works. By viewing "optimized coordinates" > I get an error that reads: > > ERROR: while executing exec sh > ../XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor ../relax.out > > pwo2xsf.xsf. > > and when I click on "Error Info" it says: > > Child process exited abnormally > > The "view latest coordinates" option produces a blank window and the > "view all coordinates as animation" option only shows one slide (the > initial structure). I think these errors were caused by a change that > was made in the wording of the output files with the update of > espresso-4.1.3 because when I compiled espresso-4.2.1, I did not have > any of these problems. Now I am using the most recent version, > espresso-4.3.1, and I am getting the same errors that I did with 4.1.3. > > What, in the code, is causing these problems to arise? Should I try > updating my version of XCrySDen (from 1.4.1)? Any incite on the matter > would be much appreciated. > > Thanks in advance. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/1cf0ee4e/attachment.htm From yhho at pub.iams.sinica.edu.tw Thu Jun 16 05:20:58 2011 From: yhho at pub.iams.sinica.edu.tw (yhho) Date: Thu, 16 Jun 2011 11:20:58 +0800 Subject: [Pw_forum] graphene phonon dispersion Message-ID: <006901cc2bd4$69af9ec0$61706d8c@mychatd6d7d1f2> Sorry I forgot it. This is matdyn.in. Thank you very much. (matdyn.in) &input asr='simple', amass(1)=12.0107, flfrc='AuC444.fc', flfrq='AuC.freq' / 121 0.00000000 0.00000000 0.00000000 1 0.00000000 -.01250000 0.00000000 2 0.00000000 -.02500000 0.00000000 3 0.00000000 -.03750000 0.00000000 4 0.00000000 -.05000000 0.00000000 5 0.00000000 -.06250000 0.00000000 6 0.00000000 -.07500000 0.00000000 7 0.00000000 -.08750000 0.00000000 8 0.00000000 -.10000000 0.00000000 9 0.00000000 -.11250000 0.00000000 10 0.00000000 -.12500000 0.00000000 11 0.00000000 -.13750000 0.00000000 12 0.00000000 -.15000000 0.00000000 13 0.00000000 -.16250000 0.00000000 14 0.00000000 -.17500000 0.00000000 15 0.00000000 -.18750000 0.00000000 16 0.00000000 -.20000000 0.00000000 17 0.00000000 -.21250000 0.00000000 18 0.00000000 -.22500000 0.00000000 19 0.00000000 -.23750000 0.00000000 20 0.00000000 -.25000000 0.00000000 21 0.00000000 -.26250000 0.00000000 22 0.00000000 -.27500000 0.00000000 23 0.00000000 -.28750000 0.00000000 24 0.00000000 -.30000000 0.00000000 25 0.00000000 -.31250000 0.00000000 26 0.00000000 -.32500000 0.00000000 27 0.00000000 -.33750000 0.00000000 28 0.00000000 -.35000000 0.00000000 29 0.00000000 -.36250000 0.00000000 30 0.00000000 -.37500000 0.00000000 31 0.00000000 -.38750000 0.00000000 32 0.00000000 -.40000000 0.00000000 33 0.00000000 -.41250000 0.00000000 34 0.00000000 -.42500000 0.00000000 35 0.00000000 -.43750000 0.00000000 36 0.00000000 -.45000000 0.00000000 37 0.00000000 -.46250000 0.00000000 38 0.00000000 -.47500000 0.00000000 39 0.00000000 -.48750000 0.00000000 40 0.00000000 -.50000000 0.00000000 41 0.00833750 -.50416950 0.00000000 42 0.01667500 -.50833900 0.00000000 43 0.02501250 -.51250850 0.00000000 44 0.03335000 -.51667800 0.00000000 45 0.04168750 -.52084750 0.00000000 46 0.05002500 -.52501700 0.00000000 47 0.05836250 -.52918650 0.00000000 48 0.06670000 -.53335600 0.00000000 49 0.07503750 -.53752550 0.00000000 50 0.08337500 -.54169500 0.00000000 51 0.09171250 -.54586450 0.00000000 52 0.10005000 -.55003400 0.00000000 53 0.10838750 -.55420350 0.00000000 54 0.11672500 -.55837300 0.00000000 55 0.12506250 -.56254250 0.00000000 56 0.13340000 -.56671200 0.00000000 57 0.14173750 -.57088150 0.00000000 58 0.15007500 -.57505100 0.00000000 59 0.15841250 -.57922050 0.00000000 60 0.16675000 -.58339000 0.00000000 61 0.17508750 -.58755950 0.00000000 62 0.18342500 -.59172900 0.00000000 63 0.19176250 -.59589850 0.00000000 64 0.20010000 -.60006800 0.00000000 65 0.20843750 -.60423750 0.00000000 66 0.21677500 -.60840700 0.00000000 67 0.22511250 -.61257650 0.00000000 68 0.23345000 -.61674600 0.00000000 69 0.24178750 -.62091550 0.00000000 70 0.25012500 -.62508500 0.00000000 71 0.25846250 -.62925450 0.00000000 72 0.26680000 -.63342400 0.00000000 73 0.27513750 -.63759350 0.00000000 74 0.28347500 -.64176300 0.00000000 75 0.29181250 -.64593250 0.00000000 76 0.30015000 -.65010200 0.00000000 77 0.30848750 -.65427150 0.00000000 78 0.31682500 -.65844100 0.00000000 79 0.32516250 -.66261050 0.00000000 80 0.33350000 -.66678000 0.00000000 81 0.32516250 -.65011050 0.00000000 82 0.31682500 -.63344100 0.00000000 83 0.30848750 -.61677150 0.00000000 84 0.30015000 -.60010200 0.00000000 85 0.29181250 -.58343250 0.00000000 86 0.28347500 -.56676300 0.00000000 87 0.27513750 -.55009350 0.00000000 88 0.26680000 -.53342400 0.00000000 89 0.25846250 -.51675450 0.00000000 90 0.25012500 -.50008500 0.00000000 91 0.24178750 -.48341550 0.00000000 92 0.23345000 -.46674600 0.00000000 93 0.22511250 -.45007650 0.00000000 94 0.21677500 -.43340700 0.00000000 95 0.20843750 -.41673750 0.00000000 96 0.20010000 -.40006800 0.00000000 97 0.19176250 -.38339850 0.00000000 98 0.18342500 -.36672900 0.00000000 99 0.17508750 -.35005950 0.00000000 100 0.16675000 -.33339000 0.00000000 101 0.15841250 -.31672050 0.00000000 102 0.15007500 -.30005100 0.00000000 103 0.14173750 -.28338150 0.00000000 104 0.13340000 -.26671200 0.00000000 105 0.12506250 -.25004250 0.00000000 106 0.11672500 -.23337300 0.00000000 107 0.10838750 -.21670350 0.00000000 108 0.10005000 -.20003400 0.00000000 109 0.09171250 -.18336450 0.00000000 110 0.08337500 -.16669500 0.00000000 111 0.07503750 -.15002550 0.00000000 112 0.06670000 -.13335600 0.00000000 113 0.05836250 -.11668650 0.00000000 114 0.05002500 -.10001700 0.00000000 115 0.04168750 -.08334750 0.00000000 116 0.03335000 -.06667800 0.00000000 117 0.02501250 -.05000850 0.00000000 118 0.01667500 -.03333900 0.00000000 119 0.00833750 -.01666950 0.00000000 120 0.00000000 0.00000000 0.00000000 121 -- Message: 3 Date: Wed, 15 Jun 2011 14:11:42 +0300 From: "yccheng.nju" Subject: Re: [Pw_forum] graphene phonon dispersion To: PWSCF Forum Cc: yhho Message-ID: <4DF8936E.7090107 at gmail.com> Content-Type: text/plain; charset="big5" >Why dont you show us your input file for matdyn.x ? I think it is due to >the wrong q-point setting. >On 15/06/11 12:28, yhho wrote: > Dear all, > I have tried many different way as I saw on pw_forum > but I still can't get a good result which is similar to tthe figure > from paper I found. > In this figure, red line is what I got and gray line is from reference > ref: *Physics Reports* > *Volume 409, > Issue 2* > *, > March 2005, Pages 47-99* > http://imageshack.us/photo/my-images/853/c2phdosvc1.jpg/ > I also found another paper shows a little different phonon dispersion > figure of graphite: > red line is my result and gray line is from reference > ref: *10.1103/PhysRevLett.92.075501* > http://imageshack.us/photo/my-images/851/c2phdosvc3.jpg/ > I have no idea to improve this > because I have tried vc-relax and relax and the structure didn't > change a lot due to that. > And I also tried increasing q-points, there's no much different from > the fewer q-points results. > Please give me some suggestion. Thanks very much. > *input file* > *(scf.in)* > &control > calculation ='scf' > restart_mode ='from_scratch' > pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' > outdir ='./' > prefix ='AuC' > / > &system > ibrav =0 > celldm(1)= 4.6514 > nat = 2 , > ntyp = 1 , > ecutwfc = 24.0, > ecutrho = 240.0, > occupations ='smearing', > degauss= 0.02 > / > &electrons > diagonalization= 'david' > conv_thr = 1.0d-12 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF > CELL_PARAMETERS (alat) > 0.984533834 0.000000000 0.000000000 > -0.492266917 0.852631311 0.000000000 > 0.000000000 0.000000000 5.328569075 > ATOMIC_POSITIONS {crystal} > C 0.481112321 1.128944752 0.517391300 > C 0.814471461 0.795556146 0.517391309 > K_POINTS > 7 > 0.0000000 0.0000000 0.0000000 0.1250000 > 0.0000000 0.2932100 0.0000000 0.2500000 > 0.0000000 -0.5864199 0.0000000 0.1250000 > 0.2539273 0.1466050 0.0000000 0.5000000 > 0.2539273 0.4398150 0.0000000 0.5000000 > -0.5078546 -0.2932100 0.0000000 0.2500000 > -0.5078546 0.0000000 0.0000000 0.2500000 > (*ph.in*) > phonons of AuC > &inputph > tr2_ph=1.0d-12, > ldisp=.true., > nq1=4, nq2=4, nq3=1 > amass(1)= 12.0107 > prefix='AuC', > outdir='./' > fildyn='AuC.dyn', > / > -- > Yu-Han Ho > Research Assistant > Institute of Atomic and Molecular Sciences(IAMS), lab503 > No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan > Tel: 886-2-2362-0212 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/525bd878/attachment-0001.htm From briquet at lippmann.lu Thu Jun 16 12:51:41 2011 From: briquet at lippmann.lu (Ludovic Briquet) Date: Thu, 16 Jun 2011 12:51:41 +0200 Subject: [Pw_forum] Bug in version 4.3.1 Message-ID: Dear all, I've installed the last version of Quantum Espresso, i.e. 4.3.1, using a pgi/mvapich2 compiler. All tests are running fine except for the scf-nccp test. I got an energy of -11.827850 Ry instead of -15.839765 Ry and a pressure of 526.54 GPa instead of 54.09 GPa. I've performed several tests to get rid of this tremendous error and it turned out I was not able to reproduce that error with version 4.3 or lower (same compilation options - same architecture). I therefore strongly suspect a bug in version 4.3.1. Regards Ludovic -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/6b2720c0/attachment.htm From cvasse at hotmail.com Thu Jun 16 13:18:51 2011 From: cvasse at hotmail.com (Vasse chis) Date: Thu, 16 Jun 2011 13:18:51 +0200 Subject: [Pw_forum] graphene phonon dispersion In-Reply-To: <006901cc2bd4$69af9ec0$61706d8c@mychatd6d7d1f2> References: <006901cc2bd4$69af9ec0$61706d8c@mychatd6d7d1f2> Message-ID: The list of q-points are in crystal coordinates, while matdyn.x requires the list in units of 2pi/a_0. That is G-M-K-G goes form (0.0, 0.0) - (0.0, 1/sqrt(3)) - (1/3, 1/sqrt(3)) - (0.0, 0.0). Good luck, Vasse From: yhho at pub.iams.sinica.edu.tw To: pw_forum at pwscf.org Date: Thu, 16 Jun 2011 11:20:58 +0800 Subject: Re: [Pw_forum] graphene phonon dispersion Sorry I forgot it. This is matdyn.in. Thank you very much. (matdyn.in) &input asr='simple', amass(1)=12.0107, flfrc='AuC444.fc', flfrq='AuC.freq' / 121 0.00000000 0.00000000 0.00000000 1 0.00000000 -.01250000 0.00000000 2 0.00000000 -.02500000 0.00000000 3 0.00000000 -.03750000 0.00000000 4 0.00000000 -.05000000 0.00000000 5 0.00000000 -.06250000 0.00000000 6 0.00000000 -.07500000 0.00000000 7 0.00000000 -.08750000 0.00000000 8 0.00000000 -.10000000 0.00000000 9 0.00000000 -.11250000 0.00000000 10 0.00000000 -.12500000 0.00000000 11 0.00000000 -.13750000 0.00000000 12 0.00000000 -.15000000 0.00000000 13 0.00000000 -.16250000 0.00000000 14 0.00000000 -.17500000 0.00000000 15 0.00000000 -.18750000 0.00000000 16 0.00000000 -.20000000 0.00000000 17 0.00000000 -.21250000 0.00000000 18 0.00000000 -.22500000 0.00000000 19 0.00000000 -.23750000 0.00000000 20 0.00000000 -.25000000 0.00000000 21 0.00000000 -.26250000 0.00000000 22 0.00000000 -.27500000 0.00000000 23 0.00000000 -.28750000 0.00000000 24 0.00000000 -.30000000 0.00000000 25 0.00000000 -.31250000 0.00000000 26 0.00000000 -.32500000 0.00000000 27 0.00000000 -.33750000 0.00000000 28 0.00000000 -.35000000 0.00000000 29 0.00000000 -.36250000 0.00000000 30 0.00000000 -.37500000 0.00000000 31 0.00000000 -.38750000 0.00000000 32 0.00000000 -.40000000 0.00000000 33 0.00000000 -.41250000 0.00000000 34 0.00000000 -.42500000 0.00000000 35 0.00000000 -.43750000 0.00000000 36 0.00000000 -.45000000 0.00000000 37 0.00000000 -.46250000 0.00000000 38 0.00000000 -.47500000 0.00000000 39 0.00000000 -.48750000 0.00000000 40 0.00000000 -.50000000 0.00000000 41 0.00833750 -.50416950 0.00000000 42 0.01667500 -.50833900 0.00000000 43 0.02501250 -.51250850 0.00000000 44 0.03335000 -.51667800 0.00000000 45 0.04168750 -.52084750 0.00000000 46 0.05002500 -.52501700 0.00000000 47 0.05836250 -.52918650 0.00000000 48 0.06670000 -.53335600 0.00000000 49 0.07503750 -.53752550 0.00000000 50 0.08337500 -.54169500 0.00000000 51 0.09171250 -.54586450 0.00000000 52 0.10005000 -.55003400 0.00000000 53 0.10838750 -.55420350 0.00000000 54 0.11672500 -.55837300 0.00000000 55 0.12506250 -.56254250 0.00000000 56 0.13340000 -.56671200 0.00000000 57 0.14173750 -.57088150 0.00000000 58 0.15007500 -.57505100 0.00000000 59 0.15841250 -.57922050 0.00000000 60 0.16675000 -.58339000 0.00000000 61 0.17508750 -.58755950 0.00000000 62 0.18342500 -.59172900 0.00000000 63 0.19176250 -.59589850 0.00000000 64 0.20010000 -.60006800 0.00000000 65 0.20843750 -.60423750 0.00000000 66 0.21677500 -.60840700 0.00000000 67 0.22511250 -.61257650 0.00000000 68 0.23345000 -.61674600 0.00000000 69 0.24178750 -.62091550 0.00000000 70 0.25012500 -.62508500 0.00000000 71 0.25846250 -.62925450 0.00000000 72 0.26680000 -.63342400 0.00000000 73 0.27513750 -.63759350 0.00000000 74 0.28347500 -.64176300 0.00000000 75 0.29181250 -.64593250 0.00000000 76 0.30015000 -.65010200 0.00000000 77 0.30848750 -.65427150 0.00000000 78 0.31682500 -.65844100 0.00000000 79 0.32516250 -.66261050 0.00000000 80 0.33350000 -.66678000 0.00000000 81 0.32516250 -.65011050 0.00000000 82 0.31682500 -.63344100 0.00000000 83 0.30848750 -.61677150 0.00000000 84 0.30015000 -.60010200 0.00000000 85 0.29181250 -.58343250 0.00000000 86 0.28347500 -.56676300 0.00000000 87 0.27513750 -.55009350 0.00000000 88 0.26680000 -.53342400 0.00000000 89 0.25846250 -.51675450 0.00000000 90 0.25012500 -.50008500 0.00000000 91 0.24178750 -.48341550 0.00000000 92 0.23345000 -.46674600 0.00000000 93 0.22511250 -.45007650 0.00000000 94 0.21677500 -.43340700 0.00000000 95 0.20843750 -.41673750 0.00000000 96 0.20010000 -.40006800 0.00000000 97 0.19176250 -.38339850 0.00000000 98 0.18342500 -.36672900 0.00000000 99 0.17508750 -.35005950 0.00000000 100 0.16675000 -.33339000 0.00000000 101 0.15841250 -.31672050 0.00000000 102 0.15007500 -.30005100 0.00000000 103 0.14173750 -.28338150 0.00000000 104 0.13340000 -.26671200 0.00000000 105 0.12506250 -.25004250 0.00000000 106 0.11672500 -.23337300 0.00000000 107 0.10838750 -.21670350 0.00000000 108 0.10005000 -.20003400 0.00000000 109 0.09171250 -.18336450 0.00000000 110 0.08337500 -.16669500 0.00000000 111 0.07503750 -.15002550 0.00000000 112 0.06670000 -.13335600 0.00000000 113 0.05836250 -.11668650 0.00000000 114 0.05002500 -.10001700 0.00000000 115 0.04168750 -.08334750 0.00000000 116 0.03335000 -.06667800 0.00000000 117 0.02501250 -.05000850 0.00000000 118 0.01667500 -.03333900 0.00000000 119 0.00833750 -.01666950 0.00000000 120 0.00000000 0.00000000 0.00000000 121 -- Message: 3 Date: Wed, 15 Jun 2011 14:11:42 +0300 From: "yccheng.nju" Subject: Re: [Pw_forum] graphene phonon dispersion To: PWSCF Forum Cc: yhho Message-ID: <4DF8936E.7090107 at gmail.com> Content-Type: text/plain; charset="big5" >Why dont you show us your input file for matdyn.x ? I think it is due to >the wrong q-point setting. >On 15/06/11 12:28, yhho wrote: > Dear all, > I have tried many different way as I saw on pw_forum > but I still can't get a good result which is similar to tthe figure > from paper I found. > In this figure, red line is what I got and gray line is from reference > ref: *Physics Reports* > *Volume 409, > Issue 2* > *, > March 2005, Pages 47-99* > http://imageshack.us/photo/my-images/853/c2phdosvc1.jpg/ > I also found another paper shows a little different phonon dispersion > figure of graphite: > red line is my result and gray line is from reference > ref: *10.1103/PhysRevLett.92.075501* > http://imageshack.us/photo/my-images/851/c2phdosvc3.jpg/ > I have no idea to improve this > because I have tried vc-relax and relax and the structure didn't > change a lot due to that. > And I also tried increasing q-points, there's no much different from > the fewer q-points results. > Please give me some suggestion. Thanks very much. > *input file* > *(scf.in)* > &control > calculation ='scf' > restart_mode ='from_scratch' > pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' > outdir ='./' > prefix ='AuC' > / > &system > ibrav =0 > celldm(1)= 4.6514 > nat = 2 , > ntyp = 1 , > ecutwfc = 24.0, > ecutrho = 240.0, > occupations ='smearing', > degauss= 0.02 > / > &electrons > diagonalization= 'david' > conv_thr = 1.0d-12 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF > CELL_PARAMETERS (alat) > 0.984533834 0.000000000 0.000000000 > -0.492266917 0.852631311 0.000000000 > 0.000000000 0.000000000 5.328569075 > ATOMIC_POSITIONS {crystal} > C 0.481112321 1.128944752 0.517391300 > C 0.814471461 0.795556146 0.517391309 > K_POINTS > 7 > 0.0000000 0.0000000 0.0000000 0.1250000 > 0.0000000 0.2932100 0.0000000 0.2500000 > 0.0000000 -0.5864199 0.0000000 0.1250000 > 0.2539273 0.1466050 0.0000000 0.5000000 > 0.2539273 0.4398150 0.0000000 0.5000000 > -0.5078546 -0.2932100 0.0000000 0.2500000 > -0.5078546 0.0000000 0.0000000 0.2500000 > (*ph.in*) > phonons of AuC > &inputph > tr2_ph=1.0d-12, > ldisp=.true., > nq1=4, nq2=4, nq3=1 > amass(1)= 12.0107 > prefix='AuC', > outdir='./' > fildyn='AuC.dyn', > / > -- > Yu-Han Ho > Research Assistant > Institute of Atomic and Molecular Sciences(IAMS), lab503 > No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan > Tel: 886-2-2362-0212 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/692ad3b0/attachment-0001.htm From giannozz at democritos.it Thu Jun 16 14:40:57 2011 From: giannozz at democritos.it (giannozz at democritos.it) Date: Thu, 16 Jun 2011 14:40:57 +0200 Subject: [Pw_forum] Bug in version 4.3.1 In-Reply-To: References: Message-ID: <20110616144057.tb8xmil9pcc8co08@mail.democritos.it> Quoting Ludovic Briquet : > All tests are running fine except for the scf-ncpp test[...] I was > not able to > reproduce that error with version 4.3 or lower (same compilation options - > same architecture). I therefore strongly suspect a bug in version 4.3.1. you are right: the code doesn't recognize any longer the simplified form 'PZ' for exchange-correlation. This is a problem only for pseudopotentials in the old 'norm-conserving' formats. If you need to use them, pending a better fix, check what you get as exchange-correlation functional, modify the XC field in the file, or explicitly specify "input_dft". Paolo -- Paolo Giannozzi, UniUdine and IOM-Democritos ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From padmaja_patnaik at yahoo.co.uk Thu Jun 16 15:20:46 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 16 Jun 2011 14:20:46 +0100 (BST) Subject: [Pw_forum] Testing pseudopotential Message-ID: <642031.52209.qm@web28510.mail.ukl.yahoo.com> Dear All I have generated fully relativistic ultr-soft pseudopotential for Cr. I am not sure of how to test it. The logarithm derivatives of all electron and pseudopotential are not exactly matching as given in the examples (examples_pseudo). below I am adding the testing portion of the output file. The value of De AE-PS is very small. Does that indicate a good generation of pseudopotential? Can anybody please mention what are the other points which should be taken care of, while testing? ?Cr ???? dirac relativistic calculation ???? atomic number is 24.00?? valence charge is? 6.00 ???? dft =PBE?? lsd =0 sic =0 latt =0? beta=0.20 tr2=1.0E-14 ???? mesh =1183 r(mesh) =? 99.18097 xmin = -7.00 dx = 0.01250 ???? n l? j? nl???????????? e AE (Ry)?????? e PS (Ry)??? De AE-PS (Ry) ???? 1 0 0.5 4S?? 1( 1.00)?????? -0.29413?????? -0.29413??????? 0.00000 ???? 3 2 1.5 3D?? 1( 4.00)?????? -0.21555?????? -0.21555??????? 0.00000 ???? 3 2 2.5 3D?? 1( 1.00)?????? -0.20988?????? -0.20988??????? 0.00000 ???? 2 1 0.5 4P?? 1( 0.00)?????? -0.07375?????? -0.07253?????? -0.00121 ???? 2 1 1.5 4P?? 1( 0.00)?????? -0.07194?????? -0.07253??????? 0.00060 ???? eps = 8.2E-15? iter = 21 ???? Etot =?? -2101.100379 Ry,?? -1050.550189 Ha,? -28586.924470 eV ???? Etotps =?? -22.414845 Ry,???? -11.207422 Ha,??? -304.969472 eV ???? Ekin =????? 11.677342 Ry,?????? 5.838671 Ha,???? 158.878313 eV ???? Encl =???? -25.691551 Ry,???? -12.845776 Ha,??? -349.551328 eV ???? Ehrt =????? 13.374298 Ry,?????? 6.687149 Ha,???? 181.966585 eV ???? Ecxc =???? -12.640375 Ry,????? -6.320188 Ha,??? -171.981050 eV ???? (Ecc =????? -8.529574 Ry,????? -4.264787 Ha,??? -116.050762 eV) ???? Epseu=????? -9.134559 Ry,????? -4.567279 Ha,??? -124.281992 eV ???? ---------------------- End of pseudopotential test ---------------------- Thanks and regards, Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/f2f62c4e/attachment.htm From pascal.boulet at univ-provence.fr Thu Jun 16 17:46:26 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Thu, 16 Jun 2011 17:46:26 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm Message-ID: <4DFA2552.3080706@univ-provence.fr> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110616/28560a20/attachment.htm From pascal.boulet at univ-provence.fr Thu Jun 16 20:53:43 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Thu, 16 Jun 2011 20:53:43 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm Message-ID: <4DFA5137.7090709@univ-provence.fr> Dear all, It seems that my first post was completely unreadable (html). Sorry for that. Here is the content. I am trying to run a CP simulation (cp.x) of a molecule in contact with a small metallic cluster of atoms. First here is the input file of my test job: &CONTROL title = 'MD', calculation = 'cp', dt = 20.d0, isave = 5, nstep = 10, etot_conv_thr = 5.d-7, prefix = 'test', pseudo_dir = '/opt/espresso-4.3.1/pseudo', restart_mode = 'from_scratch', verbosity = 'high', iprint = 1 / &SYSTEM ibrav = 0, celldm(1) = 34.015084, nat = 4, ntyp = 2, ecutwfc = 25., ecutrho = 200., occupations = 'ensemble', smearing = 'fd', degauss = 0.02, input_dft = 'PBE', nbnd = 30, assume_isolated = 'makov-payne' / &ELECTRONS conv_thr = 5.d-7, mixing_beta = 0.4d0, startingwfc = 'random', tcg = .TRUE., electron_velocities = 'zero', electron_temperature = 'nose', fnosee = 300., ekincw = 0.001, orthogonalization = 'Gram-Schmidt' / &IONS ion_dynamics = 'verlet', ion_temperature = 'nose', ion_velocities = 'random', remove_rigid_rot = .TRUE., tempw = 623.d0, ndega = -6, nhpcl = 1, fnosep = 24., / ATOMIC_SPECIES Ag 107.8682 Ag.pbe-d-rrkjus.UPF N 14.0067 N.pbe-rrkjus.UPF ATOMIC_POSITIONS angstrom Ag 6.467294548 12.585619859 10.268802850 Ag 6.293658753 10.453834050 12.214668134 N 4.165456080 10.433924294 8.842653616 N 3.807795851 10.451920023 9.956290174 CELL_PARAMETERS {cubic} 1. 0. 0. 0. 1. 0. 0. 0. 1. If I run the above input file, I get the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ions_print_info : error # 1 tcap and tnosep both true %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% What is the meaning of the variables tcap and tnosep? It seems they are not adjustable variables through the input file since they are not referenced in the manual. Indeed, if I set tcap=.false. in the input file I get the following: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 19 reading namelist ions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So, is there any contradiction in my input file? Thank you for your help Best regards Pascal From giannozz at democritos.it Thu Jun 16 21:27:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Jun 2011 21:27:15 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: <4DFA5137.7090709@univ-provence.fr> References: <4DFA5137.7090709@univ-provence.fr> Message-ID: On Jun 16, 2011, at 20:53 , pascal boulet wrote: > What is the meaning of the variables tcap and tnosep? tcap = start with random ionic velocities; > tnosep = use Nose' thermostat for ions I think you are not allowed to use ion_velocities='random' together with ion_temperature = 'nose' (not sure why). As for the clarity of the error message...this was the "style de la maison" in first-principle MD. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From crma at sissa.it Thu Jun 16 21:30:12 2011 From: crma at sissa.it (Changru Ma) Date: Thu, 16 Jun 2011 21:30:12 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: <4DFA5137.7090709@univ-provence.fr> References: <4DFA5137.7090709@univ-provence.fr> Message-ID: <8251FA6A-771A-49D3-8DB8-FA8F608DDE58@sissa.it> Dear Pascal, If you set ion_velocities = 'random' then the internal variable tcap will be true. And if ion_temperature = 'nose', the internal variable tnosep is true. These two logic variables can't be both true since the code rejects (CPV/cplib.f90 line 441). HTH, Changru On 16 Jun, 2011, at 20:53, pascal boulet wrote: > Dear all, > > It seems that my first post was completely unreadable (html). Sorry for > that. Here is the content. > > I am trying to run a CP simulation (cp.x) of a molecule in contact with > a small metallic cluster of atoms. > > > First here is the input file of my test job: > > &CONTROL > title = 'MD', > calculation = 'cp', > dt = 20.d0, > isave = 5, > nstep = 10, > etot_conv_thr = 5.d-7, > prefix = 'test', > pseudo_dir = '/opt/espresso-4.3.1/pseudo', > restart_mode = 'from_scratch', > verbosity = 'high', > iprint = 1 > / > &SYSTEM > ibrav = 0, > celldm(1) = 34.015084, > nat = 4, > ntyp = 2, > ecutwfc = 25., > ecutrho = 200., > occupations = 'ensemble', > smearing = 'fd', > degauss = 0.02, > input_dft = 'PBE', > nbnd = 30, > assume_isolated = 'makov-payne' > / > &ELECTRONS > conv_thr = 5.d-7, > mixing_beta = 0.4d0, > startingwfc = 'random', > tcg = .TRUE., > electron_velocities = 'zero', > electron_temperature = 'nose', > fnosee = 300., > ekincw = 0.001, > orthogonalization = 'Gram-Schmidt' > / > &IONS > ion_dynamics = 'verlet', > ion_temperature = 'nose', > ion_velocities = 'random', > remove_rigid_rot = .TRUE., > tempw = 623.d0, > ndega = -6, > nhpcl = 1, > fnosep = 24., > / > ATOMIC_SPECIES > Ag 107.8682 Ag.pbe-d-rrkjus.UPF > N 14.0067 N.pbe-rrkjus.UPF > > ATOMIC_POSITIONS angstrom > Ag 6.467294548 12.585619859 10.268802850 > Ag 6.293658753 10.453834050 12.214668134 > N 4.165456080 10.433924294 8.842653616 > N 3.807795851 10.451920023 9.956290174 > > CELL_PARAMETERS {cubic} > 1. 0. 0. > 0. 1. 0. > 0. 0. 1. > > > > If I run the above input file, I get the following error message: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from ions_print_info : error # 1 > tcap and tnosep both true > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > What is the meaning of the variables tcap and tnosep? > > It seems they are not adjustable variables through the input file since > they are not referenced in the manual. Indeed, if I set tcap=.false. in > the input file I get the following: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 19 > reading namelist ions > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > So, is there any contradiction in my input file? > > > Thank you for your help > > Best regards > Pascal > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- From psavita at crlindia.com Fri Jun 17 08:12:01 2011 From: psavita at crlindia.com (psavita at crlindia.com) Date: Fri, 17 Jun 2011 11:42:01 +0530 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110617/901069fc/attachment.htm From prasenjit.jnc at gmail.com Fri Jun 17 08:58:23 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 17 Jun 2011 12:28:23 +0530 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References: Message-ID: Dear Savita, I am not an expert on these type of systems.......however just a small piece of advice.....a single molecule of water has a huge dipole moment.....so a box size of 25 bohr may not be sufficient, until and unless binding to LiH quenches the dipole moment......so you may like to check whether your box is sufficiently big.....usually for a single molecule of water one uses about 35-40 bohr box or can use dipole correction. Prasenjit On 17 June 2011 11:42, wrote: > Hello, > > I have been trying to get the optimum structure of LiH..H2O that has an > intramolecular dihydrogen bond, using pwscf. > I could get the proper structure earlier using mp2 theory and 6-31++g > basis. > > For pwscf, the species is enclosed in a cubic box of 25 bohr for gamma > point calculation. > I tried the pz lda, pbe gga as well we blyp PS for the atoms in this > system, however, the first and the last > lead to H2O..LiH, the latter LiH being linear while pbe gives LiH + H2, but > no dihydrogen bond. Is there any other PS > that may lead to proper structure? Or is it that plane wave approach does > not suit systems of this kind? > > Thanks in advance and best regards, > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110617/17d0a776/attachment.htm From pascal.boulet at univ-provence.fr Fri Jun 17 10:01:10 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Fri, 17 Jun 2011 10:01:10 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: References: Message-ID: <4DFB09C6.70201@univ-provence.fr> Thank you Paolo and Changru: it works fine now. Pascal From glapenna at iccom.cnr.it Fri Jun 17 10:27:09 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Fri, 17 Jun 2011 10:27:09 +0200 (CEST) Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: <4DFA2552.3080706@univ-provence.fr> References: <4DFA2552.3080706@univ-provence.fr> Message-ID: Dear Pascal, The input shows that you are trying to carry the system to 627 K starting with random velocities and a time-step of 20 au (about 0.5 fs). I expect a huge Kel after a few time-steps, due to huge current atomic velocities, not manageable with the given time-step. Please, tell me (us) if this won't happen. Giovanni La Penna ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From tone.kokalj at ijs.si Fri Jun 17 13:28:47 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 17 Jun 2011 13:28:47 +0200 Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: <139345.24926.qm@web43410.mail.sp1.yahoo.com> References: <139345.24926.qm@web43410.mail.sp1.yahoo.com> Message-ID: <1308310127.3139.7.camel@catalyst.ijs.si> On Wed, 2011-06-15 at 10:22 -0700, Izaak Williamson wrote: > Hello everyone, > > I use XCrySDen frequently to view my structures built with Quantum > ESPRESSO. When I open old relax output files in XCrySDen that were > produced with espresso-3.2.3, I can view "latest coordinates" or "all > coordinates as animation" with no troubles. When I was using > espresso-4.1.3, there must have been a certain line (or lack of a > line) in the output files that made them not work in XCrySDen. > Specifically, when I open these outputs in XCrySDen, only the "view > initial coordinates" button works. By viewing "optimized coordinates" > I get an error that reads: > > ERROR: while executing exec > sh ../XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh > --optcoor ../relax.out > pwo2xsf.xsf. You are using an old and outdated version of xcrysden (1.4.1), which is much older then QE v4. This is also the reason of non compatibility! Why don't you try with the new version: http://www.xcrysden.org/download/xc-1.5.24-linux_x86_64-semishared.tar.gz Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From peronio at tasc.infm.it Fri Jun 17 15:54:53 2011 From: peronio at tasc.infm.it (Angelo Peronio) Date: Fri, 17 Jun 2011 15:54:53 +0200 Subject: [Pw_forum] test scf-ncpp failed Message-ID: Dear QE users, I compiled QE 4.3.1 and run the check.pw.x.j script. I found what seems to me a noticeable difference between the reference results and mine in the test named scf-ncpp. Here is the output: angelo at angelo-XPS-L501X ~/espresso/tests $ ./check-pw-mod scf-ncpp.in Checking scf-ncpp...discrepancy in total energy detected Reference: -15.839765, You got: -11.827850 discrepancy in pressure detected Reference: -54.09, You got: 526.54 Total wall time (s) spent in this run: 0.17 Reference : 0.13 I get similar results * on my laptop: Intel i7, Linux Mint 10, ifort 12.0.4.191, MKL 10.3 update 2, openmpi 1.4.3, compiled with -D__FFTW3 in DFLAGS to (in my understanding) link against MKL FFTW interface; * again on my laptop with a serial compilation and -D__FFTW to link against QE internal FFTW; * on a Mac with gfortran; * on the QE 4.3.1 pre-built on CINECA's SP6 machine. Is there a problem with the reference results or am I missing something fundamental? Regards, Angelo -- _____________________ Angelo Peronio IOM CNR laboratorio TASC AREA Science Park, edificio MM strada statale 14, km 163.5 34149 Basovizza (TS) Italy laboratory: +39 040 3756452 office: +39 040 3756458 fax: +39 040 226767 e-mail: peronio at tasc.infm.it From Heiles at cluster.pc.chemie.tu-darmstadt.de Fri Jun 17 17:54:10 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Fri, 17 Jun 2011 17:54:10 +0200 Subject: [Pw_forum] Partial density of states for bimetallic systems Message-ID: <4DFB78A2.6050809@cluster.pc.chemie.tu-darmstadt.de> Dear Quantum Espresso users. I use QE 4.2.1 and have calculated the partial density of states (pDOS) for small bimetallic AuAg Clusters. For the calculations I typically placed the clusters in a cubic box of (cluster radius + 16) AA, with 50 Ry energy cutoff (500 Ry density cutoff) and used Au.pbe-nd-rrkjus.UPF and Ag.pbe-d-rrkjus.UPF. After geometry optimization I use projwfc.x to calculate pDOS. For the pure systems and the silver rich clusters everythings looks fine. When I do the same calculations for gold rich clusters and compare the total DOS with the pDOS which is contributed from the Au and Ag atoms, respectively, I observe that the DOS form all Au atoms is higher than the total DOS (for some energies). I have observed this effect not only for one structure but for different isomers. Below you can find sample input files and I can also attach the resulting DOS if this is needed. The geometry given in the input file is the optimized geometry. Could this be due to a problem with the pseudo potentials used? Is it perhaps a problem that the two potentials use a different number of projected wavefunction (for Au s,p,d and for Ag s,d)? Many thanks in advance Best wishes Sven ---------------------------------------------- &CONTROL calculation = "relax", prefix = "Au7Ag1_IV", pseudo_dir = " . ", outdir = "/scratch/xs/", etot_conv_thr= 1.0D-5, forc_conv_thr= 1.0D-4, nstep = 500, / &SYSTEM ibrav = 0, nat = 8, ntyp = 2, ecutwfc = 50.D0, ecutrho = 400.D0, occupations = "smearing", smearing = "mp", degauss = 0.005, / &ELECTRONS conv_thr = 1.D-8, mixing_beta = 0.5D0, / &IONS / CELL_PARAMETERS cubic 35.12 0.00 0.00 0.00 35.12 0.00 0.00 0.00 35.12 ATOMIC_SPECIES Au 196.97 Au.pbe-nd-rrkjus.UPF Ag 107.87 Ag.pbe-d-rrkjus.UPF ATOMIC_POSITIONS {bohr} Au 16.406811577 13.541797257 20.987665926 Au 13.951505318 17.709867934 19.449786254 Ag 21.264908797 12.421983607 19.161370450 Au 16.077915882 21.005082800 16.003674339 Au 18.694668590 16.624463571 17.595854913 Au 20.667864709 19.918026413 14.276411488 Au 23.400513864 15.564390404 15.773691665 Au 11.463173665 21.793220893 17.973137265 K_POINTS {Gamma} -------------------------------------------------------------------------- &inputpp outdir="/scratch/xs/" prefix="Au7Ag1_IV" io_choice="both" / -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From giannozz at democritos.it Fri Jun 17 20:33:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Jun 2011 20:33:45 +0200 Subject: [Pw_forum] test scf-ncpp failed In-Reply-To: References: Message-ID: On Jun 17, 2011, at 15:54 , Angelo Peronio wrote: > I compiled QE 4.3.1 and run the check.pw.x.j script. I found what > seems to > me a noticeable difference between the reference results and mine > in the > test named scf-ncpp. http://www.democritos.it/pipermail/pw_forum/2011-June/020909.html > --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Jun 17 20:58:42 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Jun 2011 20:58:42 +0200 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References: Message-ID: <0E22B075-E8C3-4511-AA9A-69CAE2090B91@democritos.it> On Jun 17, 2011, at 8:12 , psavita at crlindia.com wrote: > Is there any other PS that may lead to proper structure? Or is > it that plane wave approach does not suit systems of this kind? what makes you think that the problem is in the pseudopotentials or in plane waves? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From both_hamad at yahoo.com Fri Jun 17 22:29:58 2011 From: both_hamad at yahoo.com (bothina hamad) Date: Fri, 17 Jun 2011 13:29:58 -0700 (PDT) Subject: [Pw_forum] phonons In-Reply-To: References: Message-ID: <475959.90077.qm@web161506.mail.bf1.yahoo.com> Dear users, I am starting phonon calculations of a full Heusler alloy ( 4 atoms per unit cell). The alloy is half-metallic (metallic in majority spin channel and semiconducting in the minority). It is also a ferromagnet with a total magnetic moment 2Bohr magnetons. Using a small grid 2x2x2, I got the phonon calculations working smoothly and I got the phonon density of states. However, I could not reach convergence for denser grids. In these calculations, I then tried to split the points and make calculations for each q point in the grid separately, I found the the convergence occur for the 3 q-points ( the same points as 2x2x2 grid), however no convergence is reached for the other point and the calculations keep oscillating until 100 iterations then stop. I tried to change some parameters such as decreasing the tr2_ph=1.0d-14 to tr2_ph=1.0d-18, and also by decreasing the mixing to 0.1, still the problem is not solved. Do you have any idea that can solve the problem Best wishes Dr. Bothina Hamad Physics Department University of Jordan Amman-11942, Jordan Tel: +962-6-5355000 ext#22030 & 22023 Fax:+962-6-5348932 From both_hamad at yahoo.com Sat Jun 18 00:43:12 2011 From: both_hamad at yahoo.com (bothina hamad) Date: Fri, 17 Jun 2011 15:43:12 -0700 (PDT) Subject: [Pw_forum] phonons Message-ID: <409773.64794.qm@web161512.mail.bf1.yahoo.com> Dear users, I am starting phonon calculations of a full Heusler alloy ( 4 atoms per unit cell). The alloy is half-metallic (metallic in majority spin channel and semiconducting in the minority). It is also a ferromagnet with a total magnetic moment 2 Bohr magnetons. Using a small grid 2x2x2, I got the phonon calculations working smoothly and I got the phonon density of states. However, I could not reach convergence for denser grids. In these calculations, I then tried to split the points and make calculations for each q point in the grid separately, I found the the convergence occur for the 3 q-points ( the same points as 2x2x2 grid), however no convergence is reached for the other point and the calculations keep oscillating until 100 iterations then stop. I tried to change some parameters such as decreasing the tr2_ph=1.0d-14 to tr2_ph=1.0d-18, and also by decreasing the mixing to 0.1, still the problem is not solved. I use espresso-4.2.1 version I attach the input of scf and phonon calculations, dyn0 file as well as the last part of the output for the second q point after which the calculations stop. Do you have any idea that can solve the problem Best wishes Dr. Bothina Hamad Physics Department University of Jordan Amman-11942, Jordan Tel: +962-6-5355000 ext#22030 & 22023 Fax:+962-6-5348932 -------------- next part -------------- A non-text attachment was scrubbed... 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Name: FCS.scf.in Type: application/octet-stream Size: 980 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110617/880a717a/attachment-0007.obj From zhaohscas at yahoo.com.cn Sat Jun 18 07:15:42 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 18 Jun 2011 13:15:42 +0800 Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: <1308310127.3139.7.camel@catalyst.ijs.si> References: <139345.24926.qm@web43410.mail.sp1.yahoo.com> <1308310127.3139.7.camel@catalyst.ijs.si> Message-ID: <4DFC347E.9030904@yahoo.com.cn> On 06/17/2011 07:28 PM, Tone Kokalj wrote: > Why don't you try with the new version: > http://www.xcrysden.org/download/xc-1.5.24-linux_x86_64-semishared.tar.gz When can I obtain the precompiled version for linux_x86. I've never been successfully compiled it from source on my Debian box. Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From njuxuyuehua at gmail.com Sat Jun 18 11:29:38 2011 From: njuxuyuehua at gmail.com (xu yuehua) Date: Sat, 18 Jun 2011 17:29:38 +0800 Subject: [Pw_forum] pwscf version 4.3 example 15 error Message-ID: hi everyone: i just update the pwscf version to 4.3. the install is finish, then i run the example 14 to test the install is ok or not, but the error exits. i run it ./run_exampel, not use mpirun....., but the error seems to be mpi. i am wondering. i search the forum, someone has encountered the similaer problem, but no answer here. my install has problem? (there is only warning during install) i also paste the make.sys here, someone would help me i will be aggreciated. thanks a lot !!! the error information : /home/yxu/espresso-4.3/espresso-4.3/examples/example15 : starting This example shows how to use pw.x and ph.x to calculate the Raman tensor for AlAs. executables directory: /home/yxu/espresso-4.3/bin pseudo directory: /home/yxu/espresso-4.3/pseudo temporary directory: /home/yxu/tmp checking that needed directories and files exist... done running pw.x as: /home/yxu/espresso-4.3/bin/pw.x running ph.x as: /home/yxu/espresso-4.3/bin/ph.x cleaning /home/yxu/tmp... done running the scf calculation... done running the response calculation...[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 done /home/yhxu/espresso-4.3/espresso-4.3/examples/example15: done - - -- - -- ----- -- ----- ------ ------------------------------------------------------------------------------------ the make.sys ?( intel compier 11.1-072, intel mpi, intel MKL) # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__INTEL -D__FFTW3 -D__MPI -D__PARA FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MOD_FLAGS = flag used by f90 compiler to locate modules # Each Makefile defines the list of needed modules in MODFLAGS MOD_FLAG = -I # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpiifort #F90 = ifort CC = icc F77 = ifort # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = mpiifort LDFLAGS = -static-intel LD_LIBS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a # BLAS_LIBS_SWITCH = internal BLAS_LIBS =-L/home/yxu/intel/Compiler/11.1/072/ifort/mkl/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -i-static BLAS_LIBS_SWITCH = external # If you have nothing better, use the local copy : # LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a # LAPACK_LIBS_SWITCH = internal # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = -L/home/yxu/intel/Compiler/11.1/072/ifort/mkl/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -i-static LAPACK_LIBS_SWITCH = external SCALAPACK_LIBS = # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) #FFT_LIBS = -lfftw3xf # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv AR = ar ARFLAGS = ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify FLIB_TARGETS = all LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS) # topdir for linking espresso libs with plugins TOPDIR = /home/giannozz/CVS/espresso -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110618/52137a5c/attachment.htm From giannozz at democritos.it Sat Jun 18 13:14:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Jun 2011 13:14:07 +0200 Subject: [Pw_forum] pwscf version 4.3 example 15 error In-Reply-To: References: Message-ID: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> On Jun 18, 2011, at 11:29 , xu yuehua wrote: > i run the example 14 [...]the error information : > > /home/yxu/espresso-4.3/espresso-4.3/examples/example15 14 /= 15 > running the response calculation...[unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 this is NOT the error message from the code. Look into results/ for the output from the response calculation P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From njuxuyuehua at gmail.com Sat Jun 18 13:21:49 2011 From: njuxuyuehua at gmail.com (xu yuehua) Date: Sat, 18 Jun 2011 19:21:49 +0800 Subject: [Pw_forum] pwscf version 4.3 example 15 error In-Reply-To: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> References: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> Message-ID: Yes , it is error, i looked into the results/ and found in the alas.ph.out : the error is labled red, I am puzzled what is the problem. thank you a lot Program PHONON v.4.3 starts on 18Jun2011 at 17:13:43 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 1 processors Ultrasoft (Vanderbilt) Pseudopotentials Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input Stick Mesh ---------- nst = 151, nstw = 61, nsts = 151 n.st n.stw n.sts n.g n.gw n.gs min 151 61 151 1243 307 1243 max 151 61 151 1243 307 1243 151 61 151 1243 307 1243 Calculation of q = 0.0000000 0.0000000 0.0000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from io_pattern : error # 1 wrong iflag %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... 2011/6/18 Paolo Giannozzi > > On Jun 18, 2011, at 11:29 , xu yuehua wrote: > > > i run the example 14 [...]the error information : > > > > /home/yxu/espresso-4.3/espresso-4.3/examples/example15 > > 14 /= 15 > > > running the response calculation...[unset]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > > this is NOT the error message from the code. Look into results/ > for the output from the response calculation > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110618/02e404a7/attachment.htm From giannozz at democritos.it Sat Jun 18 16:06:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Jun 2011 16:06:45 +0200 Subject: [Pw_forum] pwscf version 4.3 example 15 error In-Reply-To: References: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> Message-ID: <94E45583-0E23-4CDC-A950-D87E9F475541@democritos.it> On Jun 18, 2011, at 13:21 , xu yuehua wrote: > I am puzzled what is the problem it is a known bug, already fixed in v.4.3.1: see revision 7802, http://qe-forge.org/scm/browser.php?group_id=10 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pascal.boulet at univ-provence.fr Sun Jun 19 10:21:47 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Sun, 19 Jun 2011 10:21:47 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: References: Message-ID: <4DFDB19B.8060605@univ-provence.fr> Dear Giovanni, Humm... hard to say because the data are not printed in the output file. Here is what I get, for instance: >>>> nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0 nfi tempp E -T.S-mu.nbsp +K_p #Iter Step 20 0 -502.49200 -502.62143 -502.62143 6 cg_sub: missed minimum, case 1, iteration 1 cg_sub: missed minimum, case 1, iteration 2 cg_sub: missed minimum, case 1, iteration 3 cg_sub: missed minimum, case 1, iteration 4 cg_sub: missed minimum, case 1, iteration 5 NOTE: eigenvalues are not computed without ortho Occupations : 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000 1.999999 1.999999 1.999999 1.999998 1.999997 1.999995 1.999994 1.999989 1.999983 1.999977 1.999958 1.999933 1.999884 1.999793 ... 