From david.grifith at gmail.com Wed Dec 1 01:03:58 2010 From: david.grifith at gmail.com (David Grifith) Date: Wed, 1 Dec 2010 03:33:58 +0330 Subject: [Pw_forum] point charge-spin Message-ID: Dear All I am trying to calculate the point charge and the point spin density on each atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is necessary as described in INPUT_PP guide file. Calculating the point charges and spins is customary in any quantum chemistry packages and one can find such data at the end of their output files. Is it possible to calculate by PWScf ? I appreciate your help and comment in advance. Best Wishes Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101201/7605981f/attachment-0001.htm From pavel.lukashev at gmail.com Wed Dec 1 02:49:49 2010 From: pavel.lukashev at gmail.com (Lukashev Pavel) Date: Tue, 30 Nov 2010 17:49:49 -0800 Subject: [Pw_forum] Non-collinear calculations: magnetic moment relaxation Message-ID: Dear All, I am running a test calculation of bcc iron, to check if the relaxation of angle1 (theta) works correct for the non-collinear case. I have copied the file "fe.pen.in" from the examples provided on pwscf.org, and added one more Fe atom (so, I have two Fe atom unit cell). I set angle1(1)=90; angle1(2)=0.0. After self-consistent calculation I expect these angles to be aligned (ferromagnetically). Yet, I end up getting very strange result, i.e. theta(1)=70.356498; theta(2)=19.684944. Does this mean that the relaxation of atomic magnetic moments is not very reliable in case of non-collinear calculation? This is first time I am trying to include non-collinearity in my calculation, therefore I don't have much to compare with. And I did not find any published work on non-collinear systems done with PWSCF. Any help on this issue is very appreciated. I attach my input file which also includes portion from output showing magnetization magnitude/direction. Sincerely, Pavel Lukashev, Ph.D. Research Associate UNL, Department of Physics & Astronomy 208 Theodore Jorgensen Hall 855 N. 16th Street Lincoln, NE 68588-0299 Office: (402) 472-2400 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/66a90e02/attachment.htm -------------- next part -------------- &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/home/pavel/QE-4.2/espresso-4.2/pseudo/', outdir='/home/pavel/QE-4.2/espresso-4.2/examples/example13/results/TEST/tmp/', prefix='fe' / &system ibrav = 1, celldm(1) =5.217, nat= 2, ntyp= 2, ecutwfc = 25.0,ecutrho = 200.0, report=1, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 noncolin = .true. starting_magnetization(1) = 2.0 starting_magnetization(2) = 2.0 angle1(1)=90.0 angle2(1)=0.0 angle1(2)=0.0 angle2(2)=0.0 lambda = 1 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.2 / ATOMIC_SPECIES Fe1 55.847 Fe.pz-nd-rrkjus.UPF Fe2 55.847 Fe.pz-nd-rrkjus.UPF ATOMIC_POSITIONS Fe1 0.0 0.0 0.0 Fe2 0.5 0.5 0.5 K_POINTS 11 0.0625000 0.0625000 0.0625000 1.00 0.0625000 0.0625000 0.1875000 3.00 0.0625000 0.0625000 0.3125000 3.00 0.0625000 0.0625000 0.4375000 3.00 0.0625000 0.0625000 0.5625000 3.00 0.0625000 0.0625000 0.6875000 3.00 0.0625000 0.0625000 0.8125000 3.00 0.0625000 0.0625000 0.9375000 3.00 0.0625000 0.1875000 0.1875000 3.00 0.0625000 0.1875000 0.3125000 6.00 0.0625000 0.1875000 0.4375000 6.00 =========================================================== OUTPUT: atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 6.428337 magnetization : 2.269152 0.000000 0.809951 magnetization/charge: 0.352992 0.000000 0.125997 polar coord.: r, theta, phi [deg] : 2.409372 70.356498 0.000000 ============================================================================== ============================================================================== atom number 2 relative position : 0.5000 0.5000 0.5000 charge : 6.428357 magnetization : 0.811645 0.000000 2.268714 magnetization/charge: 0.126260 0.000000 0.352923 polar coord.: r, theta, phi [deg] : 2.409529 19.684944 0.000000 From sclauzer at sissa.it Wed Dec 1 09:43:50 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 1 Dec 2010 09:43:50 +0100 Subject: [Pw_forum] point charge-spin In-Reply-To: References: Message-ID: <8AD42EB9-93CB-4B6A-A734-115C0434EA9D@sissa.it> Dear David, the projwfc.x postprocessing code computes the so-called "Lowdin charges" (at the end of the output), maybe that's something similar to what you want. GS Il giorno 01/dic/2010, alle ore 01.03, David Grifith ha scritto: > Dear All > > > I am trying to calculate the point charge and the point spin density on each atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is necessary as described in INPUT_PP guide file. Calculating the point charges and spins is customary in any quantum chemistry packages and one can find such data at the end of their output files. Is it possible to calculate by PWScf ? I appreciate your help and comment in advance. Best Wishes > > > > Sincerely Yours > David G. > JCU > > _______________________________________________ > 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/20101201/38c9333b/attachment.htm From sclauzer at sissa.it Wed Dec 1 10:33:23 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 1 Dec 2010 10:33:23 +0100 Subject: [Pw_forum] Non-collinear calculations: magnetic moment relaxation In-Reply-To: References: Message-ID: <07CFA1DF-D04C-481E-A56B-C2BAC2FD15DD@sissa.it> Dear Pavel, at a first glance, it looks to me that your degauss is to large and the k-point sampling insufficient for magnetic calculations. This said, I don't understand why you get such a strange solution. With your initial choice of the angles you might be forcing some symmetry that prevents from reaching the ground state. Nevertheless, if you start from a magnetic configuration very far from the ground state you might get trapped in some local minima even with the correct symmetry, I suppose. Beware that starting_magnetization should be between -1 and 1, see Doc/INPUT_PW.txt. I remember that Paolo put some checks at some point. Which version of the code are you using? Finally, unless you include spin-orbit coupling or you consider situations with frustrated magnetism there is no need of using the noncollinear scheme. HTH GS Il giorno 01/dic/2010, alle ore 02.49, Lukashev Pavel ha scritto: > Dear All, > > I am running a test calculation of bcc iron, to check if the relaxation of angle1 (theta) works correct for the non-collinear case. I have copied the file "fe.pen.in" from the examples provided on pwscf.org, and added one more Fe atom (so, I have two Fe atom unit cell). I set angle1(1)=90; angle1(2)=0.0. After self-consistent calculation I expect these angles to be aligned (ferromagnetically). Yet, I end up getting very strange result, i.e. theta(1)=70.356498; theta(2)=19.684944. Does this mean that the relaxation of atomic magnetic moments is not very reliable in case of non-collinear calculation? This is first time I am trying to include non-collinearity in my calculation, therefore I don't have much to compare with. And I did not find any published work on non-collinear systems done with PWSCF. Any help on this issue is very appreciated. I attach my input file which also includes portion from output showing magnetization magnitude/direction. > > Sincerely, > > Pavel Lukashev, Ph.D. > Research Associate > UNL, Department of Physics & Astronomy > 208 Theodore Jorgensen Hall > 855 N. 16th Street > Lincoln, NE 68588-0299 > Office: (402) 472-2400 > _______________________________________________ > 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/20101201/8d42524c/attachment.htm From glapenna at iccom.cnr.it Wed Dec 1 10:59:27 2010 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Wed, 1 Dec 2010 10:59:27 +0100 (CET) Subject: [Pw_forum] point charge-spin In-Reply-To: References: Message-ID: As for point charges, here is a small recipe for isolated molecules (see below) for the ESP/RESP procedure [A]. Reference is Bayly et al, J. Phys. Chem., 97, 10269 (1993). Final point charges for organo-metallic molecules compare fairly well with standard or published values. Another possibility is to compute charges by integrating over atomic basins built on the basis of QT-AIM (Bader) [B]. [A] 1) From PW or CP, write into the restart directory (I guess into the charge-density.dat file) the electrostatic potential in place of electron density. This requires a call before writefile in CPV/cpr.f90 (in case of CP). Paolo Giannozzi wrote the subroutine to do this in CP. It would be nice to have it in some contrib space. In the input, it is recommended to use explicit ion_radius(i), especially if you want to compare with other programs (like CPMD, for which the default radii are all 1.2 bohr). 2) Once the restart is generated, postprocess it with PP as to print the electron density into a friendly format, like a gaussian-cube file. This file will contain the electrostatic potential on a 3d-grid. PP can process restart produced also by CP, provided disk_io='high'. 3) Write your own program to map the 3d-grid on the molecular solvent-accessible surface. This will consist in reading the 3d-grid, reading the molecular surface produced with vdw radii and a rolling probe, and finally interpolate the potential at the surface point using neighbour points in the grid. For the molecular surface, I recommend an old program called NSC (numerical surface calculation): Eisenhaber et al, J. Comput. Chem., 16, 273 (1995) WARNING: this latter step for non-periodic systems! Non-periodicity is assumed in the ESP/RESP procedure, that consists in fitting the electrostatic surface potential with a LIMITED sum of Coulomb interactions. The interpolation can be very coarse, the entire method is plenty of error sources. The output of this procedure is a list with x y z U for each point of the molecular surface. In case step 4 is performed with the aresp code that was once part of Amber, the output for a water molecule is: 3 1072 0 -0.9982123E-32 0.0000000E+00 0.2313846E+00 -0.2610123E-32 0.1494187E+01 -0.9255383E+00 -0.1829851E-15 -0.1494187E+01 -0.9255383E+00 -6.5264638e-01 2.0485851e+00 1.0162867e+00 1.6945994e+00 -7.2948945e-01 2.4209246e+00 6.0282018e-01 1.7305686e+00 ... where 3 is the number of atoms, 1072 is the number of surface points, 0 is the net charge, the three following lines are the atomic coordinates in bohr, and the following lines are x,y,z,U (bohr,kcal/mol) for the 1072 surface points. This format was once produced by Gaussian. 4) Finally, one of the RESP codes available can be used. I used the original aresp code that was part of the Amber 4.1 code. I think it is not worth to develop the RESP part in QE, but for sure steps 1-3 could be done relatively easily. And maybe with a minimum-image based periodicity. I really don't know how to do it, but I am available for testing. [B] This is simpler, but for reasons that will be apparent to everybody in a few applications, it is rarely used. 1) Postprocess the restart with PP and write the electron density on a fine 3d-grid (cube-file). The size of 10 pm associated to a density energy-cutoff of 250 Ry is rather accurate. 2) Process this electron density cube-file with a real-space QT-AIM code. I used: Sanville et al., J. Comp. Chem., 28, 899 (2007). http://theory.cm.utexas.edu/bader/ Charge are in ACF.dat. This works also for periodic systems (maybe only orthorhombic?). Problems occur with polar X-H bonds or in all cases where the zero-flux of density comes too close to atoms desribed with pseudo-potentials. Maybe, this will help, Giovanni ============================================================ 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 ============================================================ On Wed, 1 Dec 2010, David Grifith wrote: > Dear All > > > I am trying to calculate the point charge and the point spin density on each > atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is > ... From gmanyali2005 at yahoo.com Wed Dec 1 12:09:39 2010 From: gmanyali2005 at yahoo.com (george manyali) Date: Wed, 1 Dec 2010 03:09:39 -0800 (PST) Subject: [Pw_forum] error Message-ID: <252973.365.qm@web56503.mail.re3.yahoo.com> Dear all, can someone tell me how to correct the error message below: Warning: Permanently added 'cnode-1-13,172.17.200.13' (RSA) to the list of known hosts. Warning: Permanently added 'cnode-1-6,172.17.200.6' (RSA) to the list of known hosts. -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 1 with PID 11311 on node cnode-1-48 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [cnode-1-48:11307] 15 more processes have sent help message help-mpi-api.txt / mpi-abort [cnode-1-48:11307] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages here is my input file &CONTROL calculation='vc-relax', tstress=.t.,tprnfor=.t., outdir='/export/home/gmanyali/ASESMAPROJECT/Files-SiO2/tmp', pseudo_dir='/export/home/gmanyali/ASESMAPROJECT/XC_PSEUDO/PW91/' forc_conv_thr=1.d-5, !dt=30, !nstep=2000, / &SYSTEM ibrav=4, celldm(1)=9.289897331, celldm(3)=1.099552482, nat= 9, ntyp= 2, ecutwfc=90 / &ELECTRONS mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS ion_dynamics='bfgs', ! ion_dynamics='damp', / &CELL press=0, cell_dynamics='bfgs', / ATOMIC_SPECIES Si 10.0 Si_PW91.TM O 10.0 O_PW91.TM ATOMIC_POSITIONS {crystal} Si 0.469700000 0.000000000 0.000000000 Si 0.000000000 0.469700000 0.666666667 Si -0.469700000 -0.469700000 0.333333333 O 0.413500000 0.266900000 0.115800000 O -0.266900000 0.146600000 0.782466667 O -0.146600000 -0.413500000 0.449133333 O 0.266900000 0.413500000 0.550866667 O -0.413500000 -0.146600000 0.217533333 O 0.146600000 -0.266900000 -0.115800000 K_POINTS {automatic} 2 2 2 1 1 1 Mr. George Simiyu Manyali Postgraduate Student, Physics Department, Moi University-Chepkoilel Campus P.O BOX 1125,ELDORET KENYA. Phone:+254723407705 skype:gmanyali2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101201/c20602db/attachment.htm From dalcorso at sissa.it Wed Dec 1 18:39:18 2010 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Wed, 01 Dec 2010 18:39:18 +0100 Subject: [Pw_forum] Non-collinear calculations: magnetic moment relaxation In-Reply-To: References: Message-ID: <1291225158.20869.22.camel@ulisse.cm.sissa.it> k-point sampling is important in this problem. It works (meaning that the magnetic moments become parallel) for me with smearing='mp' and K-POINTS AUTOMATIC 4 4 4 1 1 1 Andrea On Tue, 2010-11-30 at 17:49 -0800, Lukashev Pavel wrote: > Dear All, > > > I am running a test calculation of bcc iron, to check if the > relaxation of angle1 (theta) works correct for the non-collinear case. > I have copied the file "fe.pen.in" from the examples provided on > pwscf.org, and added one more Fe atom (so, I have two Fe atom unit > cell). I set angle1(1)=90; angle1(2)=0.0. After self-consistent > calculation I expect these angles to be aligned (ferromagnetically). > Yet, I end up getting very strange result, i.e. theta(1)=70.356498; > theta(2)=19.684944. Does this mean that the relaxation of atomic > magnetic moments is not very reliable in case of non-collinear > calculation? This is first time I am trying to include > non-collinearity in my calculation, therefore I don't have much to > compare with. And I did not find any published work on non-collinear > systems done with PWSCF. Any help on this issue is very appreciated. I > attach my input file which also includes portion from output showing > magnetization magnitude/direction. > > > Sincerely, > > > Pavel Lukashev, Ph.D. > Research Associate > UNL, Department of Physics & Astronomy > 208 Theodore Jorgensen Hall > 855 N. 16th Street > Lincoln, NE 68588-0299 > Office: (402) 472-2400 > _______________________________________________ > 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 w2agz at w2agz.com Thu Dec 2 06:41:18 2010 From: w2agz at w2agz.com (W2AGZ) Date: Wed, 1 Dec 2010 21:41:18 -0800 Subject: [Pw_forum] Example 12 (W2AGZ) In-Reply-To: References: Message-ID: <065801cb91e3$8c701330$a5503990$@w2agz.com> All Intel Fortran Compilers (that I know about) are commercial and very expensive, even for Linux. From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of meysam pazoki Sent: Sunday, November 14, 2010 2:17 AM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Example 12 (W2AGZ) ---------- Forwarded message ---------- From: meysam pazoki Date: Sun, Nov 14, 2010 at 1:42 PM Subject: Re: Example 12 (W2AGZ) To: pw_forum at pwscf.org Dear Paul I see this message.use ifort instead of gfortran. follow this link to install ifortran in ubuntu: http://software.intel.com/en-us/articles/using-intel-compilers-for-linux-wit h-ubuntu/ Best Regards meysam pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101201/c6b679d0/attachment-0001.htm From pavel.lukashev at gmail.com Thu Dec 2 07:59:04 2010 From: pavel.lukashev at gmail.com (Lukashev Pavel) Date: Wed, 1 Dec 2010 22:59:04 -0800 Subject: [Pw_forum] Non-collinear calculations: magnetic moment relaxation In-Reply-To: <07CFA1DF-D04C-481E-A56B-C2BAC2FD15DD@sissa.it> References: <07CFA1DF-D04C-481E-A56B-C2BAC2FD15DD@sissa.it> Message-ID: Dear Gabriele and Andrea, Thank you very much. I fixed the starting_magnetization and the k-point sampling. Indeed, it appears that the problem was the insufficient number of k-points. With K-POINTS AUTOMATIC (4 4 4 1 1 1) I do get magnetic moment parallel, disregard of their starting orientations. But now I end up getting another problem. I am trying to impose a constraint on the magnetization angle (i.e. cosine of angle1, theta) by setting: constrained_magnetization='atomic direction' This doesn't seem to work, unless I start with angle1 (theta) being equal for both iron atoms. When I set them (theta's) different, they do not stay fixed anymore. I attach my input file along with the portion of the final output showing the magnetization angles. I thought that probably I have to constrain the directions separately for each atom, but I did not figure out how to do it. Simply setting constrained_magnetization(1)='atomic direction' constrained_magnetization(2)='atomic direction' results in error, and I couldn't find in the manual and/or examples any help on setting these constraints separately. Any help to resolve this issue is mostly appreciated (i.e. I want to constrain different magnetization directions on different atoms). I couldn't find the solution on PW forum archives either. Gabriele, as for your question, I am using version 4.2. And I include non-collinear scheme for this somewhat simple system mostly to test how non-collinearity works with constrained_magnetization, i.e. with fixed theta. I need this for a bit more complicated project I am currently working on. Thank you, Pavel Pavel Lukashev, Ph.D. Research Associate UNL, Department of Physics & Astronomy 208 Theodore Jorgensen Hall 855 N. 16th Street Lincoln, NE 68588-0299 Office: (402) 472-2400 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101201/efa5491e/attachment.htm -------------- next part -------------- &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/home/pavel/QE-4.2/espresso-4.2/pseudo/', outdir='/home/pavel/QE-4.2/espresso-4.2/examples/example13/results/TEST/tmp/', prefix='fe' / &system ibrav = 1, celldm(1) =5.217, nat= 2, ntyp= 2, ecutwfc = 25.0,ecutrho = 200.0, report=1, occupations='smearing', smearing='mp', degauss=0.02 noncolin =.true. starting_magnetization(1) = 0.5 starting_magnetization(2) = 0.5 angle1(1)=90.0 angle2(1)=0.0 angle1(2)=0.0 angle2(2)=0.0 constrained_magnetization='atomic direction' lambda = 1 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Fe1 55.847 Fe.pz-nd-rrkjus.UPF Fe2 55.847 Fe.pz-nd-rrkjus.UPF ATOMIC_POSITIONS Fe1 0.0 0.0 0.0 Fe2 0.5 0.5 0.5 K_POINTS AUTOMATIC 4 4 4 1 1 1 ============================================================ OUTPUT: -------------------------------------------------- ============================================================================== atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 6.406782 magnetization : 1.989301 0.000000 0.780738 magnetization/charge: 0.310499 0.000000 0.121861 polar coord.: r, theta, phi [deg] : 2.137023 68.571554 0.000000 constrained theta [deg] : 90.000000 ============================================================================== ============================================================================== atom number 2 relative position : 0.5000 0.5000 0.5000 charge : 6.406708 magnetization : 1.737036 0.000000 1.244944 magnetization/charge: 0.271128 0.000000 0.194319 polar coord.: r, theta, phi [deg] : 2.137096 54.370619 0.000000 constrained theta [deg] : 0.000000 From david.grifith at gmail.com Thu Dec 2 08:42:09 2010 From: david.grifith at gmail.com (David Grifith) Date: Thu, 2 Dec 2010 11:12:09 +0330 Subject: [Pw_forum] point charge-spin Message-ID: Dear Giovanni Many thanks for your kind attention and very detailed answer. It has raised up our knowledge around the topic. -- Sincerely Yours David G. JCU > > As for point charges, here is a small recipe for isolated > molecules (see below) for the ESP/RESP procedure [A]. > Reference is Bayly et al, J. Phys. Chem., 97, 10269 (1993). > Final point charges for organo-metallic molecules compare > fairly well with standard or published values. > Another possibility is to compute charges by integrating > over atomic basins built on the basis of QT-AIM (Bader) [B]. > > [A] > 1) From PW or CP, write into the restart > directory (I guess into the charge-density.dat file) > the electrostatic potential in place of electron > density. This requires a call before writefile > in CPV/cpr.f90 (in case of CP). Paolo Giannozzi > wrote the subroutine to do this in CP. It would be > nice to have it in some contrib space. > In the input, it is recommended to use > explicit ion_radius(i), especially if you > want to compare with other programs (like CPMD, > for which the default radii are all 1.2 bohr). > > 2) Once the restart is generated, postprocess > it with PP as to print the electron density > into a friendly format, like a gaussian-cube file. > This file will contain the electrostatic potential > on a 3d-grid. PP can process restart produced also > by CP, provided disk_io='high'. > > 3) Write your own program to map the 3d-grid on > the molecular solvent-accessible surface. This will consist in reading > the 3d-grid, reading the molecular surface produced > with vdw radii and a rolling probe, and finally > interpolate the potential at the surface point > using neighbour points in the grid. For the molecular > surface, I recommend an old program called NSC (numerical surface > calculation): > > Eisenhaber et al, J. Comput. Chem., 16, 273 (1995) > > WARNING: this latter step for non-periodic systems! > Non-periodicity is assumed in the ESP/RESP procedure, > that consists in fitting the electrostatic surface > potential with a LIMITED sum of Coulomb interactions. > > The interpolation can be very coarse, the entire method > is plenty of error sources. > The output of this procedure is a list with > x y z U > for each point of the molecular surface. > In case step 4 is performed with the aresp code > that was once part of Amber, the output for a water > molecule is: > > 3 1072 0 > -0.9982123E-32 0.0000000E+00 0.2313846E+00 > -0.2610123E-32 0.1494187E+01 -0.9255383E+00 > -0.1829851E-15 -0.1494187E+01 -0.9255383E+00 > -6.5264638e-01 2.0485851e+00 1.0162867e+00 1.6945994e+00 > -7.2948945e-01 2.4209246e+00 6.0282018e-01 1.7305686e+00 > ... > > where 3 is the number of atoms, 1072 is the number of surface points, > 0 is the net charge, the three following lines are the atomic coordinates > in bohr, and the following lines are x,y,z,U (bohr,kcal/mol) > for the 1072 surface points. This format was once produced > by Gaussian. > > 4) Finally, one of the RESP codes available can be used. > I used the original aresp code that was part of the Amber 4.1 > code. > I think it is not worth to develop the RESP part in QE, > but for sure steps 1-3 could be done relatively easily. > And maybe with a minimum-image based periodicity. > I really don't know how to do it, but I am available > for testing. > > [B] > This is simpler, but for reasons that will be apparent to > everybody in a few applications, it is rarely used. > > 1) Postprocess the restart with PP and write the electron density > on a fine 3d-grid (cube-file). The size of 10 pm associated > to a density energy-cutoff of 250 Ry is rather accurate. > > 2) Process this electron density cube-file with a real-space > QT-AIM code. I used: > > Sanville et al., J. Comp. Chem., 28, 899 (2007). > http://theory.cm.utexas.edu/bader/ > > Charge are in ACF.dat. > This works also for periodic systems (maybe only orthorhombic?). > Problems occur with polar X-H bonds or in all cases > where the zero-flux of density comes too close to atoms desribed > with pseudo-potentials. > > Maybe, this will help, > > Giovanni > > ============================================================ > 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 > ============================================================ > > On Wed, 1 Dec 2010, David Grifith wrote: > > > Dear All > > > > > > I am trying to calculate the point charge and the point spin density on > each > > atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is > > ... > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101202/76a52516/attachment.htm From miguel.martinez at ehu.es Thu Dec 2 10:14:49 2010 From: miguel.martinez at ehu.es (Miguel =?ISO-8859-1?B?TWFydO1uZXo=?=) Date: Thu, 2 Dec 2010 09:14:49 +0000 Subject: [Pw_forum] Example 12 In-Reply-To: References: <019101cb836d$b6cf3d60$246db820$@w2agz.com> Message-ID: <20101202091449.42b77502@mark> Dear Paul, Although this comes with a ton of delay, may I ask you with blas libraries are you using? I just remembered that Ubuntu (and Debian!) had a bug in the distributed Atlas libraries, affecting at least one single precision operation. Maybe some of the double precision operations are also affected: https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/363510 Additionally, the atlas libraries distributed with Ubuntu <= 10.04 and Debian Stable, which are the ones affected by this bug, are also quite old, 3.6.0, and may suffer from old, already fixed, bugs. As an alternative, you may want to try GotoBLAS, which is now a BSD library. The q-e binaries on my laptop are built with that library. Maybe others here have experience using that library. Link: http://www.tacc.utexas.edu/tacc-projects/gotoblas2/ Regards, Miguel On Sun, 14 Nov 2010 22:32:12 +0100 Paolo Giannozzi wrote: > > On Nov 13, 2010, at 21:02 , W2AGZ wrote: > > from gep_x : error # 38 error on zggev > > > > I smell a fortran compiler problem here > > > it might also be a library problem: zggev is a lapack routine, > and sometimes machine-optimized lapack do not work as > expected. That error used to be quite frequent in the past. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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. Miguel Martinez Canales Department of Physics & Astronomy University College London Gower Street, London, WC1E 6BT (UK) Fax: +44 207 679 0595 Tlf: +44 207 678 3476 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From sclauzer at sissa.it Thu Dec 2 10:41:48 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 2 Dec 2010 10:41:48 +0100 Subject: [Pw_forum] Non-collinear calculations: magnetic moment relaxation In-Reply-To: References: <07CFA1DF-D04C-481E-A56B-C2BAC2FD15DD@sissa.it> Message-ID: Il giorno 02/dic/2010, alle ore 07.59, Lukashev Pavel ha scritto: > But now I end up getting another problem. I am trying to impose a constraint on the magnetization angle (i.e. cosine of angle1, theta) by setting: > constrained_magnetization='atomic direction' If you do that, then the code will use theta(i) as the target angles (and also starting angles, I think). > This doesn't seem to work, unless I start with angle1 (theta) being equal for both iron atoms. I think that the present algorithm doesn't work if theta=90. Was this the case in your input? You may also need to play a bit with the value of lambda to get convergence. > When I set them (theta's) different, they do not stay fixed anymore. I attach my input file along with the portion of the final output showing the magnetization angles. I thought that probably I have to constrain the directions separately for each atom, but I did not figure out how to do it. Simply setting > constrained_magnetization(1)='atomic direction' > constrained_magnetization(2)='atomic direction' constrained_magnetization is not an array, it just sets a global option. You have to use theta(1)=45, theta(2)=-45,... for instance. > results in error, and I couldn't find in the manual and/or examples any help on setting these constraints separately. > Any help to resolve this issue is mostly appreciated (i.e. I want to constrain different magnetization directions on different atoms). I couldn't find the solution on PW forum archives either. > > Gabriele, as for your question, I am using version 4.2. And I include non-collinear scheme for this somewhat simple system mostly to test how non-collinearity works with constrained_magnetization, i.e. with fixed theta. I need this for a bit more complicated project I am currently working on. I think that the constrained magnetization is a seldom used feature and the code perhaps needs some improvements. If you really plan to use it extensively, you might think of some better implementation, or at least some ameliorations. Please have a look in PW/add_bfield.f90, PW/setup.f90, and PW/input.f90, it's all contained there. HTH GS > > Thank you, > > Pavel > > Pavel Lukashev, Ph.D. > Research Associate > UNL, Department of Physics & Astronomy > 208 Theodore Jorgensen Hall > 855 N. 16th Street > Lincoln, NE 68588-0299 > Office: (402) 472-2400 > _______________________________________________ > 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/20101202/144516a9/attachment.htm From sclauzer at sissa.it Thu Dec 2 10:51:29 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 2 Dec 2010 10:51:29 +0100 Subject: [Pw_forum] Example 12 (W2AGZ) In-Reply-To: <065801cb91e3$8c701330$a5503990$@w2agz.com> References: <065801cb91e3$8c701330$a5503990$@w2agz.com> Message-ID: <95DEC630-6847-417A-9A74-D1EE8A723F92@sissa.it> Il giorno 02/dic/2010, alle ore 06.41, W2AGZ ha scritto: > All Intel Fortran Compilers (that I know about) are commercial and very expensive, even for Linux. Not always very expensive, in my opinion. For Mac OSX I found a kind of student license for about 49 euros, icc&MKL included. Now I also notice that a non-commercial version of Intel compilers has reappeared on the website http://software.intel.com/en-us/articles/non-commercial-software-download/ Has anyone tried that? GS > > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of meysam pazoki > Sent: Sunday, November 14, 2010 2:17 AM > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Example 12 (W2AGZ) > > > > ---------- Forwarded message ---------- > From: meysam pazoki > Date: Sun, Nov 14, 2010 at 1:42 PM > Subject: Re: Example 12 (W2AGZ) > To: pw_forum at pwscf.org > > > Dear Paul > I see this message.use ifort instead of gfortran. > follow this link to install ifortran in ubuntu: > http://software.intel.com/en-us/articles/using-intel-compilers-for-linux-with-ubuntu/ > > Best Regards > meysam pazoki > SUT > > _______________________________________________ > 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/20101202/3c6aac87/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Thu Dec 2 10:59:03 2010 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 02 Dec 2010 10:59:03 +0100 Subject: [Pw_forum] Example 12 (W2AGZ) In-Reply-To: <95DEC630-6847-417A-9A74-D1EE8A723F92@sissa.it> References: <065801cb91e3$8c701330$a5503990$@w2agz.com> <95DEC630-6847-417A-9A74-D1EE8A723F92@sissa.it> Message-ID: In data 02 dicembre 2010 alle ore 10:51:29, Gabriele Sclauzero ha scritto: > Has anyone tried that? If I were a student I might... In any case, the XE 2011 version (==12.0.0) of intel compiler has a serious bug that miscompiles the iotk library, causing most calculations to fail. I repeat: DO NOT USE the XE 2011 version. If you do you'll most likely get this error: ######################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.2 rkind=8 rlen=-1 ######################################################################### you have been warned. However, there is a possible workaround. If for some reason you're stuck with that you can contact me for details. best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From spakinform at gmail.com Thu Dec 2 14:22:38 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Thu, 2 Dec 2010 22:22:38 +0900 Subject: [Pw_forum] pw2wannier fails to deal with USP Message-ID: Dear all, I'm a novice user of PWSCF. I've been trying to use pw2wannier90 to construct the wannier90.x inputs (.mmn and .amn) from a previously converged SCF calculation. In my calculations, I consider spin-orbit coupling so I use fully relativistic ultrasoft pseudopotentials (USP). But apparently, pw2wannier90 can not handle a noncollinear USP situation. when I run it, I get the following error message, --------------- *** Compute A --------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from pw2wannier90 : error # 1 NCLS calculation not implimented with USP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Does anybody have any workaround to fix this issue? Thanks, --- Soroush Pakseresht Advanced Science Institute (RIKEN) 2-1 Hirosawa, Wako Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101202/ec505c9a/attachment-0001.htm From lorenzo.paulatto at impmc.upmc.fr Thu Dec 2 14:25:51 2010 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 02 Dec 2010 14:25:51 +0100 Subject: [Pw_forum] pw2wannier fails to deal with USP In-Reply-To: References: Message-ID: In data 02 dicembre 2010 alle ore 14:22:38, soroush pakseresht ha scritto: > Does anybody have any workaround to fix this issue? Dear Soroush, if something is not implemented there is not much we can do to help: either you give up NCLS or USPP, or implement it yourself. You may also try to contact the developers to see if what you need is on the way. cheers > Soroush Pakseresht > Advanced Science Institute (RIKEN) > 2-1 Hirosawa, Wako > Saitama-Japan -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From giannozz at democritos.it Thu Dec 2 14:41:26 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 02 Dec 2010 14:41:26 +0100 Subject: [Pw_forum] error In-Reply-To: <252973.365.qm@web56503.mail.re3.yahoo.com> References: <252973.365.qm@web56503.mail.re3.yahoo.com> Message-ID: <4CF7A206.1090808@democritos.it> george manyali wrote: > can someone tell me how to correct the error message below: no, nobody can. A crucial piece of information is missing here: the error message in the output file. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Dec 2 15:48:09 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 02 Dec 2010 15:48:09 +0100 Subject: [Pw_forum] q2r and electron-phonon interaction In-Reply-To: References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> Message-ID: <4CF7B1A9.6070803@democritos.it> sama at ns.dcci.unipi.it wrote: > In line 358 of code q2r.f90 is read the variable *nstar*, > which for count_q=2 takes the value nstar=3. > In the next subroutine read_gamma the code expects then > a series of information dimensioned 3, while actually > in file a2Fq2r.51 the series is dimensioned 6. > In this way, in the next count_q, the code does not find > variables deg, ef and dosscf, and then stops please provide a test job so that your error can be reproduced, or file a bug report on qe-forge.org P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From spakinform at gmail.com Thu Dec 2 18:13:35 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Fri, 3 Dec 2010 02:13:35 +0900 Subject: [Pw_forum] pw2wannier fails to deal with USP In-Reply-To: References: Message-ID: Dear Lorenzo, Thanks for your quick response. I guess QE includes (supports!) some other wannier-related utilities like pmw.x and wannier_ham.x, which I haven't had any experience working with. I was wondering if they could be used to generate model hamiltonian from a noncollinear-USPP calculation. Any idea? Ciao, On Thu, Dec 2, 2010 at 10:25 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > In data 02 dicembre 2010 alle ore 14:22:38, soroush pakseresht > ha scritto: > > Does anybody have any workaround to fix this issue? > > Dear Soroush, > if something is not implemented there is not much we can do to help: > either you give up NCLS or USPP, or implement it yourself. You may also > try to contact the developers to see if what you need is on the way. > > cheers > > > Soroush Pakseresht > > Advanced Science Institute (RIKEN) > > 2-1 Hirosawa, Wako > > Saitama-Japan > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/99f2c9d6/attachment.htm From wumindt2 at zju.edu.cn Thu Dec 2 22:44:02 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Fri, 03 Dec 2010 05:44:02 +0800 Subject: [Pw_forum] wannier function Message-ID: Dear All, I'm a rookie on wannier90, and now I met a problem when i tried to test the example of Si. In the cell of Si, there are 2 inequivalent Si atoms. But in the wannier function plot with two different projections, the wannier function only located on one of the Si atoms. In the users-guide of wannier function, it said the wannier function will apply to all the atom of the type specified in the projection site. So why there is no wannier function on the other Si atom? Any idea? The two different prejections are: !! (1) Valence bands num_wann = 4 dis_froz_max = 6.5 dis_win_max = 6.5 !! !! Bond-centred s-orbitals begin projections f=-0.125,-0.125, 0.375:s f= 0.375,-0.125,-0.125:s f=-0.125, 0.375,-0.125:s f=-0.125,-0.125,-0.125:s end projections !! !! (2) Valence + conduction bands num_wann = 8 dis_froz_max = 6.5 dis_win_max = 17.0 !! !! Atom-centred sp3-orbitals begin projections Si:sp3 end projections Thanks for any help. Min Wu 2010-12-2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/d49438e7/attachment.htm From degironc at sissa.it Fri Dec 3 13:28:14 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 03 Dec 2010 13:28:14 +0100 Subject: [Pw_forum] point charge-spin In-Reply-To: References: Message-ID: <20101203132814.kyhbg31fcwgkcco8@webmail.sissa.it> dear Giovanni, I'm a bit confused... due to Gauss theorem, doesn't all the [A] procedure boil down to be the integral of the ionic+electronic charge inside the vdW radius ... I'm not sure I got what the RESP proceure does.. stefano Quoting Giovanni La Penna : > > As for point charges, here is a small recipe for isolated > molecules (see below) for the ESP/RESP procedure [A]. > Reference is Bayly et al, J. Phys. Chem., 97, 10269 (1993). > Final point charges for organo-metallic molecules compare > fairly well with standard or published values. > Another possibility is to compute charges by integrating > over atomic basins built on the basis of QT-AIM (Bader) [B]. > > [A] > 1) From PW or CP, write into the restart > directory (I guess into the charge-density.dat file) > the electrostatic potential in place of electron > density. This requires a call before writefile > in CPV/cpr.f90 (in case of CP). Paolo Giannozzi > wrote the subroutine to do this in CP. It would be > nice to have it in some contrib space. > In the input, it is recommended to use > explicit ion_radius(i), especially if you > want to compare with other programs (like CPMD, > for which the default radii are all 1.2 bohr). > > 2) Once the restart is generated, postprocess > it with PP as to print the electron density > into a friendly format, like a gaussian-cube file. > This file will contain the electrostatic potential > on a 3d-grid. PP can process restart produced also > by CP, provided disk_io='high'. > > 3) Write your own program to map the 3d-grid on > the molecular solvent-accessible surface. This will consist in reading > the 3d-grid, reading the molecular surface produced > with vdw radii and a rolling probe, and finally > interpolate the potential at the surface point > using neighbour points in the grid. For the molecular > surface, I recommend an old program called NSC (numerical surface > calculation): > > Eisenhaber et al, J. Comput. Chem., 16, 273 (1995) > > WARNING: this latter step for non-periodic systems! > Non-periodicity is assumed in the ESP/RESP procedure, > that consists in fitting the electrostatic surface > potential with a LIMITED sum of Coulomb interactions. > > The interpolation can be very coarse, the entire method > is plenty of error sources. > The output of this procedure is a list with > x y z U > for each point of the molecular surface. > In case step 4 is performed with the aresp code > that was once part of Amber, the output for a water > molecule is: > > 3 1072 0 > -0.9982123E-32 0.0000000E+00 0.2313846E+00 > -0.2610123E-32 0.1494187E+01 -0.9255383E+00 > -0.1829851E-15 -0.1494187E+01 -0.9255383E+00 > -6.5264638e-01 2.0485851e+00 1.0162867e+00 1.6945994e+00 > -7.2948945e-01 2.4209246e+00 6.0282018e-01 1.7305686e+00 > ... > > where 3 is the number of atoms, 1072 is the number of surface points, > 0 is the net charge, the three following lines are the atomic coordinates > in bohr, and the following lines are x,y,z,U (bohr,kcal/mol) > for the 1072 surface points. This format was once produced > by Gaussian. > > 4) Finally, one of the RESP codes available can be used. > I used the original aresp code that was part of the Amber 4.1 > code. > I think it is not worth to develop the RESP part in QE, > but for sure steps 1-3 could be done relatively easily. > And maybe with a minimum-image based periodicity. > I really don't know how to do it, but I am available > for testing. > > [B] > This is simpler, but for reasons that will be apparent to > everybody in a few applications, it is rarely used. > > 1) Postprocess the restart with PP and write the electron density > on a fine 3d-grid (cube-file). The size of 10 pm associated > to a density energy-cutoff of 250 Ry is rather accurate. > > 2) Process this electron density cube-file with a real-space > QT-AIM code. I used: > > Sanville et al., J. Comp. Chem., 28, 899 (2007). > http://theory.cm.utexas.edu/bader/ > > Charge are in ACF.dat. > This works also for periodic systems (maybe only orthorhombic?). > Problems occur with polar X-H bonds or in all cases > where the zero-flux of density comes too close to atoms desribed > with pseudo-potentials. > > Maybe, this will help, > > Giovanni > > ============================================================ > 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 > ============================================================ > > On Wed, 1 Dec 2010, David Grifith wrote: > >> Dear All >> >> >> I am trying to calculate the point charge and the point spin density on each >> atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is >> ... > _______________________________________________ > 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 lfhuang at theory.issp.ac.cn Fri Dec 3 14:06:12 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Fri, 03 Dec 2010 21:06:12 +0800 Subject: [Pw_forum] =?utf-8?q?_a_small_code_for_calculating_reaction_rate_?= =?utf-8?q?=28for_share=29?= Message-ID: <20101203130612.4779.qmail@ms.hfcas.ac.cn> Dear all: I have written a very small code based on hTST for calculating the zero-point energy (ZPE), ZPE correction to potential barrier, exponential prefactor, and jump frequency of a reaction process. This code can use the output files (containing vibrational freq.) of PWSCF as input. The code package can be download with the link below: http://www.sciencenet.cn/m/user_content.aspx?id=390066 Additionally, a simple example and a brief tutorial on harmonic transition state theory and on the usage of this code is included in this package. This simple code has helped me a lot, and I sincerely hope it will be of a little useful to others. Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/206350a0/attachment.htm From glapenna at iccom.cnr.it Fri Dec 3 15:33:33 2010 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Fri, 3 Dec 2010 15:33:33 +0100 (CET) Subject: [Pw_forum] point charge-spin In-Reply-To: <20101203132814.kyhbg31fcwgkcco8@webmail.sissa.it> References: <20101203132814.kyhbg31fcwgkcco8@webmail.sissa.it> Message-ID: > I'm a bit confused... > due to Gauss theorem, doesn't all the [A] procedure boil down to be > the integral of the > ionic+electronic charge inside the vdW radius ... Using for the fitting ALL the points of the electrostatic potential, one would end with the reconstruction of the potential due to the ionic charges + the diffuse valence electrons. And the Gauss theorem would work (consistently with the numerical accuracy), whatever the surface is. I understood that using in the fitting a sub-set of points (like those laying on a surface) of electrostatic potential means using a different estimate of the electric field on the spanned surface. This latter estimate satisfies the Gauss theorem with different charges. The ESP idea (see the Kollman & Co. citations in Bayly et al 1993) was to use ONLY the points on (or around) the molecular solvent accessible surface. Empirically, the more points you collect away from the surface and the closer to the real (original) charge distribution you get. Apparently, the worse is the definition of the electric field on the given surface (due to the inaccuracy of the potential in providing a good field by finite differences) and the better are the point charges (at least for chemists!, but I would say for describing intermolecular interactions, the main goal of the ESP/RESP procedure). Maybe I increased the confusion. As I said, I gave a recipe for providing results consistent with another recipe. Giovanni ============================================================ 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 jgrz2010 at yahoo.com.mx Fri Dec 3 15:34:43 2010 From: jgrz2010 at yahoo.com.mx (JAIME GUSTAVO RODRIGUEZ ZAVALA) Date: Fri, 3 Dec 2010 06:34:43 -0800 (PST) Subject: [Pw_forum] Fermi level in DOS In-Reply-To: Message-ID: <69251.26995.qm@web112418.mail.gq1.yahoo.com> Dear PW_Forum users When you calculate the density of states, where is located the Fermi level? best regards. Jaime Gustavo Rodr?guez Zavala Universidad de Guadalajara, Mex. --- El vie 3-dic-10, pw_forum-request at pwscf.org escribi?: > De: pw_forum-request at pwscf.org > Asunto: Pw_forum Digest, Vol 42, Issue 6 > A: pw_forum at pwscf.org > Fecha: viernes, 3 de diciembre de 2010, 2:47 > Send Pw_forum mailing list > submissions to > ??? pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > ??? http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' > to > ??? pw_forum-request at pwscf.org > > You can reach the person managing the list at > ??? pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > ???1. Re: pw2wannier fails to deal with USP > (Lorenzo Paulatto) > ???2. Re: error (Paolo Giannozzi) > ???3. Re: q2r and electron-phonon > interaction (Paolo Giannozzi) > ???4. Re: pw2wannier fails to deal with USP > (soroush pakseresht) > ???5. wannier function (wumindt2) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 02 Dec 2010 14:25:51 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] pw2wannier fails to deal with USP > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; > delsp=yes > > In data 02 dicembre 2010 alle ore 14:22:38, soroush > pakseresht? > > ha scritto: > > Does anybody have any workaround to fix this issue? > > Dear Soroush, > if something is not implemented there is not much we can do > to help:? > either you give up NCLS or USPP, or implement it yourself. > You may also? > try to contact the developers to see if what you need is on > the way. > > cheers > > > Soroush Pakseresht > > Advanced Science Institute (RIKEN) > > 2-1 Hirosawa, Wako > > Saitama-Japan > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www:???http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA? &? DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www:???http://people.sissa.it/~paulatto/ > > > ------------------------------ > > Message: 2 > Date: Thu, 02 Dec 2010 14:41:26 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] error > To: PWSCF Forum > Message-ID: <4CF7A206.1090808 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > george manyali wrote: > > > can someone tell me how to correct the error message > below: > > no, nobody can. A crucial piece of information is missing > here: the error message in the output file. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Dec 2010 15:48:09 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] q2r and electron-phonon > interaction > To: PWSCF Forum > Message-ID: <4CF7B1A9.6070803 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > sama at ns.dcci.unipi.it > wrote: > > > In line 358 of code q2r.f90 is read the variable > *nstar*, > > which for count_q=2 takes the value nstar=3. > > In the next subroutine read_gamma the code expects > then > >? a series of information dimensioned 3, while > actually > > in file a2Fq2r.51 the series is dimensioned 6. > > In this way, in the next count_q, the code does not > find > > variables deg, ef and dosscf, and then stops > > please provide a test job so that your error can be > reproduced, > or file a bug report on qe-forge.org > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 4 > Date: Fri, 3 Dec 2010 02:13:35 +0900 > From: soroush pakseresht > Subject: Re: [Pw_forum] pw2wannier fails to deal with USP > To: PWSCF Forum > Message-ID: > ??? > Content-Type: text/plain; charset="iso-8859-1" > > Dear Lorenzo, > > Thanks for your quick response. I guess QE includes > (supports!) some other > wannier-related utilities like pmw.x and wannier_ham.x, > which I haven't had > any experience working with. I was wondering if they could > be used to > generate model hamiltonian from a noncollinear-USPP > calculation. Any idea? > > Ciao, > > > > > On Thu, Dec 2, 2010 at 10:25 PM, Lorenzo Paulatto < > lorenzo.paulatto at impmc.upmc.fr> > wrote: > > > In data 02 dicembre 2010 alle ore 14:22:38, soroush > pakseresht > > > ha scritto: > > > Does anybody have any workaround to fix this > issue? > > > > Dear Soroush, > > if something is not implemented there is not much we > can do to help: > > either you give up NCLS or USPP, or implement it > yourself. You may also > > try to contact the developers to see if what you need > is on the way. > > > > cheers > > > > > Soroush Pakseresht > > > Advanced Science Institute (RIKEN) > > > 2-1 Hirosawa, Wako > > > Saitama-Japan > > > > > > -- > > Lorenzo Paulatto > > post-doc @ IMPMC/UPMC - Universit? Paris 6 > > phone: +33 (0)1 44 27 74 89 > > www:???http://www-int.impmc.upmc.fr/~paulatto/ > > > > previously (take note of the change!): > > phd student @ SISSA? &? DEMOCRITOS > (Trieste) > > phone: +39 040 3787 511 > > www:???http://people.sissa.it/~paulatto/ > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Soroush Pakseresht > Advanced Science Institute (RIKEN) > Saitama-Japan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/99f2c9d6/attachment.html > > > ------------------------------ > > Message: 5 > Date: Fri, 03 Dec 2010 05:44:02 +0800 > From: "wumindt2" > Subject: [Pw_forum] wannier function > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear All, > > I'm a rookie on wannier90, and now I met a problem when i > tried to test the example of Si. > In the cell of Si, there are 2 inequivalent Si atoms. But > in the wannier function plot with two different > projections, the wannier function only located on one of > the Si atoms. > In the users-guide of wannier function, it said the wannier > function will apply to all the atom of the type > specified in the projection site. So why there is no > wannier function on the other Si atom? > Any idea? > > The two different prejections are: > > !! (1) Valence bands > num_wann? ? ? ? =???4 > dis_froz_max? ? =???6.5 > dis_win_max? ???=???6.5 > !! !! Bond-centred s-orbitals > begin projections > f=-0.125,-0.125, 0.375:s > f= 0.375,-0.125,-0.125:s > f=-0.125, 0.375,-0.125:s > f=-0.125,-0.125,-0.125:s > end projections > > > !! !! (2) Valence + conduction bands > ???num_wann? ? ? ? > =???8 > ???dis_froz_max? ? > =???6.5 > ???dis_win_max? > ???=? 