0.001473 0.000546 0.000502 0.000278 0.000134 0.000079 0.000033 0.000019 0.000000 nfi tempp E -T.S-mu.nbsp +K_p #Iter Step 21 0 -502.49200 -502.62143 -502.62143 6 <<<<< etc. So, there is nothing about ekinc, temph, tempp, ... However, the data "nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0" look like those given in the file xxx.evp (except for one missing column). If this is right, then in this file ekinc = 0. during the whole simulation. That's strange! So, I guess there is something wrong somewhere in my input. Pascal > Date: Fri, 17 Jun 2011 10:27:09 +0200 (CEST) > From: Giovanni La Penna > Subject: Re: [Pw_forum] CP simulation with ensemble-dft algorithm > To: PWSCF Forum > Message-ID: > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > > Dear Pascal, > > The input shows that you are trying to > carry the system to 627 K starting with > random velocities and a time-step of 20 au (about 0.5 fs). > I expect a huge Kel after a few time-steps, due > to huge current atomic velocities, not manageable > with the given time-step. > Please, tell me (us) if this won't happen. > > Giovanni La Penna > > * * Anglais * Fran?ais * Anglais * Fran?ais From abmus007 at gmail.com Sun Jun 19 10:30:18 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 19 Jun 2011 03:30:18 -0500 Subject: [Pw_forum] cell parameters (celldm(1)-(4)) and atomic positions optimization Message-ID: Dear QE Users Pls I am working on a triclinic system and I want to ask how to optimize the celldm(1)-celldm(4) and also the atomic positions. In addition I want to ask if it is neccessary to optimize both or just atomic positions optimization would be ok thanks in anticipation of yuor fvourable reply Musari A.A Dept of physics University of Agriculture, Abeokuta Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110619/d4d62326/attachment.htm From njuxuyuehua at gmail.com Sun Jun 19 10:44:33 2011 From: njuxuyuehua at gmail.com (xu yuehua) Date: Sun, 19 Jun 2011 16:44:33 +0800 Subject: [Pw_forum] pwscf version 4.3 example 15 error In-Reply-To: <94E45583-0E23-4CDC-A950-D87E9F475541@democritos.it> References: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> <94E45583-0E23-4CDC-A950-D87E9F475541@democritos.it> Message-ID: thank you, when i update to 4.3.1, the error disappears. however, my results of example 15 has a liittle difference in alas.ph.out. i think it can not be neglected?? thank you very much. my results are : ************************************************************************** omega( 1) = -0.154428 [THz] = -5.151172 [cm-1] omega( 2) = -0.154428 [THz] = -5.151172 [cm-1] omega( 3) = -0.154428 [THz] = -5.151172 [cm-1] omega( 4) = 10.583082 [THz] = 353.013616 [cm-1] omega( 5) = 10.583082 [THz] = 353.013616 [cm-1] omega( 6) = 10.583082 [THz] = 353.013616 [cm-1] ************************************************************************** Mode symmetry, T_d (-43m) point group: omega( 1 - 3) = -5.2 [cm-1] --> T_2 G_15 P_4 I+R omega( 4 - 6) = 353.0 [cm-1] --> T_2 G_15 P_4 I+R ************************************************************************** the reference are ************************************************************************** omega( 1) = 0.044075 [THz] = 1.470192 [cm-1] omega( 2) = 0.044075 [THz] = 1.470192 [cm-1] omega( 3) = 0.044075 [THz] = 1.470192 [cm-1] omega( 4) = 10.582824 [THz] = 353.007358 [cm-1] omega( 5) = 10.582824 [THz] = 353.007358 [cm-1] omega( 6) = 10.582824 [THz] = 353.007358 [cm-1] ************************************************************************** Mode symmetry, T_d (-43m) point group: omega( 1 - 3) = 1.5 [cm-1] --> T_2 G_15 P_4 I+R omega( 4 - 6) = 353.0 [cm-1] --> T_2 G_15 P_4 I+R ************************************************************************** 2011/6/18 Paolo Giannozzi > > On Jun 18, 2011, at 13:21 , xu yuehua wrote: > > > I am puzzled what is the problem > > it is a known bug, already fixed in v.4.3.1: see revision 7802, > http://qe-forge.org/scm/browser.php?group_id=10 > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110619/bb3a7f9b/attachment.htm From abmus007 at gmail.com Sun Jun 19 11:02:19 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 19 Jun 2011 04:02:19 -0500 Subject: [Pw_forum] cell(dm) In-Reply-To: <20110425105803.otrlndpgggkww8w4@webmail.sissa.it> References: <20110424150614.kvw50iurokccswwc@webmail.sissa.it> <20110425105803.otrlndpgggkww8w4@webmail.sissa.it> Message-ID: Sir< Thank you very much for the assistance but where am so confused here is that the cell parameters (a 3x3x3 matrix)? are they the new cell parameters 'a b and c' that am looking for? and if yes which one would be my a b and c among them Thanks in anticipation of your favourable reply Abolore On Mon, Apr 25, 2011 at 3:58 AM, Emine Kucukbenli wrote: > Dear Abolore, > Sorry I couldnt understand your first question.Please rephrase it. > For the second one: > During the vc-relax run, at each step towards convergence, new cell > parameters are written on the output. Look for CELL_PARAMETERS (a 3x3 > matrix) values.The final one should be the relaxed one. (Please verify > this before progressing further, check stress, pressure ) > > You may want to examine the VCSexample directory and examples therein, > before dong anything , actually. (It is different than example03, > which you have been dong similar calculations till now, in which only > the atomic positions are relaxed) > best, > emine kucukbenli, phd student, sissa, it > > Quoting Abolore Musari : > > > Dear sir, am glad for the info thanks, but first if my celldm(4) = > > -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab) > > where a and b r in bohr, secondly hw do l locate my answer? afta d vc > > relax cos ve done it using example03 of the expresso. THANKS > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110619/e8361fa5/attachment.htm From lapenna.giovanni at gmail.com Sun Jun 19 11:51:53 2011 From: lapenna.giovanni at gmail.com (Giovanni La Penna) Date: Sun, 19 Jun 2011 11:51:53 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: <4DFDB19B.8060605@univ-provence.fr> References: <4DFDB19B.8060605@univ-provence.fr> Message-ID: Dear Pascal and QE-users, In the *.evp (and in stdout) of CP, ekinc (Kel) and actual T are printed, as, respectively, columns 2 and 4 (in *.evp). Kel is the fictitious kinetic energy of electronic variables. Empirically, I found that: Kel/Kion < 1/10 for a reliable CP-MD run, with Kion= 3/2 Ndeg R T . Since Kel is (please confirm) in Ha, R must be converted in Ha/K. Even though the word reliable may be an opinion, when the ratio becomes larger, then Kel starts diverging very quickly (while in the other case only a slow drift occurs). I would be glad if other CP users could confirm this empirical observation. Giovanni La Penna (Cnr-Iccom, Italy) From abmus007 at gmail.com Sun Jun 19 12:51:43 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 19 Jun 2011 05:51:43 -0500 Subject: [Pw_forum] VC RELAX Message-ID: Dear all, In the vc relax example of the expresso l want to ask how the cell parameter (3x3 matrix) of the system are gotten. thanks in anticapation of your favourable reply. Abolore, Phy dept UNAAB From nicola.marzari at materials.ox.ac.uk Sun Jun 19 18:24:28 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sun, 19 Jun 2011 17:24:28 +0100 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm In-Reply-To: <4DFDB19B.8060605@univ-provence.fr> References: <4DFDB19B.8060605@univ-provence.fr> Message-ID: <4DFE22BC.2040008@materials.ox.ac.uk> Dear All, just to clear up a few things - the ensemble-DFT algorithm coded in the CP code is a direct minimization algorithm, to do Born-Oppenheimer molecular dynamics in metallic systems, and not to do Car-Parrinello molecular dynamics (this latter breaks down in the absence of a gap). Hence, the ion dynamics parameters are typical of BOMD (large ionic steps, of the order of 0.5 to 5 fs, i.e. 20 to 200 a.u.), while for the electrons there is no fictitious electronic kinetic energy (ekinc). Although the code has been used very little, it does seem to work (actually very well - we just checked it last week for some tungsten clusters, that were impossible to converge with another of the popular codes, and it did get convergence in ~40 conjugate gradient steps). Pascal, let us know if you encounter problems. nicola On 6/19/11 9:21 AM, pascal boulet wrote: > > Dear Giovanni, > > Humm... hard to say because the data are not printed in the output file. > Here is what I get, for instance: > >>>>> > nfi ekinc temph tempp etot enthal econs > econt vnhh xnhh0 vnhp xnhp0 > nfi tempp E -T.S-mu.nbsp +K_p #Iter > Step 20 0 -502.49200 -502.62143 -502.62143 6 > cg_sub: missed minimum, case 1, iteration 1 > cg_sub: missed minimum, case 1, iteration 2 > cg_sub: missed minimum, case 1, iteration 3 > cg_sub: missed minimum, case 1, iteration 4 > cg_sub: missed minimum, case 1, iteration 5 > NOTE: eigenvalues are not computed without ortho > Occupations : > 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000 1.999999 1.999999 > 1.999999 1.999998 > 1.999997 1.999995 1.999994 1.999989 1.999983 1.999977 1.999958 1.999933 > 1.999884 1.999793 ... 0.001473 0.000546 0.000502 0.000278 0.000134 > 0.000079 0.000033 0.000019 0.000000 > nfi tempp E -T.S-mu.nbsp +K_p #Iter > Step 21 0 -502.49200 -502.62143 -502.62143 6 > > <<<<< > etc. > > > So, there is nothing about ekinc, temph, tempp, ... > > > However, the data "nfi ekinc temph tempp etot enthal > econs econt vnhh xnhh0 vnhp xnhp0" look > like those given in the file xxx.evp (except for one missing column). > If this is right, then in this file ekinc = 0. during the whole > simulation. That's strange! > So, I guess there is something wrong somewhere in my input. > > Pascal > > >> Date: Fri, 17 Jun 2011 10:27:09 +0200 (CEST) >> From: Giovanni La Penna >> Subject: Re: [Pw_forum] CP simulation with ensemble-dft algorithm >> To: PWSCF Forum >> Message-ID: >> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >> >> >> Dear Pascal, >> >> The input shows that you are trying to >> carry the system to 627 K starting with >> random velocities and a time-step of 20 au (about 0.5 fs). >> I expect a huge Kel after a few time-steps, due >> to huge current atomic velocities, not manageable >> with the given time-step. >> Please, tell me (us) if this won't happen. >> >> Giovanni La Penna >> >> > > * > * Anglais > * Fran?ais > > * Anglais > * Fran?ais > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From giannozz at democritos.it Sun Jun 19 23:35:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 19 Jun 2011 23:35:09 +0200 Subject: [Pw_forum] pwscf version 4.3 example 15 error In-Reply-To: References: <9155DEB8-A0AC-4E09-B75B-2F3706B507FD@democritos.it> <94E45583-0E23-4CDC-A950-D87E9F475541@democritos.it> Message-ID: <6D4E9975-94D3-4AE4-8656-3F4CCCDE1407@democritos.it> On Jun 19, 2011, at 10:44 , xu yuehua wrote: > my results of example 15 has a liittle difference in alas.ph.out. > i think it can not be neglected?? the difference between "true" frequencies is very small. The non-zero value for the acoustic frequency is a well-known and hard to solve problem. Those number vary a lot from machine to machine and from version to version, but as long as they are small and disappear by applying the Acoustic Sum Rule, they are not a problem P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From flux_ray12 at 163.com Mon Jun 20 02:56:23 2011 From: flux_ray12 at 163.com (=?UTF-8?Q?GAO=C2=A0Zhe?=) Date: Mon, 20 Jun 2011 08:56:23 +0800 (CST) Subject: [Pw_forum] q not allowed while using q2r.x Message-ID: <5ce70676.7afc.130aa8c5bec.Coremail.flux_ray12@163.com> Dear PWscf Developers and Users: I am using PWscf 4.3.1 at two computers, one is i7-860 with CentOS 5.6 x86_64, another Phenom 1090T with Scientific Linux 6 x86_64. These days, when I calculated phonon, a problem occurred in both of these two computers. After phonon calculation by ph.x, q2r.x showed error " from init : error # 1 q not allowed " while I was changing phonon to real space. My input file is: cat >A0.ph.in <A0.ph.out echo -e " done" cat >A0.q2r.in <A0.q2r.out echo -e " done" The error information in A0.q2r.out is: reading grid info from file A0.dyn0 reading force constants from file A0.dyn1 Dielectric Tensor not found nqs= 1 q= 0.00000000 0.00000000 0.00000000 reading force constants from file A0.dyn2 nqs= 6 q= 0.00000000 0.00000000 0.33345931 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from init : error # 1 q not allowed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The structure is SC with 8 atoms. What should I do to avoid such a problem and overcome it? Thank you. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/30baf55a/attachment.htm From njuxuyuehua at gmail.com Mon Jun 20 03:29:37 2011 From: njuxuyuehua at gmail.com (xu yuehua) Date: Mon, 20 Jun 2011 09:29:37 +0800 Subject: [Pw_forum] raman intensity for few layer graphene Message-ID: hi everyone: Recenlt, i want to calculate the raman intensity fo Few layer graphene.(there are many experimental data). As everyone known, many Few layer graphene is metal or semi-metal. so i am wondering pwscf can calculate these case? thank you ! -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/89f78f1b/attachment.htm From hqzhou at nju.edu.cn Mon Jun 20 05:07:57 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 20 Jun 2011 11:07:57 +0800 Subject: [Pw_forum] VC RELAX References: Message-ID: <922C88D6CF594481902CA9DEE9D899BE@solarflare> Abolore, There are two , actually one, "implicit" methods for defining the matrix: 1. set ibrav = 1 to 14 to define a suitable lattice, then celldm(i), i = 1 to 6, to define the cell parameters; 2. set ibrav again, as well as A, B, C, cosAB, cosAC and cosBC to define cell parameters; There is one explicit method for defining the cell vector matrix, too: set ibrav = 0 with celldm(1) = alat or without celldm(1), then define the three vectors as suitable for your purpose in the CELL_PARAMETER card. For detail, please read the input_PW.html. Manual is always your first aid! zhou huiqun @earth sciences and engineering, nanjing university, china ----- Original Message ----- From: "Abolore Musari" To: Sent: Sunday, June 19, 2011 6:51 PM Subject: [Pw_forum] VC RELAX > Dear all, In the vc relax example of the expresso l want to ask how > the cell parameter (3x3 matrix) of the system are gotten. thanks in > anticapation of your favourable reply. Abolore, Phy dept UNAAB > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From psavita at crlindia.com Mon Jun 20 06:54:18 2011 From: psavita at crlindia.com (psavita at crlindia.com) Date: Mon, 20 Jun 2011 10:24:18 +0530 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/ec0b5436/attachment.htm From yccheng.nju at gmail.com Mon Jun 20 06:54:59 2011 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 20 Jun 2011 07:54:59 +0300 Subject: [Pw_forum] raman intensity for few layer graphene In-Reply-To: References: Message-ID: Have you ever seen any paper calculating Raman Intensity of graphene by using PWscf? If NO, I think the answer for your question is "NO". 2011/6/20 xu yuehua > hi everyone: > Recenlt, i want to calculate the raman intensity fo Few layer > graphene.(there are many experimental data). > As everyone known, many Few layer graphene is metal or semi-metal. so i am > wondering pwscf can calculate these case? > thank you ! > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/bc6be882/attachment.htm From baroni at sissa.it Mon Jun 20 08:01:35 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Jun 2011 08:01:35 +0200 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References:

Message-ID: <7EBA4B00-75E4-4F45-B302-F62DF4BB7109@sissa.it> By comparing MP2 all-electron calculations performed using localized basis sets and free boundary conditions, with DFT pseudopotential calcs, done with plane waves and periodic boundary conditions you have succeeded in making the two calculations as heterogeneous as possible. Well done (converged) calculations should not depend on the basis set, pseudopotential, or boundary conditions, but they certainly will on the level of theory you use. Getting very different results with MP2 and DFT should make you suspect that some kind of inter-molecular correlation effects may play an important role. The first thing I would do is to repeat the calculation with localized basis sets at the DFT level, and see if the structure you obtain matches the one you get with QE. SB On Jun 20, 2011, at 6:54 AM, psavita at crlindia.com wrote: > Dear Prof. Ghosh, > > As per your suggestion, I performed the structure relaxation of LiH--H2O system using a bigger cubic box of dimension 50 a.u. > and I still find H2 abstraction instead of an intramolecular dihydrogen bond. > Do you think the box is still inadequate? > For such systems, would it be better to put some constraints initially? > How do we do this in QE? > > Thanks for your suggestion and best regards, > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > > > -----pw_forum-bounces at pwscf.org wrote: ----- > > > > > > > Dear Savita, > > I am not an expert on these type of systems.......however just a small piece > of advice.....a single molecule of water has a huge dipole moment.....so a > box size of 25 bohr may not be sufficient, until and unless binding to LiH > quenches the dipole moment......so you may like to check whether your box is > sufficiently big.....usually for a single molecule of water one uses about > 35-40 bohr box or can use dipole correction. > > Prasenjit > > On 17 June 2011 11:42, wrote: > > > Hello, > > > > I have been trying to get the optimum structure of LiH..H2O that has an > > intramolecular dihydrogen bond, using pwscf. > > I could get the proper structure earlier using mp2 theory and 6-31++g > > basis. > > > > For pwscf, the species is enclosed in a cubic box of 25 bohr for gamma > > point calculation. > > I tried the pz lda, pbe gga as well we blyp PS for the atoms in this > > system, however, the first and the last > > lead to H2O..LiH, the latter LiH being linear while pbe gives LiH + H2, but > > no dihydrogen bond. Is there any other PS > > that may lead to proper structure? Or is it that plane wave approach does > > not suit systems of this kind? > > > > Thanks in advance and best regards, > > > > Savita Pundlik > > Computational Materials Applied Research Group > > Computational Research Laboratories Ltd., > > Taco House, Damle Path, Off Law College Road > > Pune - 411004, India. > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > PRASENJIT GHOSH, > Assistant Professor, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110617/17d0a776/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 48, Issue 45 > **************************************** > > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/df976ac6/attachment-0001.htm From prasenjit.jnc at gmail.com Mon Jun 20 08:29:51 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 20 Jun 2011 11:59:51 +0530 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References:

Message-ID: Dear Savita, It is hard to tell....You can try plotting total energy vs. the box size and see how the energies are changing....if the change is of the order of a meV then I would say that your calculations are converged wrt box size....... However, I think it is good idea to follow Stefano's suggestion........using the same basis set you have been using for your mp2 calculation, you try to calculate the same thing using DFT and see whether you get similar results.....if you get different results, then it will suggest that DFT is not properly describing the electronic correlations. Prasenjit On 20 June 2011 10:24, wrote: > Dear Prof. Ghosh, > > As per your suggestion, I performed the structure relaxation of LiH--H2O > system using a bigger cubic box of dimension 50 a.u. > and I still find H2 abstraction instead of an intramolecular dihydrogen > bond. > Do you think the box is still inadequate? > For such systems, would it be better to put some constraints initially? > How do we do this in QE? > > Thanks for your suggestion and best regards, > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > > > -----pw_forum-bounces at pwscf.org wrote: ----- > > > > > > > Dear Savita, > > I am not an expert on these type of systems.......however just a small > piece > of advice.....a single molecule of water has a huge dipole moment.....so a > box size of 25 bohr may not be sufficient, until and unless binding to LiH > quenches the dipole moment......so you may like to check whether your box > is > sufficiently big.....usually for a single molecule of water one uses about > 35-40 bohr box or can use dipole correction. > > Prasenjit > > On 17 June 2011 11:42, wrote: > > > Hello, > > > > I have been trying to get the optimum structure of LiH..H2O that has an > > intramolecular dihydrogen bond, using pwscf. > > I could get the proper structure earlier using mp2 theory and 6-31++g > > basis. > > > > For pwscf, the species is enclosed in a cubic box of 25 bohr for gamma > > point calculation. > > I tried the pz lda, pbe gga as well we blyp PS for the atoms in this > > system, however, the first and the last > > lead to H2O..LiH, the latter LiH being linear while pbe gives LiH + H2, > but > > no dihydrogen bond. Is there any other PS > > > that may lead to proper structure? Or is it that plane wave approach does > > not suit systems of this kind? > > > > Thanks in advance and best regards, > > > > Savita Pundlik > > Computational Materials Applied Research Group > > Computational Research Laboratories Ltd., > > Taco House, Damle Path, Off Law College Road > > Pune - 411004, India. > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > PRASENJIT GHOSH, > Assistant Professor, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110617/17d0a776/attachment-0001.htm > > > ------------------------------ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 48, Issue 45 > **************************************** > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/90bf5020/attachment.htm From jibanez008 at ikasle.ehu.es Mon Jun 20 09:21:23 2011 From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz) Date: Mon, 20 Jun 2011 09:21:23 +0200 Subject: [Pw_forum] Testing pseudopotential In-Reply-To: <642031.52209.qm@web28510.mail.ukl.yahoo.com> References: <642031.52209.qm@web28510.mail.ukl.yahoo.com> Message-ID: Hi Padmaja, I think that in general it cannot be said that a PP is good or bad looking just at the value you mention of AE-PS. Maybe you can try testing your PP in some system in which you know the answer, for instance calculate the band structure of bulk Cr and compare with known results. I see that in the repository of QE PP there are a couple of scalar-relativistic Cr PP's, you can check if their band structures match with yours (with lspinorb=.false. in the case of your fully relat PP). Also you can try to compare this band structure with some all-electron band structure. And finally, it is very good to compare the lattice parameter obtained with your PP in bulk Cr with the real value, I think they should differ at most in 5%. Hope this helps, -- ?======================================== Julen Iba?ez Azpiroz Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015326 Mail: jibanez008 at ikasle.ehu.es ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/3dbf194c/attachment.htm From pascal.boulet at univ-provence.fr Mon Jun 20 10:53:52 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Mon, 20 Jun 2011 10:53:52 +0200 Subject: [Pw_forum] CP simulation with ensemble-dft algorithm Message-ID: <4DFF0AA0.9010608@univ-provence.fr> Dear Nicola, I confirm that I have no problem to converge the density with the ensemble-DFT algorithm. I am working on silver nanoparticules. With a small one (13 atoms only) the convergence is reach within 10 cycles. I am going to try with a bigger one soon (38 atoms). Regards Pascal * * Anglais * Fran?ais * Anglais * Fran?ais From pascal.boulet at univ-provence.fr Mon Jun 20 11:23:55 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Mon, 20 Jun 2011 11:23:55 +0200 Subject: [Pw_forum] optimized cell parameters with pw version 4.2.1 versus 4.3.1 Message-ID: <4DFF11AB.6080701@univ-provence.fr> Dear all, I am optimizing the cell parameters of some compounds. With pw.x version 4.2.1 the optimized parameters are given at the end of the output. It seems that it is not the case with version 4.3.1, even with verbosity='high'. Is it possible to reactivate the priniting of the optimized parameters? Regards Pascal From psavita at crlindia.com Mon Jun 20 11:44:46 2011 From: psavita at crlindia.com (psavita at crlindia.com) Date: Mon, 20 Jun 2011 15:14:46 +0530 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/c97a32de/attachment.htm From pascal.boulet at univ-provence.fr Mon Jun 20 11:42:05 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Mon, 20 Jun 2011 11:42:05 +0200 Subject: [Pw_forum] optimized cell parameters with pw version 4.2.1 versus 4.3.1 Message-ID: <4DFF15ED.9070905@univ-provence.fr> Hello again, Please, forget my previous message: I did not noticed there is a final SCF cycle at the optimized structure! Sorry for that. regards Pascal From giuseppe.mattioli at mlib.ism.cnr.it Mon Jun 20 13:56:28 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Mon, 20 Jun 2011 13:56:28 +0200 Subject: [Pw_forum] Suitable pseudopotentials for LiH..H2O In-Reply-To: References:

Message-ID: <20110620135628.yr2bfrkcg48wsg8k@webmail.sic.rm.cnr.it> Dear Savita It is generally suggested that high-level post-HF methods (as MP2) account for van der Waals interactions far better than standard DFT calculations (i.e., LDA or GGA calculations). Within QE (actually, by using pw.x), you could try to use either a semi-empirical dispersion correction (london=.true. flag), or an improved xc functional containing a long-range correlation contribution (input_dft="vdw-df" flag) in order to simulate van der Waals interactions in a reliable way. HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting psavita at crlindia.com: > Dear Prof. Ghosh, > > I should have done this before, but now I have performed structure > relaxation of LiH..H2O using DFT with 6-31++g basis set, > the same one that was used for mp2 calculations, and found that DFT > does not give intramolecular H-bond. > Thus, in general, DFT does not seem suitable for such systems and > hence there has been difficulty with QE. > > I agree with Paolo that the problem is not with plane wave approach. > > Thanks once again and best regards, > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > -----pw_forum-bounces at pwscf.org wrote: ----- > > To: pw_forum at pwscf.org > From: pw_forum-request at pwscf.org > Sent by: pw_forum-bounces at pwscf.org > Date: 06/20/2011 01:17PM > Subject: Pw_forum Digest, Vol 48, Issue 51 > > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum[1] > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > Today's Topics: > > 1. Re: Suitable pseudopotentials for LiH..H2O (Prasenjit Ghosh) > 2. Re: Testing pseudopotential (Julen Ibanez Azpiroz) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Jun 2011 11:59:51 +0530 > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] Suitable pseudopotentials for LiH..H2O > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Savita, > > It is hard to tell....You can try plotting total energy vs. the box > size and > see how the energies are changing....if the change is of the order of > a meV > then I would say that your calculations are converged wrt box > size....... > > However, I think it is good idea to follow Stefano's > suggestion........using > the same basis set you have been using for your mp2 calculation, you > try to > calculate the same thing using DFT and see whether you get similar > results.....if you get different results, then it will suggest that > DFT is > not properly describing the electronic correlations. > > Prasenjit > > On 20 June 2011 10:24, wrote: > >> Dear Prof. Ghosh, >> >> As per your suggestion, I performed the structure relaxation of > LiH--H2O >> system using a bigger cubic box of dimension 50 a.u. >> and I still find H2 abstraction instead of an intramolecular > dihydrogen >> bond. >> Do you think the box is still inadequate? >> For such systems, would it be better to put some constraints > initially? >> How do we do this in QE? >> >> Thanks for your suggestion and best regards, >> >> Savita Pundlik >> Computational Materials Applied Research Group >> Computational Research Laboratories Ltd., >> Taco House, Damle Path, Off Law College Road >> Pune - 411004, India. >> >> >> >> -----pw_forum-bounces at pwscf.org wrote: ----- >> >> >> >> >> >> >> Dear Savita, >> >> I am not an expert on these type of systems.......however just a > small >> piece >> of advice.....a single molecule of water has a huge dipole > moment.....so a >> box size of 25 bohr may not be sufficient, until and unless binding > to LiH >> quenches the dipole moment......so you may like to check whether > your box >> is >> sufficiently big.....usually for a single molecule of water one > uses about >> 35-40 bohr box or can use dipole correction. >> >> Prasenjit >> >> On 17 June 2011 11:42, > wrote: >> >> > Hello, >> > >> > I have been trying to get the optimum structure of LiH..H2O that > has an >> > intramolecular dihydrogen bond, using pwscf. >> > I could get the proper structure earlier using mp2 theory and > 6-31++g >> > basis. >> > >> > For pwscf, the species is enclosed in a cubic box of 25 bohr for > gamma >> > point calculation. >> > I tried the pz lda, pbe gga as well we blyp PS for the atoms in > this >> > system, however, the first and the last >> > lead to H2O..LiH, the latter LiH being linear while pbe gives LiH > + H2, >> but >> > no dihydrogen bond. Is there any other PS >> >> > that may lead to proper structure? Or is it that plane wave > approach does >> > not suit systems of this kind? >> > >> > Thanks in advance and best regards, >> > >> > Savita Pundlik >> > Computational Materials Applied Research Group >> > Computational Research Laboratories Ltd., >> > Taco House, Damle Path, Off Law College Road >> > Pune - 411004, India. >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum[2] >> > >> > >> >> >> -- >> PRASENJIT GHOSH, >> Assistant Professor, >> IISER Pune, >> First floor, Central Tower, Sai Trinity Building >> Garware Circle, Sutarwadi, Pashan >> Pune, Maharashtra 411021, India >> >> Phone: +91 (20) 2590 8203 >> Fax: +91 (20) 2589 9790 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > http://www.democritos.it/pipermail/pw_forum/attachments/20110617/17d0a776/attachment-0001.htm[3] >> >> >> ------------------------------ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum[4] >> >> >> End of Pw_forum Digest, Vol 48, Issue 45 >> **************************************** >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum[5] >> >> > > -- > PRASENJIT GHOSH, > Assistant Professor, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110620/90bf5020/attachment.html[6] > > > ------------------------------ > > Message: 2 > Date: Mon, 20 Jun 2011 09:21:23 +0200 > From: Julen Ibanez Azpiroz > Subject: Re: [Pw_forum] Testing pseudopotential > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Hi Padmaja, > > I think that in general it cannot be said that a PP is good or bad > looking > just at the value you mention of AE-PS. Maybe you can try testing > your PP in > some system in which you know the answer, for instance calculate the > band > structure of bulk Cr and compare with known results. I see that in > the > repository of QE PP there are a couple of scalar-relativistic Cr > PP's, you > can check if their band structures match with yours (with > lspinorb=.false. > in the case of your fully relat PP). Also you can try to compare this > band > structure with some all-electron band structure. And finally, it is > very > good to compare the lattice parameter obtained with your PP in bulk > Cr with > the real value, I think they should differ at most in 5%. Hope this > helps, > > -- > > ?======================================== > Julen Iba?ez Azpiroz > Materia Kondentsatuaren Fisika Saila > Zientzia eta Teknologia Fakultatea > Euskal Herriko Unibertsitatea > 644 Posta Kutxatila, 48080 Bilbo, Spain > > Telefonoa: +34 946015326 > Mail: jibanez008 at ikasle.ehu.es > ======================================== > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110620/3dbf194c/attachment-0001.htm[7] > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum[8] > > End of Pw_forum Digest, Vol 48, Issue 51 > **************************************** > > > > Links: > ------ > [1] http://www.democritos.it/mailman/listinfo/pw_forum > [2] http://www.democritos.it/mailman/listinfo/pw_forum > [3] > http://www.democritos.it/pipermail/pw_forum/attachments/20110617/17d0a776/attachment-0001.htm > [4] http://www.democritos.it/mailman/listinfo/pw_forum > [5] http://www.democritos.it/mailman/listinfo/pw_forum > [6] > http://www.democritos.it/pipermail/pw_forum/attachments/20110620/90bf5020/attachment.html > [7] > http://www.democritos.it/pipermail/pw_forum/attachments/20110620/3dbf194c/attachment-0001.htm > [8] http://www.democritos.it/mailman/listinfo/pw_forum > From gm030212 at gmail.com Mon Jun 20 14:19:11 2011 From: gm030212 at gmail.com (Fen Hong) Date: Mon, 20 Jun 2011 21:19:11 +0900 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error Message-ID: Dear all I tried to generate Ti norm conserving semi-core pseudopotential using PBE functional. The 3s 3p orbitals are supposed to include. But there is error showing " from ld1_readin : error # 1 Two wavefunctions for the same l" I checked the examples in the atomic_doc and did not find this kind input. so does there anyone know how to solve the problem. Thank you very much. The input file is " &input iswitch=3, rlderiv=1.5, eminld=-8.0, emaxld=5.0, deld=0.01d0, nld=3, rel=1, zed=22.0, config="[Ne] 3s2 3p6 3d2 4s2 4p-1" dft='PBE', / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/73074718/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Jun 20 14:46:19 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 20 Jun 2011 14:46:19 +0200 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: In data 20 giugno 2011 alle ore 14:19:11, Fen Hong ha scritto: > The input file is Dear Fen Hong, the part of the input you attached is perfectly correct; the error must be in the rest of the input. best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From gm030212 at gmail.com Mon Jun 20 16:03:47 2011 From: gm030212 at gmail.com (Fen Hong) Date: Mon, 20 Jun 2011 23:03:47 +0900 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: Dear Paulatto Thank you very much. I paste the whole input now. &input iswitch=3, rlderiv=1.5, eminld=-8.0, emaxld=5.0, deld=0.01d0, nld=3, rel=1, zed=22.0, config="[Ne] 3s2 3p6 3d2 4s2 4p-1" dft='PBE', / &inputp lloc=1, pseudotype=1, file_pseudopw='Ti-pbe-semi.UPF', zval=12.0, tm = .true. / 5 3S 1 0 2.00 0.00 2.20 2.20 3P 2 1 6.00 0.00 2.20 2.20 3D 3 2 2.00 0.00 2.20 2.20 4S 1 0 2.00 0.00 2.40 2.40 4P 2 1 0.00 -0.10 2.40 2.40 2011/6/20 Lorenzo Paulatto > In data 20 giugno 2011 alle ore 14:19:11, Fen Hong ha > scritto: > > The input file is > > Dear Fen Hong, > the part of the input you attached is perfectly correct; the error must be > in the rest of the input. > > best regards > > > -- > Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/c0121a69/attachment.htm From chengyu.young at gmail.com Mon Jun 20 16:35:40 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 20 Jun 2011 10:35:40 -0400 Subject: [Pw_forum] Setting parameters about carbon nanotube/metal system Message-ID: Dear All, I am now working on a project about carbon nanotube interacting with metal atoms. And I've got some problems: 1. I forgot how I defined the celldm parameters. Generally, I use a script for a (6,6) carbon nanotube like this: &SYSTEM ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 27,ntyp = 2,ecutwfc = 75 , occupations='smearing', smearing='gaussian', degauss=0.02 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF Cu 63.55 Cu.pz-d-rrkjus.UPF The celldm(1) and celldm(3), I don't quite understand their meaning and how they came out. Although I could calculate the lattice parameters for carbon nanotube, like the diameter d and the translation parameter t, I still couldn't make connections between these parameters and the values I got here. I forgot how I got them, and now I need to calculate a (8,8) cnt, while I need a larger space between the carbon nanotubes, cause they are now too crowded using the same structure data. I don't know how could I change them. 2. I don't know what kind of pseudopotential I should choose, there are several potentials for each element, while I am just looking for a general calculation. 3. I keep the other parameters like the ecutwfc, the conv-thr, and the mixing-beta the same for different metal elements, does that do harm to my calculations? I am not quite sure. Well, thank you for your time. I know my questions are somehow silly, but hope one could teach me. Thanks. Regards. Chengyu Yang MMAE department, University of Central Florida USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/961cacc7/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Jun 20 16:37:36 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 20 Jun 2011 16:37:36 +0200 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: In data 20 giugno 2011 alle ore 16:03:47, Fen Hong ha scritto: > pseudotype=1, I think just setting pseudotype=2 should do the trick. best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From izaakw89 at yahoo.com Tue Jun 21 01:15:48 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 20 Jun 2011 16:15:48 -0700 (PDT) Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO Message-ID: <392694.27520.qm@web43405.mail.sp1.yahoo.com> Thanks for all the responses. I guess it was my outdated version of XCrySDen that was causing the problem. On Fri, Jun 17 13:28:47 CEST 2011, Tone Kokalj wrote: >Why don't you try with the new version: >http://www.xcrysden.org/download/xc-1.5.24-linux_x86_64-semishared.tar.gz I downloaded this version and used ./xcConfigure to configure the program. Because my previous version was still installed, I had to manually put the following lines into my .bashrc file: #------------------------------------------------------------------------ # this is for XCRYSDEN 1.5.24; added by XCRYSDEN installation on # Mon Jun 20 16:22:44 PDT 2011 #------------------------------------------------------------------------ XCRYSDEN_TOPDIR=/home/Izaak/XCrySDen/XCrySDen-1.5.24-bin-semishared XCRYSDEN_SCRATCH=/home/Izaak/xcrys-tmp/ export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" After using the command ". ~/.bashrc" to source it, I try running xcrysden and this is what is produced: +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*-----------------------------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2009 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.5.24 Please report bugs to: Tone.Kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. TCL_LIBRARY=/home/Izaak/XCrySDen/XCrySDen-1.5.24-bin-semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home/Izaak/XCrySDen/XCrySDen-1.5.24-bin-semishared XCRYSDEN_SCRATCH=/home/Izaak/xcrys-tmp/ ./xcrysden: line 224: /home/Izaak/XCrySDen/XCrySDen-1.5.24-bin-semishared/bin/xcrys: cannot execute binary file What does this error mean? What can I do to correct this? Also, I tried compiling XCrySDen-1.5.24-bin-shared but the same error occurred. Thanks -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110620/095cd012/attachment-0001.htm From gm030212 at gmail.com Tue Jun 21 02:45:21 2011 From: gm030212 at gmail.com (Fen Hong) Date: Tue, 21 Jun 2011 09:45:21 +0900 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: Thank you very much, But there is still something wrong. another error showed " Computing logarithmic derivative in 1.49590 WARNING! Expected number of nodes: 0= 2- 1- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) WARNING! Expected number of nodes: 0= 3- 2- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from run_pseudo : error # 1 Errors in PS-KS equation " On the Pw_forum list, there is such kind of error, the answer is "The pseudization radii shouldn't differ too much either" The radii I used is similar, and it still not correct. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/6cb62c70/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue Jun 21 09:01:53 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 21 Jun 2011 09:01:53 +0200 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: In data 21 giugno 2011 alle ore 02:45:21, Fen Hong ha scritto: > WARNING! Expected number of nodes: 0= 2- 1- 1, number of > nodes found: 1. > Setting wfc to zero for this iteration. > (This warning will only be printed once per wavefunction) > > > WARNING! Expected number of nodes: 0= 3- 2- 1, number of > nodes found: 1. > Setting wfc to zero for this iteration. > (This warning will only be printed once per wavefunction) In norm conserving pseudopotentials, pseduo-wavefunctions have to be orthogonal to each other. Thus, if they have the same angular omentum they need to have a different number of nodes. In short, change these two lines 4S 1 0 2.00 0.00 2.40 2.40 4P 2 1 0.00 -0.10 2.40 2.40 to 4S 2 0 2.00 0.00 2.40 2.40 4P 3 1 0.00 -0.10 2.40 2.40 regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From siobhan.ohalloran at tyndall.ie Tue Jun 21 13:12:41 2011 From: siobhan.ohalloran at tyndall.ie (Siobhan O'Halloran) Date: Tue, 21 Jun 2011 12:12:41 +0100 Subject: [Pw_forum] Reading fildvscf Message-ID: <2DD66562E02F11409F54329AC3ECF4C57CC534@MAIL.tyndall.ie> Hi all, I would like to read the variation of the potential from fildvscf. As somebody who has little programming experience, how would I do that? Regards, Siobhan O Halloran Materials Theory Group Tyndall National Institute Cork, Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/1a214a7f/attachment.htm From jorge.gallardo at cab.cnea.gov.ar Tue Jun 21 15:00:02 2011 From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar) Date: Tue, 21 Jun 2011 10:00:02 -0300 (ART) Subject: [Pw_forum] filepp(1) too short In-Reply-To: References:

<59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar> Message-ID: <55984.200.0.233.52.1308661202.squirrel@mail.cab.cnea.gov.ar> Hello all Someone knows how to enlarge the data matrix stored in filepp(1), when calculating electronic density using pp.x? That file is limited up to 140 MB (using iflag = 3, output_format = 3) so it stores a 3d-matrix 432x432x45, but I would need a biger one. thank you in advance! ____ Lic. Jorge A. Garc?a Gallardo Materiales Metalicos y Nanoestructurados TeMaDi Bariloche Atomic Center CNEA From baroni at sissa.it Tue Jun 21 15:47:00 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 21 Jun 2011 15:47:00 +0200 Subject: [Pw_forum] filepp(1) too short In-Reply-To: <55984.200.0.233.52.1308661202.squirrel@mail.cab.cnea.gov.ar> References:

<59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar> <55984.200.0.233.52.1308661202.squirrel@mail.cab.cnea.gov.ar> Message-ID: <1E3BD8CD-C0D7-4ACF-A00D-423F0D60FD0D@sissa.it> sounds like a system limitation, not anything intrinsic to pp.x (or so I believe ...) SB On Jun 21, 2011, at 3:00 PM, jorge.gallardo at cab.cnea.gov.ar wrote: > Hello all > > Someone knows how to enlarge the data matrix stored in filepp(1), when > calculating electronic density using pp.x? That file is limited up to 140 > MB (using iflag = 3, output_format = 3) so it stores a 3d-matrix > 432x432x45, but I would need a biger one. > > thank you in advance! > > > ____ > > Lic. Jorge A. Garc?a Gallardo > Materiales Metalicos y Nanoestructurados > TeMaDi > Bariloche Atomic Center > CNEA > > _______________________________________________ > 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://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/77fa133b/attachment.htm From vv0210 at gmail.com Tue Jun 21 16:40:02 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Tue, 21 Jun 2011 10:40:02 -0400 Subject: [Pw_forum] init_london Error Message-ID: Dear All, I am trying to relax my WS2 unit cell structure using vc-relax (using PBE pps) and I want to include disperson corrections to it. So, I tried using the london flag = .true. However, on starting my job I got an error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from init_london : error # 1 atom W not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% After going through mm_dispersion.f90, I found that the vdw_radius and c_6 parameters are given for first 54 atoms only (which corresponds to first 5 periods of periodic table). Tungsten (W), with atomic number of 74 is in 6th period. I emailed Prof. Stefan Grimme (author of the references that are mentioned in mm_dispersion.f90) if anything was further pursued. He replied mentioning that they have approached this problem further and referred me to his website, http://toc.uni-muenster.de/DFTD3/ and told me that this has already been implemented into major QM codes. Mentioning that, I have few questions. 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. 2. Are there any other ways to incorporate dispersion interactions in calculations in DFT. Currently, I am running my simulations on 4.2 version of the code that I downloaded few months ago. I would high appreciate your insights in how should I go about solving this problem regarding dispersion interactions in Tungsten. Looking forward for a positive reply. Best Regards, Vikas Varshney, Computational Materials Scientist, Wright-Patterson Air Force Base, Dayton-OH (USA). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/c01661b2/attachment.htm From ttduyle at gmail.com Tue Jun 21 16:51:03 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 21 Jun 2011 10:51:03 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: References: Message-ID: Dear Vikas, One simplest thing you can do is to read the DFT-D2 part of DFT-D3 code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/) You will be able to find all necessary coefficients for all atoms with Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE, then you are good to go. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney wrote: > Dear All, > > I am trying to relax my WS2 unit cell structure using vc-relax (using PBE > pps) and I want to include disperson corrections to it. So, I tried using > the london flag = .true. However, on starting my job I got an error > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > ???? from? init_london? : error #???????? 1 > ???? atom W?? not found > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > After going through mm_dispersion.f90, I found that the vdw_radius and c_6 > parameters are given for first 54 atoms only (which corresponds to first 5 > periods of periodic table). Tungsten (W), with atomic number of 74 is in 6th > period. > > I emailed Prof. Stefan Grimme (author of the references that are mentioned > in mm_dispersion.f90) if anything was further pursued. He replied mentioning > that they have approached this problem further and referred me to his > website, > > http://toc.uni-muenster.de/DFTD3/ > > and told me that this has already been implemented into major QM codes. > > Mentioning that, I have few questions. > 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. > 2. Are there any other ways to incorporate dispersion interactions in > calculations in DFT. > > Currently, I am running my simulations on 4.2 version of the code that I > downloaded few months ago. I would high appreciate your insights in how > should I go about solving this problem regarding dispersion interactions in > Tungsten. > > Looking forward for a positive reply. > > Best Regards, > > Vikas Varshney, > Computational Materials Scientist, > Wright-Patterson Air Force Base, Dayton-OH (USA). > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From prasenjit.jnc at gmail.com Tue Jun 21 17:09:03 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 21 Jun 2011 20:39:03 +0530 Subject: [Pw_forum] Estimation of cpu time required without actually doing the calculation Message-ID: Dear all, Is there some way to estimate the time required for doing an scf iteration using pw.x, without actually performing the calculation ? I tried to make an estimate following the guideline given in the manual and compared it with the actual CPU time required......the two results are not matching......I am getting an abnormally high estimate of the CPU time required........most probably I am doing something wrong. By the way, in what units will I get the time by using the procedure mentioned in the manual? With regards, Prasenjit -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/cebad61d/attachment.htm From vv0210 at gmail.com Tue Jun 21 17:27:55 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Tue, 21 Jun 2011 11:27:55 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: References:

Message-ID: Dear Duy, Thank you very much for the input. I will look into that today itself. Best Regards, Vikas On Tue, Jun 21, 2011 at 10:51 AM, Duy Le wrote: > Dear Vikas, > One simplest thing you can do is to read the DFT-D2 part of DFT-D3 > code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/) > You will be able to find all necessary coefficients for all atoms with > Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE, > then you are good to go. > -------------------------------------------------- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney wrote: > > Dear All, > > > > I am trying to relax my WS2 unit cell structure using vc-relax (using PBE > > pps) and I want to include disperson corrections to it. So, I tried using > > the london flag = .true. However, on starting my job I got an error > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from init_london : error # 1 > > atom W not found > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > After going through mm_dispersion.f90, I found that the vdw_radius and > c_6 > > parameters are given for first 54 atoms only (which corresponds to first > 5 > > periods of periodic table). Tungsten (W), with atomic number of 74 is in > 6th > > period. > > > > I emailed Prof. Stefan Grimme (author of the references that are > mentioned > > in mm_dispersion.f90) if anything was further pursued. He replied > mentioning > > that they have approached this problem further and referred me to his > > website, > > > > http://toc.uni-muenster.de/DFTD3/ > > > > and told me that this has already been implemented into major QM codes. > > > > Mentioning that, I have few questions. > > 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. > > 2. Are there any other ways to incorporate dispersion interactions in > > calculations in DFT. > > > > Currently, I am running my simulations on 4.2 version of the code that I > > downloaded few months ago. I would high appreciate your insights in how > > should I go about solving this problem regarding dispersion interactions > in > > Tungsten. > > > > Looking forward for a positive reply. > > > > Best Regards, > > > > Vikas Varshney, > > Computational Materials Scientist, > > Wright-Patterson Air Force Base, Dayton-OH (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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/88b07477/attachment-0001.htm From ar_ma86 at libero.it Tue Jun 21 19:41:07 2011 From: ar_ma86 at libero.it (ar_ma86 at libero.it) Date: Tue, 21 Jun 2011 19:41:07 +0200 (CEST) Subject: [Pw_forum] Smearing and tot_magnetization Message-ID: <19657556.2129651308678067087.JavaMail.defaultUser@defaultHost> Hi guys, I'm new with pw and I've got a question. It seems to me that for a spin polarized calculation the program has errors if I try to impose occupation equation to smearing and tot_magnetization fixed for a certain value. I guess that fixing total magnetization the program fixes the occupation numbers of the bands and so it cannot make a smearing. But is it correct? are the tow options compatible or not? Thanks to anyone who's gonna answer. Hope to enjoy pw :) Bye From vv0210 at gmail.com Tue Jun 21 21:19:06 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Tue, 21 Jun 2011 15:19:06 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: References:

Message-ID: Dear Duy, All, I have converted the R0 from the dftd3.f code to QE code (from Angs to Bohr with 1.1 further scaling factor). However, I dont know what is the scaling factor that is used for C6 in mm_dispersion.f90. Any insight will be highly appreciated. Best Regards, Vikas Varshney, Computational Materials Scientist, Wright-Patterson Air Force Base, Dayton-OH (USA). On Tue, Jun 21, 2011 at 11:27 AM, Vikas Varshney wrote: > Dear Duy, > Thank you very much for the input. I will look into that today itself. > > Best Regards, > Vikas > > > On Tue, Jun 21, 2011 at 10:51 AM, Duy Le wrote: > >> Dear Vikas, >> One simplest thing you can do is to read the DFT-D2 part of DFT-D3 >> code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/) >> You will be able to find all necessary coefficients for all atoms with >> Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE, >> then you are good to go. >> -------------------------------------------------- >> Duy Le >> PhD Candidate >> Department of Physics >> University of Central Florida. >> >> "Men don't need hand to do things" >> >> >> >> On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney >> wrote: >> > Dear All, >> > >> > I am trying to relax my WS2 unit cell structure using vc-relax (using >> PBE >> > pps) and I want to include disperson corrections to it. So, I tried >> using >> > the london flag = .true. However, on starting my job I got an error >> > >> > >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> > from init_london : error # 1 >> > atom W not found >> > >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> > >> > After going through mm_dispersion.f90, I found that the vdw_radius and >> c_6 >> > parameters are given for first 54 atoms only (which corresponds to first >> 5 >> > periods of periodic table). Tungsten (W), with atomic number of 74 is in >> 6th >> > period. >> > >> > I emailed Prof. Stefan Grimme (author of the references that are >> mentioned >> > in mm_dispersion.f90) if anything was further pursued. He replied >> mentioning >> > that they have approached this problem further and referred me to his >> > website, >> > >> > http://toc.uni-muenster.de/DFTD3/ >> > >> > and told me that this has already been implemented into major QM codes. >> > >> > Mentioning that, I have few questions. >> > 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. >> > 2. Are there any other ways to incorporate dispersion interactions in >> > calculations in DFT. >> > >> > Currently, I am running my simulations on 4.2 version of the code that I >> > downloaded few months ago. I would high appreciate your insights in how >> > should I go about solving this problem regarding dispersion interactions >> in >> > Tungsten. >> > >> > Looking forward for a positive reply. >> > >> > Best Regards, >> > >> > Vikas Varshney, >> > Computational Materials Scientist, >> > Wright-Patterson Air Force Base, Dayton-OH (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 >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110621/21d02100/attachment.htm From giannozz at democritos.it Tue Jun 21 21:45:18 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 21 Jun 2011 21:45:18 +0200 Subject: [Pw_forum] Reading fildvscf In-Reply-To: <2DD66562E02F11409F54329AC3ECF4C57CC534@MAIL.tyndall.ie> References: <2DD66562E02F11409F54329AC3ECF4C57CC534@MAIL.tyndall.ie> Message-ID: <9C2ACA16-2A5D-4BDB-8CB2-581C80EF66A8@democritos.it> On Jun 21, 2011, at 13:12 , Siobhan O'Halloran wrote: > I would like to read the variation of the potential from fildvscf. > As somebody who has little programming experience, how would I do > that? > as a rule, binary files must be read exactly in the same way as they are written P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Jun 21 21:52:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 21 Jun 2011 21:52:19 +0200 Subject: [Pw_forum] Smearing and tot_magnetization In-Reply-To: <19657556.2129651308678067087.JavaMail.defaultUser@defaultHost> References: <19657556.2129651308678067087.JavaMail.defaultUser@defaultHost> Message-ID: <978BE797-1C99-44C0-B6E8-202516988C5E@democritos.it> On Jun 21, 2011, at 19:41 , ar_ma86 at libero.it wrote: > I'm new with pw definitely so: http://www.quantum-espresso.org/wiki/index.php/Pw_users, notably the second item. > I guess that fixing total magnetization the program fixes the > occupation numbers of the bands and so it cannot make a > smearing. But is it correct? it is > are the two options compatible or not? no P. -- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ttduyle at gmail.com Tue Jun 21 23:52:13 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 21 Jun 2011 17:52:13 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: References:

Message-ID: I don't remember. You can always calculate it easily: the ratio between C6 (or R0) of Cacbon in mm_dispersion.f90 and in dft-d3 code will give you an idea how to convert them. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, Jun 21, 2011 at 3:19 PM, Vikas Varshney wrote: > Dear Duy, All, > I have converted the R0 from the dftd3.f code to QE code (from Angs to Bohr > with 1.1 further scaling factor). However, I dont know what is the scaling > factor that is used for C6 in mm_dispersion.f90. Any insight will be highly > appreciated. > > Best Regards, > > Vikas Varshney, > Computational Materials Scientist, > Wright-Patterson Air Force Base, Dayton-OH (USA). > > On Tue, Jun 21, 2011 at 11:27 AM, Vikas Varshney wrote: >> >> Dear Duy, >> Thank you very much for the input. I will look into that today itself. >> >> Best Regards, >> Vikas >> >> On Tue, Jun 21, 2011 at 10:51 AM, Duy Le wrote: >>> >>> Dear Vikas, >>> One simplest thing you can do is to read the DFT-D2 part of DFT-D3 >>> code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/) >>> You will be able to find all necessary coefficients for all atoms with >>> Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE, >>> then you are good to go. >>> -------------------------------------------------- >>> Duy Le >>> PhD Candidate >>> Department of Physics >>> University of Central Florida. >>> >>> "Men don't need hand to do things" >>> >>> >>> >>> On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney >>> wrote: >>> > Dear All, >>> > >>> > I am trying to relax my WS2 unit cell structure using vc-relax (using >>> > PBE >>> > pps) and I want to include disperson corrections to it. So, I tried >>> > using >>> > the london flag = .true. However, on starting my job I got an error >>> > >>> > >>> > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> > ???? from? init_london? : error #???????? 1 >>> > ???? atom W?? not found >>> > >>> > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> > >>> > After going through mm_dispersion.f90, I found that the vdw_radius and >>> > c_6 >>> > parameters are given for first 54 atoms only (which corresponds to >>> > first 5 >>> > periods of periodic table). Tungsten (W), with atomic number of 74 is >>> > in 6th >>> > period. >>> > >>> > I emailed Prof. Stefan Grimme (author of the references that are >>> > mentioned >>> > in mm_dispersion.f90) if anything was further pursued. He replied >>> > mentioning >>> > that they have approached this problem further and referred me to his >>> > website, >>> > >>> > http://toc.uni-muenster.de/DFTD3/ >>> > >>> > and told me that this has already been implemented into major QM codes. >>> > >>> > Mentioning that, I have few questions. >>> > 1. I wanted to ask if QE has incorporated the additions DFT-D, >>> > recently. >>> > 2. Are there any other ways to incorporate dispersion interactions in >>> > calculations in DFT. >>> > >>> > Currently, I am running my simulations on 4.2 version of the code that >>> > I >>> > downloaded few months ago. I would high appreciate your insights in how >>> > should I go about solving this problem regarding dispersion >>> > interactions in >>> > Tungsten. >>> > >>> > Looking forward for a positive reply. >>> > >>> > Best Regards, >>> > >>> > Vikas Varshney, >>> > Computational Materials Scientist, >>> > Wright-Patterson Air Force Base, Dayton-OH (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 >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From gm030212 at gmail.com Wed Jun 22 03:44:57 2011 From: gm030212 at gmail.com (Fen Hong) Date: Wed, 22 Jun 2011 10:44:57 +0900 Subject: [Pw_forum] Norm-conserving semi-core pseudopotential generation error In-Reply-To: References: Message-ID: Thank you very much. But there is still error "WARNING! Expected number of nodes: 0= 3- 2- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from run_pseudo : error # 1 Errors in PS-KS equation " So I think I need read the details about the pseudopotential generation. Thank you very much again -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110622/d79fb05a/attachment.htm From subhra at iitg.ernet.in Wed Jun 22 03:04:16 2011 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Wed, 22 Jun 2011 06:34:16 +0530 (IST) Subject: [Pw_forum] Smearing and tot_magnetization In-Reply-To: <978BE797-1C99-44C0-B6E8-202516988C5E@democritos.it> References: <19657556.2129651308678067087.JavaMail.defaultUser@defaultHost> <978BE797-1C99-44C0-B6E8-202516988C5E@democritos.it> Message-ID: <50433.172.16.109.56.1308704656.squirrel@webmail.iitg.ernet.in> I have one question regarding this. I am calculating the relaxed structure of a metallic system with fixed total magnetization. Since the magnetization is fixed, I am not supposed to use smearing. On the other hand, it has been suggested in the documentation that the tetrahedra method is not suitable for relaxation. Therefore, do I need to use only 'occupations=fixed'? Regards, Subhradip > > On Jun 21, 2011, at 19:41 , ar_ma86 at libero.it wrote: > >> I'm new with pw > > definitely so: http://www.quantum-espresso.org/wiki/index.php/Pw_users, > notably the second item. > >> I guess that fixing total magnetization the program fixes the >> occupation numbers of the bands and so it cannot make a >> smearing. But is it correct? > > it is > >> are the two options compatible or not? > > no > > P. > -- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > > ************************************************************************ Dr. Subhradip Ghosh Associate Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From wang.riping.81 at gmail.com Wed Jun 22 05:22:29 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Wed, 22 Jun 2011 12:22:29 +0900 Subject: [Pw_forum] compiling QHA Message-ID: Dear all, When I compile QHA in espresso-4.3, the following error occur: [wang at solei QHA]$ ./Compile ifort -O3 -c tetra.f ifort -O3 -c k_brillouin.f ifort -O3 -c generate_tetra.f ifort -O3 -c det3.f ifort -O3 -c det4.f ifort -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o det3.o det4.o ld: cannot find -lm ld: cannot find -lpthread ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [tetra] Error 1 ifort -O3 -c Debye.f90 ifort -O3 -c Debye_T.f ifort -O3 -c debye3.f ifort -O3 -c cheval.f ifort -O3 -c d1mach.f ifort -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o ld: cannot find -lm ld: cannot find -lpthread ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [Debye_x] Error 1 ifort -FR -c Mean_square_displacement.f90 ifort -static -o Mean_square_displacement.x Mean_square_displacement.o ld: cannot find -lm ld: cannot find -lpthread ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [MSD] Error 1 Could you please help me ? Thank you very much. WANG Riping 2011.6.22 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), +81-858-43-1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110622/2bbc6497/attachment-0001.htm From faridtaherkhani at gmail.com Wed Jun 22 10:31:34 2011 From: faridtaherkhani at gmail.com (farid taherkhani) Date: Wed, 22 Jun 2011 01:31:34 -0700 Subject: [Pw_forum] Installing Quantum espresso on GPU or CPU Message-ID: Dear Quantum QE users We want to install quantum Espresso in parallel version. Installing quantum espresso on GPU system is better or on CPU system? Which one has high performance for computational job? Which one is more stable? Which one has less error message in during computational job? Any help will be appreciated. All the Best, Farid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110622/27936b9d/attachment.htm From lmartinsamos at gmail.com Wed Jun 22 10:53:20 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 22 Jun 2011 10:53:20 +0200 Subject: [Pw_forum] Installing Quantum espresso on GPU or CPU In-Reply-To: References: Message-ID: Dear Farid, the GPU implementation for QE is still experimental, while the combined openmp/mpi is well established. Indeed, there is still non official release enabling calculations combining CPU-GPU. As long as I know, if your architecture is a parallel computer with CPU and GPU, you can always install traditional mpi espresso without using the GPU. bests Layla 2011/6/22 farid taherkhani > > > Dear Quantum QE users > > We want to install quantum Espresso in parallel version. Installing quantum > espresso on GPU system is better or on CPU system? Which one has high > performance for computational job? Which one is more stable? Which one has > less error message in during computational job? Any help will be > appreciated. > > All the Best, > > Farid > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110622/c3905220/attachment.htm From vv0210 at gmail.com Wed Jun 22 15:27:27 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 22 Jun 2011 09:27:27 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: References:

Message-ID: Thanks Duy, I appreciate it very much. I did that. I wanted to see how the units were converted. Best Regards, Vikas On Tue, Jun 21, 2011 at 5:52 PM, Duy Le wrote: > I don't remember. You can always calculate it easily: > the ratio between C6 (or R0) of Cacbon in mm_dispersion.f90 and in > dft-d3 code will give you an idea how to convert them. > -------------------------------------------------- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Tue, Jun 21, 2011 at 3:19 PM, Vikas Varshney wrote: > > Dear Duy, All, > > I have converted the R0 from the dftd3.f code to QE code (from Angs to > Bohr > > with 1.1 further scaling factor). However, I dont know what is the > scaling > > factor that is used for C6 in mm_dispersion.f90. Any insight will be > highly > > appreciated. > > > > Best Regards, > > > > Vikas Varshney, > > Computational Materials Scientist, > > Wright-Patterson Air Force Base, Dayton-OH (USA). > > > > On Tue, Jun 21, 2011 at 11:27 AM, Vikas Varshney > wrote: > >> > >> Dear Duy, > >> Thank you very much for the input. I will look into that today itself. > >> > >> Best Regards, > >> Vikas > >> > >> On Tue, Jun 21, 2011 at 10:51 AM, Duy Le wrote: > >>> > >>> Dear Vikas, > >>> One simplest thing you can do is to read the DFT-D2 part of DFT-D3 > >>> code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/) > >>> You will be able to find all necessary coefficients for all atoms with > >>> Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE, > >>> then you are good to go. > >>> -------------------------------------------------- > >>> Duy Le > >>> PhD Candidate > >>> Department of Physics > >>> University of Central Florida. > >>> > >>> "Men don't need hand to do things" > >>> > >>> > >>> > >>> On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney > >>> wrote: > >>> > Dear All, > >>> > > >>> > I am trying to relax my WS2 unit cell structure using vc-relax (using > >>> > PBE > >>> > pps) and I want to include disperson corrections to it. So, I tried > >>> > using > >>> > the london flag = .true. However, on starting my job I got an error > >>> > > >>> > > >>> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >>> > from init_london : error # 1 > >>> > atom W not found > >>> > > >>> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >>> > > >>> > After going through mm_dispersion.f90, I found that the vdw_radius > and > >>> > c_6 > >>> > parameters are given for first 54 atoms only (which corresponds to > >>> > first 5 > >>> > periods of periodic table). Tungsten (W), with atomic number of 74 is > >>> > in 6th > >>> > period. > >>> > > >>> > I emailed Prof. Stefan Grimme (author of the references that are > >>> > mentioned > >>> > in mm_dispersion.f90) if anything was further pursued. He replied > >>> > mentioning > >>> > that they have approached this problem further and referred me to his > >>> > website, > >>> > > >>> > http://toc.uni-muenster.de/DFTD3/ > >>> > > >>> > and told me that this has already been implemented into major QM > codes. > >>> > > >>> > Mentioning that, I have few questions. > >>> > 1. I wanted to ask if QE has incorporated the additions DFT-D, > >>> > recently. > >>> > 2. Are there any other ways to incorporate dispersion interactions in > >>> > calculations in DFT. > >>> > > >>> > Currently, I am running my simulations on 4.2 version of the code > that > >>> > I > >>> > downloaded few months ago. I would high appreciate your insights in > how > >>> > should I go about solving this problem regarding dispersion > >>> > interactions in > >>> > Tungsten. > >>> > > >>> > Looking forward for a positive reply. > >>> > > >>> > Best Regards, > >>> > > >>> > Vikas Varshney, > >>> > Computational Materials Scientist, > >>> > Wright-Patterson Air Force Base, Dayton-OH (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 > >> > > > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110622/22b84c21/attachment.htm From peronio at tasc.infm.it Wed Jun 22 16:40:26 2011 From: peronio at tasc.infm.it (Angelo Peronio) Date: Wed, 22 Jun 2011 16:40:26 +0200 Subject: [Pw_forum] esm and phonons Message-ID: <29a83cca0f1f3b52e533423df1c9a248@tasc.infm.it> Dear QE users, is it possible to perform a phonon calculation after a SCF one which employed the Effective Screening Medium by Otani and Sugino (assume_isolated = 'esm')? I tried (NO molecule between two electrodes) and did not succeed: ph.x outputs [...] Representation # 1 mode # 1 Self-consistent Calculation kpoint 1 ibnd 8 solve_linter: root not converged NaNQ Pert. # 1: Fermi energy shift (Ry) = NaNQ NaNQ iter # 1 total cpu time : 22.5 secs av.it.: 200.0 thresh= 0.100E-01 alpha_mix = 0.300 |ddv_scf|^2 = NaNQ [...] and so on, up to a crash: "from broyden : error # 1 factorization". Attached you can find pw.x and ph.x inputs and outputs, the run was done with the QE 4.3.1 pre-built on CINECA's SP6 machine. This was only a preliminary test: what I am trying to do is to study the effect of an electric field on the vibrational modes of molecule adsorbed on a metal surface. I already did it with the "tefield" implementation of electric field and since the effect is tiny I would like to have a consistency check. Thanks in advance for any help, comment or suggestion. Angelo -- _____________________ Angelo Peronio IOM CNR laboratorio TASC AREA Science Park, edificio MM strada statale 14, km 163.5 34149 Basovizza (TS) Italy laboratory: +39 040 3756452 office: +39 040 3756458 fax: +39 040 226767 e-mail: peronio at tasc.infm.it -------------- next part -------------- &CONTROL calculation = 'relax', prefix = 'no-gas-ph-esm-02', pseudo_dir = '/gpfs/scratch/userexternal/aperonio/pseudo', outdir = '/gpfs/scratch/userexternal/aperonio/outdirs/no-gas-ph-esm-02', disk_io = 'low', wf_collect = .false., ! max_seconds = 120, ! restart_mode = 'restart', / &SYSTEM ibrav = 1, celldm(1) = 20, nat = 2, ntyp = 2, ecutwfc = 30, ecutrho = 240, occupations = 'smearing', smearing = 'marzari-vanderbilt', degauss = 0.02, nspin = 2, starting_magnetization(1)=0.7, starting_magnetization(2)=0.3, assume_isolated = 'esm', esm_bc = 'pbc', ! esm_w = esm_efield = 0.0d0, ! esm_nfit = / &ELECTRONS conv_thr = 1.0d-10, / &IONS / ATOMIC_SPECIES N 14.0067 N.pbe-van_bm.UPF O 15.9994 O.pbe-van_bm.UPF ATOMIC_POSITIONS {bohr} N 0.0 0.0 -1.1013d0 0 0 0 O 0.0 0.0 1.1013d0 K_POINTS {automatic} 1 1 1 0 0 0 -------------- next part -------------- Program PWSCF v.4.3.1 starts on 22Jun2011 at 15:42:26 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 16 processors K-points division: npool = 2 R & G space division: proc/pool = 8 Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Reading PseudoPotential from /gpfs/scratch/userexternal/aperonio/pseudo/N.pbe-van_bm.UPF Reading PseudoPotential from /gpfs/scratch/userexternal/aperonio/pseudo/O.pbe-van_bm.UPF Subspace diagonalization in iterative solution of the eigenvalue problem: parallel, distributed-memory algorithm (size of sub-group: 2* 2 procs) Stick Mesh ---------- nst = 7645, nstw = 949, nsts = 3809 n.st n.stw n.sts n.g n.gw n.gs min 955 118 476 62807 2762 22180 max 956 119 477 62812 2767 22202 7645 949 3809 502479 22119 177509 bravais-lattice index = 1 lattice parameter (alat) = 20.0000 a.u. unit-cell volume = 8000.0000 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 2 number of electrons = 11.00 number of Kohn-Sham states= 10 kinetic-energy cutoff = 30.0000 Ry charge density cutoff = 240.0000 Ry convergence threshold = 1.0E-10 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0) EXX-fraction = 0.00 nstep = 50 Effective Screening Medium Method ================================= field strength (Ry/a.u.) = 0.00 ESM offset from cell edge (a.u.) = 0.00 grid points for fit at edges = 4 Ordinary Periodic Boundary Conditions celldm(1)= 20.000000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of alat) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) reciprocal axes: (cart. coord. in units 2 pi/alat) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 1.000000 ) PseudoPot. # 1 for N read from