17.0 > !! !! Atom-centred sp3-orbitals > ???begin projections > ???Si:sp3 > ? ? end projections > > > Thanks for any help. > > Min Wu > 2010-12-2 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/d49438e7/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 42, Issue 6 > *************************************** > From Lorenzo.Paulatto at impmc.upmc.fr Fri Dec 3 15:46:03 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 03 Dec 2010 15:46:03 +0100 Subject: [Pw_forum] Fermi level in DOS In-Reply-To: <69251.26995.qm@web112418.mail.gq1.yahoo.com> References: <69251.26995.qm@web112418.mail.gq1.yahoo.com> Message-ID: On Fri, 03 Dec 2010 15:34:43 +0100, JAIME GUSTAVO RODRIGUEZ ZAVALA wrote: > When you calculate the density of states, where is > located the Fermi level? \int_{-\infty}^{E_f} \theta(\epsilon) d\epsilon = N_e where: \theta(\epsilon) is the DOS, E_f is the Fermi energy, N_e is the number of electrons (per unit cell). In any case, if you system is metallic, the value of E_f (in eV) is printed on output by pw.x during the calculation. regards -- Lorenzo Paulatt (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From sama at ns.dcci.unipi.it Fri Dec 3 18:07:27 2010 From: sama at ns.dcci.unipi.it (sama at ns.dcci.unipi.it) Date: Fri, 3 Dec 2010 18:07:27 +0100 Subject: [Pw_forum] q2r and electron-phonon interaction In-Reply-To: <4CF7B1A9.6070803@democritos.it> References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> <4CF7B1A9.6070803@democritos.it> Message-ID: <5609feefb956a697e5f3084b8abfe9ab.squirrel@www.dcci.unipi.it> Dear Paolo, plase find here the input file and the related error message which is outputted. The test works until the execution of q2r; at that point the calculation stops. The error message is: running q2r...At line 356 of file q2r.f90 (unit = 51, file = 'a2Fq2r.51') Fortran runtime error: Bad real number in item 1 of list input Error condition encountered during test: exit status = 137 Aborting I know there are too few k and q points to obtain a reliable calculation; this was only a simple test to make the error show up. Thanks Samantha > sama at ns.dcci.unipi.it wrote: > >> In line 358 of code q2r.f90 is read the variable *nstar*, >> which for count_q=2 takes the value nstar=3. >> In the next subroutine read_gamma the code expects then >> a series of information dimensioned 3, while actually >> in file a2Fq2r.51 the series is dimensioned 6. >> In this way, in the next count_q, the code does not find >> variables deg, ef and dosscf, and then stops > > please provide a test job so that your error can be reproduced, > or file a bug report on qe-forge.org > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: run_grafene Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/5b7721d4/attachment.txt From sama at ns.dcci.unipi.it Fri Dec 3 18:13:55 2010 From: sama at ns.dcci.unipi.it (sama at ns.dcci.unipi.it) Date: Fri, 3 Dec 2010 18:13:55 +0100 Subject: [Pw_forum] Measure units in electron-phonon interaction In-Reply-To: <253975.48718.qm@web65705.mail.ac4.yahoo.com> References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> Message-ID: <0fed6dd8dc471ff301dfaa71e1c377bc.squirrel@www.dcci.unipi.it> Dear all, I'm trying to calculate the electron-phonon absorption/emission scattering rate in a graphene sheet. I tried to extrapolate the value of the transition matrix element for each k ---> k+q transition, to be integrated as a function of q in order to obtain the scattering rate. I'm not able to understand the measure unit of the transition matrix element, as it is calculated from elphel subroutine. Any hint would be welcome. Thanks Samantha From elbuesta at icqmail.com Fri Dec 3 18:27:45 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Fri, 03 Dec 2010 12:27:45 -0500 Subject: [Pw_forum] Oxygen molecule binding energy Message-ID: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> Dear all, I recently evaluated with PW the binding energy of a O2 molecule using the regular ultra-soft PP from the webpage. I noticed that the energy obtained could be 5.7eV or 6.7eV depending if the flag "nosym=.true." is used or not in the energy evaluation of the isolated oxygen atom. I would like to know if anyone could help me understand why such a large difference is obtained for this system, since for many other systems (such as metals) the inclusion of "nosym=.true." for the isolated atom do not affect so much (or not at all) the value of the binding/cohesive energy. Thanks very much for your time, and all best for all! Fabio Negreiros IPCF - CNR, Pisa - Italia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: O2-iso.scf.in Type: application/octet-stream Size: 730 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0008.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: O2-iso.scf.out Type: application/octet-stream Size: 43953 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0009.obj -------------- next part -------------- A non-text attachment was scrubbed... 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Name: O-iso.scf.in Type: application/octet-stream Size: 656 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0013.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: O_nosym-iso.scf.in Type: application/octet-stream Size: 656 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0014.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: O_nosym-iso.scf.out Type: application/octet-stream Size: 13042 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101203/3cd7d50d/attachment-0015.obj From giannozz at democritos.it Fri Dec 3 20:25:54 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 3 Dec 2010 20:25:54 +0100 Subject: [Pw_forum] Measure units in electron-phonon interaction In-Reply-To: <0fed6dd8dc471ff301dfaa71e1c377bc.squirrel@www.dcci.unipi.it> References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> <0fed6dd8dc471ff301dfaa71e1c377bc.squirrel@www.dcci.unipi.it> Message-ID: <3630533F-B1D9-4DE0-A7AB-77DAB5D5391F@democritos.it> On Dec 3, 2010, at 18:13 , sama at ns.dcci.unipi.it wrote: > I'm not able to understand the measure unit of the transition matrix > element, as it is calculated from elphel subroutine. in the absence of different explicit specifications: everything should be in atomic units (Rydberg: e^2=2, \hbar=1, m=1/2) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From science35 at gmail.com Sat Dec 4 09:17:10 2010 From: science35 at gmail.com (patriot pershing) Date: Sat, 4 Dec 2010 09:17:10 +0100 Subject: [Pw_forum] i have a problem with pseudofiles converted from fhi98PP code Message-ID: dear all : i have created a pseudofiles for Zn and O to use in ZnO study, the pseudopotentials were norm conserving created using the haman scheme in the non local form using lmax = 2. ( d ). i have tested these PP using the fhi98md code using d as local channel, and the obtained results were nice ( force, direct gap,,,,) then i have converted the same pp files to upf format using fhi2upf.x utility and i choise lmax=2 (espresso stantard lmax value also) but when i have running the test the result was completely different from fhimd code ( the force , the gap was indirect ....) i don't know where is the problem here since the 2 codes use plane wave . so if any one have a suggestion please send to me a reply best regards M; lahmer university of constantine algeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101204/9ae02f7a/attachment.htm From kirtinandan07 at gmail.com Sun Dec 5 07:23:13 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Sun, 5 Dec 2010 11:53:13 +0530 Subject: [Pw_forum] cohesive energy of tungsten Message-ID: Hi I am trying to calculate the cohesive energy for tungsten. the code is attached. I am able to get the lattice parameter of 3.19 ang while experimental is 3.16 angs. Then i calculated the cohesive energy of w by calculating the energy of isolated w atom by changing lattice parameter up to 25. I got the cohesive energy of 11.1 ev/atom while reported value is 8.9 ev/atom. This is way too high. can anybody help me. I have varied the K point as well as The E_cut but no advantage. vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101205/f1fcaf6b/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: W-12.in Type: application/octet-stream Size: 737 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101205/f1fcaf6b/attachment.obj From nicola.marzari at materials.ox.ac.uk Sat Dec 4 22:27:44 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 04 Dec 2010 21:27:44 +0000 Subject: [Pw_forum] Oxygen molecule binding energy In-Reply-To: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> References: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> Message-ID: <4CFAB250.7090401@materials.ox.ac.uk> Dear Fabio, a wild guess on my favourite topic - it could be the difference between a spherical and a cylindric atom... I.e. if the O is in the origin, and there is symmetry, the charge density will be sphericized, but by imposing nosym=.true., you'll be left with 2 of the p orbitals doubly occupied (i.e. a cylindrical atom). I've never managed to get from anyone, including some of the luminaries in the fundamentals of DFT, a clear answer to which solution is the "correct" one. Note that even with nosym=.true. you ahve the option of having occupation 2.0 on 2 of the p orbitals, or occupation 1.3333333 on oeach of the 3 p orbitals - the latter solution would probably be similar to the symmetrized solution (but shouldn't be identical). nicola On 12/3/10 5:27 PM, elbuesta at icqmail.com wrote: > Dear all, > > I recently evaluated with PW the binding energy of a O2 molecule using > the regular ultra-soft PP from the webpage. I noticed that the energy > obtained could be 5.7eV or 6.7eV depending if the flag "nosym=.true." is > used or not in the energy evaluation of the isolated oxygen atom. I > would like to know if anyone could help me understand why such a large > difference is obtained for this system, since for many other systems > (such as metals) the inclusion of "nosym=.true." for the isolated atom > do not affect so much (or not at all) the value of the binding/cohesive > energy. > > > Thanks very much for your time, and all best for all! > > Fabio Negreiros > IPCF - CNR, Pisa - Italia -- ---------------------------------------------------------------------- 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 tscale at asu.edu Sun Dec 5 18:44:25 2010 From: tscale at asu.edu (Timothy Cale) Date: Sun, 5 Dec 2010 10:44:25 -0700 Subject: [Pw_forum] openmp in 4.2.1 Message-ID: I am trying to use openmp with espresso-4.2.1 with 64-bit ubuntu 10.04 (gcc et al. 4.4.3), running on an 8 core single processor (i7 930). 4.2.1 runs the test and examples when compiled without modifying "configure". After configuring with --enable-openmp, make crashes in pw.x, with a large number of "undefined reference to", e.g.; omp_get_num_threads opm_get_thread_number GOMP_parallel_start GOMP_parallel_end among many others. It looks like there are issues with several functions in libpw.a, ../Modules/libqemod.a, and ../flib/flib.a. I am new to openmp, but I think I have installed the required libraries (even 32 bit), and used LIBDIRS with configure. I successfully ran openmp demos using simple programs. Any suggestions as to where I might be going astray will be appreciated. Thanks, Tim -- Dr. Timothy S. Cale Center for Solid State Science Arizona State University tscale at asu.edu 480-381-2228 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101205/7408bb20/attachment.htm From giannozz at democritos.it Sun Dec 5 20:57:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 5 Dec 2010 20:57:49 +0100 Subject: [Pw_forum] openmp in 4.2.1 In-Reply-To: References: Message-ID: On Dec 5, 2010, at 18:44 , Timothy Cale wrote: > After configuring with --enable-openmp, make crashes in pw.x what you are describing is a problem with the linker, not with make > with a large number of "undefined reference to", e.g.; > omp_get_num_threads please look into file make.sys (whose syntax is quite obvious) and check whether all the required compiler, linker and library options (if any) are present. --enable-openmp has been tested in a limited number of cases and may not work properly for all compilers P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Mon Dec 6 06:34:10 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 6 Dec 2010 09:04:10 +0330 Subject: [Pw_forum] Model pseudopotential References: Message-ID: Dear QE experts, Is it possible to do pwscf calculations with a simple model pseudopotential (for example, Ashcroft empty-core) without doing much effort on pw code? Best regards, Mahmoud Payami Physics Group, AEOI, Tehran, Iran From mohnish.iitk at gmail.com Mon Dec 6 07:51:58 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 6 Dec 2010 12:21:58 +0530 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: References: Message-ID: Dear Vicky! Check the convergence of energy of isolated atoms also. Normally convergence threshold for energy for isolated species is higher than the crystal system. Check for different values of ecut and use the converged value. And next thing is you are doing calculations for bulk system so all the degrees of freedom should be relaxed for geometry optimization so instead of flag "relax" use "vc-relax".. The former one will converge the forces but not the stress and latter one converges the stress also... On Sun, Dec 5, 2010 at 11:53 AM, vicky singh wrote: > Hi > > I am trying to calculate the cohesive energy for tungsten. the code is > attached. I am able to get the lattice parameter of 3.19 ang while > experimental is 3.16 angs. Then i calculated the cohesive energy of w by > calculating the energy of isolated w atom by changing lattice parameter up > to 25. I got the cohesive energy of 11.1 ev/atom while reported value is 8.9 > ev/atom. This is way too high. can anybody help me. I have varied the K > point as well as The E_cut but no advantage. > > vicky singh > research student > Bangalore > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101206/42b627a2/attachment.htm From kazempoor2000 at yahoo.com Mon Dec 6 09:00:36 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 6 Dec 2010 00:00:36 -0800 (PST) Subject: [Pw_forum] HSE Message-ID: <192742.57809.qm@web114409.mail.gq1.yahoo.com> Dear All The implemented version of HSE hybrid functional? in cvs version is from HSE03 or HSE06? Thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101206/75999ce8/attachment.htm From giannozz at democritos.it Mon Dec 6 09:32:44 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 6 Dec 2010 09:32:44 +0100 Subject: [Pw_forum] Model pseudopotential In-Reply-To: References: Message-ID: <044EAD37-5134-4FBD-9601-1C9DEC2772EC@democritos.it> On Dec 6, 2010, at 6:34 , Mahmoud Payami wrote: > Is it possible to do pwscf calculations with a simple model > pseudopotential > (for example, Ashcroft empty-core) without doing much effort on pw > code? if the model pseudopotential can be written as a "normal" pseudopotential in separable form, you just have to fill the pseudopotential file with what you want P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Dec 6 09:33:39 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 6 Dec 2010 09:33:39 +0100 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: References: Message-ID: <9CA3B60B-D296-4C8E-88B8-854448632787@democritos.it> On Dec 5, 2010, at 7:23 , vicky singh wrote: > This is way too high other results in the literature? P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Mon Dec 6 09:45:58 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 06 Dec 2010 09:45:58 +0100 Subject: [Pw_forum] Oxygen molecule binding energy In-Reply-To: <4CFAB250.7090401@materials.ox.ac.uk> References: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> <4CFAB250.7090401@materials.ox.ac.uk> Message-ID: <4CFCA2C6.1050909@sissa.it> Nicola Marzari wrote: > I've never managed to get from anyone, including some of the luminaries > in the fundamentals of DFT, a clear answer to which solution is the > "correct" one. Note that even with nosym=.true. you ahve the option > of having occupation 2.0 on 2 of the p orbitals, or occupation > 1.3333333 on oeach of the 3 p orbitals - the latter solution > would probably be similar to the symmetrized solution (but shouldn't > be identical). > I think there's no general consensus whether it's "more correct" to have the lowest possible energy giving up the known symmetry of the true GS or to constraint the system to the expected symmetry accepting a slightly higher energy... Of course the "true" xc functional would not put you in this dilemma, but while awaiting for it, I think the important thing is to be aware of the two alternatives and clearly state which one one chooses to conpare with. stefano > nicola > > > > On 12/3/10 5:27 PM, elbuesta at icqmail.com wrote: > >> Dear all, >> >> I recently evaluated with PW the binding energy of a O2 molecule using >> the regular ultra-soft PP from the webpage. I noticed that the energy >> obtained could be 5.7eV or 6.7eV depending if the flag "nosym=.true." is >> used or not in the energy evaluation of the isolated oxygen atom. I >> would like to know if anyone could help me understand why such a large >> difference is obtained for this system, since for many other systems >> (such as metals) the inclusion of "nosym=.true." for the isolated atom >> do not affect so much (or not at all) the value of the binding/cohesive >> energy. >> >> >> Thanks very much for your time, and all best for all! >> >> Fabio Negreiros >> IPCF - CNR, Pisa - Italia >> > > > From janfelix.binder at epfl.ch Mon Dec 6 10:18:47 2010 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Mon, 06 Dec 2010 10:18:47 +0100 Subject: [Pw_forum] HSE In-Reply-To: <192742.57809.qm@web114409.mail.gq1.yahoo.com> References: <192742.57809.qm@web114409.mail.gq1.yahoo.com> Message-ID: <4CFCAA77.5020405@epfl.ch> It is HSE06. ali kazempour wrote: > Dear All > The implemented version of HSE hybrid functional in cvs version is > from HSE03 or HSE06? > Thanks a lot > > Ali Kazempour > > > > Fritz-Haber-Institut fax : ++49-30-8413 4701 > der Max-Planck-Gesellschaft > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de > D-14 195 Berlin-Dahlem / German > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From f_kalantary_f at yahoo.com Mon Dec 6 12:18:27 2010 From: f_kalantary_f at yahoo.com (Forough Kalantary) Date: Mon, 6 Dec 2010 03:18:27 -0800 (PST) Subject: [Pw_forum] AlN Message-ID: <831541.6988.qm@web110205.mail.gq1.yahoo.com> Hi I wanted to know if the best lattice parameter (a) for nanotubes should be fit with murnagon equation. How much is the best value for Al-N nanotubes. Regards.? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101206/93d1a949/attachment.htm From mpayami at aeoi.org.ir Mon Dec 6 12:28:29 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 6 Dec 2010 14:58:29 +0330 Subject: [Pw_forum] Model pseudopotential References: <044EAD37-5134-4FBD-9601-1C9DEC2772EC@democritos.it> Message-ID: <700E793BA3904ADCAFF9C4339C1EC093@b> Dear Paolo, Thank you very much for your reply. > if the model pseudopotential can be written as a "normal" > pseudopotential in separable form, you just have to fill > the pseudopotential file with what you want my special interest is the pseudopotential given by: V_{ion}^{ps}(r) = 0.0, for r <= r_c, = -z/r, for r>r_c. It is not nonlocal and therefore I think the separablity has nothing to do in this simple case (?!) The r_c parameter is material dependent which can be determined somehow. Best regards, mahmoud > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 > > From w2agz at w2agz.com Tue Dec 7 08:33:43 2010 From: w2agz at w2agz.com (W2AGZ) Date: Mon, 6 Dec 2010 23:33:43 -0800 Subject: [Pw_forum] iotk error - again Message-ID: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> While trying to run an electron-phonon calculation (PH) on my Ubuntu 8.04 box within QE 4.0 (a very stable configuration), I get the following immediately after start-up: ############################################################################ ############################################ # FROM IOTK LIBRARY, VERSION 1.1.0development # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.spp:211) # CVS Revision: 1.7 # foundl # ERROR IN: iotk_close_read (iotk_files.spp:589) # CVS Revision: 1.3 I've run at least four or five other e-p sessions on the above box without problem. If helpful, I can post my input file later. Drilling around the Forum, I found this: ************************************************************************* alan chen chenhanghuipwscf at gmail.com Wed Aug 13 23:33:56 CEST 2008 Previous message: [Pw_forum] npwx in pwscf v.4.0 Next message: [Pw_forum] IOTK library Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Dear PWSCF users, I have encountered this problem many times and I checked the archive but I still did not get how to fix the problem. Some of my jobs are killed by the following errors: ############################################################################ ############################################ # FROM IOTK LIBRARY, VERSION 1.1.0development # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_getline (iotk_scan.spp:812) # CVS Revision: 1.7 # iostat=-1 # ERROR IN: iotk_scan_tag (iotk_scan.spp:516) # CVS Revision: 1.7 # ERROR IN: iotk_scan (iotk_scan.spp:710) # CVS Revision: 1.7 # ERROR IN: iotk_scan_end (iotk_scan.spp:211) # CVS Revision: 1.7 # foundl # ERROR IN: iotk_close_read (iotk_files.spp:589) # CVS Revision: 1.3 ############################################################################ ############################################ Paolo suggested a quick fix: change Q_REAL in Q_REAL_SPACE in Modules/xml_io_base.f90 (thanks to Giovanni Bussi). Does that mean: replace Q_REAL_SPACE by Q_REAL? Could any one provide more specific procedures to fix the bug? Thank you very much. Hanghui Chen Department of Physics, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/d86fccae/at tachment.htm PMG Comment: Paolo responded "replace q_real by q_real_space." Is this the fix? Paul Grant, IBM Research Staff Member Emeritus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101206/d6a7baf7/attachment.htm From scandolo at ictp.it Tue Dec 7 09:14:06 2010 From: scandolo at ictp.it (Sandro Scandolo) Date: Tue, 07 Dec 2010 09:14:06 +0100 Subject: [Pw_forum] Oxygen molecule binding energy In-Reply-To: <4CFCA2C6.1050909@sissa.it> References: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> <4CFAB250.7090401@materials.ox.ac.uk> <4CFCA2C6.1050909@sissa.it> Message-ID: <4CFDECCE.2030608@ictp.it> In the specific case of the O2 molecule, in a molecular orbital picture O2 has two degenerate pi-star HOMO orbitals that need to be filled with 2 electrons. The ground state is a triplet S=1 (up,up), (up,down)+(down,up),(down,down), the next state is a singlet (up,down)-(down,up). A good representation of the triplet should be given by the ground state of a spin-polarized calculation. The ground state should have nup-ndown=2, and the two unpaired electrons fill the two pi-star orbitals (with the same spin). I believe you don't need to impose any symmetry to find this ground state. If you force the system to have total spin=0 (in a spin-polarized calculation), you should obtain the state (up,down) (or its degenerate counterpart (down,up)). This state does not satisfy the correct symmetry of the 2-electron wfc, so in principle does not correspond to any of the correct many-electron states above. However this spurious state can be expressed as a linear combination (sum or difference) of one of the triplet states ((up,down)+(down,up)) and the singlet state ((up,down)-(down,up)). Perhaps its energy corresponds to the average energy of the triplet and the singlet??!? Best regards Sandro On 06/12/2010 09:45, Stefano de Gironcoli wrote: > Nicola Marzari wrote: >> I've never managed to get from anyone, including some of the luminaries >> in the fundamentals of DFT, a clear answer to which solution is the >> "correct" one. Note that even with nosym=.true. you ahve the option >> of having occupation 2.0 on 2 of the p orbitals, or occupation >> 1.3333333 on oeach of the 3 p orbitals - the latter solution >> would probably be similar to the symmetrized solution (but shouldn't >> be identical). >> > I think there's no general consensus whether it's "more correct" to have > the lowest possible energy giving up the known symmetry of the true GS > or to constraint the system to the expected symmetry accepting a > slightly higher energy... Of course the "true" xc functional would not > put you in this dilemma, but while awaiting for it, I think the > important thing is to be aware of the two alternatives and clearly state > which one one chooses to conpare with. > > stefano > > > >> nicola >> >> >> >> On 12/3/10 5:27 PM, elbuesta at icqmail.com wrote: >> >>> Dear all, >>> >>> I recently evaluated with PW the binding energy of a O2 molecule using >>> the regular ultra-soft PP from the webpage. I noticed that the energy >>> obtained could be 5.7eV or 6.7eV depending if the flag "nosym=.true." is >>> used or not in the energy evaluation of the isolated oxygen atom. I >>> would like to know if anyone could help me understand why such a large >>> difference is obtained for this system, since for many other systems >>> (such as metals) the inclusion of "nosym=.true." for the isolated atom >>> do not affect so much (or not at all) the value of the binding/cohesive >>> energy. >>> >>> >>> Thanks very much for your time, and all best for all! >>> >>> Fabio Negreiros >>> IPCF - CNR, Pisa - Italia >>> >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sandro Scandolo -- http:/www.ictp.it/~scandolo From sclauzer at sissa.it Tue Dec 7 09:58:48 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 7 Dec 2010 09:58:48 +0100 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: References: Message-ID: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> Dear Mohnish Il giorno 06/dic/2010, alle ore 07.51, mohnish pandey ha scritto: > Dear Vicky! > Check the convergence of energy of isolated atoms also. Normally convergence threshold for energy for isolated species is higher than the crystal system. I'm sorry, but I hope you'll let me disagree on this point. What makes you say this? > Check for different values of ecut and use the converged value. One usually uses the same ecutwfc value for both bulk and atomic calculations, in order to take advantage of some error cancellation. Indeed, if you plot the difference between the bulk and atomic total energies as a function of ecutwfc, you should see that it converges much faster than any of the two energies taken alone. > And next thing is you are doing calculations for bulk system so all the degrees of freedom should be relaxed for geometry optimization so instead of flag "relax" use "vc-relax".. The former one will converge the forces but not the stress and latter one converges the stress also... I agree that the "vc-relax" option is useful, but maybe not so much in this case. I think that bulk W is bcc, hence it can be studied with one atom per cell and there are no internal parameters to relax. You can simply scan the total energy as a function of the lattice parameter to get the equilibrium value, as Vicky already did. There are many other issues that come in, especially in the atomic calculation (see recent discussions on the forum). Even when you get a converged DFT value, in some cases this might be considerably far from the experimental value. Best regards, GS > On Sun, Dec 5, 2010 at 11:53 AM, vicky singh wrote: > Hi > > I am trying to calculate the cohesive energy for tungsten. the code is attached. I am able to get the lattice parameter of 3.19 ang while experimental is 3.16 angs. Then i calculated the cohesive energy of w by calculating the energy of isolated w atom by changing lattice parameter up to 25. I got the cohesive energy of 11.1 ev/atom while reported value is 8.9 ev/atom. This is way too high. can anybody help me. I have varied the K point as well as The E_cut but no advantage. > > vicky singh > research student > Bangalore > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > _______________________________________________ > 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/20101207/a3e0bc6e/attachment.htm From rolf.oettking at etit.tu-chemnitz.de Tue Dec 7 11:57:34 2010 From: rolf.oettking at etit.tu-chemnitz.de (Rolf =?iso-8859-1?b?1nR0a2luZw==?