file N.pbe-van_bm.UPF MD5 check sum: 90d10febe142ad51ac9d5be1deb811c4 Pseudo is Ultrasoft, Zval = 5.0 Generated by new atomic code, or converted to UPF format Using radial grid of 729 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 PseudoPot. # 2 for O read from file O.pbe-van_bm.UPF MD5 check sum: ca2828d9fb1f294809e918903b7648d1 Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 737 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 atomic species valence mass pseudopotential N 5.00 14.00670 N ( 1.00) O 6.00 15.99940 O ( 1.00) Starting magnetic structure atomic species magnetization N 0.700 O 0.300 8 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (alat units) 1 N tau( 1) = ( 0.0000000 0.0000000 -0.0550650 ) 2 O tau( 2) = ( 0.0000000 0.0000000 0.0550650 ) number of k points= 2 Marzari-Vanderbilt smearing, width (Ry)= 0.0200 cart. coord. in units 2pi/alat k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000 k( 2) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000 G cutoff = 2431.7084 ( 502479 G-vectors) FFT grid: (110,110,110) G cutoff = 1215.8542 ( 177509 G-vectors) smooth grid: ( 70, 70, 70) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.42 Mb ( 2767, 10) NL pseudopotentials 0.68 Mb ( 2767, 16) Each V/rho on FFT grid 5.17 Mb ( 169400, 2) Each G-vector array 0.48 Mb ( 62812) G-vector shells 0.02 Mb ( 2016) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 1.69 Mb ( 2767, 40) Each subspace H/S matrix 0.02 Mb ( 40, 40) Each matrix 0.00 Mb ( 16, 10) Arrays for rho mixing 20.68 Mb ( 169400, 8) Initial potential from superposition of free atoms Check: negative starting charge=(component1): -0.002084 Check: negative starting charge=(component2): -0.001185 starting charge 10.99999, renormalised to 11.00000 negative rho (up, down): 0.208E-02 0.118E-02 Starting wfc are 8 atomic + 2 random wfc total cpu time spent up to now is 2.39 secs per-process dynamical memory: 197.4 Mb Self-consistent Calculation iteration # 1 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 6.0 negative rho (up, down): 0.252E-02 0.199E-02 total cpu time spent up to now is 4.03 secs total energy = -51.65926069 Ry Harris-Foulkes estimate = -51.44041938 Ry estimated scf accuracy < 0.21844163 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.14 Bohr mag/cell iteration # 2 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.99E-03, avg # of iterations = 2.0 negative rho (up, down): 0.305E-02 0.251E-02 total cpu time spent up to now is 5.53 secs total energy = -51.65146146 Ry Harris-Foulkes estimate = -51.73300180 Ry estimated scf accuracy < 0.21580913 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.05 Bohr mag/cell iteration # 3 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.96E-03, avg # of iterations = 2.0 negative rho (up, down): 0.276E-02 0.253E-02 total cpu time spent up to now is 7.02 secs total energy = -51.71705264 Ry Harris-Foulkes estimate = -51.72770453 Ry estimated scf accuracy < 0.07169371 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.05 Bohr mag/cell iteration # 4 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 6.52E-04, avg # of iterations = 1.5 negative rho (up, down): 0.274E-02 0.265E-02 total cpu time spent up to now is 8.51 secs total energy = -51.72855187 Ry Harris-Foulkes estimate = -51.72799460 Ry estimated scf accuracy < 0.00069238 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 5 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 6.29E-06, avg # of iterations = 16.5 negative rho (up, down): 0.270E-02 0.269E-02 total cpu time spent up to now is 10.26 secs total energy = -51.72905395 Ry Harris-Foulkes estimate = -51.72895663 Ry estimated scf accuracy < 0.00010165 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 6 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.24E-07, avg # of iterations = 13.5 negative rho (up, down): 0.268E-02 0.271E-02 total cpu time spent up to now is 11.98 secs total energy = -51.72910574 Ry Harris-Foulkes estimate = -51.72909107 Ry estimated scf accuracy < 0.00001217 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 7 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.11E-07, avg # of iterations = 2.5 negative rho (up, down): 0.268E-02 0.271E-02 total cpu time spent up to now is 13.56 secs total energy = -51.72911799 Ry Harris-Foulkes estimate = -51.72911738 Ry estimated scf accuracy < 0.00000073 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 8 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 6.60E-09, avg # of iterations = 2.5 negative rho (up, down): 0.268E-02 0.271E-02 total cpu time spent up to now is 15.11 secs total energy = -51.72911884 Ry Harris-Foulkes estimate = -51.72911878 Ry estimated scf accuracy < 0.00000003 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 9 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.72E-10, avg # of iterations = 2.5 negative rho (up, down): 0.268E-02 0.271E-02 total cpu time spent up to now is 16.68 secs total energy = -51.72911887 Ry Harris-Foulkes estimate = -51.72911887 Ry estimated scf accuracy < 6.6E-10 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell iteration # 10 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.97E-12, avg # of iterations = 2.0 negative rho (up, down): 0.268E-02 0.271E-02 total cpu time spent up to now is 18.03 secs End of self-consistent calculation ------ SPIN UP ------------ k = 0.0000 0.0000 0.0000 ( 22119 PWs) bands (ev): -31.2947 -16.8855 -12.6879 -12.6879 -11.5761 -4.4472 -4.4472 -0.4962 0.7319 0.7723 ------ SPIN DOWN ---------- k = 0.0000 0.0000 0.0000 ( 22119 PWs) bands (ev): -30.8017 -16.0562 -11.7974 -11.7974 -10.9813 -3.0901 -3.0901 -0.4338 0.7944 0.8554 the Fermi energy is -4.4093 ev ! total energy = -51.72911887 Ry Harris-Foulkes estimate = -51.72911887 Ry estimated scf accuracy < 3.1E-11 Ry The total energy is the sum of the following terms: one-electron contribution = -103.00652293 Ry hartree contribution = 52.78098676 Ry xc contribution = -11.64948453 Ry ewald contribution = 10.15246548 Ry smearing contrib. (-TS) = -0.00656366 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization = 1.03 Bohr mag/cell ESM Charge and Potential ======================== z (A) rho (e) Avg v_hartree Avg v_local Avg v_hart+v_loc (eV/A) (eV/A) (eV/A) ========================================================================== -5.196 -0.00002 -13.9264976 14.2712723 0.3447748 -5.099 0.00002 -13.8974847 14.2433913 0.3459066 -5.003 -0.00002 -13.8391001 14.1861335 0.3470333 -4.907 0.00002 -13.7513427 14.0995026 0.3481599 -4.811 0.00000 -13.6342133 13.9835046 0.3492912 -4.714 0.00001 -13.4877116 13.8381248 0.3504132 -4.618 0.00001 -13.3118376 13.6633852 0.3515476 -4.522 0.00000 -13.1065917 13.4592583 0.3526666 -4.426 0.00003 -12.8719735 13.2257750 0.3538015 -4.330 -0.00001 -12.6079840 12.9629033 0.3549193 -4.233 0.00004 -12.3146223 12.6706738 0.3560516 -4.137 0.00001 -11.9918898 12.3490595 0.3571696 -4.041 0.00006 -11.6397859 11.9980820 0.3582961 -3.945 0.00004 -11.2583121 11.6177264 0.3594143 -3.849 0.00008 -10.8474683 11.2080000 0.3605316 -3.752 0.00010 -10.4072561 10.7689034 0.3616473 -3.656 0.00013 -9.9376768 10.3004282 0.3627514 -3.560 0.00020 -9.4387319 9.8025901 0.3638582 -3.464 0.00023 -8.9104248 9.2753669 0.3649421 -3.367 0.00038 -8.3527585 8.7187860 0.3660276 -3.271 0.00046 -7.7657393 8.1328164 0.3670771 -3.175 0.00071 -7.1493735 7.5174909 0.3681175 -3.079 0.00093 -6.5036727 6.8727765 0.3691038 -2.983 0.00135 -5.8286503 6.1987049 0.3700546 -2.886 0.00188 -5.1243279 5.4952473 0.3709193 -2.790 0.00266 -4.3907346 4.7624278 0.3716932 -2.694 0.00377 -3.6279124 4.0002286 0.3723161 -2.598 0.00529 -2.8359209 3.2086597 0.3727388 -2.502 0.00756 -2.0148430 2.3877204 0.3728774 -2.405 0.01067 -1.1647998 1.5374006 0.3726009 -2.309 0.01530 -0.2859609 0.6577228 0.3717620 -2.213 0.02172 0.6214258 -0.2513497 0.3700761 -2.117 0.03105 1.5570118 -1.1897644 0.3672474 -2.020 0.04421 2.5202955 -2.1575914 0.3627041 -1.924 0.06331 3.5105641 -3.1547418 0.3558223 -1.828 0.09084 4.5267870 -4.1813248 0.3454622 -1.732 0.13041 5.5674778 -5.2372107 0.3302672 -1.636 0.18694 6.6305011 -6.3225495 0.3079516 -1.539 0.26664 7.7128117 -7.4371723 0.2756394 -1.443 0.37971 8.8101061 -8.5812648 0.2288413 -1.347 0.53804 9.9162954 -9.7546247 0.1616708 -1.251 0.75679 11.0228510 -10.9574670 0.0653841 -1.155 1.03962 12.1180768 -12.1894531 -0.0713763 -1.058 1.38402 13.1868805 -13.4524122 -0.2655317 -0.962 1.77275 14.2109278 -14.7561650 -0.5452372 -0.866 2.12333 15.1698382 -16.0731229 -0.9032847 -0.770 2.33264 16.0453749 -17.3176295 -1.2722546 -0.673 2.37679 16.8264704 -18.3889554 -1.5624850 -0.577 2.32638 17.5104278 -19.2037165 -1.6932887 -0.481 2.25285 18.0995999 -19.7309585 -1.6313585 -0.385 2.15719 18.5979300 -20.0092095 -1.4112795 -0.289 2.03191 19.0105744 -20.1254095 -1.1148351 -0.192 1.91772 19.3440342 -20.1806255 -0.8365912 -0.096 1.87358 19.6041279 -20.2555020 -0.6513741 0.000 -287.51570 19.7931416 -20.3708587 -0.5777171 0.096 -286.04631 19.9088070 -20.5172867 -0.6084797 0.192 -282.40604 19.9441223 -20.7063017 -0.7621794 0.289 -276.81219 19.8861134 -20.9127531 -1.0266398 0.385 -269.61565 19.7166175 -21.0431534 -1.3265359 0.481 -261.15867 19.4166405 -20.9730835 -1.5564430 0.577 -251.64729 18.9712676 -20.5956396 -1.6243720 0.673 -241.16305 18.3727057 -19.8673076 -1.4946019 0.770 -229.75048 17.6226661 -18.8227858 -1.2001197 0.866 -217.37361 16.7353553 -17.5637779 -0.8284226 0.962 -203.86939 15.7371031 -16.2150613 -0.4779582 1.058 -189.03428 14.6601590 -14.8763509 -0.2161920 1.155 -175.48462 13.5344885 -13.5804525 -0.0459640 1.251 -635.36735 12.3835347 -12.3161422 0.0673925 1.347 0.45944 11.2246977 -11.0808868 0.1438109 1.443 0.30658 10.0703485 -9.8752192 0.1951293 1.539 0.20477 8.9287758 -8.6987326 0.2300432 1.636 0.13743 7.8054861 -7.5518013 0.2536848 1.732 0.09166 6.7041357 -6.4340751 0.2700607 1.828 0.06126 5.6271936 -5.3458742 0.2813194 1.924 0.04093 4.5763084 -4.2869143 0.2893941 2.020 0.02758 3.5525788 -3.2574376 0.2951411 2.117 0.01872 2.5567291 -2.2572474 0.2994816 2.213 0.01265 1.5892399 -1.2864924 0.3027474 2.309 0.00865 0.6504379 -0.3450711 0.3053668 2.405 0.00577 -0.2594581 0.5669603 0.3075022 2.502 0.00402 -1.1402955 1.4496171 0.3093216 2.598 0.00267 -1.9919762 2.3029196 0.3109434 2.694 0.00192 -2.8144302 3.1268188 0.3123886 2.790 0.00127 -3.6076143 3.9213848 0.3137705 2.886 0.00091 -4.3714954 4.6865343 0.3150390 2.983 0.00062 -5.1060528 5.4223560 0.3163032 3.079 0.00042 -5.8112711 6.1287631 0.3174919 3.175 0.00032 -6.4871400 6.8058341 0.3186941 3.271 0.00019 -7.1336534 7.4535039 0.3198504 3.367 0.00018 -7.7508052 8.0718206 0.3210154 3.464 0.00007 -8.3385935 8.6607551 0.3221616 3.560 0.00011 -8.8970144 9.2203171 0.3233027 3.656 0.00003 -9.4260677 9.7505154 0.3244478 3.752 0.00006 -9.9257508 10.2513250 0.3255742 3.849 0.00002 -10.3960640 10.7227839 0.3267198 3.945 0.00002 -10.8370061 11.1648450 0.3278389 4.041 0.00002 -11.2485770 11.5775601 0.3289831 4.137 0.00000 -11.6307764 11.9608773 0.3301009 4.233 0.00003 -11.9836035 12.3148445 0.3312410 4.330 -0.00002 -12.3070592 12.6394213 0.3323621 4.426 0.00003 -12.6011421 12.9346378 0.3334957 4.522 -0.00002 -12.8658534 13.2004760 0.3346226 4.618 0.00002 -13.1011919 13.4369412 0.3357493 4.714 -0.00001 -13.3071586 13.6440407 0.3368821 4.811 0.00001 -13.4837526 13.8217561 0.3380035 4.907 0.00000 -13.6309744 13.9701151 0.3391407 5.003 -0.00001 -13.7488238 14.0890832 0.3402594 5.099 0.00001 -13.8373007 14.1786982 0.3413975 5.196 -0.00002 -13.8964055 14.2389220 0.3425165 5.292 0.00002 -13.9261374 14.2697901 0.3436527 convergence has been achieved in 10 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 -0.00086155 atom 2 type 2 force = 0.00000000 0.00000000 0.00086155 Total force = 0.000862 Total SCF correction = 0.000012 BFGS Geometry Optimization bfgs converged in 1 scf cycles and 0 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02) End of BFGS Geometry Optimization Final energy = -51.7291188729 Ry Begin final coordinates ATOMIC_POSITIONS (bohr) N 0.000000000 0.000000000 -1.101300000 0 0 0 O 0.000000000 0.000000000 1.101300000 End final coordinates Writing output data file no-gas-ph-esm-02.save init_run : 0.98s CPU 2.00s WALL ( 1 calls) electrons : 7.53s CPU 15.84s WALL ( 1 calls) forces : 0.32s CPU 0.64s WALL ( 1 calls) Called by init_run: wfcinit : 0.03s CPU 0.09s WALL ( 1 calls) potinit : 0.41s CPU 0.82s WALL ( 1 calls) Called by electrons: c_bands : 0.96s CPU 1.99s WALL ( 10 calls) sum_band : 1.90s CPU 3.84s WALL ( 10 calls) v_of_rho : 3.07s CPU 6.23s WALL ( 11 calls) newd : 1.13s CPU 2.29s WALL ( 11 calls) mix_rho : 0.34s CPU 0.69s WALL ( 10 calls) Called by c_bands: init_us_2 : 0.02s CPU 0.05s WALL ( 21 calls) cegterg : 0.90s CPU 1.87s WALL ( 10 calls) Called by *egterg: h_psi : 0.73s CPU 1.46s WALL ( 65 calls) s_psi : 0.02s CPU 0.03s WALL ( 65 calls) g_psi : 0.00s CPU 0.02s WALL ( 54 calls) cdiaghg : 0.09s CPU 0.18s WALL ( 64 calls) Called by h_psi: add_vuspsi : 0.01s CPU 0.03s WALL ( 65 calls) General routines calbec : 0.00s CPU 0.04s WALL ( 76 calls) fft : 1.99s CPU 3.99s WALL ( 335 calls) ffts : 0.03s CPU 0.12s WALL ( 42 calls) fftw : 0.67s CPU 1.30s WALL ( 746 calls) interpolate : 0.34s CPU 0.71s WALL ( 42 calls) davcio : 0.00s CPU 0.00s WALL ( 1 calls) Parallel routines fft_scatter : 0.96s CPU 1.95s WALL ( 1123 calls) PWSCF : 8.97s CPU 19.08s WALL This run was terminated on: 15:42:45 22Jun2011 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= -------------- next part -------------- NO gas phase phonons at Gamma. &inputph prefix='no-gas-ph-esm-02', outdir='/gpfs/scratch/userexternal/aperonio/outdirs/no-gas-ph-esm-02', fildyn='no-gas-ph-esm-02.dynmat', alpha_mix(1) = 0.3, tr2_ph = 1d-14, / 0.0 0.0 0.0 -------------- next part -------------- Program PHONON v.4.3.1 starts on 22Jun2011 at 15:43:12 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 16 processors K-points division: npool = 2 R & G space division: proc/pool = 8 Ultrasoft (Vanderbilt) Pseudopotentials Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input Reading PseudoPotential from /gpfs/scratch/userexternal/aperonio/outdirs/no-gas-ph-esm-02/no-gas-ph-esm-02.save/N.pbe-van_bm.UPF Reading PseudoPotential from /gpfs/scratch/userexternal/aperonio/outdirs/no-gas-ph-esm-02/no-gas-ph-esm-02.save/O.pbe-van_bm.UPF Stick Mesh ---------- nst = 7645, nstw = 949, nsts = 3809 n.st n.stw n.sts n.g n.gw n.gs min 955 118 476 62807 2762 22180 max 956 119 477 62812 2767 22202 7645 949 3809 502479 22119 177509 negative rho (up, down): 0.268E-02 0.271E-02 Calculation of q = 0.0000000 0.0000000 0.0000000 bravais-lattice index = 1 lattice parameter (alat) = 20.0000 a.u. unit-cell volume = 8000.0000 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 2 kinetic-energy cut-off = 30.0000 Ry charge density cut-off = 240.0000 Ry convergence threshold = 1.0E-14 beta = 0.3000 number of iterations used = 4 Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0) EXX-fraction = 0.00 celldm(1)= 20.00000 celldm(2)= 0.00000 celldm(3)= 0.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of alat) a(1) = ( 1.0000 0.0000 0.0000 ) a(2) = ( 0.0000 1.0000 0.0000 ) a(3) = ( 0.0000 0.0000 1.0000 ) reciprocal axes: (cart. coord. in units 2 pi/alat) b(1) = ( 1.0000 0.0000 0.0000 ) b(2) = ( 0.0000 1.0000 0.0000 ) b(3) = ( 0.0000 0.0000 1.0000 ) Atoms inside the unit cell: Cartesian axes site n. atom mass positions (alat units) 1 N 14.0067 tau( 1) = ( 0.00000 0.00000 -0.05506 ) 2 O 15.9994 tau( 2) = ( 0.00000 0.00000 0.05506 ) Computing dynamical matrix for q = ( 0.0000000 0.0000000 0.0000000 ) 9 Sym.Ops. (with q -> -q+G ) G cutoff = 2431.7084 ( 62812 G-vectors) FFT grid: (110,110,110) G cutoff = 1215.8542 ( 22190 G-vectors) smooth grid: ( 70, 70, 70) number of k points= 2 Marzari-Vanderbilt smearing, width (Ry)= 0.0200 cart. coord. in units 2pi/alat k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000 k( 2) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000 PseudoPot. # 1 for N read from file N.pbe-van_bm.UPF MD5 check sum: 643e1b9210c5596d3e8220b7f5116234 Pseudo is Ultrasoft, Zval = 5.0 Generated by new atomic code, or converted to UPF format Using radial grid of 729 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 PseudoPot. # 2 for O read from file O.pbe-van_bm.UPF MD5 check sum: 7ee51cec6b4d96081c02596cd828ca05 Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 737 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 k=gamma and q=gamma tricks are used Atomic displacements: There are 6 irreducible representations Representation 1 1 modes - To be done Representation 2 1 modes - To be done Representation 3 1 modes - To be done Representation 4 1 modes - To be done Representation 5 1 modes - To be done Representation 6 1 modes - To be done Alpha used in Ewald sum = 2.5000 PHONON : 6.66s CPU 13.95s WALL Representation # 1 mode # 1 Self-consistent Calculation kpoint 1 ibnd 8 solve_linter: root not converged NaNQ Pert. # 1: Fermi energy shift (Ry) = NaNQ NaNQ iter # 1 total cpu time : 22.5 secs av.it.: 200.0 thresh= 0.100E-01 alpha_mix = 0.300 |ddv_scf|^2 = NaNQ kpoint 1 ibnd 8 solve_linter: root not converged NaNQ Pert. # 1: Fermi energy shift (Ry) = NaNQ NaNQ iter # 2 total cpu time : 31.1 secs av.it.: 200.0 thresh= NaNQ alpha_mix = 0.300 |ddv_scf|^2 = NaNQ kpoint 1 ibnd 8 solve_linter: root not converged NaNQ Pert. # 1: Fermi energy shift (Ry) = NaNQ NaNQ iter # 3 total cpu time : 39.7 secs av.it.: 200.0 thresh= NaNQ alpha_mix = 0.300 |ddv_scf|^2 = NaNQ kpoint 1 ibnd 8 solve_linter: root not converged NaNQ Pert. # 1: Fermi energy shift (Ry) = NaNQ NaNQ -------------- next part -------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 9 from broyden : error # 1 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From woozydude at gmail.com Wed Jun 22 23:24:07 2011 From: woozydude at gmail.com (Woozy) Date: Thu, 23 Jun 2011 00:24:07 +0300 Subject: [Pw_forum] Mailman will remind you of your Message-ID: Normally, Mailman will remind you of your http://tut.by mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110623/39245daa/attachment.htm From hqzhou at nju.edu.cn Thu Jun 23 09:50:31 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Thu, 23 Jun 2011 15:50:31 +0800 Subject: [Pw_forum] Reading fildvscf References: <2DD66562E02F11409F54329AC3ECF4C57CC534@MAIL.tyndall.ie> Message-ID: <6D58A59D8CDE4BA29DDFEAC472C8A1FF@solarflare> Reading fildvscfYou need to find out the piece of source code that write the file fildvscf, then you can mimic the code, for example, open the file as "old", replace "write" with "read", and make use of the original "format" statements, to write your program to read the file in. It should be very simple even for those who have very little experience of programming. zhou huiqun @earth scieces, nanjing university, china ----- Original Message ----- From: Siobhan O'Halloran To: pw_forum at pwscf.org Sent: Tuesday, June 21, 2011 7:12 PM Subject: [Pw_forum] Reading fildvscf Hi all, I would like to read the variation of the potential from fildvscf. As somebody who has little programming experience, how would I do that? Regards, Siobhan O Halloran Materials Theory Group Tyndall National Institute Cork, Ireland ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110623/f42c5068/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu Jun 23 11:52:33 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 23 Jun 2011 11:52:33 +0200 Subject: [Pw_forum] init_london Error In-Reply-To: References: Message-ID: <201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it> Dear Vikas You can also use the ab-initio implementation of vdW forces by switching on the input_dft="vdw-df" flag. HTH Giuseppe On Tuesday 21 June 2011 16:40:02 Vikas Varshney wrote: > Dear All, > > I am trying to relax my WS2 unit cell structure using vc-relax (using PBE > pps) and I want to include disperson corrections to it. So, I tried using > the london flag = .true. However, on starting my job I got an error > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% from init_london : error # 1 > atom W not found > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% > > After going through mm_dispersion.f90, I found that the vdw_radius and c_6 > parameters are given for first 54 atoms only (which corresponds to first 5 > periods of periodic table). Tungsten (W), with atomic number of 74 is in > 6th period. > > I emailed Prof. Stefan Grimme (author of the references that are mentioned > in mm_dispersion.f90) if anything was further pursued. He replied > mentioning that they have approached this problem further and referred me > to his website, > > http://toc.uni-muenster.de/DFTD3/ > > and told me that this has already been implemented into major QM codes. > > Mentioning that, I have few questions. > 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. > 2. Are there any other ways to incorporate dispersion interactions in > calculations in DFT. > > Currently, I am running my simulations on 4.2 version of the code that I > downloaded few months ago. I would high appreciate your insights in how > should I go about solving this problem regarding dispersion interactions in > Tungsten. > > Looking forward for a positive reply. > > Best Regards, > > Vikas Varshney, > Computational Materials Scientist, > Wright-Patterson Air Force Base, Dayton-OH (USA). -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From tone.kokalj at ijs.si Thu Jun 23 12:06:57 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 23 Jun 2011 12:06:57 +0200 Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: <4DFC347E.9030904@yahoo.com.cn> References: <139345.24926.qm@web43410.mail.sp1.yahoo.com> <1308310127.3139.7.camel@catalyst.ijs.si> <4DFC347E.9030904@yahoo.com.cn> Message-ID: <1308823617.3857.7.camel@catalyst.ijs.si> On Sat, 2011-06-18 at 13:15 +0800, Hongsheng Zhao wrote: > On 06/17/2011 07:28 PM, Tone Kokalj wrote: > > Why don't you try with the new version: > > http://www.xcrysden.org/download/xc-1.5.24-linux_x86_64-semishared.tar.gz > > When can I obtain the precompiled version for linux_x86. The 32bit compiled version has been just made available: http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz (btw: I thought the 32bit machines are dead species) Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From s.heidari at ucl.ac.uk Thu Jun 23 14:45:32 2011 From: s.heidari at ucl.ac.uk (Heidari, Sareh) Date: Thu, 23 Jun 2011 12:45:32 +0000 Subject: [Pw_forum] Layers of different materials Message-ID: <66AA506EF5B85548B59A4C6C1667C728051BFF@AMSPRD0104MB100.eurprd01.prod.exchangelabs.com> Dear QE users, I am quite new to using Quantum Espresso. Apologies in advance for this very elementary question. I would like to do an scf calculation on a structure that has layers of different materials. For example, 7 layers of Cu in an fcc structure (100) surface, followed by two layers of CuN (100) surface. I started by calculating bulk Cu and then bulk CuN. However, I could not find how to create layers without making a very large supercell that is 9 layers (7+2) thick. Is there another way for me to approach this problem that would allow me to use smaller unit cells? Or is the approach I mentioned above the recommended one? Again, I am sorry if this has been asked before; I have tried searching the archive, user guide and other sources but hadn't come across an answer. Many thanks in advance. Kind regards, Sareh _____________________________ Sareh Heidari PhD Student London Centre for Nanotechnology University College London 17-19 Gordon Street, London, WC1H 0AH. ____________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110623/62d14cfe/attachment.htm From zhaohscas at yahoo.com.cn Thu Jun 23 16:32:15 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Thu, 23 Jun 2011 22:32:15 +0800 Subject: [Pw_forum] Compatibility between XCrySDen and Quantum ESPRESSO In-Reply-To: <1308823617.3857.7.camel@catalyst.ijs.si> References: <139345.24926.qm@web43410.mail.sp1.yahoo.com> <1308310127.3139.7.camel@catalyst.ijs.si> <4DFC347E.9030904@yahoo.com.cn> <1308823617.3857.7.camel@catalyst.ijs.si> Message-ID: <4E034E6F.7030805@yahoo.com.cn> On 06/23/2011 06:06 PM, Tone Kokalj wrote: > The 32bit compiled version has been just made available: > http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz > > (btw: I thought the 32bit machines are dead species) In my case, at home, I use a pc with the the cpu info as this: "Intel(R) Core(TM) i7 CPU 920 @ 2.67GHz". I think this should belong to the x86_64 family. On the other hand, in my office, I use a pc with another type of cpu ( I forget the specific info ). Though both of them are belong to x86_64 architecture, in my experience, the pc of my office cann't run smoothly when I install the amd64 distribution of Debian (i.e., x86_64 OS). I don't know the reason. Based on the above situation, I use i386 distribution of Debian . Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From baroni at sissa.it Thu Jun 23 21:21:33 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 23 Jun 2011 21:21:33 +0200 Subject: [Pw_forum] Layers of different materials In-Reply-To: <66AA506EF5B85548B59A4C6C1667C728051BFF@AMSPRD0104MB100.eurprd01.prod.exchangelabs.com> References: <66AA506EF5B85548B59A4C6C1667C728051BFF@AMSPRD0104MB100.eurprd01.prod.exchangelabs.com> Message-ID: <47BE2F38-8D6F-4DAA-BBF9-FB2649C87F88@sissa.it> Sareh: sorry for you, but I'm afraid there is no free lunch. If what you are after depends on the actual geometry of the system, there is no other way than simulating the supercell . SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 23/giu/2011, at 14:45, "Heidari, Sareh" wrote: > Dear QE users, > > I am quite new to using Quantum Espresso. Apologies in advance for this very elementary question. > > I would like to do an scf calculation on a structure that has layers of different materials. For example, 7 layers of Cu in an fcc structure (100) surface, followed by two layers of CuN (100) surface. > I started by calculating bulk Cu and then bulk CuN. However, I could not find how to create layers without making a very large supercell that is 9 layers (7+2) thick. > > Is there another way for me to approach this problem that would allow me to use smaller unit cells? Or is the approach I mentioned above the recommended one? > > Again, I am sorry if this has been asked before; I have tried searching the archive, user guide and other sources but hadn't come across an answer. Many thanks in advance. > > Kind regards, > Sareh > > _____________________________ > Sareh Heidari > PhD Student > London Centre for Nanotechnology > University College London > 17-19 Gordon Street, > London, WC1H 0AH. > ____________________________ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110623/10891588/attachment.htm From member at linkedin.com Fri Jun 24 05:19:58 2011 From: member at linkedin.com (Weiguang Chen via LinkedIn) Date: Fri, 24 Jun 2011 03:19:58 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <2056766942.3763785.1308885598020.JavaMail.app@ela4-bed32.prod> LinkedIn ------------ Weiguang Chen requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Weiguang Accept invitation from Weiguang Chen http://www.linkedin.com/e/bpp12m-gpakov28-5i/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I64595856_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvdzkUdjARd3p9bTtymAlJoBtCbP8Rcj4PcjgVe34LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Weiguang Chen http://www.linkedin.com/e/bpp12m-gpakov28-5i/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I64595856_60/0MdBYSdjwRejkQdAALqnpPbOYWrSlI/svi/ ------------------------------------------ Why might connecting with Weiguang Chen be a good idea? Have a question? Weiguang Chen's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Weiguang Chen and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/bpp12m-gpakov28-5i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/9774ade0/attachment-0001.htm From songsong19840614 at gmail.com Fri Jun 24 06:04:12 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 24 Jun 2011 12:04:12 +0800 Subject: [Pw_forum] Could calculate the structure of high temperature? Message-ID: Hi, The first principle is based on 0K. So, I want to ask if I could calculate sturucture of high temperature. Such as, some structure are znic-blend,but it will transform to wurtzite at high temperature. Could I calculate property of wurtzite of these materials using pwscf ? Such as phonon dispersion, thermal properties. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/2fec9a21/attachment.htm From lmartinsamos at gmail.com Fri Jun 24 08:17:43 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 24 Jun 2011 08:17:43 +0200 Subject: [Pw_forum] Could calculate the structure of high temperature? In-Reply-To: References: Message-ID: Hi, with pwscf you can perform Born-Oppenheimer molecular dynamics ---> with temperature. But if you just want eletronic structure of wurtzite and phonons, you set the atomic positions to wurtzite, by hand, relax the atomic positions and the cell, and you are done! bests regards Layla 2011/6/24 lucking-pine > Hi, > The first principle is based on 0K. So, I want to ask if I could calculate > sturucture of high temperature. Such as, some structure are znic-blend,but > it will transform to wurtzite at high temperature. Could I calculate > property of wurtzite of these materials using pwscf ? Such as phonon > dispersion, thermal properties. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/6959ef58/attachment.htm From thisisasafeaccount at gmail.com Fri Jun 24 09:25:10 2011 From: thisisasafeaccount at gmail.com (tian kong) Date: Fri, 24 Jun 2011 15:25:10 +0800 Subject: [Pw_forum] how to choose ibrav Message-ID: i have read the help document about INPUT_PW.htm again and again, but since i'm a newbie, i still don't know whice one i should choose. can you help me? here is the problem: A=10, B=C=8, cosAB=cosBC=cosAC=0. can you tell me ibrav=? thx a lot !!! *>>>>>>>>?this is an email sent by tiankong?* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/f638aa92/attachment.htm From flux_ray12 at 163.com Fri Jun 24 09:35:30 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 24 Jun 2011 15:35:30 +0800 (CST) Subject: [Pw_forum] how to choose ibrav In-Reply-To: References: Message-ID: <7a2c9a72.ed87.130c09332fd.Coremail.flux_ray12@163.com> In your case, this structure must be simple tetragonal or body centered tetragonal. Please check your model more carefully from PDF-card or ICSD database. P.S.: the choice of ibrav depends on the knowledge of crystallography, please learn it before you do ab-initio calculation, since symmetry is a very important and foundamental thing in this area. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-06-24 15:25:10?"tian kong" wrote: i have read the help document about INPUT_PW.htm again and again, but since i'm a newbie, i still don't know whice one i should choose. can you help me? here is the problem: A=10, B=C=8, cosAB=cosBC=cosAC=0. can you tell me ibrav=? thx a lot !!! >>>>>>>>?this is an email sent bytiankong? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/8c47de64/attachment.htm From s.heidari at ucl.ac.uk Fri Jun 24 10:10:58 2011 From: s.heidari at ucl.ac.uk (Heidari, Sareh) Date: Fri, 24 Jun 2011 08:10:58 +0000 Subject: [Pw_forum] Layers of different materials In-Reply-To: <47BE2F38-8D6F-4DAA-BBF9-FB2649C87F88@sissa.it> References: <66AA506EF5B85548B59A4C6C1667C728051BFF@AMSPRD0104MB100.eurprd01.prod.exchangelabs.com>, <47BE2F38-8D6F-4DAA-BBF9-FB2649C87F88@sissa.it> Message-ID: <562653D7-9B55-4C9D-A58F-4D489AB279FB@ucl.ac.uk> Dear Stefano, Thank you for your reply. That's fine; I don't mind using the supercell. I just wanted to know that I wasn't missing something else! Thanks again, Sareh _____________________________ Sareh Heidari PhD Student London Centre for Nanotechnology University College London 17-19 Gordon Street, London, WC1H 0AH. On 23 Jun 2011, at 20:22, Stefano Baroni > wrote: Sareh: sorry for you, but I'm afraid there is no free lunch. If what you are after depends on the actual geometry of the system, there is no other way than simulating the supercell . SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 23/giu/2011, at 14:45, "Heidari, Sareh" <s.heidari at ucl.ac.uk> wrote: Dear QE users, I am quite new to using Quantum Espresso. Apologies in advance for this very elementary question. I would like to do an scf calculation on a structure that has layers of different materials. For example, 7 layers of Cu in an fcc structure (100) surface, followed by two layers of CuN (100) surface. I started by calculating bulk Cu and then bulk CuN. However, I could not find how to create layers without making a very large supercell that is 9 layers (7+2) thick. Is there another way for me to approach this problem that would allow me to use smaller unit cells? Or is the approach I mentioned above the recommended one? Again, I am sorry if this has been asked before; I have tried searching the archive, user guide and other sources but hadn't come across an answer. Many thanks in advance. Kind regards, Sareh _____________________________ Sareh Heidari PhD Student London Centre for Nanotechnology University College London 17-19 Gordon Street, London, WC1H 0AH. ____________________________ _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/6f41f70a/attachment.htm From BarnardEP at ufs.ac.za Fri Jun 24 11:16:49 2011 From: BarnardEP at ufs.ac.za (Egbert Barnard) Date: Fri, 24 Jun 2011 11:16:49 +0200 Subject: [Pw_forum] NEB: enexpected number of dimensons in ngg Message-ID: <4E0472210200009A00030D40@gwinter.ufs.ac.za> I seem to have solved the problem I had experienced with Quantum espresso 4.2.1 in the NEB code. I got the following error: Unexpected number if dimensions in ngg.If you make the number of pools 1 then no error occurs. So I assume there is a bug in that part of the code, where you parallelize with respect to your k-points. Pieter Barnard University of the Free State Bloemfontein South Africa _____________________________________________________________________ University of the Free State: This message and its contents are subject to a disclaimer. Please refer to http://www.ufs.ac.za/disclaimer for full details. Universiteit van die Vrystaat: Hierdie boodskap en sy inhoud is aan 'n vrywaringsklousule onderhewig. Volledige besonderhede is by http://www.ufs.ac.za/vrywaring beskikbaar. _____________________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/729b8bb7/attachment.htm From baroni at sissa.it Fri Jun 24 11:17:58 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 24 Jun 2011 11:17:58 +0200 Subject: [Pw_forum] Could calculate the structure of high temperature? In-Reply-To: References: Message-ID: <92BA9AD9-4184-45D1-AF09-D39712DB3709@sissa.it> of course, you can also calculate phonons and study thermal properties in the quasi-harmonic approximation SB On Jun 24, 2011, at 8:17 AM, Layla Martin-Samos wrote: > Hi, with pwscf you can perform Born-Oppenheimer molecular dynamics ---> with temperature. But if you just want eletronic structure of wurtzite and phonons, you set the atomic positions to wurtzite, by hand, relax the atomic positions and the cell, and you are done! > > bests regards > > Layla > > 2011/6/24 lucking-pine > Hi, > The first principle is based on 0K. So, I want to ask if I could calculate sturucture of high temperature. Such as, some structure are znic-blend,but it will transform to wurtzite at high temperature. Could I calculate property of wurtzite of these materials using pwscf ? Such as phonon dispersion, thermal properties. > > _______________________________________________ > 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 --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/048b5259/attachment.htm From zhaohscas at yahoo.com.cn Fri Jun 24 12:49:10 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 24 Jun 2011 18:49:10 +0800 Subject: [Pw_forum] About the naming rule for k points. Message-ID: <4E046BA6.9040400@yahoo.com.cn> Hi all, It's known to all that in the BZ, we usually use specific lables to denoting k points, say, G, L, M, K, H, and so on. But I'm very confused on the naming rule for k points, i.e, for a specific k point, which lable should I use? Could someone please give me some hints? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From zhaohscas at yahoo.com.cn Fri Jun 24 12:55:17 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 24 Jun 2011 18:55:17 +0800 Subject: [Pw_forum] Compute the distance between two point in reciprocal lattice. Message-ID: <4E046D15.9000101@yahoo.com.cn> Hi all, In gereral case, for a tri-clinic lattice, based on the fractional positions of two k-points relative to the reciprocal space lattice vectors, how can I compute the distance between these two points in reciprocal space? Does someone here have the script/tools for this purpose? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From zhaohscas at yahoo.com.cn Fri Jun 24 12:54:44 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 24 Jun 2011 18:54:44 +0800 Subject: [Pw_forum] Compute the distance between two point in reciprocal lattice. Message-ID: <4E046CF4.60209@yahoo.com.cn> Hi all, In gereral case, for a tri-clinic lattice, based on the fractional positions of two k-points relative to the reciprocal space lattice vectors, how can I compute the distance between these two points in reciprocal space? Does someone here have the script/tools for this purpose? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From jenaparadies at googlemail.com Fri Jun 24 13:04:59 2011 From: jenaparadies at googlemail.com (Lars Matthes) Date: Fri, 24 Jun 2011 13:04:59 +0200 Subject: [Pw_forum] About the naming rule for k points. In-Reply-To: <4E046BA6.9040400@yahoo.com.cn> References: <4E046BA6.9040400@yahoo.com.cn> Message-ID: Hi, you can find a very nice overview about high symmetry points for all(?) BZs in wikipedia: http://en.wikipedia.org/wiki/Brillouin_zone Ciao Lars 2011/6/24 Hongsheng Zhao > Hi all, > > It's known to all that in the BZ, we usually use specific lables to > denoting k points, say, G, L, M, K, H, and so on. But I'm very > confused on the naming rule for k points, i.e, for a specific k point, > which lable should I use? Could someone please give me some hints? > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Lars Matthes Institut f?r Festk?rpertheorie und -optik Friedrich-Schiller-Universit?t Jena Max-Wien-Platz 1 07743 Jena Germany Phone: +49.3641.947163 Mail: Lars.Matthes at uni-jena.de Universit? degli Studi di Roma Tor Vergata Dipartimento di Fisica Teorie di Fisica della materia via della Ricerca Scientifica 1 00133 Rome Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/182063ae/attachment.htm From zhaohscas at yahoo.com.cn Fri Jun 24 13:23:52 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 24 Jun 2011 19:23:52 +0800 Subject: [Pw_forum] About the naming rule for k points. In-Reply-To: References: <4E046BA6.9040400@yahoo.com.cn> Message-ID: <4E0473C8.2050806@yahoo.com.cn> On 06/24/2011 07:04 PM, Lars Matthes wrote: > Hi, > > you can find a very nice overview about high symmetry points > for all(?) BZs in wikipedia: > http://en.wikipedia.org/wiki/Brillouin_zone Even though, it's difficult to remember them. Are there some tools/scripts to obtain them automatically? Regards. > > Ciao > Lars > > 2011/6/24 Hongsheng Zhao > > > Hi all, > > It's known to all that in the BZ, we usually use specific lables to > denoting k points, say, G, L, M, K, H, and so on. But I'm very > confused on the naming rule for k points, i.e, for a specific k point, > which lable should I use? Could someone please give me some hints? > > Regards. > -- > Hongsheng Zhao > > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > Lars Matthes > Institut f?r Festk?rpertheorie und -optik > Friedrich-Schiller-Universit?t Jena > Max-Wien-Platz 1 > 07743 Jena > Germany > > Phone: +49.3641.947163 > Mail: Lars.Matthes at uni-jena.de > > Universit? degli Studi di Roma Tor Vergata > Dipartimento di Fisica > Teorie di Fisica della materia > via della Ricerca Scientifica 1 > 00133 Rome > Italy > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From Lorenzo.Paulatto at impmc.upmc.fr Fri Jun 24 13:30:35 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 24 Jun 2011 13:30:35 +0200 Subject: [Pw_forum] About the naming rule for k points. In-Reply-To: <4E0473C8.2050806@yahoo.com.cn> References: <4E046BA6.9040400@yahoo.com.cn> <4E0473C8.2050806@yahoo.com.cn> Message-ID: On Fri, 24 Jun 2011 13:23:52 +0200, Hongsheng Zhao wrote: > Even though, it's difficult to remember them. Are there some > tools/scripts to obtain them automatically? Not in Quantum Espresso AFAIK. Seriously, how many times do you have to find the high symmetry point? Even if you spend 10 minutes on it won't be the end of the World... -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From vv0210 at gmail.com Fri Jun 24 15:39:50 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Fri, 24 Jun 2011 09:39:50 -0400 Subject: [Pw_forum] init_london Error In-Reply-To: <201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it> References: <201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Giuseppe, Thanks for your email. Although, I finished my calculations successfully by .london. flag, I wanted to ask if input=dft="vdw-df" does the same thing? Best Regards, Vikas On Thu, Jun 23, 2011 at 5:52 AM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > > Dear Vikas > You can also use the ab-initio implementation of vdW forces by switching on > the input_dft="vdw-df" flag. > HTH > Giuseppe > > > On Tuesday 21 June 2011 16:40:02 Vikas Varshney wrote: > > Dear All, > > > > I am trying to relax my WS2 unit cell structure using vc-relax (using PBE > > pps) and I want to include disperson corrections to it. So, I tried using > > the london flag = .true. However, on starting my job I got an error > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >%%% from init_london : error # 1 > > atom W not found > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >%%% > > > > After going through mm_dispersion.f90, I found that the vdw_radius and > c_6 > > parameters are given for first 54 atoms only (which corresponds to first > 5 > > periods of periodic table). Tungsten (W), with atomic number of 74 is in > > 6th period. > > > > I emailed Prof. Stefan Grimme (author of the references that are > mentioned > > in mm_dispersion.f90) if anything was further pursued. He replied > > mentioning that they have approached this problem further and referred me > > to his website, > > > > http://toc.uni-muenster.de/DFTD3/ > > > > and told me that this has already been implemented into major QM codes. > > > > Mentioning that, I have few questions. > > 1. I wanted to ask if QE has incorporated the additions DFT-D, recently. > > 2. Are there any other ways to incorporate dispersion interactions in > > calculations in DFT. > > > > Currently, I am running my simulations on 4.2 version of the code that I > > downloaded few months ago. I would high appreciate your insights in how > > should I go about solving this problem regarding dispersion interactions > in > > Tungsten. > > > > Looking forward for a positive reply. > > > > Best Regards, > > > > Vikas Varshney, > > Computational Materials Scientist, > > Wright-Patterson Air Force Base, Dayton-OH (USA). > > > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110624/23ea7bda/attachment.htm From vv0210 at gmail.com Fri Jun 24 19:52:29 2011 From: vv0210 at gmail.com (Vikas Varshney) Date: Fri, 24 Jun 2011 13:52:29 -0400 Subject: [Pw_forum] Clarification of a confusion related to q vector specifications in ph.x Message-ID: Dear QE usesrs, I wanted to have a clarification on the following sentence from the phonon calculations part of the manual: "After the namelist you must specify the q-vector of the phonon mode. This must be the same q-vector given in the input of pw.x.". The link for the following text is given below. http://www.quantum-espresso.org/user_guide/node31.html In ph.x, we specify three values for q-vector (0,0,0) for gamma point, for example. However, in pw.x, the k points are often specified as K_POINTS automatic 4 4 2 0 0 0. I wanted to understand if these are related. If not, what does the above sentence mean. I am not sure but it might be a silly question to ask but I am trying to clear it in my head. Any insights will be highly appreciated. Best Regards, Vikas Varshney Computational Materials Scientist, Wright Patterson Air Force Base, Dayton OH From songsong19840614 at gmail.com Sat Jun 25 02:40:43 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Sat, 25 Jun 2011 08:40:43 +0800 Subject: [Pw_forum] Could calculate the structure of high temperature? In-Reply-To: <92BA9AD9-4184-45D1-AF09-D39712DB3709@sissa.it> References: <92BA9AD9-4184-45D1-AF09-D39712DB3709@sissa.it> Message-ID: Hi,Thank Stefano Baroni for your help so that I can do my work continuously. 