=) Date: Tue, 07 Dec 2010 11:57:34 +0100 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. Message-ID: <20101207115734.169030wfl42gbh26@mail.tu-chemnitz.de> Dear all, I am referring to the posting of Ngoc Linh Nguyen from Tue Apr 13 10:25:09 CEST 2010, where the dos-calculation of SI using the PBE0 EXX functional enforced by input_dft='pbe0' is said to run properly. However, if I use the same input files (see below), after running the scf calculation, in the nscf run the PWSCF v.4.2.1 code replies %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from setup : error # 1 HYBRID XC not allowed in non-scf calculations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I understand that the calculation of the DOS using hybrid functionals causes problems, but, if so, how can the files "work well" as said by Linh? With best regards Rolf input file for dos calculation &CONTROL title = 'Si-0', calculation = 'nscf', prefix = 'Si-0.pw', pseudo_dir = './pseudo' outdir = './Si-0', restart_mode='restart', / &system ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =12.0, nbnd = 5, input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, / &electrons mixing_beta = 0.7 / ATOMIC_SPECIES Si 28.086 Si.pz-vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 From degironc at sissa.it Tue Dec 7 12:44:09 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 07 Dec 2010 12:44:09 +0100 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. In-Reply-To: <20101207115734.169030wfl42gbh26@mail.tu-chemnitz.de> References: <20101207115734.169030wfl42gbh26@mail.tu-chemnitz.de> Message-ID: <4CFE1E09.7030208@sissa.it> the problem is not the DOS calculation but, as the error states, the nscf calculation with hybrid functionals.. you need to run an scf calculation and plot the corresponding dos without doing a nscf calculation. stefano Rolf ?ttking wrote: > Dear all, > > I am referring to the posting of Ngoc Linh Nguyen from Tue Apr 13 > 10:25:09 CEST 2010, where the dos-calculation of SI using the PBE0 EXX > functional enforced by input_dft='pbe0' is said to run properly. > > However, if I use the same input files (see below), after running the > scf calculation, in the nscf run the PWSCF v.4.2.1 code replies > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from setup : error # 1 > HYBRID XC not allowed in non-scf calculations > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I understand that the calculation of the DOS using hybrid functionals > causes problems, but, if so, how can the files "work well" as said by > Linh? > > With best regards > > Rolf > > input file for dos calculation > > &CONTROL > title = 'Si-0', > calculation = 'nscf', > prefix = 'Si-0.pw', > pseudo_dir = './pseudo' > outdir = './Si-0', > restart_mode='restart', > / > > &system > ibrav= 2, > celldm(1) =10.20, > nat= 2, > ntyp= 1, > ecutwfc =12.0, > nbnd = 5, > input_dft='pbe0', > nqx1 = 1, nqx2 = 1, nqx3 = 1, > / > > &electrons > mixing_beta = 0.7 > / > > ATOMIC_SPECIES > Si 28.086 Si.pz-vbc.UPF > > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > > K_POINTS > 10 > 0.1250000 0.1250000 0.1250000 1.00 > 0.1250000 0.1250000 0.3750000 3.00 > 0.1250000 0.1250000 0.6250000 3.00 > 0.1250000 0.1250000 0.8750000 3.00 > 0.1250000 0.3750000 0.3750000 3.00 > 0.1250000 0.3750000 0.6250000 6.00 > 0.1250000 0.3750000 0.8750000 6.00 > 0.1250000 0.6250000 0.6250000 3.00 > 0.3750000 0.3750000 0.3750000 1.00 > 0.3750000 0.3750000 0.6250000 3.00 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From elcortogm at googlemail.com Tue Dec 7 18:13:23 2010 From: elcortogm at googlemail.com (Steve Schmerler) Date: Tue, 7 Dec 2010 18:13:23 +0100 Subject: [Pw_forum] nstep not honored in vc-md Message-ID: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> Hello I'm using QE for a while now and I'm quite happy with it. Thank you for working on this. I'm trying some basic variable cell MD (pw.x, vc-md) and I found that the code does not stop after 'nstep' steps with cell_dynamics='w' or 'pr', while it does so with normal 'md' and 'vc-relax' (cell_dynamics='damp-w'). This is with 4.2.1 and 4.1.2 . Attached are input (pw.in) and output (pw.out, killed after 9 steps, nstep=3 in pw.in). "nstep=3" is mentioned correctly in the output, though. Thank you for your help. best, Steve -- Steve Schmerler Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392797 -------------- next part -------------- A non-text attachment was scrubbed... Name: pw.in.gz Type: application/octet-stream Size: 587 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101207/1d6ae3d5/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: pw.out.gz Type: application/octet-stream Size: 22302 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101207/1d6ae3d5/attachment-0003.obj From mirnezhad.mm at gmail.com Tue Dec 7 19:34:14 2010 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Tue, 7 Dec 2010 10:34:14 -0800 Subject: [Pw_forum] hi,effect of temperature Message-ID: Dear all, I used Q.E to calculate the Youngs mudulud of Boron-Nitride nanotube and h-Bn the result are in agrement with previous calculation. At this stage i want to calcualte the effect of temperature on the Young mudulus of Boron-Nitride structres. Can Q.E do such calcualtions? Tahnks for your reply. mirnezhad, msc guilan .iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101207/75903279/attachment.htm From eyvaz_isaev at yahoo.com Wed Dec 8 01:26:45 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 7 Dec 2010 16:26:45 -0800 (PST) Subject: [Pw_forum] hi,effect of temperature In-Reply-To: References: Message-ID: <759409.98534.qm@web65712.mail.ac4.yahoo.com> Hi, The short answer is "No" as DFT deals with T=0K. But you can try Molecular Dynamics and supercells to deal with finite temperature. > Can Q.E do such calcualtions? Can you do such calculations? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Mahdi Mirnezhad To: pw_forum Sent: Tue, December 7, 2010 7:34:14 PM Subject: [Pw_forum] hi,effect of temperature Dear all, I used Q.E to calculate the Youngs mudulud of Boron-Nitride nanotube and h-Bn the result are in agrement with previous calculation. At this stage i want to calcualte the effect of temperature on the Young mudulus of Boron-Nitride structres. Can Q.E do such calcualtions? Tahnks for your reply. mirnezhad, msc guilan .iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101207/2e02ef9c/attachment.htm From mayankaditya at gmail.com Wed Dec 8 06:35:56 2010 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 8 Dec 2010 11:05:56 +0530 Subject: [Pw_forum] Total energy convergence Message-ID: Dear All I am interested in phonon calculation. I want to know for phonon calculation what is the order of total energy convergence and k mesh size should be taken in scf calculation? Should I take larger value than the band calculation parameters. M K Gupta From ac.rain at inbox.com Wed Dec 8 08:15:51 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Tue, 7 Dec 2010 23:15:51 -0800 Subject: [Pw_forum] QE and mpich2, Linux Message-ID: <47BD3257D74.00000656ac.rain@inbox.com> hi all, I am having troubles getting MPICH2 working with Quantum Espresso, it seems to be working somewhat but with errors. There may be an issue with my environment setup, some is guess-work as I couldn't find much documentation for espresso and mpich2. server4 is the system the user will submit from. server3 and server5 are extra nodes on the same subnet. mpich2 was built with gfortran support and ssh keys are setup with no message-Of-Day so nodes can talk properly. The espresso directory /usr/local/espresso-4.2.1 is located on server4 and NFS shared out to server3 and server5 with read/write mode (when I initially had NFS set to read-only, espresso was unable to write a temp file to the tests directory so I made it a read-write NFS export). This means all 3 systems have read-write access to the same espresso directory, is this correct? extra info: inside the examples/environment_variables file I have the line "TMP_DIR=/home/mpiexec_espresso_tmp" however no files were written there (each system has its own instance of that dir) it seems to just use /usr/local/espresso-4.2.1/tmp ,as I can see files from today's date. This is fine with me if it prefers to use the NFS partition. I tried messing with PARA_PREFIX and PARA_POSTFIX inside the variables file but I only ran into worse issues. here is my test command... mpiexec -f ~/mpiMachinefile.txt -n 10 -wdir /usr/local/espresso-4.2.1/tests ./check-pw.x.j here is the contents of my ~/mpiMachinefile.txt file... server3:24 server4:24 server5:24 I have also tried with -n 30 and it seemed to put most of the process on the first server in the list as expected, however I never saw 10 or more process using 100% of the core in 'top'. When there were many processes at once they were only using small percentage of resources, with one of the process using 100% of core/cpu. From my understanding there should be 24 different process per machine at 100%, depending on what it's doing. In summary: the errors are troubling, and I don't think the system(s) are using their full potential for simulating. below is the first part of command-line output, from the mpiexec using the -n 10 option. any advice appreciated, thanks, Nick - Linux Administrator $ mpiexec -f ~/mpiMachinefile.txt -n 10 -wdir /usr/local/espresso-4.2.1/tests ./check-pw.x.j Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...Checking atom...passed Checking atom-lsda...passed Checking atom-pbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...passed Checking atom-lsda...passed Checking atom-lsda...passed Checking atom-lsda...passed Checking atom-lsda...passed Checking atom-lsda...passed Checking atom-lsda...passed Checking atom-lsda...passed passed awk: cmd. line:6: fatal: cannot open file `atom.tmp' for reading (No such file or directory) /bin/rm: cannot remove `atom.tmp': No such file or directory Checking atom-lsda...Checking atom-lsda...STOP 2 FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting STOP 2 STOP 2 FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting STOP 2 FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting STOP 2 FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting STOP 2 FAILED with error condition! Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref Aborting discrepancy in number of scf iterations detected Reference: 7, You got: 11 Checking atom-pbe...discrepancy in number of scf iterations detected Reference: 7, You got: 11 Checking atom-pbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...STOP 2 FAILED with error condition! Input: atom-sigmapbe.in, Output: atom-sigmapbe.out, Reference: atom-sigmapbe.ref Aborting discrepancy in number of scf iterations detected Reference: 7, You got: 25 Checking atom-pbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...discrepancy in total energy detected Reference: -31.491047, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 16, You got: discrepancy in pressure detected Reference: -15.02, You got: Checking berry...passed Checking berry, step 2 ...discrepancy in number of scf iterations detected Reference: 16, You got: 34 discrepancy in pressure detected Reference: -15.02, You got: -15.11 Checking berry...STOP 2 FAILED with error condition! Input: berry.in2, Output: berry.out2, Reference: berry.ref2 Aborting passed Checking berry, step 2 ...STOP 2 FAILED with error condition! Input: berry.in2, Output: berry.out2, Reference: berry.ref2 Aborting discrepancy in number of scf iterations detected Reference: 16, You got: 32 discrepancy in pressure detected Reference: -15.02, You got: -14.98 Checking berry...passed Checking berry, step 2 ... end. ____________________________________________________________ Publish your photos in seconds for FREE TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if4 From giannozz at democritos.it Wed Dec 8 09:42:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 8 Dec 2010 09:42:06 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <47BD3257D74.00000656ac.rain@inbox.com> References: <47BD3257D74.00000656ac.rain@inbox.com> Message-ID: <560747B7-8F80-4B51-828A-78E8262FF819@democritos.it> On Dec 8, 2010, at 8:15 , ac.rain at inbox.com wrote: > $ mpiexec -f ~/mpiMachinefile.txt -n 10 -wdir /usr/local/ > espresso-4.2.1/tests ./check-pw.x.j the correct way to start the tests in parallel is to edit PARA_PREFIX and PARA_POSTFIX in the "check-pw.x.j" script P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gyalcin at sakarya.edu.tr Wed Dec 8 09:52:47 2010 From: gyalcin at sakarya.edu.tr (Battal Gazi =?ISO-8859-9?Q?YAL=C7IN?=) Date: Wed, 08 Dec 2010 10:52:47 +0200 Subject: [Pw_forum] band_structure_alloys Message-ID: Hello all, I want to calculate band structure of Gax(In1-x)As, (x =0.25, 0.50, 0.75) for x =0.25 I have done it, but the others the program don t work, and it give us following result; c_bands:2 eigenvalues not converged &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& from cdiaghg : error# 91 diagonalization (ZHEGV*) failed &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& I have never run into like this problem. What can I do, I don t know, If you help me it will be very very good. Thanks a lot ___________________________________________________________________________________________ Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : http://www.mail.sakarya.edu.tr/ Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : http://www.sakarya.edu.tr/ ___________________________________________________________________________________________ From mohnish.iitk at gmail.com Wed Dec 8 10:27:10 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 8 Dec 2010 14:57:10 +0530 Subject: [Pw_forum] speed becomes very slow after some electronic or ionic relaxation cycles Message-ID: Dear QE users, I am trying to simulate supercell of ZnO zincblende structure with 56 atoms. I have checked the structure with Xcrysden and it is right. But the problem is after performing some electronic cycle the speed becomes very slow and the calculations are stuck. When I reduce the "ecut" value it performs some ionic relaxation step but the same problem come after some ionic relaxation steps. Can anybody please help whats wrong with the calculation? -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101208/3c9cf56d/attachment.htm From nazari at iasbs.ac.ir Wed Dec 8 09:55:44 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 8 Dec 2010 12:25:44 +0330 (IRST) Subject: [Pw_forum] band_structure_alloys In-Reply-To: References: Message-ID: <31926.85.185.211.90.1291798544.squirrel@mail.iasbs.ac.ir>
Check the nbnd. > Hello all, I want to calculate band structure of Gax(In1-x)As, (x =0.25, > 0.50, 0.75) for x =0.25 I have done it, but the others the program don t > work, and it give us following result; > > c_bands:2 eigenvalues not converged > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > from cdiaghg : error# 91 > diagonalization (ZHEGV*) failed > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > I have never run into like this problem. > > What can I do, I don t know, If you help me it will be very very good. > > Thanks a lot > ___________________________________________________________________________________________ > > Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : > http://www.mail.sakarya.edu.tr/ > Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : > http://www.sakarya.edu.tr/ > ___________________________________________________________________________________________ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- 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/20101208/66af74c2/attachment.htm From sclauzer at sissa.it Wed Dec 8 10:34:24 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 8 Dec 2010 10:34:24 +0100 Subject: [Pw_forum] speed becomes very slow after some electronic or ionic relaxation cycles In-Reply-To: References: Message-ID: You are not giving enough information to understand the problem. Please read this: http://quantum-espresso.org/wiki/index.php/Bugs Regards, GS Il giorno 08/dic/2010, alle ore 10.27, mohnish pandey ha scritto: > Dear QE users, > I am trying to simulate supercell of ZnO zincblende structure with 56 atoms. I have checked the structure with Xcrysden and it is right. But the problem is after performing some electronic cycle the speed becomes very slow and the calculations are stuck. When I reduce the "ecut" value it performs some ionic relaxation step but the same problem come after some ionic relaxation steps. Can anybody please help whats wrong with the calculation? > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > _______________________________________________ > 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/20101208/d48f230e/attachment.htm From sclauzer at sissa.it Wed Dec 8 10:35:26 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 8 Dec 2010 10:35:26 +0100 Subject: [Pw_forum] band_structure_alloys In-Reply-To: References: Message-ID: <8A3F557F-6C82-4574-8F6F-A8366930CE5E@sissa.it> You are not giving enough information to understand the problem. Please read this: http://quantum-espresso.org/wiki/index.php/Bugs Regards, GS Il giorno 08/dic/2010, alle ore 09.52, Battal Gazi YAL?IN ha scritto: > Hello all, I want to calculate band structure of Gax(In1-x)As, (x =0.25, 0.50, 0.75) for x =0.25 I have done it, but the others the program don t work, and it give us following result; > > c_bands:2 eigenvalues not converged > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > from cdiaghg : error# 91 > diagonalization (ZHEGV*) failed > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > I have never run into like this problem. > > What can I do, I don t know, If you help me it will be very very good. > > Thanks a lot > ___________________________________________________________________________________________ > > Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : http://www.mail.sakarya.edu.tr/ > Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : http://www.sakarya.edu.tr/ > ___________________________________________________________________________________________ > > > _______________________________________________ > 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/20101208/f9a342cc/attachment.htm From giannozz at democritos.it Wed Dec 8 10:49:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 8 Dec 2010 10:49:12 +0100 Subject: [Pw_forum] iotk error - again In-Reply-To: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> Message-ID: On Dec 7, 2010, at 8:33 , W2AGZ wrote: > ?replace q_real by q_real_space.? Is this the fix? > no. This is the fix for a very specific case, and the only one I remember in which an error was issued by iotk for a good reason (i.e. a variable was written with one name and read with another). All other instances of iotk errors I remember are related to miscompilation. Try first of all to compile iotk with reduced optimization (e.g. using $(MAKE) FFLAGS="$(FFLAGS_NOOPT)" ) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gregor.mali at ki.si Wed Dec 8 12:31:43 2010 From: gregor.mali at ki.si (Gregor Mali) Date: Wed, 8 Dec 2010 12:31:43 +0100 Subject: [Pw_forum] GIPAW and updates? In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D25602535656@postar.ki.si> Dear QE/GIPAW developers, during the CECAM Tutorial 'Computational spectroscopy using Quantum Espresso and related codes' in July 2010 in Trieste it was mentioned that the GIPAW module of QE will be updated/rewritten. I wonder if a new version of this modul is perhaps already available? I am particularly interested in the 'incorporation' of core-relaxation for calculation of hyperfine couplings and in the possibility of using different (PAW, US) pseudopotentials with the GIPAW code. I also wonder if it is (will be) possible to use pseudopotentials without the 'GIPAW reconstruction part' for atoms for which we are not interested in NMR or EPR parameters. In the current version of GIPAW module, pseudopotentials files of all the atomic species have to include the GIPAW reconstruction part, otherwise the calculation stops with error. Since only a limited set of 'GIPAW pseudopotentials' is available, it would be very welcome if other PPs could be used at least for those species for which we are not seeking NMR/EPR data. Thank you very much. Gregor Gregor Mali National Institute of Chemistry Ljubljana, Slovenia From eyvaz_isaev at yahoo.com Wed Dec 8 13:20:11 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 8 Dec 2010 04:20:11 -0800 (PST) Subject: [Pw_forum] band_structure_alloys In-Reply-To: <31926.85.185.211.90.1291798544.squirrel@mail.iasbs.ac.ir> References: <31926.85.185.211.90.1291798544.squirrel@mail.iasbs.ac.ir> Message-ID: <25407.15987.qm@web65705.mail.ac4.yahoo.com> Dear Nazari, This is well known (and OLD) error, if you search the forum archive. Please take time to learn from the archive why this happens. Or see Troubleshooting in User Guides in /Doc. You will be surprised how many reasons there are for this error. And see possible solution. Please also give correct Subject for your message, as the error is not connected to any alloy calculation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: "nazari at iasbs.ac.ir" To: PWSCF Forum Sent: Wed, December 8, 2010 9:55:44 AM Subject: Re: [Pw_forum] band_structure_alloys Check the nbnd. > Hello all, I want to calculate band structure of Gax(In1-x)As, (x =0.25, > 0.50, 0.75) for x =0.25 I have done it, but the others the program don t > work, and it give us following result; > > c_bands:2 eigenvalues not converged > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > from cdiaghg : error# 91 > diagonalization (ZHEGV*) failed > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > I have never run into like this problem. > > What can I do, I don t know, If you help me it will be very very good. > > Thanks a lot >___________________________________________________________________________________________ >_ > > > Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : > http://www.mail.sakarya.edu.tr/ > Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : > http://www.sakarya.edu.tr/ >___________________________________________________________________________________________ >_ > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- 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/20101208/6030d7d3/attachment.htm From kucukben at sissa.it Wed Dec 8 13:40:11 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 08 Dec 2010 13:40:11 +0100 Subject: [Pw_forum] GIPAW and updates? In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D25602535656@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256017CDA42@postar.ki.si> <8C0B47760A05FB4AB504C9BCAD32D256017CDA5F@postar.ki.si> <8C0B47760A05FB4AB504C9BCAD32D25602535656@postar.ki.si> Message-ID: <20101208134011.8hgegszs00ss8gkk@webmail.sissa.it> Dear Gregor, The module is ready for production runs (there is still a lot of room for improvement though) but I believe it will be ready for release once we collate and organize a manual and perhaps a tutorial. It works well with PAW and US pseudopotentials..and involves an easy way around for generating GIPAW suitable pseudos from existing PAW ones, so you can keep on using your favorite PAW pseudos :) As far as I know there is also a pseudo dataset generation study going on, from which GIPAW users can benefit greatly. Hope to get back to you with release notes soon. Thanks for your interest, emine kucukbenli, phd student, sissa, italy. Quoting Gregor Mali : > Dear QE/GIPAW developers, > > during the CECAM Tutorial 'Computational spectroscopy using Quantum > Espresso and related codes' in July 2010 in Trieste it was mentioned > that the GIPAW module of QE will be updated/rewritten. I wonder if a new > version of this modul is perhaps already available? > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From giannozz at democritos.it Wed Dec 8 14:07:47 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 8 Dec 2010 14:07:47 +0100 Subject: [Pw_forum] nstep not honored in vc-md In-Reply-To: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> References: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> Message-ID: <43EB0A05-5DC1-4DAF-83E5-4EA2482E047F@democritos.it> On Dec 7, 2010, at 18:13 , Steve Schmerler wrote: > I'm trying some basic variable cell MD (pw.x, vc-md) and I found that > the code does not stop after 'nstep' steps with cell_dynamics='w' or > 'pr', while it does so with normal 'md' and 'vc-relax' > (cell_dynamics='damp-w'). this is an old problem, whose origin goes back to the way the different pieces of codes, written by diferent people in different times, were integrated into QE. It wouldn't be that difficult to solve it, but the various MD and structural optimization codes need some major reorganization anyway, so this will be fixed in due time (in a not too distant future, I hope) Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elcortogm at googlemail.com Wed Dec 8 14:31:26 2010 From: elcortogm at googlemail.com (Steve Schmerler) Date: Wed, 8 Dec 2010 14:31:26 +0100 Subject: [Pw_forum] nstep not honored in vc-md In-Reply-To: <43EB0A05-5DC1-4DAF-83E5-4EA2482E047F@democritos.it> References: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> <43EB0A05-5DC1-4DAF-83E5-4EA2482E047F@democritos.it> Message-ID: <20101208133126.GA19103@cartman.physik.tu-freiberg.de> On Dec 08 14:07 +0100, Paolo Giannozzi wrote: > > On Dec 7, 2010, at 18:13 , Steve Schmerler wrote: > > > I'm trying some basic variable cell MD (pw.x, vc-md) and I found that > > the code does not stop after 'nstep' steps with cell_dynamics='w' or > > 'pr', while it does so with normal 'md' and 'vc-relax' > > (cell_dynamics='damp-w'). > > this is an old problem, whose origin goes back to the way the > different pieces of codes, written by diferent people in different > times, were integrated into QE. It wouldn't be that difficult to > solve it, but the various MD and structural optimization codes > need some major reorganization anyway, so this will be fixed > in due time (in a not too distant future, I hope) Ah OK. I figured that it's not too difficult (some if-statements), but rather time-consuming for someone without proper knowledge of the code. I had a look at PW/vcsmd.f90 and others but did not find an immediate solution or one which I could investigate further at the moment. Thank you. best, Steve PS: My first message seems to have been wrongly threaded (as an answer) in the mailing list archive. -- Steve Schmerler Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany From giannozz at democritos.it Wed Dec 8 14:36:34 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 8 Dec 2010 14:36:34 +0100 Subject: [Pw_forum] nstep not honored in vc-md In-Reply-To: <20101208133126.GA19103@cartman.physik.tu-freiberg.de> References: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> <43EB0A05-5DC1-4DAF-83E5-4EA2482E047F@democritos.it> <20101208133126.GA19103@cartman.physik.tu-freiberg.de> Message-ID: <84A86773-9075-4CB0-BF36-B47FDE1EAC18@democritos.it> On Dec 8, 2010, at 14:31 , Steve Schmerler wrote: > PS: My first message seems to have been wrongly > threaded (as an answer) in the mailing list archive. did you use "Reply" to a previous message and edited the subject? P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Wed Dec 8 14:37:54 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 8 Dec 2010 05:37:54 -0800 (PST) Subject: [Pw_forum] Total energy convergence In-Reply-To: References: Message-ID: <890100.12690.qm@web65708.mail.ac4.yahoo.com> Hi, ----- Original Message ---- From: mayank gupta > I am interested in phonon calculation. I want to know for phonon > calculation what is the order of total energy convergence and k mesh > size should be taken in scf calculation? Should I take larger value > than the band calculation parameters. First, you can use the convergence criteria used in example06 (10^{-8} for scf and 10^{-12} for ph), then decide you are satisfied or not. As concerns k-points, just keep in mind phonon calculations are time consumable, so, more k-points, more time is required. So, the best choice is "trial and fail". That means you are responsible for your own choice and results. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From w2agz at w2agz.com Wed Dec 8 15:25:05 2010 From: w2agz at w2agz.com (W2AGZ) Date: Wed, 8 Dec 2010 06:25:05 -0800 Subject: [Pw_forum] iotk error - again In-Reply-To: References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> Message-ID: <02c401cb96e3$b7039900$250acb00$@w2agz.com> Thanks, Paolo. I'll look into it ths week. -Paul -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Wednesday, December 08, 2010 1:49 AM To: PWSCF Forum Subject: Re: [Pw_forum] iotk error - again On Dec 7, 2010, at 8:33 , W2AGZ wrote: > "replace q_real by q_real_space." Is this the fix? > no. This is the fix for a very specific case, and the only one I remember in which an error was issued by iotk for a good reason (i.e. a variable was written with one name and read with another). All other instances of iotk errors I remember are related to miscompilation. Try first of all to compile iotk with reduced optimization (e.g. using $(MAKE) FFLAGS="$(FFLAGS_NOOPT)" ) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, 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 From elcortogm at googlemail.com Wed Dec 8 16:02:30 2010 From: elcortogm at googlemail.com (Steve Schmerler) Date: Wed, 8 Dec 2010 16:02:30 +0100 Subject: [Pw_forum] nstep not honored in vc-md In-Reply-To: <84A86773-9075-4CB0-BF36-B47FDE1EAC18@democritos.it> References: <20101207171323.GA9408@cartman.physik.tu-freiberg.de> <43EB0A05-5DC1-4DAF-83E5-4EA2482E047F@democritos.it> <20101208133126.GA19103@cartman.physik.tu-freiberg.de> <84A86773-9075-4CB0-BF36-B47FDE1EAC18@democritos.it> Message-ID: <20101208150230.GB21993@cartman.physik.tu-freiberg.de> On Dec 08 14:36 +0100, Paolo Giannozzi wrote: > did you use "Reply" to a previous message and edited > the subject? No, that's why I wondered. As far as I can see, there are no In-Reply-To, References (or some such) headers in the message. best, Steve -- Steve Schmerler Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany From eariel99 at gmail.com Wed Dec 8 17:08:44 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 8 Dec 2010 13:08:44 -0300 Subject: [Pw_forum] Restarting nscf calculations Message-ID: Hi all, I need to do a PW nscf calculation with many k-points, so many that the wave functions files fill the hard disk. I think the only way to avoid filling the hard disk is using disk_io='none' . However, I need to do a few restarts, because the queue system does not allows such long calculation at once. However, when I restart, the calculation begin again by the first k-point. (I checked that if disk_io='default', the calculation restarts by the first non computed k-point). I assume that in order to compute the DOS, the wavefunctions are not needed, just the energies and weights are needed. Hence, I wonder if this behaviour is a bug or if this is the intended procedure. The version of espresso is 4.0.4. Thanks Eduardo -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101208/175579f3/attachment-0001.htm From eariel99 at gmail.com Wed Dec 8 17:51:15 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 8 Dec 2010 13:51:15 -0300 Subject: [Pw_forum] hi,effect of temperature Message-ID: >I used Q.E to calculate the Youngs mudulud of Boron-Nitride nanotube and h-Bn the result are >in agrement with previous calculation. At this stage i want to calcualte the effect of temperature >on the Young mudulus of Boron-Nitride structres. Can Q.E do such calcualtions? >Tahnks for your reply. >mirnezhad, msc guilan .iran Yes, you can calculate the temperature effects on the Young modulus. You must also take into account the thermal dilation. For that, you may calculate the phonon density of states and the free energy. Also, use finite temperature DFT, with smearing='fermi-dirac'. The Young modulos is the second derivative of the free energy with respect to the apropriate deformation, divided by the unstressed unit cell volume (mimimum free energy for a given temperature). Take a look at Phys. Rev. B 76, 054117 (2007) I Guess that the QHA automates the proccess of the Free energy calculations. Using molecular dynamics you can also study the thermal effects, but not it is not equivalent to the free energy calculation. Molecular dynamics is classic for the motion of the atomic nuclei, hence you lose the quantum effects that you obtain from a phonon calculation. Hence, for low temperatures you should always do the phonon calculations and obtain the free energies, and derive them to get the Young modulus. For high temperatures, the anharmonic effects are more important than the quantum effects, so, do molecular dynamics and obtain the Young moduli from average stresses. I do not know what is "low" and "high" temperature, maybe comparing with the Debye temperature. I am not sure if the average stress in a molecular dynamics is all the stress. I guess it is not. For example, the pressure reported by PWSCF is the pressure due to the interatomic forces, it depends only on the positions, but not on velocities. To obtain the total pressure at a given temperature one must add the term NkT/V (ideal gas). The pressure is the trace of the stress tensor, hence, the stress tensor must be corrected with the ideal gas term, at least in the diagonal elements. Best regards Eduardo -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101208/1cb4b93a/attachment.htm From giannozz at democritos.it Wed Dec 8 17:54:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 8 Dec 2010 17:54:25 +0100 Subject: [Pw_forum] Restarting nscf calculations In-Reply-To: References: Message-ID: <93AEB988-7937-4F1E-A3C2-67DC39DC7B3C@democritos.it> On Dec 8, 2010, at 17:08 , Eduardo Ariel Menendez Proupin wrote: > Hence, I wonder if this behaviour is a bug or if this is the > intended procedure. none of the above. The imagination of QE users vastly exceeds the resources of QE developers. When I implemented the disk_io='none' option, I couldn't imagine that somebody was going to use it in such a way. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mayankaditya at gmail.com Thu Dec 9 05:29:14 2010 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 9 Dec 2010 09:59:14 +0530 Subject: [Pw_forum] Phonon Calculation Message-ID: Hi I have performed phonon calculation for silver oxide with mesh size 8x8x8 and ecut off is 70 Ry erhocut=1050 Ry. I have tested the total energy convergence. We have used the pseudopotetial generated by using PBE . After SCF calculation we performed phonon calculation at different pressure with 2x2x2 q point using default cutoff parameters and calculate the gruneisen parameters. The calculated Gruneisen parameter and thermal expansion are in agreement with our previous calculation using potential model lattice dynamics as well as with experimental results. Again I have performed the same calculation with 4x4x4 q point mesh I find the entirely different result. my main concern is around q=0 because around that I found the significant change in phonon frequency. I have used matdyn.x to generate phonon frequency at intermediate point. Further in acoustic sum rule if I used asr=simple I am getting the negative frequency while asr=crystal I didn't get any negative phonon frequency. So I am confused which sum rule should use and how much q point I have to calculate. Kindly suggest me . Thanks A lot M K gupta From lfhuang at theory.issp.ac.cn Thu Dec 9 09:38:15 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 09 Dec 2010 16:38:15 +0800 Subject: [Pw_forum] =?utf-8?q?How_to_estimate_the_memory_requirement_of_ph?= =?utf-8?b?Lng/?= Message-ID: <20101209083815.10056.qmail@ms.hfcas.ac.cn> Dear QE developers and users: I am calculating the vibrational frequencies of a graphene supercell (90 atoms total). I used 24N_p = 6N_pk*4N_pr first, and the pw.x calculation completed perfectly with about 500 MB memory per-processor. However, the ph.x calculation always stopped after several hours at the place as below: ****************************************************** Atomic displacements: There are 270 irreducible representations Representation 1 1 modes -A To be done Representation 2 1 modes -A To be done ...... Representation 270 1 modes -A To be done STOPPED HERE due to the breakdown of some processors. ******************************************************* If I use 24N_p = 24N_pr?the ph.x can also completed perfectly with about 80 MB (.=500/6) per-processor in the pw.x calculation. From DFPT, it is understandable that ph.x requires more memory than pw.x. But how to estimate it to be qualitatively precise? The architecture of the machine I am using is that: One node has 8 processors with shared memory of 24GB (3GB per processor). How can a 3GB processor breaks down when doing a ph.x job, when the requirement of it pw.x job is just 500MB? By the way, is it better to assign the N_pr to be m**2 (m=2,3,4...) than other values (e.g. 6, 10, 11, 14...) if I want to divide the R-&G-space in parallelization? I'd like to highly appreciate any help from you! Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101209/0d2f2921/attachment.htm From elie.moujaes at hotmail.co.uk Thu Dec 9 19:00:08 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 9 Dec 2010 18:00:08 +0000 Subject: [Pw_forum] gdir value Message-ID: Dear all, I am doing some band structure calculations in graphene under the effect of the electric field. I need to specify gdir which in this case refers to the direction of the electric field. If my electric field is in the z-direction, does it mean that gdir = 3? Thanks Elie Moujaes University of Nottingham UK NG7 2 RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101209/fc5d89bd/attachment.htm From wumindt2 at zju.edu.cn Fri Dec 10 00:16:59 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Fri, 10 Dec 2010 07:16:59 +0800 Subject: [Pw_forum] wannier function Message-ID: Dear all, I tested the example of wannier90.x and have a problem here. For the Si calculation (example11), we need to include the 4 highest valence bands and the 4 lowest conduction bands to make a sp3 projection on Si atoms. However, in the case of Silane (example07), we only need all the 4 bands to make a sp3 projection on Si atom. Why we need different number of bands to form sp3 projection for these two material? Thanks for any idea. Min Wu 2010-12-9 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101210/e5869952/attachment.htm From nicola.marzari at materials.ox.ac.uk Fri Dec 10 03:42:42 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Fri, 10 Dec 2010 02:42:42 +0000 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: <4D0193A2.10509@materials.ox.ac.uk> Dear Min Wu, you need, at a minimum, to mix 4 bands for each silicon atom, to get 4 sp3 hybrids for each silicon atom. In the first case, you have two silicon atoms per unit cell; in the second case, one. nicola On 12/9/10 11:16 PM, wumindt2 wrote: > Dear all, > > I tested the example of wannier90.x and have a problem here. > For the Si calculation (example11), we need to include the 4 highest > valence bands and the 4 lowest conduction bands > to make a sp3 projection on Si atoms. > However, in the case of Silane (example07), we only need all the 4 bands > to make a sp3 projection on Si atom. > > Why we need different number of bands to form sp3 projection for these > two material? > > Thanks for any idea. > > Min Wu > 2010-12-9 > -- ---------------------------------------------------------------------- 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 ac.rain at inbox.com Fri Dec 10 07:54:18 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Thu, 9 Dec 2010 22:54:18 -0800 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <560747B7-8F80-4B51-828A-78E8262FF819@democritos.it> References: <47bd3257d74.00000656ac.rain@inbox.com> Message-ID: <60B257887FC.000006D5ac.rain@inbox.com> Hi Paolo, Thank you for your assistance. that is looking better, This is the line I added to the script check-pw.x.j ... PARA_PREFIX="mpiexec -n 60 -f /home/user/mpiMachinefile.txt" when launched with "./check-pw.x.j" many 100% processes showed on each system. however I am not sure what it was doing because nothing else happened besides the text output "Checking atom...". Usually this test completes in less than an hour on 1 core, many cores should reduce the completion time, after a couple of hours I saw nothing more than "Checking atom..." so I pressed Ctrl+C on the terminal and it printed some more information... $ ./check-pw.x.j Checking atom...Killed by signal 2. [mpiexec at server4] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:99): one of the processes terminated badly; aborting [mpiexec at server4] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting for completion [mpiexec at server4] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:352): bootstrap server returned error waiting for completion [mpiexec at server4] main (./ui/mpich/mpiexec.c:294): process manager error waiting for completion FAILED with error condition! Input: atom.in, Output: atom.out, Reference: atom.ref Aborting $ I also tried adding "-wdir /usr/local/espresso-4.2.1/tests" at the end of PARA_PREFIX and gave the same result. I also tried uncommenting PARA_POSTFIX="./check-pw.x.j" and it gave the same result. thanks & regards, Nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Wed, 8 Dec 2010 09:42:06 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE and mpich2, Linux > > > On Dec 8, 2010, at 8:15 , ac.rain at inbox.com wrote: > >> $ mpiexec -f ~/mpiMachinefile.txt -n 10 -wdir /usr/local/ >> espresso-4.2.1/tests ./check-pw.x.j > > the correct way to start the tests in parallel is to edit PARA_PREFIX > and PARA_POSTFIX > in the "check-pw.x.j" script > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth From giannozz at democritos.it Fri Dec 10 08:20:45 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 10 Dec 2010 08:20:45 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <60B257887FC.000006D5ac.rain@inbox.com> References: <47bd3257d74.00000656ac.rain@inbox.com> <60B257887FC.000006D5ac.rain@inbox.com> Message-ID: <34977170-99D5-4EB3-BC21-7AF1EA719897@democritos.it> Run interactively and look what happens. If nothing happens, use option "-inp file" to read from file "file". --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Dec 10 08:22:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 10 Dec 2010 08:22:53 +0100 Subject: [Pw_forum] gdir value In-Reply-To: References: Message-ID: <9D2A50BE-8D0E-4B5C-9780-506E5263A8CE@democritos.it> On Dec 9, 2010, at 19:00 , Elie Moujaes wrote: > If my electric field is in the z-direction, does it mean that gdir > = 3? in most cases, yes. Crystal axis are reprinted in the output P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pnyawere at gmail.com Fri Dec 10 11:54:09 2010 From: pnyawere at gmail.com (Phillip Nyawere) Date: Fri, 10 Dec 2010 11:54:09 +0100 Subject: [Pw_forum] Ghost States Message-ID: Dear pwscf I am doing a "relax" calculation by shifting the position of an atom in a supercell. Some sites appear unfavorable and one of them is hear below showing the presence of a ghost state. Could anyone give me an idear of how to remove the ghost sites (energy) in a calculation? Part of the output is here: k = 0.0000 0.0000 0.0000 ( 36612 PWs) bands (ev): -30.6867 -19.5462 -19.4947 -19.4037 -19.3662 -19.3332 -19.2705 -19.2304 -19.1717 -19.1681 -19.1466 -19.1386 -19.1164 -19.1036 -19.0976 -19.0943 -19.0939 -19.0851 -19.0845 -19.0825 -19.0527 -19.0276 -19.0078 -18.9858 -18.9681 -18.9567 -18.9032 -18.8883 -18.8418 -18.8179 -18.8140 -18.7612 -16.0244 -16.0133 -15.9881 -15.9532 -15.9512 -15.9385 -15.9291 -15.9228 -15.9189 -15.9102 -15.9075 -15.8753 -15.8739 -15.8689 -15.8610 -15.8544 -15.8478 -15.8397 -15.8373 -15.8212 -15.8090 -15.8056 -15.8013 -15.8011 -15.7823 -15.7817 -15.7715 -15.7649 -15.7627 -15.7584 -15.7468 -15.7436 -15.7351 -15.7292 -15.7268 -15.7206 -15.7142 -15.7116 -15.6975 -15.6971 -15.6943 -15.6870 -15.6812 -15.6688 -15.6646 -15.6594 -15.6557 -15.6490 -15.6428 -15.6409 -15.6229 -15.6099 -15.6036 -15.6026 -15.5933 -15.5905 -15.5677 -15.4540 -15.2097 -15.0390 -14.9480 -14.9457 -13.8970 -8.5916 -8.4985 -6.7400 -4.8562 -4.8507 -4.7891 -4.7626 -4.7525 -4.7343 -4.6927 -4.6912 -4.6645 -4.6403 -4.6237 -4.6234 -4.6209 -4.6134 -4.6053 -4.5858 -4.5672 -4.5576 -4.5273 -4.5016 -4.4944 -4.4676 -4.4578 -4.4492 -4.4396 -4.4155 -4.4061 -4.3838 -4.3792 -4.3767 -4.3725 -4.3714 -4.3711 -4.3593 -4.3566 -4.3515 -4.3489 -4.3463 -4.3440 -4.3399 -4.3383 -4.3366 -4.3351 -4.3343 -4.3326 -4.3321 -4.3299 -4.3266 -4.3264 -4.3241 -4.3239 -4.3229 -4.3224 -4.3206 -4.3189 -4.3165 -4.3158 -4.3152 -4.3045 -4.3029 -4.2829 -4.2798 -- Phillip W. Otieno Nyawere, International Center for Theoretical Physics, ICTP, Strada Costiera, 11 - 34014217, Leonardo Building, Office 305, Trieste, Italy. Tel +393382213805 office +39 040 2240 217 pnyawere at gmail.com, potieno at kabarak.ac.ke God raises the meek from the ground and sits them with Kings. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101210/f6725057/attachment.htm From giannozz at democritos.it Fri Dec 10 12:33:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 10 Dec 2010 12:33:20 +0100 Subject: [Pw_forum] How to estimate the memory requirement of ph.x? In-Reply-To: <20101209083815.10056.qmail@ms.hfcas.ac.cn> References: <20101209083815.10056.qmail@ms.hfcas.ac.cn> Message-ID: <4D021000.5050302@democritos.it> lfhuang wrote: > it is understandable that ph.x requires more memory than pw.x. > But how to estimate it to be qualitatively precise? sum the size of large arrays. I do not know any other way. If the code runs, a call to "memstat" returns the size of dynamically allocated memory (on operating systems that support it). Not sure how much of the total memory is reported, though. Apparently the question "how much memory does a process use" has become difficult to answer in modern operating systems. > How can a 3GB processor breaks down when doing a ph.x job, when the > requirement of it pw.x job is just 500MB? the phonon code uses more arrays and distributes less of them across processors. > By the way, is it better to assign the N_pr to be m**2 (m=2,3,4...) than > other values (e.g. 6, 10, 11, 14...) if I want to divide the R-&G-space > in parallelization? I think it depends upon the specific communication hardware and MPI implementation. Not sure though. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From kucukben at sissa.it Fri Dec 10 12:55:24 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Fri, 10 Dec 2010 12:55:24 +0100 Subject: [Pw_forum] Ghost States In-Reply-To: <20101210120728.9khtoc28g8ooc400@webmail.sissa.it> References: <20101210120728.9khtoc28g8ooc400@webmail.sissa.it> Message-ID: <20101210125524.wjtpt4hzmsso404o@webmail.sissa.it> Dear Phillip, ghost states are related to pseudopotentials. if you are _sure_ that you have a ghost state, the safest thing would be changing the pseudo for that particular atom. Please let us know if it is one of the pp's from QE-database. cheers, emine kucukbenli, phd student, sissa, italy Quoting Phillip Nyawere : >> Dear pwscf >> I am doing a "relax" calculation by shifting the position of an atom in a >> supercell. Some sites appear unfavorable and one of them is hear below >> showing the presence of a ghost state. Could anyone give me an idear of how >> to remove the ghost sites (energy) in a calculation? Part of the output is >> here: >> >> k = 0.0000 0.0000 0.0000 ( 36612 PWs) bands (ev): >> -30.6867 -19.5462 -19.4947 -19.4037 -19.3662 -19.3332 -19.2705 -19.2304 > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From david.grifith at gmail.com Sat Dec 11 02:54:16 2010 From: david.grifith at gmail.com (David Grifith) Date: Sat, 11 Dec 2010 05:24:16 +0330 Subject: [Pw_forum] Lowdin Charge- sign Message-ID: Dear QE Users My calculated "Lowdin Charge" values are "positive" as shown below. I thought that they must be the charge of the valence electron ! but the sign is positive. Also, I don't know that a pseudopotential package like Quantum Espresso considers the "core" charge to be calculated or not ? Atom # 1: total charge = 3.9571, s = 0.9145, p = 3.0426, d = 0.0000, spin up = 1.9786, s = 0.4573, p = 1.5213, d = 0.0000, spin down = 1.9786, s = 0.4573, p = 1.5213, d = 0.0000, polarization = 0.0000, s = 0.0000, p = 0.0000, d = 0.0000, Atom # 2: total charge = 3.9569, s = 0.9154, p = 3.0415, d = 0.0000, spin up = 1.9785, s = 0.4577, p = 1.5208, d = 0.0000, spin down = 1.9785, s = 0.4577, p = 1.5208, d = 0.0000, polarization = 0.0000, s = 0.0000, p = 0.0000, d = 0.0000, Atom # 3: total charge = 3.9554, s = 0.9153, p = 3.0402, d = 0.0000, spin up = 1.9777, s = 0.4576, p = 1.5201, d = 0.0000, spin down = 1.9777, s = 0.4576, p = 1.5201, d = 0.0000, polarization = 0.0000, s = 0.0000, p = 0.0000, d = 0.0000, Atom # 4: total charge = 3.9573, s = 0.9164, p = 3.0408, d = 0.0000, spin up = 1.9786, s = 0.4582, p = 1.5204, d = 0.0000, spin down = 1.9786, s = 0.4582, p = 1.5204, d = 0.0000, polarization = 0.0000, s = 0.0000, p = 0.0000, d = 0.0000, Atom # 5: total charge = 3.9607, s = 0.9155, p = 3.0452, d = 0.0000, spin up = 1.9804, s = 0.4578, p = 1.5226, d = 0.0000, spin down = 1.9804, s = 0.4578, p = 1.5226, d = 0.0000, polarization = -0.0000, s = -0.0000, p = -0.0000, d = 0.0000, Atom # 6: total charge = 3.9599, s = 0.9146, p = 3.0453, d = 0.0000, spin up = 1.9800, s = 0.4573, p = 1.5227, d = 0.0000, spin down = 1.9800, s = 0.4573, p = 1.5227, d = 0.0000, polarization = -0.0000, s = -0.0000, p = -0.0000, d = 0.0000, Atom # 7: total charge = 3.9600, s = 0.9148, p = 3.0452, d = 0.0000, spin up = 1.9800, s = 0.4574, p = 1.5226, d = 0.0000, spin down = 1.9800, s = 0.4574, p = 1.5226, d = 0.0000, polarization = -0.0000, s = -0.0000, p = -0.0000, d = 0.0000, -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/5723819b/attachment.htm From w2agz at w2agz.com Sat Dec 11 07:38:53 2010 From: w2agz at w2agz.com (W2AGZ) Date: Fri, 10 Dec 2010 22:38:53 -0800 Subject: [Pw_forum] example07...again Message-ID: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> Eyvaz, I still get gfortran errors in QE-4.2.1 after "re-making" the changes you sent last August. See below: running pw.x as: /home/pmpgrant/espresso-4.2.1/bin/pw.x running ph.x as: /home/pmpgrant/espresso-4.2.1/bin/ph.x running q2r.x as: /home/pmpgrant/espresso-4.2.1/bin/q2r.x running matdyn.x as: /home/pmpgrant/espresso-4.2.1/bin/matdyn.x running lambda.x as: /home/pmpgrant/espresso-4.2.1/bin/lambda.x cleaning /home/pmpgrant/tmp... done running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... done running q2r... done running matdyn for frequency calculation... done running matdyn for a2F(omega) calculation... done running lambda.x for lambda calculation...At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.000000. 0.000000. 0.000000') Fortran runtime error: Constant string in input format (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4) ^ Error condition encountered during test: exit status = 2 Aborting -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101210/b24e5a88/attachment.htm From heatherjkulik at gmail.com Sat Dec 11 07:59:52 2010 From: heatherjkulik at gmail.com (Heather Kulik) Date: Fri, 10 Dec 2010 22:59:52 -0800 Subject: [Pw_forum] Lowdin Charge- sign In-Reply-To: References: Message-ID: Dear David, You are right in that the Lowdin charges here refer to the valence electrons of your system. The Lowdin charges are calculated as a sum of the projections of the extended plane wave valence states onto a pseudo-atomic basis (characterized by the highest valence s, p, d, f states per your output). The numbers are positive and not negative, as you pointed out, because they refer to the *number* of electrons (i.e. s, p, and so on). In your example, there appears to be approximately four electrons: 1 s-type and 3 p-type valence electrons attributed to each atom. The code should also a 'spilling parameter' at the bottom of your output that tells you how well the projections are capturing the description of the valence states. For instance, the projection is capturing 3.96 electrons per atom in your example. So, if you expect in your example to have four valence electrons per atom, then the pseudo-atomic basis is capturing your extended valence states pretty well. Hope that helps! -- Heather K Postdoc at Stanford University On Fri, Dec 10, 2010 at 5:54 PM, David Grifith wrote: > Dear QE Users > > My calculated "Lowdin Charge" values are "positive" as shown below. I > thought that they must be the charge of the valence electron ! but the sign > is positive. Also, I don't know that a pseudopotential package like Quantum > Espresso considers the "core" charge to be calculated or not ? > > > > Atom # 1: total charge = 3.9571, s = 0.9145, p = 3.0426, d = > 0.0000, > spin up = 1.9786, s = 0.4573, p = 1.5213, d = > 0.0000, > spin down = 1.9786, s = 0.4573, p = 1.5213, d = > 0.0000, > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > 0.0000, > Atom # 2: total charge = 3.9569, s = 0.9154, p = 3.0415, d = > 0.0000, > spin up = 1.9785, s = 0.4577, p = 1.5208, d = > 0.0000, > spin down = 1.9785, s = 0.4577, p = 1.5208, d = > 0.0000, > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > 0.0000, > Atom # 3: total charge = 3.9554, s = 0.9153, p = 3.0402, d = > 0.0000, > spin up = 1.9777, s = 0.4576, p = 1.5201, d = > 0.0000, > spin down = 1.9777, s = 0.4576, p = 1.5201, d = > 0.0000, > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > 0.0000, > Atom # 4: total charge = 3.9573, s = 0.9164, p = 3.0408, d = > 0.0000, > spin up = 1.9786, s = 0.4582, p = 1.5204, d = > 0.0000, > spin down = 1.9786, s = 0.4582, p = 1.5204, d = > 0.0000, > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > 0.0000, > Atom # 5: total charge = 3.9607, s = 0.9155, p = 3.0452, d = > 0.0000, > spin up = 1.9804, s = 0.4578, p = 1.5226, d = > 0.0000, > spin down = 1.9804, s = 0.4578, p = 1.5226, d = > 0.0000, > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > 0.0000, > Atom # 6: total charge = 3.9599, s = 0.9146, p = 3.0453, d = > 0.0000, > spin up = 1.9800, s = 0.4573, p = 1.5227, d = > 0.0000, > spin down = 1.9800, s = 0.4573, p = 1.5227, d = > 0.0000, > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > 0.0000, > Atom # 7: total charge = 3.9600, s = 0.9148, p = 3.0452, d = > 0.0000, > spin up = 1.9800, s = 0.4574, p = 1.5226, d = > 0.0000, > spin down = 1.9800, s = 0.4574, p = 1.5226, d = > 0.0000, > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > 0.0000, > > -- > Sincerely Yours > David G. > JCU > > > _______________________________________________ > 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/20101210/ea1f482a/attachment-0001.htm From lfhuang at theory.issp.ac.cn Sat Dec 11 08:32:18 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Sat, 11 Dec 2010 15:32:18 +0800 Subject: [Pw_forum] =?utf-8?q?How_to_estimate_the_memory_requirement_of_ph?= =?utf-8?b?Lng/?= Message-ID: <20101211073218.9863.qmail@ms.hfcas.ac.cn> Dear prof. P. Giannozzi: Thank you very much for your helpful and clear response! I appreciate very much! Best Wishes! Yours Sincerely L. F. Huang > Date: Fri, 10 Dec 2010 12:33:20 +0100 > From: Paolo Giannozzi > > lfhuang wrote: > > > it is understandable that ph.x requires more memory than pw.x. > > But how to estimate it to be qualitatively precise? > > sum the size of large arrays. I do not know any other way. If the > code runs, a call to "memstat" returns the size of dynamically > allocated memory (on operating systems that support it). Not sure > how much of the total memory is reported, though. Apparently the > question "how much memory does a process use" has become difficult > to answer in modern operating systems. > > > How can a 3GB processor breaks down when doing a ph.x job, when the > > requirement of it pw.x job is just 500MB? > > the phonon code uses more arrays and distributes less of them across > processors. > > > By the way, is it better to assign the N_pr to be m**2 (m=2,3,4...) than > > other values (e.g. 6, 10, 11, 14...) if I want to divide the R-&G-space > > in parallelization? > > I think it depends upon the specific communication hardware and > MPI implementation. Not sure though. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/afe689a2/attachment.htm From david.grifith at gmail.com Sat Dec 11 09:08:43 2010 From: david.grifith at gmail.com (David Grifith) Date: Sat, 11 Dec 2010 11:38:43 +0330 Subject: [Pw_forum] Lowdin Charge- sign Message-ID: Dear Heather Thanks for your comments. I think that this type of charge (Lowdin) which is nearly the number of valence electrons can not speak about the details of the system. Some electrons are bonding and also, the effect of the core (core electron + nucleus ) is not negligible. I want to compare the real charge of two atoms in my system with each other not their valence electrons. I appreciate your help in advance. -- Sincerely Yours David G. JCU Dear David, > > You are right in that the Lowdin charges here refer to the valence > electrons > of your system. > > The Lowdin charges are calculated as a sum of the projections of the > extended plane wave valence states onto a pseudo-atomic basis > (characterized > by the highest valence s, p, d, f states per your output). > > The numbers are positive and not negative, as you pointed out, because they > refer to the *number* of electrons (i.e. s, p, and so on). In your > example, > there appears to be approximately four electrons: 1 s-type and 3 p-type > valence electrons attributed to each atom. > > The code should also a 'spilling parameter' at the bottom of your output > that tells you how well the projections are capturing the description of > the > valence states. For instance, the projection is capturing 3.96 electrons > per atom in your example. So, if you expect in your example to have four > valence electrons per atom, then the pseudo-atomic basis is capturing your > extended valence states pretty well. > > Hope that helps! > -- > Heather K > Postdoc at Stanford University > > On Fri, Dec 10, 2010 at 5:54 PM, David Grifith >wrote: > > > Dear QE Users > > > > My calculated "Lowdin Charge" values are "positive" as shown below. I > > thought that they must be the charge of the valence electron ! but the > sign > > is positive. Also, I don't know that a pseudopotential package like > Quantum > > Espresso considers the "core" charge to be calculated or not ? > > > > > > > > Atom # 1: total charge = 3.9571, s = 0.9145, p = 3.0426, d = > > 0.0000, > > spin up = 1.9786, s = 0.4573, p = 1.5213, d = > > 0.0000, > > spin down = 1.9786, s = 0.4573, p = 1.5213, d = > > 0.0000, > > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > > 0.0000, > > Atom # 2: total charge = 3.9569, s = 0.9154, p = 3.0415, d = > > 0.0000, > > spin up = 1.9785, s = 0.4577, p = 1.5208, d = > > 0.0000, > > spin down = 1.9785, s = 0.4577, p = 1.5208, d = > > 0.0000, > > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > > 0.0000, > > Atom # 3: total charge = 3.9554, s = 0.9153, p = 3.0402, d = > > 0.0000, > > spin up = 1.9777, s = 0.4576, p = 1.5201, d = > > 0.0000, > > spin down = 1.9777, s = 0.4576, p = 1.5201, d = > > 0.0000, > > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > > 0.0000, > > Atom # 4: total charge = 3.9573, s = 0.9164, p = 3.0408, d = > > 0.0000, > > spin up = 1.9786, s = 0.4582, p = 1.5204, d = > > 0.0000, > > spin down = 1.9786, s = 0.4582, p = 1.5204, d = > > 0.0000, > > polarization = 0.0000, s = 0.0000, p = 0.0000, d = > > 0.0000, > > Atom # 5: total charge = 3.9607, s = 0.9155, p = 3.0452, d = > > 0.0000, > > spin up = 1.9804, s = 0.4578, p = 1.5226, d = > > 0.0000, > > spin down = 1.9804, s = 0.4578, p = 1.5226, d = > > 0.0000, > > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > > 0.0000, > > Atom # 6: total charge = 3.9599, s = 0.9146, p = 3.0453, d = > > 0.0000, > > spin up = 1.9800, s = 0.4573, p = 1.5227, d = > > 0.0000, > > spin down = 1.9800, s = 0.4573, p = 1.5227, d = > > 0.0000, > > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > > 0.0000, > > Atom # 7: total charge = 3.9600, s = 0.9148, p = 3.0452, d = > > 0.0000, > > spin up = 1.9800, s = 0.4574, p = 1.5226, d = > > 0.0000, > > spin down = 1.9800, s = 0.4574, p = 1.5226, d = > > 0.0000, > > polarization = -0.0000, s = -0.0000, p = -0.0000, d = > > 0.0000, > > > > -- > > Sincerely Yours > > David G. > > JCU > > > > > > _______________________________________________ > > 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/20101210/ea1f482a/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 42, Issue 19 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/9da9e3da/attachment.htm From degironc at sissa.it Sat Dec 11 10:29:12 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 11 Dec 2010 10:29:12 +0100 Subject: [Pw_forum] Lowdin Charge- sign In-Reply-To: References: Message-ID: <4D034468.4040809@sissa.it> In a pseudopotential calculation core electrons are not there so if you want to "see" the core electrons you need to do an all-electron calculation or a PAW calculation where the total charge is reconstructed. If you are interested in knowing a total atomic charge this is easy... just add to the valence electron charge the number of (completely filled) core electrons, change sign and add the nuclear charge.. notice however that the decomposition of a charge distribution in atomic contribution is a somewhat ill defined procedure and Lowdin procedure is just one possibility, so do not attach too much significance to minor changes from system to system... Something that can be useful to identify bonding in your system can be the analysis of the projected density of states on atomic levels of nearest-neighbor atoms. It is sometime possible to see peaks occurring in the same energy range for the two atoms that signal that electronic states in that energy range are shared between the two atoms as one expect in a covalent bond. Hope it helps. Stefano de Gironcoli David Grifith wrote: > Dear Heather > > Thanks for your comments. I think that this type of charge (Lowdin) which is > nearly the number of valence electrons can not speak about the details of > the system. > Some electrons are bonding and also, the effect of the core (core electron + > nucleus ) is not negligible. I want to compare the real charge of two atoms > in my system with each other not their valence electrons. I appreciate your > help in advance. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Sat Dec 11 10:47:22 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 11 Dec 2010 10:47:22 +0100 Subject: [Pw_forum] example07...again In-Reply-To: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> References: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> Message-ID: <3C47CAD6-493F-40DE-A5E7-C07D1B0C34B7@democritos.it> On Dec 11, 2010, at 7:38 , W2AGZ wrote: > At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.000000. > 0.000000. 0.000000') > > Fortran runtime error: Constant string in input format > > (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4) > some compilers do not like formats like the one reported above. Workaround: replace it with (26x,f7.3,12x,i4), or do not use lambda.f90 (I think it is obsolete) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Sat Dec 11 12:36:17 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 11 Dec 2010 03:36:17 -0800 (PST) Subject: [Pw_forum] example07...again In-Reply-To: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> References: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> Message-ID: <535388.46466.qm@web65702.mail.ac4.yahoo.com> Paul, I will look at asap to fix it. Bests, Eyvaz. ________________________________ From: W2AGZ To: pw_forum at pwscf.org Sent: Sat, December 11, 2010 7:38:53 AM Subject: [Pw_forum] example07...again Eyvaz, I still get gfortran errors in QE-4.2.1 after ?re-making? the changes you sent last August. See below: running pw.x as: /home/pmpgrant/espresso-4.2.1/bin/pw.x running ph.x as: /home/pmpgrant/espresso-4.2.1/bin/ph.x running q2r.x as: /home/pmpgrant/espresso-4.2.1/bin/q2r.x running matdyn.x as: /home/pmpgrant/espresso-4.2.1/bin/matdyn.x running lambda.x as: /home/pmpgrant/espresso-4.2.1/bin/lambda.x cleaning /home/pmpgrant/tmp... done running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... done running q2r... done running matdyn for frequency calculation... done running matdyn for a2F(omega) calculation... done running lambda.x for lambda calculation...At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.000000. 0.000000. 0.000000') Fortran runtime error: Constant string in input format (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4) ^ Error condition encountered during test: exit status = 2 Aborting -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/1190db22/attachment.htm From eyvaz_isaev at yahoo.com Sat Dec 11 14:32:59 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 11 Dec 2010 05:32:59 -0800 (PST) Subject: [Pw_forum] example07...again In-Reply-To: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> References: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> Message-ID: <95815.20948.qm@web65704.mail.ac4.yahoo.com> Dear Paul, May I suppose, you used an old version of lambda.f90, as I can see from the last edition of lambda.f90 a line with "(5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4)" is commented. Besides, as already it was pointed out by Paolo, lambda.f90 somewhat obsolete, but will be supported, I guess. Now lambda can be calculated by means of matdyn.x. Bests, Eyvaz ________________________________ From: W2AGZ To: pw_forum at pwscf.org Sent: Sat, December 11, 2010 7:38:53 AM Subject: [Pw_forum] example07...again Eyvaz, I still get gfortran errors in QE-4.2.1 after ?re-making? the changes you sent last August. See below: running pw.x as: /home/pmpgrant/espresso-4.2.1/bin/pw.x running ph.x as: /home/pmpgrant/espresso-4.2.1/bin/ph.x running q2r.x as: /home/pmpgrant/espresso-4.2.1/bin/q2r.x running matdyn.x as: /home/pmpgrant/espresso-4.2.1/bin/matdyn.x running lambda.x as: /home/pmpgrant/espresso-4.2.1/bin/lambda.x cleaning /home/pmpgrant/tmp... done running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... done running q2r... done running matdyn for frequency calculation... done running matdyn for a2F(omega) calculation... done running lambda.x for lambda calculation...At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.000000. 0.000000. 0.000000') Fortran runtime error: Constant string in input format (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4) ^ Error condition encountered during test: exit status = 2 Aborting -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/f6da03e4/attachment.htm From giannozz at democritos.it Sat Dec 11 15:36:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 11 Dec 2010 15:36:10 +0100 Subject: [Pw_forum] q2r and electron-phonon interaction In-Reply-To: References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> Message-ID: <81D8253E-5FAA-455A-B211-BF71206194F6@democritos.it> On Nov 29, 2010, at 22:59 , sama at ns.dcci.unipi.it wrote: > In line 358 of code q2r.f90 is read the variable *nstar*, which for > count_q=2 takes the value nstar=3. In the next subroutine read_gamma > the code expects then a series of information dimensioned 3, while > actually in file a2Fq2r.51 the series is dimensioned 6. this is actually a bug, that happens whenever -q is not in the star of q. In this case, there is still a symmetry operation (time reversal) sending q into -q, but it is not a point group symmetry. Or at least, this is what I vaguely remember. The code writes the number nq of q's in the star, then it writes the results for all q's, plus those for all -q's. Workaround: in file PH/elphon.f90, locate line write(iuelph,*) nq replace with IF ( imq == 0 ) THEN write(iuelph,*) 2*nq ELSE write(iuelph,*) nq ENDIF No warranty! Thank you for the detailed report. By the way: 1) in principle you should use pseuopotentials generated for the same exchange-correlation potential 2) If you use norm-conserving pseudopopotentials, you should not set a value of ecutrho (it will be set to 4*ecutwfc) 3) "la2F=.true." should be set only in the first scf run, the one with very dense k-point grid Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From david.grifith at gmail.com Sat Dec 11 18:48:46 2010 From: david.grifith at gmail.com (David Grifith) Date: Sat, 11 Dec 2010 21:18:46 +0330 Subject: [Pw_forum] Lowdin Charge - sign Message-ID: Dear Stefano de Gironcoli Thanks a lot for your instructive and informative comments. -- Sincerely Yours David G. JCU > In a pseudopotential calculation core electrons are not there so if you > want to "see" the core electrons you need to do an all-electron > calculation or a PAW calculation where the total charge is reconstructed. > If you are interested in knowing a total atomic charge this is easy... > just add to the valence electron charge the number of (completely > filled) core electrons, change sign and add the nuclear charge.. > notice however that the decomposition of a charge distribution in > atomic contribution is a somewhat ill defined procedure and Lowdin > procedure is just one possibility, so do not attach too much > significance to minor changes from system to system... > > Something that can be useful to identify bonding in your system can be > the analysis of the projected density of states on atomic levels of > nearest-neighbor atoms. It is sometime possible to see peaks occurring > in the same energy range for the two atoms that signal that electronic > states in that energy range are shared between the two atoms as one > expect in a covalent bond. > > Hope it helps. > > Stefano de Gironcoli > David Grifith wrote: >* Dear Heather *>* *>* Thanks for your comments. I think that this type of charge (Lowdin) which is *>* nearly the number of valence electrons can not speak about the details of *>* the system. *>* Some electrons are bonding and also, the effect of the core (core electron + *>* nucleus ) is not negligible. I want to compare the real charge of two atoms *>* in my system with each other not their valence electrons. I appreciate your *>* help in advance. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/123a3b5d/attachment-0001.htm From w2agz at w2agz.com Sat Dec 11 21:56:37 2010 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 11 Dec 2010 12:56:37 -0800 Subject: [Pw_forum] example07...again In-Reply-To: <95815.20948.qm@web65704.mail.ac4.yahoo.com> References: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> <95815.20948.qm@web65704.mail.ac4.yahoo.com> Message-ID: <00ce01cb9975$e814ed20$b83ec760$@w2agz.com> Eyvaz, thanks for getting back so fast. My bad (mea culpa). I thought I had inserted the ?new Fortran code? you sent me a few months ago, but on replacement and ?make,? I must have screwed up something...I?ll check. In the meantime, you state the new matdyn.x ?replaces all the old stuff, e.g. lambda.x? used in example07. Is there an ?updated example07? that illustrates the new methodology? I follow the path illustrated in example07 a fair amount in my attempts to simulate electron-phonon mediated Eliashberg-McMillan pairing. Last September you sent me a tar-file with the f90 code for elphon, lambda, matdyn, phcom and qr2 along with matdyn.in.dos and qr2.in. I take it all are required to ?fix? example07? Or just matdyn? I see the two text input files must be ?plugged into? run_example because of the new nsig flag. Anyway, I?ll see if I can get the ?old? example07 to work. BTW, I?ve observed one can have gfortran compiler issues with example07...go to http://www.democritos.it/pipermail/pw_forum/2010-March/016356.html I note phq_readin still contains the error message 'The phonon code with LDA+U is not yet available.' Any idea when it might be available? I would be a very willing beta tester. BTW (again), I?m having occasional iotk problems running the PH code on both 4.0 and 4.2.1...see my original forum posting at http://www.democritos.it/pipermail/pw_forum/2010-March/016356.html and Paolo?s reply http://www.democritos.it/pipermail/pw_forum/2010-December/018852.html On the other hand, backing off to 3.2.3 always works! :-) Regards, -Paul http://www.w2agz.com w2agz at w2agz.com From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Eyvaz Isaev Sent: Saturday, December 11, 2010 5:33 AM To: PWSCF Forum Subject: Re: [Pw_forum] example07...again Dear Paul, May I suppose, you used an old version of lambda.f90, as I can see from the last edition of lambda.f90 a line with "(5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4)" is commented. Besides, as already it was pointed out by Paolo, lambda.f90 somewhat obsolete, but will be supported, I guess. Now lambda can be calculated by means of matdyn.x. Bests, Eyvaz _____ From: W2AGZ To: pw_forum at pwscf.org Sent: Sat, December 11, 2010 7:38:53 AM Subject: [Pw_forum] example07...again Eyvaz, I still get gfortran errors in QE-4.2.1 after ?re-making? the changes you sent last August. See below: running pw.x as: /home/pmpgrant/espresso-4.2.1/bin/pw.x running ph.x as: /home/pmpgrant/espresso-4.2.1/bin/ph.x running q2r.x as: /home/pmpgrant/espresso-4.2.1/bin/q2r.x running matdyn.x as: /home/pmpgrant/espresso-4.2.1/bin/matdyn.x running lambda.x as: /home/pmpgrant/espresso-4.2.1/bin/lambda.x cleaning /home/pmpgrant/tmp... done running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... done running q2r... done running matdyn for frequency calculation... done running matdyn for a2F(omega) calculation... done running lambda.x for lambda calculation...At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.000000. 0.000000. 0.000000') Fortran runtime error: Constant string in input format (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4) ^ Error condition encountered during test: exit status = 2 Aborting -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101211/a9fdc114/attachment.htm From eyvaz_isaev at yahoo.com Sun Dec 12 19:26:46 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 12 Dec 2010 10:26:46 -0800 (PST) Subject: [Pw_forum] example07...again In-Reply-To: <00ce01cb9975$e814ed20$b83ec760$@w2agz.com> References: <003101cb98fe$15a76c40$40f644c0$@w2agz.com> <95815.20948.qm@web65704.mail.ac4.yahoo.com> <00ce01cb9975$e814ed20$b83ec760$@w2agz.com> Message-ID: <637371.20240.qm@web65705.mail.ac4.yahoo.com> Hi Paul, ________________________________ From: W2AGZ >My bad (mea culpa). I thought I had inserted the ?new Fortran code? you sent me >a >few months ago, but on replacement and ?make,? I must have screwed up >>something...I?ll check. Please check it. >In the meantime, you state the new matdyn.x ?replaces all the old stuff, e.g. >>lambda.x? used in example07. Is there an ?updated example07? that illustrates >the >new methodology? I follow the path illustrated in example07 a fair amount >in my >attempts to simulate electron-phonon mediated Eliashberg-McMillan >pairing. > No, I will update this example. Thanks bringing this inconsistency to our attention. But lambda.f90 should work. >Last September you sent me a tar-file with the f90 code for elphon, lambda, >>matdyn, phcom and qr2 along with matdyn.in.dos and qr2.in. I take it all are >>required to ?fix? example07? Or just matdyn? I see the two text input files >must be >?plugged into? run_example because of the new nsig flag. Anyway, I?ll >see if I can >get the ?old? example07 to work. I suppose you should take all these files. "nsig" by default is 10. But these files were tested for 4.2 version. >BTW, I?ve observed one can have gfortran compiler issues with example07...go to >>http://www.democritos.it/pipermail/pw_forum/2010-March/016356.html Fortunately, I have never got such kind misbehavior of the code due to a compiler. For me the code always worked smoothly. Only once I got very unusual lambda's, but it was due to a system error, as when I restarted it was OK. >I note phq_readin still contains the error message 'The phonon code with LDA+U >is >not yet available.' Any idea when it might be available? I would be a very >willing >beta tester. As far as I remember Matteo C. said "phonons with LDA+U" is almost ready, but still there are some problems, I guess. Sorry, but I am the first in the queue list. Let us ask Matteo again about this opportunity. >BTW (again), I?m having occasional iotk problems running the PH code on both 4.0 >>and 4.2.1...see my original forum posting at http://www.democritos.it/pipermail >/pw_forum/2010-March/016356.htmland Paolo?s reply >http://www.democritos.it/pipermail >/pw_forum/2010-December/018852.html Sorry, but the first link was posted by Miguel, not you. Nevertheless, I remember. Have you tried g95? Bests, Eyvaz. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101212/3309a095/attachment.htm From priyankagoud8 at gmail.com Mon Dec 13 07:42:35 2010 From: priyankagoud8 at gmail.com (priyanka goud) Date: Mon, 13 Dec 2010 12:12:35 +0530 Subject: [Pw_forum] Problem in Finding x.kpath file in pwtools Message-ID: Hello, Iam Priyanka, recently started using pwscf version(QuantumEspesso-4.0.1) I would like to generate the list of k-points by using utility program X.KPATH in PWTOOLS. (Mentioned in http://www.tcd.ie/Physics/People/Claude.Ederer/teaching/PG5009/exercise3.pdf) But I couldn't find any of such file in pwtools.Can you please suggest where can I find that file or the process to generate list of K-points of high symmetry lines. Regards, Priyanka From nazari at iasbs.ac.ir Mon Dec 13 07:53:02 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 13 Dec 2010 10:23:02 +0330 (IRST) Subject: [Pw_forum] Problem in Finding x.kpath file in pwtools In-Reply-To: References: Message-ID: <5013.85.185.211.90.1292223182.squirrel@mail.iasbs.ac.ir>