2011/6/24 Stefano Baroni > of course, you can also calculate phonons and study thermal properties in > the quasi-harmonic approximation SB > > bests regards > Pine > On Jun 24, 2011, at 8:17 AM, Layla Martin-Samos wrote: > > Hi, with pwscf you can perform Born-Oppenheimer molecular dynamics ---> > with temperature. But if you just want eletronic structure of wurtzite and > phonons, you set the atomic positions to wurtzite, by hand, relax the atomic > positions and the cell, and you are done! > > bests regards > > Layla > > 2011/6/24 lucking-pine > >> Hi, >> The first principle is based on 0K. So, I want to ask if I could calculate >> sturucture of high temperature. Such as, some structure are znic-blend,but >> it will transform to wurtzite at high temperature. Could I calculate >> property of wurtzite of these materials using pwscf ? Such as phonon >> dispersion, thermal properties. >> >> _______________________________________________ >> 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 > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110625/6c25e2c1/attachment-0001.htm From sclauzer at sissa.it Sat Jun 25 10:31:20 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 25 Jun 2011 10:31:20 +0200 Subject: [Pw_forum] About the naming rule for k points. In-Reply-To: <4E0473C8.2050806@yahoo.com.cn> References: <4E046BA6.9040400@yahoo.com.cn> <4E0473C8.2050806@yahoo.com.cn> Message-ID: There is something in XCrysDen, at least for the most common symmetries (cubic, hexagonal,...) http://www.xcrysden.org/doc/kpath.html HTH GS Il giorno 24/giu/2011, alle ore 13.23, Hongsheng Zhao ha scritto: > On 06/24/2011 07:04 PM, Lars Matthes wrote: >> Hi, >> >> you can find a very nice overview about high symmetry points >> for all(?) BZs in wikipedia: >> http://en.wikipedia.org/wiki/Brillouin_zone > > Even though, it's difficult to remember them. Are there some > tools/scripts to obtain them automatically? > > Regards. >> >> Ciao >> Lars >> >> 2011/6/24 Hongsheng Zhao > > >> >> Hi all, >> >> It's known to all that in the BZ, we usually use specific lables to >> denoting k points, say, G, L, M, K, H, and so on. But I'm very >> confused on the naming rule for k points, i.e, for a specific k point, >> which lable should I use? Could someone please give me some hints? >> >> Regards. >> -- >> Hongsheng Zhao > >> School of Physics and Electrical Information Science, >> Ningxia University, Yinchuan 750021, China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> -- >> Lars Matthes >> Institut f?r Festk?rpertheorie und -optik >> Friedrich-Schiller-Universit?t Jena >> Max-Wien-Platz 1 >> 07743 Jena >> Germany >> >> Phone: +49.3641.947163 >> Mail: Lars.Matthes at uni-jena.de >> >> Universit? degli Studi di Roma Tor Vergata >> Dipartimento di Fisica >> Teorie di Fisica della materia >> via della Ricerca Scientifica 1 >> 00133 Rome >> Italy >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110625/02b78496/attachment.htm From giannozz at democritos.it Sat Jun 25 10:59:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 25 Jun 2011 10:59:09 +0200 Subject: [Pw_forum] Clarification of a confusion related to q vector specifications in ph.x In-Reply-To: References: Message-ID: <2737D72C-78C9-472C-82A8-BCD8281795E9@democritos.it> On Jun 24, 2011, at 19:52 , Vikas Varshney wrote: > "After the namelist you must specify the q-vector of the phonon mode. in cartesian corrdinates, 2\pi/a units > This must be the same q-vector given in the input of pw.x." obsolete statement from the old procedure, please ignore P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ar_ma86 at libero.it Sat Jun 25 12:01:20 2011 From: ar_ma86 at libero.it (ar_ma86 at libero.it) Date: Sat, 25 Jun 2011 12:01:20 +0200 (CEST) Subject: [Pw_forum] exctracting data from evc.dat Message-ID: <7130001.3435521308996080442.JavaMail.defaultUser@defaultHost> Hi, I'm trying to read the values of the kohn-sham wavefunction even for points different from the gamma one (otherwise I used pp.x) . I managed to obtain a file "evc.dat" that should contain the information, but it is unformatted and I don't know it's structure (in that case I could use a read statement from fortran). How can I extract and understand my data? Sorry for the questions of a beginner, but I got stuck. Regards Marcolongo Aris Scuola Internazionale Superiore di Studi Avanzati, Trieste From mirnezhad.mm at gmail.com Sat Jun 25 13:47:08 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Sat, 25 Jun 2011 04:47:08 -0700 Subject: [Pw_forum] Help for a NC PS for Zn Message-ID: Dear Users, I need a NC PS for ZN, any suggestion appreciated, Thanks in advance, ----------------------------------------------------- Mahdi Mirnezhad MSc student of Mechanical engineering, Guilan University. From nicola.marzari at materials.ox.ac.uk Sat Jun 25 14:00:14 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 25 Jun 2011 13:00:14 +0100 Subject: [Pw_forum] Help for a NC PS for Zn In-Reply-To: References: Message-ID: <4E05CDCE.9040602@materials.ox.ac.uk> On 6/25/11 12:47 PM, Mahdi Mirnezhad wrote: > Dear Users, > I need a NC PS for ZN, > any suggestion appreciated, > Thanks in advance, You can download FHI98PP (google it), generate the Troullier-Martins pseudo there, and convert it to UPF using the QE upftools program fhi2upf. nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From ferretti at mit.edu Sat Jun 25 14:09:20 2011 From: ferretti at mit.edu (Andrea Ferretti) Date: Sat, 25 Jun 2011 14:09:20 +0200 (CEST) Subject: [Pw_forum] exctracting data from evc.dat Message-ID: Hi Aris, once you've managed to get the files evc.dat, I think the easiest way to read them (together with more or less all the data produced and dumped by QE) is to use the QEXML library. This lib (you can find in PP/qexml.f90 ) is meant to be used also by third party codes and can be compiled easily also out of QE and in connection with other codes... Note you need to link the iotk lib, but that is compiled by espresso (have a look at make.sys to see how to link it) you may want to have a look at the routines: qexml_init, qexml_openfile, qexml_closefile qexml_read_planewaves qexml_read_gk qexml_read_wfc (feel free to have alook inside the library) The idea is that these routines are written to first read the dimensions of the data you need, then you can allocate the needed workspace, and then you can call the routine again to get the massive data... For some examples about how to use them, you can have a look at PP/qexml_example.f90 or inside the sources of WanT (downloadable at qe-forge), just grep "qexml_" in want/wannier/*.f90 hope it helps andrea > > I'm trying to read the values of the kohn-sham wavefunction even for points > different from the gamma one (otherwise I used pp.x) . I managed to obtain a > file "evc.dat" that should contain the information, but it is unformatted and > I > don't know it's structure (in that case I could use a read statement from > fortran). How can I extract and understand my data? > > Sorry for the questions of a beginner, but I got stuck. > > Regards > > Marcolongo Aris > > Scuola Internazionale Superiore di Studi Avanzati, Trieste > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Andrea Ferretti S3 Center, Istituto Nanoscienze, CNR via Campi 213/A, 41100, Modena, Italy Tel: +39 059 2055300; Skype: andrea_ferretti URL: http://www.nano.cnr.it From giannozz at democritos.it Sat Jun 25 15:05:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 25 Jun 2011 15:05:33 +0200 Subject: [Pw_forum] init_london Error In-Reply-To: References: <201106231152.33600.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <31E55D94-9D24-4F80-8449-3F08E9A39561@democritos.it> On Jun 24, 2011, at 15:39 , Vikas Varshney wrote: > I wanted to ask if input_dft="vdw-df" does the same thing? no, it uses the nonlocal functional by Dion et al (vdW-DF) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From thisisasafeaccount at gmail.com Sat Jun 25 15:49:38 2011 From: thisisasafeaccount at gmail.com (tian kong) Date: Sat, 25 Jun 2011 21:49:38 +0800 Subject: [Pw_forum] how to choose ibrav In-Reply-To: <7a2c9a72.ed87.130c09332fd.Coremail.flux_ray12@163.com> References: <7a2c9a72.ed87.130c09332fd.Coremail.flux_ray12@163.com> Message-ID: yeah, i think you are right. but what really matters is how to set ibrav in pwscf. ibrav structure celldm(2)-celldm(6) 6 Tetragonal P (st) celldm(3)=c/a 7 Tetragonal I (bct) celldm(3)=c/a simple tetragonal (p) ==================== v1 = a(1,0,0), v2 = a(0,1,0), v3 = a(0,0,c/a) body centered tetragonal (i) ================================ v1 = (a/2)(1,-1,c/a), v2 = (a/2)(1,1,c/a), v3 = (a/2)(-1,-1,c/a). it seems that: if ibrav=6, then A=B?C. if ibrav=7, then A=B=C. but what i need is A?B=C. i don't know if i can choose ibrav=6 or 7, and should i need to change the atoms position after i choose ibrav=6 or 7 ? *>>>>>>>>?this is an email sent by tiankong?* 2011/6/24 GAO Zhe > In your case, this structure must be simple tetragonal or body centered > tetragonal. Please check your model more carefully from PDF-card or ICSD > database. > P.S.: the choice of ibrav depends on the knowledge of crystallography, > please learn it before you do ab-initio calculation, since symmetry is a > very important and foundamental thing in this area. > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-06-24 15:25:10?"tian kong" wrote: > > i have read the help document about INPUT_PW.htm again and again, but since > i'm a newbie, i still don't know whice one i should choose. can you help me? > here is the problem: > A=10, B=C=8, cosAB=cosBC=cosAC=0. > can you tell me ibrav=? > thx a lot !!! > *>>>>>>>>?this is an email sent by tiankong?* > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110625/fad76fbb/attachment-0001.htm From scipioni at mpip-mainz.mpg.de Sat Jun 25 15:46:14 2011 From: scipioni at mpip-mainz.mpg.de (Roberto Scipioni) Date: Sat, 25 Jun 2011 15:46:14 +0200 Subject: [Pw_forum] cp + wannier dynamics ---> Segmentation fault Message-ID: <4E05E6A6.6030108@mpip-mainz.mpg.de> Dear all, I am trying to run a CP MD with the code cp.x with the option cp-wf. I am running 48 water molecules with NOSE thermalised with 4 thermostats (frequencies) the input is : ------------------------ &control title = ' 48 Waters ', calculation = 'cp-wf', ! cp restart_mode = 'restart', ! 'restart', from_scratch ndr = 222, ndw = 222, nstep = 200, iprint = 100, isave = 1000 tstress = .TRUE., tprnfor = .TRUE., dt = 5.0d0, etot_conv_thr = 5.d-6, ekin_conv_thr = 5.d-5, forc_conv_thr = 5.d-4, prefix = 'h2o', pseudo_dir='/u/robechan/work/QUANTUM_EXPRESSO/espresso-4.2.1/pseudo/', outdir='/u/robechan/work/ICE_PROJECT/TEST_48H2O/TEST_WF/RESTART/tmp', / &system ibrav = 14, celldm(1) = 17.0075419, celldm(2) = 0.86602222, celldm(3) = 2.4400000, celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0, nat = 144, ntyp = 2, nbnd = 192 , ecutwfc = 70.0, ecfixed = 68.0, input_dft = 'PBE', / &electrons emass = 400.d0, emass_cutoff = 2.5d0, ortho_max = 40, ! electron_dynamics = 'cg', electron_dynamics = 'verlet', ! electron_velocities = 'zero', ! after first run remove / &ions ion_dynamics = 'verlet', ! ion_dynamics = 'none' ! ion_dynamics = 'sd' ion_temperature = 'nose', ! ion_velocities = 'zero', ! after first run remove nhpcl = 4 fnosep = 12.0 24.0 36.0 48.0 ! fnosep = 35.0, tempw = 270.0 ! tranp(1) = .TRUE., ! tranp(2) = .TRUE., ! amprp(1) = 0.01 ! amprp(2) = 0.01 / &wannier nsteps = 10, ! wfsd = 3 / &cell cell_dynamics = 'none', cell_velocities = 'zero', / ATOMIC_SPECIES O 16.0d0 oxygen-pbe.UPF ! 16.0d0 H 1.0079d0 hydrogen-pbe.UPF ! 1.0079d0 ATOMIC_POSITIONS (bohr) O 0.420884E+01 0.235900E+01 0.145438E-01 H 0.577544E+01 0.326552E+01 -0.566406E+00 H 0.425217E+01 0.240412E+01 0.191095E+01 ..... ..... -------------------------------------------------------------------------------- an I get in the output ---------------------------------------- ............... ............... ................ ------------------------DYNAMICS IN THE WANNIER BASIS-------------------------- DYNAMICS PARAMETERS FICTITIOUS MASS PARAMETER USED FOR SPREAD OPTIMIZATION = 1500.0 TIME STEP USED FOR DAMPED DYNAMICS = 5.0000000 DAMPING COEFFICIENT USED FOR WANNIER FUNCTION SPREAD OPTIMIZATION = 0.3000000 10 STEPS OF DAMPED MOLECULAR DYNAMICS FOR OPTIMIZATION OF THE SPREAD AVERAGE WANNIER FUNCTION SPREAD WRITTEN TO FORT.24 INDIVIDUAL WANNIER FUNCTION SPREAD WRITTEN TO /u/robechan/work/ICE_PROJECT/TEST_48H2O/TEST_WF/RESTART/tmp/h2o.spr WANNIER CENTERS WRITTEN TO /u/robechan/work/ICE_PROJECT/TEST_48H2O/TEST_WF/RESTART/tmp/h2o.wfc SOME PERTINENT RUN-TIME INFORMATION WRITTEN TO FORT.27 ------------------------------------------------------------------------------- IBRAV SELECTED: 14 WANNIER SETUP : check G vectors and weights inw = 1: 1 0 0 1.000000 inw = 2: 0 1 0 0.749994 inw = 3: 0 0 1 5.953600 inw = 4: 1 1 0 0.000000 inw = 5: 0 1 1 0.000000 inw = 6: 1 0 1 0.000000 Translations to be done 6 ibrav selected: 14 ---------------------------------------------------- I get segmentation fault and a bunch of coredir directories ANY INSIGHT ? Thanks RS From giannozz at democritos.it Sat Jun 25 16:15:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 25 Jun 2011 16:15:33 +0200 Subject: [Pw_forum] how to choose ibrav In-Reply-To: References: <7a2c9a72.ed87.130c09332fd.Coremail.flux_ray12@163.com> Message-ID: <5844AF2A-3EBE-4181-983E-583CA350CEA4@democritos.it> On Jun 25, 2011, at 15:49 , tian kong wrote: > > what i need is A?B=C. i don't know if i can choose ibrav=6 or 7, > and should i need to change the atoms position after i choose > ibrav=6 or 7 ? set ibrav=0, provide the lattice vectors via the CELL_PARAMETERS card --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Jun 25 16:17:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 25 Jun 2011 16:17:01 +0200 Subject: [Pw_forum] cp + wannier dynamics ---> Segmentation fault In-Reply-To: <4E05E6A6.6030108@mpip-mainz.mpg.de> References: <4E05E6A6.6030108@mpip-mainz.mpg.de> Message-ID: <82793D93-8E42-4877-B646-F6C295FC217B@democritos.it> On Jun 25, 2011, at 15:46 , Roberto Scipioni wrote: > I get segmentation fault and a bunch of coredir directories > ANY INSIGHT ? "segmentation fault" == "no insight" --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From syuva2987 at gmail.com Sat Jun 25 18:14:43 2011 From: syuva2987 at gmail.com (yuva rani) Date: Sat, 25 Jun 2011 21:44:43 +0530 Subject: [Pw_forum] Constraints In-Reply-To: <20110613084223.12439bllg1135bnz@webmail.chem.leidenuniv.nl> References: <20110613084223.12439bllg1135bnz@webmail.chem.leidenuniv.nl> Message-ID: Sir with your suggestions I have constrained two pentacene molecules stacked one above the other using flags. But it did not worked. so please provide me a detailed definition and syntax for using constraints. I also have another doubt, I am constructing a metal-organic interface.I built an layered structure using matreial studio and the cartesian coordinates are taken using chemcraft. How should I input the coordinates in quantum espresso, whether cartesian or fractional and the also cell parameters of the specified layered structure. Thanks in advance. On 6/13/11, m.g.p.krishna at chem.leidenuniv.nl wrote: > Hi Yuva, > > If you look at the previous post, you can see a small example script, > where a CONSTRAINT card is used. Also to use CONSTRAINT card you > SHOULD use 'damp' rather than 'bfgs'. It is easy to use 'distance' > constraint. > > But I failed to fix the coordination number for selected atoms (using > 'atom_coord' and 'type_coord') as It described in the previous mail. > > Moreover some strange things are there, for example > from the previous input, it do a relaxation if you use: > > CONSTRAINTS > 1 0.5 > 'atom_coord' 5 1 3.5 0.5 > > > and you will get an ERROR message if you swap the atom index (VERY > STRANGE): ie. > > CONSTRAINTS > 1 0.5 > 'atom_coord' 1 5 3.5 0.5 > > So someone can help us to give a working/reliable example script on > 'atom_coord' and 'type_coord' constraints. It will be very useful, > since the default examples dont include this... > > otherwise I am going to do a Quantum-Espresso plugin for ASE/CamD just > for a reliable geometry optimization. :-( > > With best regards > > Krishna Mohan GP > Center for Superfunctional Materials > POSTECH > Sotuh Korea. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From abmus007 at gmail.com Sat Jun 25 23:39:42 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Sat, 25 Jun 2011 16:39:42 -0500 Subject: [Pw_forum] ibrav and celldm(4) In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Abolore Musari Date: Sat, 25 Jun 2011 16:32:45 -0500 Subject: ibrav and celldm(4) To: pw-forum at pwscf.org Dear QE user, l am working on monoclinic system and from textbook monoclinic system alpha equal beta equal 90 degree and from literature of my system beta was gotten from reitveld refinement to be 113.81. so i dont know if my celldm(4) which is equal to cos(ab) should be cos90 or cos113.81 or tell me the appropriate way to get celldm(4)=cos(ab). i will appreciate ur assistance. abolore dept of phy UNAAB From m.saghayezhian at gmail.com Sun Jun 26 10:27:27 2011 From: m.saghayezhian at gmail.com (Mohammad Saghayezhian) Date: Sun, 26 Jun 2011 04:27:27 -0400 Subject: [Pw_forum] -rsh error in phonon calculation Message-ID: Hello everybody, I have a job file that perform a scf calculation (pw.x) and phonon calculation (ph.x). the script runs good for pw.x but when It reaches to run ph.x it gives me this error: Unable to read script file because of error: ERROR! invalid option argument "-rsh" mpi is fine and the espresso version is 4.1.2 and it does good for any other calculation but for phonon calculation that error appears here is the script: #!/bin/csh -f #$ -N Auphon #$ -S /bin/csh #$ -pe mpi_o_* 16 #$ -M m.saghayezhian at gmail.com #$ -m baes #$ -o $JOB_NAME.$JOB_ID.out #$ -notify #$ -cwd #$ -l h_rt=200:00:00 set mpi="/home-fs4/sp0088/mpi/xeon/mvapich-1.1/bin/mpirun_rsh" set pwx="/home-fs4/hp0070/softs/espresso-4.1.2/bin/pw.x" set phx="/home-fs4/hp0070/softs/espresso-4.1.2/bin/ph.x" set case=aup set wdir=`pwd` set scratchfile="/scratch/hp0070/$case" #set makdir="mkdir -p $scratchfile" #set deldir="rm -rf $scratchfile" set HOSTFILE="$TMPDIR/machines" cat $HOSTFILE > $wdir/$case.host set nodes=16 setenv MKL_NUM_THREADS 1 setenv OMP_NUM_THREADS 1 mkdir -p $scratchfile @ i=1 while ( $i <= $nodes ) set node=` head -$i $wdir/$case.host | tail -1 ` rsh $node $makdir @ i= $i + 4 end # cat $PE_HOSTFILE | cut -c 1-6 > .hostfile # HOSTFILE=".hostfile" # HOSTFILE=$PE_HOSTFILE echo $NSLOTS ### Here we have a real running command $mpi -rsh -np 16 -legacy -hostfile $wdir/$case.host $pwx -npool 2 < $wdir/au-a3.90108 > $wdir/scf.out cat << end2 > $wdir/ph.in phonon &inputph tr2_ph=1.0d-14, prefix='Au', ldisp=.true., nq1=4 , nq2=4 , nq3=4, amass(1)=196.96655, outdir='./', fildyn='au.dyn', / end2 $mpi -rsh -np 16 -legacy -hostfile $wdir/$case.host $phx -npool 2 < $wdir/ ph.in > $wdir/ph.out rm -rf $scratchfile #./job1 #/homes/hp0070/bin/killpwx ./$case.host rm -rf $scratchfile @ i=1 while ( $i <= $nodes ) set node=` head -$i $wdir/$case.host | tail -1 ` rsh $node $deldir @ i= $i + 4 end echo finished ------------------------------------------------------------------- Mohammad Saghayezhian Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Isfahan, Iran Tel lab: +98 311 391 3731 Fax Office: +98311 391 3746 ------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110626/3cb65978/attachment.htm From degironc at sissa.it Sun Jun 26 15:15:14 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 26 Jun 2011 15:15:14 +0200 Subject: [Pw_forum] Clarification of a confusion related to q vector specifications in ph.x In-Reply-To: References: Message-ID: <20110626151514.v64m746rcw0gcc00@webmail.sissa.it> Dear Vikas Varshney , the second part of the sentence is obsolete and referred to the case in which the single point calculation was done combining a nscf call to pw.x and one to ph.x... the two call ought obviously to be consistent. As stated somewhat above in the manual page you linked "NOTE: the alternative procedure in which a band-structure calculation with calculation='phonon was performed as an intermediate step is no longer implemented since version 4.1. It is also no longer needed to specify lnscf=.true. for q$ \ne$ 0 . " so just specify the q point you desire and the code wil run the nscf+dfpt calculation in sequence. stefano Quoting Vikas Varshney : > Dear QE usesrs, > > I wanted to have a clarification on the following sentence from the > phonon calculations part of the manual: "After the namelist you must > specify the q-vector of the phonon mode. This must be the same > q-vector given in the input of pw.x.". The link for the following text > is given below. > http://www.quantum-espresso.org/user_guide/node31.html > > In ph.x, we specify three values for q-vector (0,0,0) for gamma point, > for example. > > However, in pw.x, the k points are often specified as > > K_POINTS automatic > 4 4 2 0 0 0. > > I wanted to understand if these are related. If not, what does the > above sentence mean. I am not sure but it might be a silly question to > ask but I am trying to clear it in my head. > > Any insights will be highly appreciated. > > Best Regards, > > Vikas Varshney > Computational Materials Scientist, > Wright Patterson Air Force Base, Dayton OH > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From brad.malone at gmail.com Sun Jun 26 20:02:43 2011 From: brad.malone at gmail.com (Brad Malone) Date: Sun, 26 Jun 2011 11:02:43 -0700 Subject: [Pw_forum] Convergence of imaginary modes Message-ID: Hello QE users, I am calculating the lattice dynamical properties of a high-pressure phase. As has been documented in this forum, phonon frequencies can be quite sensitive to the various other parameter of the calculation (wavefunction cutoff, BZ sampling, etc.) and it's important to test this explicitly and not rely on the parameters one finds converged for say, a total-energy SCF calculation. In the testing of my phonon frequencies with respect to the density of the k-point sampling in the SCF calculation prior to the phonon calculation, I decided to test a uniform grid of q-points rather than simply the Gamma phonon since I don't know of any a priori reason to expect that all phonon frequencies converge identically (although in my prior experience this is approximately true). I found that almost all frequencies are converged to within about 1% or so at a "small" kgrid sampling of about 40x40x40. However, one mode is wildly unconverged at this point, and differences on the order of 100s of cm^1 can be found by going to a kgrid sampling of 80x80x80. So I just kept increasing the kpoint sampling until I converged this mode. The mode didn't fully converge until 200x200x200, although it is pretty close at 160x160x160.The mode finally converged to a negative value (although was positive until the kpoint sampling was in the triple digits in each direction). This negative mode signals an instability of the structure along the path corresponding to the phonon displacement pattern. That's all well and good. I know that this structure is thermodynamically unstable at pressures in the ballpark of the calculation, and so if it's dynamically unstable too no problem. Since the structure becomes more thermodynamically stable at higher presures, I increased the pressure and tested the phonon frequencies again. I found that the negative mode goes positive, and increases in frequency as the pressure is increased (as one might guess). However, this mode still depends very sensitively on the kpoint sampling and doesn't get close to full convergence until about 160x160x160 similarly to the calculation at lower pressures. In previous lattice dynamical calculations, I've always been blessed with positive frequencies (at least those that can't be ASRed away) and I'm curious as to whether the more sensitive convergence of imaginary modes (and those that are close to being unstable) is a property that others have found in their calculations or whether it is something unusual with the system that I am studying. Thanks, Brad Malone UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110626/514877af/attachment.htm From germaneau at gucas.ac.cn Mon Jun 27 12:50:39 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Mon, 27 Jun 2011 06:50:39 -0400 Subject: [Pw_forum] Too many r-vectors? Message-ID: <4E08607F.1060705@gucas.ac.cn> Dear QE users, I recently my self consistent calculations have crashed (pw.x) with the error "too many r-vectors". I did not find the meaning and how to avoid it. Well, I guess it has something to do with real space vectors but that's it. So, I may need your light here. Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110627/e15d2e14/attachment.htm From nicola.marzari at materials.ox.ac.uk Mon Jun 27 02:38:12 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Mon, 27 Jun 2011 01:38:12 +0100 Subject: [Pw_forum] Convergence of imaginary modes In-Reply-To: References: Message-ID: <4E07D0F4.9080404@materials.ox.ac.uk> On 6/26/11 7:02 PM, Brad Malone wrote: > In previous lattice dynamical calculations, I've always been blessed > with positive frequencies (at least those that can't be ASRed away) and > I'm curious as to whether the more sensitive convergence of imaginary > modes (and those that are close to being unstable) is a property that > others have found in their calculations or whether it is something > unusual with the system that I am studying. > > Thanks, > Brad Malone > UC Berkeley Dear Brad, if you have a Kohn anomaly it's not unusual to require that high of a k-point sampling - comparable numbers are needed to converge some of the optical modes in graphene/graphite (do check some of the early papers of Mauri/Lazzeri). I haven't heard of other cases where such high-sampling is needed for phonons, unless your system was a metal, and you were not using a smearing scheme (or way too small a smearing). nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From hqzhou at nju.edu.cn Mon Jun 27 05:29:25 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 27 Jun 2011 11:29:25 +0800 Subject: [Pw_forum] how to choose ibrav References: <7a2c9a72.ed87.130c09332fd.Coremail.flux_ray12@163.com> Message-ID: Hi, It's your own responsibility to make clear what crystal class your system belongs to. Do you know the symbol of space group of your system? For your case, if it's Pxxx, the system should be simple tetragonal (ibrav=6), if it's Ixxx, it should be base centered tetragonal (ibrav=7). zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: tian kong To: PWSCF Forum Sent: Saturday, June 25, 2011 9:49 PM Subject: Re: [Pw_forum] how to choose ibrav yeah, i think you are right. but what really matters is how to set ibrav in pwscf. ibrav structure celldm(2)-celldm(6) 6 Tetragonal P (st) celldm(3)=c/a 7 Tetragonal I (bct) celldm(3)=c/asimple tetragonal (p) ==================== v1 = a(1,0,0), v2 = a(0,1,0), v3 = a(0,0,c/a) body centered tetragonal (i) ================================ v1 = (a/2)(1,-1,c/a), v2 = (a/2)(1,1,c/a), v3 = (a/2)(-1,-1,c/a). it seems that: if ibrav=6, then A=B?C. if ibrav=7, then A=B=C.but what i need is A?B=C. i don't know if i can choose ibrav=6 or 7, and should i need to change the atoms position after i choose ibrav=6 or 7 ? >>>>>>>>?this is an email sent by tiankong? 2011/6/24 GAO Zhe