?The exe fileis : ?kpoints.x regards > Hello, > > Iam Priyanka, recently started using pwscf > version(QuantumEspesso-4.0.1) > I would like to generate the list of k-points by using utility program > X.KPATH in PWTOOLS. > (Mentioned in > http://www.tcd.ie/Physics/People/Claude.Ederer/teaching/PG5009/exercise3.pdf) > > But I couldn't find any of such file in pwtools.Can you > please suggest where can I find that > file or the process to generate list of K-points of high symmetry lines. > > > Regards, > Priyanka > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- 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/20101213/e191197a/attachment.htm From giannozz at democritos.it Mon Dec 13 08:53:42 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 13 Dec 2010 08:53:42 +0100 Subject: [Pw_forum] Problem in Finding x.kpath file in pwtools In-Reply-To: References: Message-ID: On Dec 13, 2010, at 7:42 , priyanka goud wrote: > I would like to generate the list of k-points by using utility program > X.KPATH in PWTOOLS. it is not part of the "official" QE distribution P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From songsong19840614 at gmail.com Mon Dec 13 12:24:38 2010 From: songsong19840614 at gmail.com (=?GB2312?B?uMTN9dauzfW4xM311q7N9Q==?=) Date: Mon, 13 Dec 2010 19:24:38 +0800 Subject: [Pw_forum] Problem in Finding x.kpath file in pwtools Message-ID: I always use "xcrysden" to generate high symmetry k-point and then use this "bk.exe" (I have upload file)to generate all k-point which is along high symmetry.I never use pwtool,butI guess it may be the "kpoint.x". -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101213/8cd8828d/attachment.htm From sclauzer at sissa.it Mon Dec 13 12:36:27 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 13 Dec 2010 12:36:27 +0100 Subject: [Pw_forum] Problem in Finding x.kpath file in pwtools In-Reply-To: References: Message-ID: I think that kpoints.x in pwtools does a different thing. It generates a regular b1 x n2 x n3 grid of k-points (reduced by the symmetry of the Bravais lattice) which can be used to sample the BZ. It is not meant to generate a path in k-space (i.e. a sequence of points that can be used to plot a band structure). HTH GS Il giorno 13/dic/2010, alle ore 12.24, ???????? ha scritto: > I always use "xcrysden" to generate high symmetry k-point and then use this "bk.exe" (I have upload file)to generate all k-point which is along high symmetry.I never use pwtool,butI guess it may be the "kpoint.x". _______________________________________________ > 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/20101213/dfc9dba1/attachment.htm From 1009ukumar at gmail.com Mon Dec 13 12:44:49 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Mon, 13 Dec 2010 17:14:49 +0530 Subject: [Pw_forum] kpoints along sym directions in k-lattice of hexagonal, valence and core charge density in atomic code ? Message-ID: Dear all QE users, i have 2 questions? 1) what are the k points along symmetry directions ( gamma-M-K-gamma-A-L-H-A, M-L, K-H ) of reciprocal lattice of hexagonal unit cell ? is there any tool to do so? kpoint.x doesn't produce kpoints along symmetry directions. 2) how to output the valence and core charge density in PP generation using atomic code? what does " ld1.pwe" file contain? hope that i haven't asked too many q's. with regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101213/5204895f/attachment.htm From elie.moujaes at hotmail.co.uk Mon Dec 13 13:57:36 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 13 Dec 2010 12:57:36 +0000 Subject: [Pw_forum] Bilayer graphene subject to an electric field Message-ID: Dear all, I am trying to get the band structure of bilayer graphene under the effect of an external electric field. I have done the scf calculations without the inclusion of an electric field , then again did teh scf calculation with an electric field included in the z-direction (of value 0.1 Ry). However the convergence is not achieved and it stopped after 100 iterations giving the following message: total cpu time spent up to now is 83435.11 secs total energy = -52.83248336 Ry Harris-Foulkes estimate = -45.80937450 Ry estimated scf accuracy < 0.00524127 Ry End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping You will find below the inout file for the scf calculation when an electric field is applied: &control prefix='bielgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., nberrycyc= 1, pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_mode='local-TF' mixing_beta=0.1D0 efield_cart(1) = 0.000, efield_cart(2) = 0.000, efield_cart(3) = 0.10, / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 C 0.000000 0.000000 0.257692 C 0.333333 -0.33333 0.000000 C -0.333333 0.33333 0.257692 K_POINTS automatic 25 25 1 0 0 0 Thanks Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101213/4850afb4/attachment.htm From ac.rain at inbox.com Tue Dec 14 05:00:54 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Mon, 13 Dec 2010 20:00:54 -0800 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <34977170-99D5-4EB3-BC21-7AF1EA719897@democritos.it> References: <47bd3257d74.00000656ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> Message-ID: <9179582E6FA.00000849ac.rain@inbox.com> Hi Paolo thanks for your response. What do you mean exactly by "run interactively"? at first I tried running from the command line with mpi commands and then we moved to putting the info inside the PARA_PREFIX and PARA_PREFIX inside the actual script called "check-pw.x.j". to run this i have been doing "./check_pw.x.j" ,which is running interactively but only prints "Checking atom..." then sits there for long time, the machines working at 100% without doing anything. I tried to add "-inp file" to PARA_PREFIX I just get "unrecognized argument inp" then fail, when I add it to PARA_POSTFIX I don't get error but get the same results as previously with the hung output. (I have not required input file before? just trying to get a test working with the least amount of complexity possible). PARA_PREFIX="mpiexec -n 60 -f /home/user/mpiMachinefile.txt -wdir /usr/local/espresso-4.2.1/tests" PARA_POSTFIX="./check-pw.x.j -inp file" regards, Nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Fri, 10 Dec 2010 08:20:45 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE and mpich2, Linux > > Run interactively and look what happens. If nothing > happens, use option "-inp file" to read from file "file". > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth From sclauzer at sissa.it Tue Dec 14 11:19:44 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 14 Dec 2010 11:19:44 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <9179582E6FA.00000849ac.rain@inbox.com> References: <47bd3257d74.00000656ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <9179582E6FA.00000849ac.rain@inbox.com> Message-ID: <2535D195-AC71-4965-8379-243A44A796B0@sissa.it> Il giorno 14/dic/2010, alle ore 05.00, ac.rain at inbox.com ha scritto: > Hi Paolo thanks for your response. > > What do you mean exactly by "run interactively"? > > at first I tried running from the command line with mpi commands and then we moved to putting the info inside the PARA_PREFIX and PARA_PREFIX inside the actual script called "check-pw.x.j". > > to run this i have been doing "./check_pw.x.j" ,which is running interactively but only prints "Checking atom..." then sits there for long time, the machines working at 100% without doing anything. > > I tried to add "-inp file" to PARA_PREFIX I just get "unrecognized argument inp" then fail, when I add it to PARA_POSTFIX I don't get error but get the same results as previously with the hung output. > > (I have not required input file before? just trying to get a test working with the least amount of complexity possible). > > PARA_PREFIX="mpiexec -n 60 -f /home/user/mpiMachinefile.txt -wdir /usr/local/espresso-4.2.1/tests" > PARA_POSTFIX="./check-pw.x.j -inp file" This is not correct! Please retry with PARA_POSTFIX="-inp" PARA_PREFIX and PARA_POSTFIX will be automatically placed before and after the executable command name (e.g. /usr/local/espresso-4.2.1/bin/pw.x) and the resulting command line will be called by the script check-pw.j GS > > regards, > > Nick > >> -----Original Message----- >> From: giannozz at democritos.it >> Sent: Fri, 10 Dec 2010 08:20:45 +0100 >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] QE and mpich2, Linux >> >> Run interactively and look what happens. If nothing >> happens, use option "-inp file" to read from file "file". >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics, 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 > > ____________________________________________________________ > FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! > Check it out at http://www.inbox.com/earth > _______________________________________________ > 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/20101214/3a35bced/attachment.htm From giannozz at democritos.it Tue Dec 14 11:30:45 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 14 Dec 2010 11:30:45 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <2535D195-AC71-4965-8379-243A44A796B0@sissa.it> References: <47bd3257d74.00000656ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <9179582E6FA.00000849ac.rain@inbox.com> <2535D195-AC71-4965-8379-243A44A796B0@sissa.it> Message-ID: <4D074755.3020701@democritos.it> Gabriele Sclauzero wrote: > This is not correct! Please retry with > PARA_POSTFIX="-inp" no, this is not going to work. The correct way is to replace the "<" in the two lines $PARA_PREFIX $ESPRESSO_ROOT/bin/pw.x $PARA_POSTFIX < $TESTDIR/$name.in \ > $TESTDIR/$name.out with "-inp" P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Tue Dec 14 11:34:08 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 14 Dec 2010 11:34:08 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <4D074755.3020701@democritos.it> References: <47bd3257d74.00000656ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <9179582E6FA.00000849ac.rain@inbox.com> <2535D195-AC71-4965-8379-243A44A796B0@sissa.it> <4D074755.3020701@democritos.it> Message-ID: OK, admittedly I don't know that script well enough :) GS Il giorno 14/dic/2010, alle ore 11.30, Paolo Giannozzi ha scritto: > Gabriele Sclauzero wrote: > >> This is not correct! Please retry with >> PARA_POSTFIX="-inp" > > no, this is not going to work. The correct way is to replace the "<" > in the two lines > $PARA_PREFIX $ESPRESSO_ROOT/bin/pw.x $PARA_POSTFIX < $TESTDIR/$name.in \ >> $TESTDIR/$name.out > with "-inp" > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? 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/20101214/8b066eb1/attachment.htm From lhe.oum at gmail.com Tue Dec 14 22:40:22 2010 From: lhe.oum at gmail.com (chaou oum) Date: Tue, 14 Dec 2010 22:40:22 +0100 Subject: [Pw_forum] modeling junction with Q.E Message-ID: DEAR USER Q.E : CAN MODELING THE JUNCTION WITH Q.E? AND IF POSSIBLE GIVE ME AN EXAMPLE FOR PN OR PNP JUNCTION AND THE STEPS. THANK YOU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101214/ff308b99/attachment.htm From eyvaz_isaev at yahoo.com Tue Dec 14 22:40:59 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 14 Dec 2010 13:40:59 -0800 (PST) Subject: [Pw_forum] Bilayer graphene subject to an electric field In-Reply-To: References: Message-ID: <376278.95406.qm@web65706.mail.ac4.yahoo.com> Hi, A couple of comments that might be useful. 1. As you use an US pseudopotential, reduce ecutwfc down to ~30Ry. I do not see any reason for such kind of high cutoff energy, unless you performed some tests and proved that 60Ry is better. Besides, for the same reason (US PsP), you should use more ecutrho (8-12 times of ecutwfc). By default ecutrho=4*ecutwfc (why so, think about) and this works for norm-conserving PsPs. As a reference see N.Mounet and N. Marzari, Phys. Rev. B 71, 205214 (2005), where they used ecutoff=40Ry for graphene and other C-based structures. 2. I have noticed that the job started to converge when I used smaller efield_cart(3)=0.05, after 49 iteration I had estimated scf accuracy < 0.00007068 Ry but then my notebook turned off due to a heating problem, I suggest. As I just tried to test the problem I used only 2x2x1 k-points set, and mixing_beta(1)=0.05. But when I used efield_cart(3)=0.005 (with mixing coefficient 0.1) the job finished after 11 iterations. Hope this helps. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, December 13, 2010 1:57:36 PM Subject: [Pw_forum] Bilayer graphene subject to an electric field Dear all, I am trying to get the band structure of bilayer graphene under the effect of an external electric field. I have done the scf calculations without the inclusion of an electric field , then again did teh scf calculation with an electric field included in the z-direction (of value 0.1 Ry). However the convergence is not achieved and it stopped after 100 iterations giving the following message: total cpu time spent up to now is 83435.11 secs total energy = -52.83248336 Ry Harris-Foulkes estimate = -45.80937450 Ry estimated scf accuracy < 0.00524127 Ry End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping You will find below the inout file for the scf calculation when an electric field is applied: &control prefix='bielgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., nberrycyc= 1, pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_mode='local-TF' mixing_beta=0.1D0 efield_cart(1) = 0.000, efield_cart(2) = 0.000, efield_cart(3) = 0.10, / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 C 0.000000 0.000000 0.257692 C 0.333333 -0.33333 0.000000 C -0.333333 0.33333 0.257692 K_POINTS automatic 25 25 1 0 0 0 Thanks Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101214/5b9bc55e/attachment-0001.htm From ac.rain at inbox.com Wed Dec 15 06:55:52 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Tue, 14 Dec 2010 21:55:52 -0800 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <4D074755.3020701@democritos.it> References: <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <47bd3257d74.00000656ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> Message-ID: <9F0CFC29994.000009E2ac.rain@inbox.com> I am not using $TESTDIR, I am not using $name , I am not using < or >, I am not using -inp, I am not using pw.x directly but the script may be calling it. I have used some of these when trying to get it working but no luck yet so simplifying as much as possible to get something working at least. I do not understand your PARA_ lines in the below message, is it related to the two PARA lines in the script? or are you requesting that I modify the script elsewhere and approach this another way? How to run one of the test programs with mpich2 ? I don't mind which test it is.. but very frustrating staring at code and documentation all day without any progress just brick walls and errors... regards, Nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Tue, 14 Dec 2010 11:30:45 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE and mpich2, Linux > > Gabriele Sclauzero wrote: > >> This is not correct! Please retry with >> PARA_POSTFIX="-inp" > > no, this is not going to work. The correct way is to replace the "<" > in the two lines > $PARA_PREFIX $ESPRESSO_ROOT/bin/pw.x $PARA_POSTFIX < $TESTDIR/$name.in \ > > $TESTDIR/$name.out > with "-inp" > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ____________________________________________________________ Send your photos by email in seconds... TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if3 Works in all emails, instant messengers, blogs, forums and social networks. From masoudnahali at live.com Wed Dec 15 09:31:36 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Wed, 15 Dec 2010 12:01:36 +0330 Subject: [Pw_forum] electron configuration of Ni Message-ID: Dear Quantum Espresso Users I have used Ni.pbe-nd-rrkjus.UPF pseudo-potential for nickel in my project. In the info part of this pseudopotential has been written : Info: Ni PBE 3d9 4s1 RRKJ3 US But I know that the well established electron configuration for nickel is "3d8 4s2" and now I am too worry that it may cause an error in my work. May it ? I appreciate your help to understand the point in advance. Many Thanks Best Wishes * ----------------- Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101215/1f51f2bf/attachment.htm From giannozz at democritos.it Wed Dec 15 09:35:37 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 15 Dec 2010 09:35:37 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <9F0CFC29994.000009E2ac.rain@inbox.com> References: <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <47bd3257d74.00000656ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <9F0CFC29994.000009E2ac.rain@inbox.com> Message-ID: On Dec 15, 2010, at 6:55 , ac.rain at inbox.com wrote: > How to run one of the test programs with mpich2 ? mpirun -np 2 ../bin/pw.x -inp atom.in or mpiexec -n 2 ../bin/pw.x -inp atom.in --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From heatherjkulik at gmail.com Wed Dec 15 18:09:31 2010 From: heatherjkulik at gmail.com (Heather Kulik) Date: Wed, 15 Dec 2010 09:09:31 -0800 Subject: [Pw_forum] electron configuration of Ni In-Reply-To: References: Message-ID: Dear Masoud, You are correct in that the pseudopotential was generated in the state 3d9 4s1. One minor point is that according to NIST ( http://physics.nist.gov/PhysRefData/ASD/levels_form.html), the low-lying experimental atomic energy levels of Ni are: ^3F(3d84s2) ~0 and ^3D(3d94s1) ~ <0.1 eV, ^1D(3d94s1) ~ <0.5 eV. However, the good news is that, the state in which the pseudopotential was generated should not prevent you from accurately describing states that have 3d84s2 character since the core electrons from a 3d94s1 and 3d84s2 Ni should be described fairly similarly. You can also verify the character of your electronic states using any of the postprocessing codes (e.g. projected density of states from projwfc.x) Note: A more serious problem is that if your extended system (i.e. more than one atom) has numerous solutions close in energy comparable to the character of the atomic system, most x-c functionals will likely fail to predict the correct ordering. You should try comparing the relative energies you get for a few representative systems to experimental data where possible to identify if the GGA (or LDA) suffers from any particular bias in the relative ordering of these states. Hope that helps! -- Heather K Postdoc at Stanford University On Wed, Dec 15, 2010 at 12:31 AM, Masoud Nahali wrote: > Dear Quantum Espresso Users > > I have used Ni.pbe-nd-rrkjus.UPF pseudo-potential for nickel in my project. > In the info part of this pseudopotential has been written : > > Info: Ni PBE 3d9 4s1 RRKJ3 US > > But I know that the well established electron configuration for nickel is > "3d8 4s2" and now I am too worry that it may cause an error in my work. May > it ? > I appreciate your help to understand the point in advance. Many Thanks > > > > Best Wishes > * > > ----------------- > > Masoud Nahali > > PhD Student of Physical Chemistry > Sharif University of Technology > * > > > _______________________________________________ > 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/20101215/a251f8be/attachment.htm From masoudnahali at live.com Wed Dec 15 21:57:32 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Thu, 16 Dec 2010 00:27:32 +0330 Subject: [Pw_forum] electron configuration of Ni Message-ID: Dear Heather and QE Users Many thanks for your attention and answer. The case of study is a Ni atom which is connected to 4 carbon atoms in a graphite-like structure. The projected DOS calculation by projwfc.x (lowdin charge analysis) after relaxation procedure shows that the Ni electronic configuration is : 4s[0.4023] + 3d[8.8971]. As I know the initial guess of this pseudo-potential is 3d[9] 4s[1] for Ni and I wanna to know that if the initial guess was 3d[8] 4s[2], would I get 4s[0.4023] + 3d[8.8971] again after the relaxation procedure or not ? I appreciate any suggestion in advance. Best Wishes * ----------------- Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * Heather Kulik wrote : > > Dear Masoud, > > You are correct in that the pseudopotential was generated in the state 3d9 > 4s1. > > One minor point is that according to NIST ( > http://physics.nist.gov/PhysRefData/ASD/levels_form.html), the low-lying > experimental atomic energy levels of Ni are: > > ^3F(3d84s2) ~0 and ^3D(3d94s1) ~ <0.1 eV, ^1D(3d94s1) ~ <0.5 eV. > > However, the good news is that, the state in which the pseudopotential was > generated should not prevent you from accurately describing states that > have > 3d84s2 character since the core electrons from a 3d94s1 and 3d84s2 Ni > should > be described fairly similarly. > > You can also verify the character of your electronic states using any of > the > postprocessing codes (e.g. projected density of states from projwfc.x) > > Note: A more serious problem is that if your extended system (i.e. more > than > one atom) has numerous solutions close in energy comparable to the > character > of the atomic system, most x-c functionals will likely fail to predict the > correct ordering. > > You should try comparing the relative energies you get for a few > representative systems to experimental data where possible to identify if > the GGA (or LDA) suffers from any particular bias in the relative ordering > of these states. > > Hope that helps! > -- > Heather K > Postdoc at Stanford University > > > On Wed, Dec 15, 2010 at 12:31 AM, Masoud Nahali > >wrote: > >* Dear Quantum Espresso Users *>* *>* I have used Ni.pbe-nd-rrkjus.UPF pseudo-potential for nickel in my project. *>* In the info part of this pseudopotential has been written : *>* *>* Info: Ni PBE 3d9 4s1 RRKJ3 US *>* *>* But I know that the well established electron configuration for nickel is *>* "3d8 4s2" and now I am too worry that it may cause an error in my work. May *>* it ? *>* I appreciate your help to understand the point in advance. Many Thanks *>* *>* *>* *>* Best Wishes *>* * *>* *>* ----------------- *>* *>* Masoud Nahali *>* *>* PhD Student of Physical Chemistry *>* Sharif University of Technology *>* * *>* * ** ** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101216/6adaa95d/attachment.htm From giannozz at democritos.it Wed Dec 15 22:19:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 15 Dec 2010 22:19:12 +0100 Subject: [Pw_forum] electron configuration of Ni In-Reply-To: References: Message-ID: <13279247-E896-425D-BDFE-E4CA4C59133C@democritos.it> On Dec 15, 2010, at 21:57 , Masoud Nahali wrote: > The projected DOS calculation [...] shows that the Ni electronic > configuration is > 4s[0.4023] + 3d[8.8971]. As I know the initial guess of this pseudo- > potential is > 3d[9] 4s[1] for Ni this is not "an initial guess". This is "the reference electronic configuration" for the pseudopotential. In principle, you can choose any reference electronic configuration: if the pseudopotential is transferrable, it will work in other environments as well > and I wanna to know please don't write like rappers talk: "want", not "wanna" > that if the initial guess was 3d[8] 4s[2], would I get 4s[0.4023] + > 3d[8.8971] again you will never get exactly the same numbers, but you should get very similar numbers, as long as both pseudopotentials are sufficiently tranferrable Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mcminis2 at illinois.edu Wed Dec 15 23:03:12 2010 From: mcminis2 at illinois.edu (Jeremy McMinis) Date: Wed, 15 Dec 2010 16:03:12 -0600 (CST) Subject: [Pw_forum] Broken degeneracy using B3LYP Message-ID: <20101215160312.CWU05639@expms5.cites.uiuc.edu> Hello, I am using the B3LYP functional and notice that degeneracies are being broken. Do I need to use a specific diagonalization method or is there something else I need to be doing to avoid this problem? I am running with sym and inv .false. because I want the k-points to generate orbitals. This doesn't effect the LDA calculation. ====================================== For instance, running Silicon Carbide in a cubic cell and 2x2x2 K-point tiling I get the lowest occupied orbitals from LDA as, energy=-0.27368 k=( 0.0000, 0.0000, 0.0000) energy=-0.13866 k=( 0.3813, 0.3813, 0.3813) energy=-0.13866 k=(-0.3813, 0.3813, -0.3813) energy=-0.13866 k=(-0.3813, -0.3813, 0.3813) energy=-0.13866 k=(-0.3813, 0.3813, 0.3813) energy=-0.08071 k=( 0.0000, 0.0000, 0.7626) energy=-0.08071 k=( 0.0000, 0.7626, 0.0000) energy=-0.08071 k=(-0.7626, 0.0000, 0.0000) energy=-0.00732 k=(-0.3813, 0.3813, 0.3813) energy=-0.00732 k=(-0.3813, -0.3813, 0.3813) energy=-0.00732 k=(-0.3813, 0.3813, -0.3813) energy=-0.00732 k=( 0.3813, 0.3813, 0.3813) energy= 0.01591 k=(-0.7626, 0.0000, 0.0000) energy= 0.01591 k=( 0.0000, 0.0000, 0.7626) energy= 0.01591 k=( 0.0000, 0.7626, 0.0000) energy= 0.19069 k=( 0.0000, 0.7626, 0.0000) energy= 0.19069 k=( 0.0000, 0.0000, 0.7626) energy= 0.19069 k=(-0.7626, 0.0000, 0.0000) energy= 0.19069 k=(-0.7626, 0.0000, 0.0000) energy= 0.19069 k=( 0.0000, 0.0000, 0.7626) energy= 0.19069 k=( 0.0000, 0.7626, 0.0000) energy= 0.26820 k=( 0.3813, 0.3813, 0.3813) energy= 0.26820 k=(-0.3813, -0.3813, 0.3813) energy= 0.26820 k=(-0.3813, 0.3813, -0.3813) energy= 0.26820 k=(-0.3813, 0.3813, 0.3813) energy= 0.26820 k=( 0.3813, 0.3813, 0.3813) energy= 0.26820 k=(-0.3813, 0.3813, -0.3813) energy= 0.26820 k=(-0.3813, 0.3813, 0.3813) energy= 0.26820 k=(-0.3813, -0.3813, 0.3813) energy= 0.30662 k=( 0.0000, 0.0000, 0.0000) energy= 0.30662 k=( 0.0000, 0.0000, 0.0000) energy= 0.30662 k=( 0.0000, 0.0000, 0.0000) and from B3LYP as : energy=-0.21040 k=( 0.0000, 0.0000, 0.0000) energy=-0.07163 k=(-0.3813, 0.3813, -0.3813) energy=-0.07163 k=( 0.3813, 0.3813, 0.3813) energy=-0.07163 k=(-0.3813, -0.3813, 0.3813) energy=-0.07162 k=(-0.3813, 0.3813, 0.3813) energy=-0.01393 k=(-0.7626, 0.0000, 0.0000) energy=-0.01393 k=( 0.0000, 0.7626, 0.0000) energy=-0.01393 k=( 0.0000, 0.0000, 0.7626) energy= 0.03976 k=(-0.3813, 0.3813, 0.3813) energy= 0.03977 k=(-0.3813, -0.3813, 0.3813) energy= 0.03977 k=( 0.3813, 0.3813, 0.3813) energy= 0.03978 k=(-0.3813, 0.3813, -0.3813) energy= 0.06856 k=( 0.0000, 0.0000, 0.7626) energy= 0.06856 k=( 0.0000, 0.7626, 0.0000) energy= 0.06856 k=(-0.7626, 0.0000, 0.0000) energy= 0.24708 k=(-0.7626, 0.0000, 0.0000) energy= 0.24708 k=( 0.0000, 0.7626, 0.0000) energy= 0.24708 k=( 0.0000, 0.0000, 0.7626) energy= 0.24708 k=( 0.0000, 0.0000, 0.7626) energy= 0.24708 k=(-0.7626, 0.0000, 0.0000) energy= 0.24708 k=( 0.0000, 0.7626, 0.0000) energy= 0.33069 k=(-0.3813, -0.3813, 0.3813) energy= 0.33069 k=(-0.3813, 0.3813, -0.3813) energy= 0.33070 k=( 0.3813, 0.3813, 0.3813) energy= 0.33070 k=(-0.3813, 0.3813, 0.3813) energy= 0.33070 k=(-0.3813, 0.3813, -0.3813) energy= 0.33071 k=(-0.3813, 0.3813, 0.3813) energy= 0.33071 k=( 0.3813, 0.3813, 0.3813) energy= 0.33071 k=(-0.3813, -0.3813, 0.3813) energy= 0.37074 k=( 0.0000, 0.0000, 0.0000) energy= 0.37075 k=( 0.0000, 0.0000, 0.0000) energy= 0.37076 k=( 0.0000, 0.0000, 0.0000) ====================================== &control prefix= "dft.sic.222", pseudo_dir = '../', outdir='.', wf_collect=.true., / &system ibrav= 2, celldm(1) =8.2392, nat= 2, ntyp= 2, ecutwfc = 200, nelec=8, nbnd=6, input_dft= "B3LYP", nosym=.true., noinv=.true., / &electrons / ATOMIC_SPECIES C 14.0 C.DF.upf Si 28.086 Si.DF.upf ATOMIC_POSITIONS C 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS automatic 2 2 2 0 0 0 From Lorenzo.Paulatto at impmc.upmc.fr Thu Dec 16 09:46:45 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 16 Dec 2010 09:46:45 +0100 Subject: [Pw_forum] Broken degeneracy using B3LYP In-Reply-To: <20101215160312.CWU05639@expms5.cites.uiuc.edu> References: <20101215160312.CWU05639@expms5.cites.uiuc.edu> Message-ID: On Wed, 15 Dec 2010 23:03:12 +0100, Jeremy McMinis wrote: > I am using the B3LYP functional and notice that degeneracies are being > broken. Do I need to use a specific diagonalization method or is there > something else I need to be doing to avoid this problem? I am running > with sym and inv .false. because I want the k-points to generate > orbitals. This doesn't effect the LDA calculation. > [...] > nosym=.true., > noinv=.true., Dear Jeremy, I don't think the problem is b3lyp itself, but the just the gradient correction: it can be quite noisy and thus break the symmetry of the crystal. If you wish the symmetry to be actively enforced you have to lease nosym to its default value, namely .false. best regards -- Lorenzo Paulatt (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From spakinform at gmail.com Thu Dec 16 10:33:31 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Thu, 16 Dec 2010 18:33:31 +0900 Subject: [Pw_forum] SCF loop fails to converge when tefield is switched on Message-ID: Dear all, I'm trying to do finite electric field calculation for a thin slab with hexagonal symmetry. I consider a saw-like electric field (as large as 0.0005 au~0.03 eV/A) exerted along c-axis of my hexagonal unit cell. My input settings (partly) are as follows: &CONTROL title = Ta_slab , calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './tmp/' , pseudo_dir = './' , prefix = 'tao' , tstress = .true. , tprnfor = .true. , tefield = .true. , dipfield = .true. , / &SYSTEM ibrav = 4, celldm(1) = 6.90415879, celldm(3) = 21.57221207, nat = 18, ntyp = 3, ecutwfc = 50 , noncolin = .true. , lspinorb = .true. , nbnd = 152, edir = 3 , eamp = 0.0005834 , emaxpos = 0.75 , eopreg = 0.4 , / &ELECTRONS conv_thr = 1.0d-6 , . . . Using these settings, the calculation appears to be going well for the first few iterations with rather sharp convergence in total energy, but then it becomes slower and slower and eventually ends up with a dE much larger than conv_thr. Without electric field, there is no such a problem. Any idea how to improve the SCF convergence while tefield is on? Any help is appreciated, Sincerely -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101216/9a534b69/attachment.htm From glapenna at iccom.cnr.it Thu Dec 16 12:50:54 2010 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Thu, 16 Dec 2010 12:50:54 +0100 (CET) Subject: [Pw_forum] Electron sharing by PW calculations In-Reply-To: References: Message-ID: Dear QE users and developers, I would like to know if there is a method, that does not imply projections onto atomic orbitals, for calculating the number of shared electrons between two atoms (bond order, delocalization index, or whatever) and when the electronic structure is calculated in terms of plane-waves expansions. Many thanks in advance, 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 giannozz at democritos.it Thu Dec 16 18:49:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Dec 2010 18:49:16 +0100 Subject: [Pw_forum] SCF loop fails to converge when tefield is switched on In-Reply-To: References: Message-ID: <4D0A511C.5060103@democritos.it> soroush pakseresht wrote: > I consider a saw-like electric field (as large as 0.0005 au~0.03 eV/A) > exerted along c-axis of my hexagonal unit cell[...] the calculation [...] > becomes slower and slower and eventually ends up with a dE much larger > than conv_thr are you sure that your sawtooth potential doesn't changs sign in the middle of atoms? misunderstanding of the form of the sawtooth potential is a frequent reason for bad or no convergence P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From spakinform at gmail.com Thu Dec 16 19:33:41 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Fri, 17 Dec 2010 03:33:41 +0900 Subject: [Pw_forum] SCF loop fails to converge when tefield is switched on In-Reply-To: <4D0A511C.5060103@democritos.it> References: <4D0A511C.5060103@democritos.it> Message-ID: Dear Paolo, In my calculations, the sawtooth potential is defined as follows edir = 3 , eamp = 0.0005834 , emaxpos = 0.75 , eopreg = 0.4 , The emaxpos is slightly above the topmost layer of the slab and (emaxpos+eopreg-1) is just below the bottom layer. Basically this should correspond to a sawlike potential linearly increasing from one end to the other end of the slab without any sign change. So, I don't think this should be the reason for my problem. Soroush On Fri, Dec 17, 2010 at 2:49 AM, Paolo Giannozzi wrote: > soroush pakseresht wrote: > > > I consider a saw-like electric field (as large as 0.0005 au~0.03 eV/A) > > exerted along c-axis of my hexagonal unit cell[...] the calculation [...] > > becomes slower and slower and eventually ends up with a dE much larger > > than conv_thr > > are you sure that your sawtooth potential doesn't changs sign in the > middle of atoms? misunderstanding of the form of the sawtooth potential > is a frequent reason for bad or no convergence > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/08dee2ac/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Thu Dec 16 21:21:21 2010 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 16 Dec 2010 21:21:21 +0100 Subject: [Pw_forum] SCF loop fails to converge when tefield is switched on In-Reply-To: References: <4D0A511C.5060103@democritos.it> Message-ID: In data 16 dicembre 2010 alle ore 19:33:41, soroush pakseresht ha scritto: > slightly above > just below Dear Soroush, "safely far" is a wiser distance quantifier than "slightly" and "just" when using sawtooth potential. Ideally there should be absolutely *zero* charge density in the inversion region (from emaxpos to eopreg). This is easier to achieve if you use a small inversion region (eopreg ~ 0.05) and a lot of vacuum in the slab geometry. Keep in mind that the charge density of an atom can still be important far behyond its conventional covalent or ionic radius (I would say >5 bohr). best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From kirtinandan07 at gmail.com Fri Dec 17 06:39:11 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Fri, 17 Dec 2010 11:09:11 +0530 Subject: [Pw_forum] lattice parameter of Co Message-ID: Hi I am trying to determine the lattice parameter of hcp Co. The reported experimental results is a = 4.74 bohr c/a = 1.62 but i am getting a = 4.675 and c/a = 1.58 . I am using the GGA PP Co.pbe-nd-rrkjus.UPF which is expected to overestimate the lattice parameter as compared to LDA PP but here it is underestimating the lattice parameter by around 2%. am i doing any thing wrong or this value i should proceed with this result for my further calculation. I am attaching the input file and the plot of E vs lattice parameter. Please help. Thanks in advance. vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/05c02e88/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: E_vs_latt_par_compare2.pdf Type: application/pdf Size: 3599 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101217/05c02e88/attachment-0001.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: Co.in Type: application/octet-stream Size: 795 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101217/05c02e88/attachment-0001.obj From kirtinandan07 at gmail.com Fri Dec 17 06:47:46 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Fri, 17 Dec 2010 11:17:46 +0530 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> References: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> Message-ID: sorry for late reply. so what is your suggestion for getting the accurate value for cohesive energy for W. I also tried another BCC material Ta and its cohesive energy is also more than 22% higher than the reported value (kittel). But when i calculated the cohesive energy for FCC Ni and Al the difference from experimental result is around 6 % (on the higher side) Thanks in advance Vicky singh Bangalore On Tue, Dec 7, 2010 at 2:28 PM, Gabriele Sclauzero wrote: > Dear Mohnish > > Il giorno 06/dic/2010, alle ore 07.51, mohnish pandey ha scritto: > > Dear Vicky! > Check the convergence of energy of isolated atoms also. > Normally convergence threshold for energy for isolated species is higher > than the crystal system. > > > I'm sorry, but I hope you'll let me disagree on this point. What makes you > say this? > > Check for different values of ecut and use the converged value. > > > One usually uses the same ecutwfc value for both bulk and atomic > calculations, in order to take advantage of some error cancellation. Indeed, > if you plot the difference between the bulk and atomic total energies as a > function of ecutwfc, you should see that it converges much faster than any > of the two energies taken alone. > > And next thing is you are doing calculations for bulk system so all the > degrees of freedom should be relaxed for geometry optimization so instead of > flag "relax" use "vc-relax".. The former one will converge the forces but > not the stress and latter one converges the stress also... > > > I agree that the "vc-relax" option is useful, but maybe not so much in this > case. I think that bulk W is bcc, hence it can be studied with one atom per > cell and there are no internal parameters to relax. You can simply scan the > total energy as a function of the lattice parameter to get the equilibrium > value, as Vicky already did. > > There are many other issues that come in, especially in the atomic > calculation (see recent discussions on the forum). Even when you get a > converged DFT value, in some cases this might be considerably far from the > experimental value. > > Best regards, > > GS > > On Sun, Dec 5, 2010 at 11:53 AM, vicky singh wrote: > >> Hi >> >> I am trying to calculate the cohesive energy for tungsten. the code is >> attached. I am able to get the lattice parameter of 3.19 ang while >> experimental is 3.16 angs. Then i calculated the cohesive energy of w by >> calculating the energy of isolated w atom by changing lattice parameter up >> to 25. I got the cohesive energy of 11.1 ev/atom while reported value is 8.9 >> ev/atom. This is way too high. can anybody help me. I have varied the K >> point as well as The E_cut but no advantage. >> >> vicky singh >> research student >> Bangalore >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > _______________________________________________ > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/554922d3/attachment.htm From kirtinandan07 at gmail.com Fri Dec 17 06:57:01 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Fri, 17 Dec 2010 11:27:01 +0530 Subject: [Pw_forum] lattice parameter of Co In-Reply-To: References: Message-ID: Hi I am extremly sorry to attach wrong code for Co. Kindly ignore it. I am attaching the correct code. vicky singh On Fri, Dec 17, 2010 at 11:09 AM, vicky singh wrote: > Hi > I am trying to determine the lattice parameter of hcp Co. The reported > experimental results is a = 4.74 bohr c/a = 1.62 but i am getting a = 4.675 > and c/a = 1.58 . I am using the GGA PP Co.pbe-nd-rrkjus.UPF which is > expected to overestimate the lattice parameter as compared to LDA PP but > here it is underestimating the lattice parameter by around 2%. am i doing > any thing wrong or this value i should proceed with this result for my > further calculation. I am attaching the input file and the plot of E vs > lattice parameter. > > Please help. Thanks in advance. > > vicky singh > research student > Bangalore > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/75e642b1/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Co-4.75.in Type: application/octet-stream Size: 833 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101217/75e642b1/attachment.obj From giuseppe.mattioli at mlib.ism.cnr.it Fri Dec 17 08:26:36 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 17 Dec 2010 08:26:36 +0100 Subject: [Pw_forum] lattice parameter of Co In-Reply-To: References: Message-ID: <201012170826.37128.giuseppe.mattioli@mlib.ism.cnr.it> Dear vicky singh I've done more than few calculations with that same Co pseudopotential. Your wavefunction cutoff is far too low. I used 35/280 Ry. Which kind of cell optimisation have you performed? Have you tried vc-relax with bfgs? What about nspin=2? As you know, Co is a ferromagnetic metal... However, your calculated parameters do not seem so bad to me. Hope this help Giuseppe On Friday 17 December 2010 06:57:01 you wrote: > Hi > I am extremly sorry to attach wrong code for Co. Kindly ignore it. I am > attaching the correct code. > > vicky singh > > On Fri, Dec 17, 2010 at 11:09 AM, vicky singh wrote: > > Hi > > I am trying to determine the lattice parameter of hcp Co. The reported > > experimental results is a = 4.74 bohr c/a = 1.62 but i am getting a = > > 4.675 and c/a = 1.58 . I am using the GGA PP Co.pbe-nd-rrkjus.UPF which > > is expected to overestimate the lattice parameter as compared to LDA PP > > but here it is underestimating the lattice parameter by around 2%. am i > > doing any thing wrong or this value i should proceed with this result for > > my further calculation. I am attaching the input file and the plot of E > > vs lattice parameter. > > > > Please help. Thanks in advance. > > > > vicky singh > > research student > > Bangalore -- ******************************************************** - 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 sclauzer at sissa.it Fri Dec 17 10:12:02 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 17 Dec 2010 10:12:02 +0100 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: References: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> Message-ID: <4D0B2962.8050806@sissa.it> On 12/17/2010 06:47 AM, vicky singh wrote: > sorry for late reply. so what is your suggestion for getting the > accurate value for cohesive energy for W. I also tried another BCC > material Ta and its cohesive energy is also more than 22% higher than > the reported value (kittel). Which kind of value? Is it from experimental results, from HF, DFT, or more sophisticated calculations? Have you tried bcc iron, for instance? I think that for this material you would be able to find many DFT results to compare with in the literature. In order to get a well converged value there are many critical points to take care of in the calculation, especially that for the atom. There has been several discussions about that in the last month on the forum, and for sure many others earlier. Please take a few minutes to browse the archives. GS > But when i calculated the cohesive energy for FCC Ni and Al the > difference from experimental result is around 6 % (on the higher side) > > Thanks in advance > > Vicky singh > Bangalore -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From spakinform at gmail.com Fri Dec 17 13:07:30 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Fri, 17 Dec 2010 21:07:30 +0900 Subject: [Pw_forum] SCF loop fails to converge when tefield is switched on In-Reply-To: References: <4D0A511C.5060103@democritos.it> Message-ID: Dear Lorenzo, You are right. My inversion region looks too thick. I will redo the calculations using larger (smaller) emaxpos (eopreg). Hope this will solve the problem. Thanks, Soroush On Fri, Dec 17, 2010 at 5:21 AM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > In data 16 dicembre 2010 alle ore 19:33:41, soroush pakseresht > ha scritto: > > slightly above > > just below > > Dear Soroush, > "safely far" is a wiser distance quantifier than "slightly" and "just" > when using sawtooth potential. Ideally there should be absolutely *zero* > charge density in the inversion region (from emaxpos to eopreg). This is > easier to achieve if you use a small inversion region (eopreg ~ 0.05) and > a lot of vacuum in the slab geometry. Keep in mind that the charge density > of an atom can still be important far behyond its conventional covalent or > ionic radius (I would say >5 bohr). > > best regards > > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/5b981299/attachment.htm From kirtinandan07 at gmail.com Fri Dec 17 14:55:08 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Fri, 17 Dec 2010 19:25:08 +0530 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: <4D0B2962.8050806@sissa.it> References: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> <4D0B2962.8050806@sissa.it> Message-ID: sorry, i think i was not clear about the reported value of the cohesive energy of W, Ni, Al and Ta . It is the experimental result from kittel. I need to calculate the cohesive energy of W, Ni, Al and Ta and not Fe. with regards vicky singh On Fri, Dec 17, 2010 at 2:42 PM, Gabriele Sclauzero wrote: > On 12/17/2010 06:47 AM, vicky singh wrote: > > sorry for late reply. so what is your suggestion for getting the > > accurate value for cohesive energy for W. I also tried another BCC > > material Ta and its cohesive energy is also more than 22% higher than > > the reported value (kittel). > > Which kind of value? Is it from experimental results, from HF, DFT, or > more sophisticated calculations? Have you tried bcc iron, > for instance? I think that for this material you would be able to find > many DFT results to compare with in the literature. > In order to get a well converged value there are many critical points to > take care of in the calculation, especially that for the atom. There has > been several discussions about that in the last month on the forum, and > for sure many others earlier. Please take a few minutes to browse the > archives. > > > GS > > > But when i calculated the cohesive energy for FCC Ni and Al the > > difference from experimental result is around 6 % (on the higher side) > > > > Thanks in advance > > > > Vicky singh > > Bangalore > -- > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/aa35d261/attachment.htm From giannozz at democritos.it Fri Dec 17 15:03:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Dec 2010 15:03:10 +0100 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: References: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> <4D0B2962.8050806@sissa.it> Message-ID: <4D0B6D9E.3080808@democritos.it> vicky singh wrote: > > I need to calculate the cohesive energy of W, Ni, Al and Ta and not Fe. this is an inappropriate answer. You need to LEARN to calculate the cohesive energy. Gabriele has suggested to start from a simple and well-known case, and you should take his suggestion seriously. -- Paolo Giannozzi, Democritos and University of Udine, Italy From Silvia.Bahmann at physik.tu-freiberg.de Fri Dec 17 15:06:35 2010 From: Silvia.Bahmann at physik.tu-freiberg.de (Silvia Bahmann) Date: Fri, 17 Dec 2010 15:06:35 +0100 Subject: [Pw_forum] Band structure of non-metallic antiferromagnet Message-ID: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> Hi all, I would like to calculate the band structure of an antiferromagnetic insulator. In v. 4.2.1 of QE one has to define antiferromagnetism in an insulator like this: starting_magnetization(1) = 1, starting_magnetization(2) = -1, tot_magnetization = 0 This is considered as constrained magnetization which is not allowed to use with the bands code. Is there another way to define the antiferromagnetism since nelup and neldw are not available anymore? And why is the bands code not working? Thanks in advance for your help, Silvia Bahmann Institute for Theoretical Physics TU Bergakademie Freiberg Germany From elie.moujaes at hotmail.co.uk Fri Dec 17 16:47:51 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 17 Dec 2010 15:47:51 +0000 Subject: [Pw_forum] Bilayer graphene subject to an electric field In-Reply-To: <376278.95406.qm@web65706.mail.ac4.yahoo.com> References: , <376278.95406.qm@web65706.mail.ac4.yahoo.com> Message-ID: Dear Prof. Eyvaz, Thanks a lot for the information. Everything is solved now.. Elie Date: Tue, 14 Dec 2010 13:40:59 -0800 From: eyvaz_isaev at yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Bilayer graphene subject to an electric field Hi, A couple of comments that might be useful. 1. As you use an US pseudopotential, reduce ecutwfc down to ~30Ry. I do not see any reason for such kind of high cutoff energy, unless you performed some tests and proved that 60Ry is better. Besides, for the same reason (US PsP), you should use more ecutrho (8-12 times of ecutwfc). By default ecutrho=4*ecutwfc (why so, think about) and this works for norm-conserving PsPs. As a reference see N.Mounet and N. Marzari, Phys. Rev. B 71, 205214 (2005), where they used ecutoff=40Ry for graphene and other C-based structures. 2. I have noticed that the job started to converge when I used smaller efield_cart(3)=0.05, after 49 iteration I had estimated scf accuracy < 0.00007068 Ry but then my notebook turned off due to a heating problem, I suggest. As I just tried to test the problem I used only 2x2x1 k-points set, and mixing_beta(1)=0.05. But when I used efield_cart(3)=0.005 (with mixing coefficient 0.1) the job finished after 11 iterations. Hope this helps. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, December 13, 2010 1:57:36 PM Subject: [Pw_forum] Bilayer graphene subject to an electric field Dear all, I am trying to get the band structure of bilayer graphene under the effect of an external electric field. I have done the scf calculations without the inclusion of an electric field , then again did teh scf calculation with an electric field included in the z-direction (of value 0.1 Ry). However the convergence is not achieved and it stopped after 100 iterations giving the following message: total cpu time spent up to now is 83435.11 secs total energy = -52.83248336 Ry Harris-Foulkes estimate = -45.80937450 Ry estimated scf accuracy < 0.00524127 Ry End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping You will find below the inout file for the scf calculation when an electric field is applied: &control prefix='bielgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., nberrycyc= 1, pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_mode='local-TF' mixing_beta=0.1D0 efield_cart(1) = 0.000, efield_cart(2) = 0.000, efield_cart(3) = 0.10, / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 C 0.000000 0.000000 0.257692 C 0.333333 -0.33333 0.000000 C -0.333333 0.33333 0.257692 K_POINTS automatic 25 25 1 0 0 0 Thanks Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ 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/20101217/733d6536/attachment-0001.htm From natalia at npavlenko.com Fri Dec 17 19:19:56 2010 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Fri, 17 Dec 2010 10:19:56 -0800 (PST) Subject: [Pw_forum] Problems with generation of GGA pseudopotential for Rb Message-ID: <229757.26331.qm@web1107.biz.mail.sk1.yahoo.com> Dear users, I am trying to build a GGA-type pseudopotential (pbe or PW91) for Rb, but experience problems. I would be very grateful for any advice, below I attach my input code for generation of pbe-pseudopotential for Rb and the output reports of the errors. Thanks in advance for any possible help, N.Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine -------------------- input for generation of Rb pseudopotential--- &input title='Rb', zed=37.0, rel=0, lsd=0, iswitch=3, rlderiv=1.80, eminld=-2.0, emaxld=2.0, deld=0.01, nld=2, config='[Ar] 3d10 4s2 4p6 5s1 5p-1.0', dft='PBE' / &inputp pseudotype=3, lloc=0, file_pseudopw='Rb_pbe.UPF' rcloc=2.5, rcore=2.2 / 4 4S 1 0 2.00 0.00 1.80 1.80 4P 2 1 6.00 0.00 2.20 2.20 5P 2 1 0.00 0.10 2.00 2.00 5S 1 0 1.00 0.00 1.80 1.80 -------------------------------- ---output file with error warning--------------------- --------------------- Generating US pseudopotential Generating local pot.: lloc=0, matching radius rcloc = 1.8000 Wfc 4S rcut= 1.802 Estimated cut-off energy= 39.82 Ry This function has 0 nodes for 0 < r < 1.802 0 1220 1219 100.895173059079 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from compute_chi : error # 1 n is too large %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... --------------------------- From neto.baldini at gmail.com Fri Dec 17 23:15:58 2010 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Fri, 17 Dec 2010 20:15:58 -0200 Subject: [Pw_forum] NEB Calculation with Ti and Graphene Message-ID: Dear users, I'm playing with a NEB calculation involving one Ti atom in a graphene monolayer. The calculation crashes due to diagonalization problems according to the message below. ******************************************* task # 8 from cdiaghg : error # 434 diagonalization (ZHEGV*) failed ******************************************** In what follows I copied my input file (without the atomic positions in order to make it small for the readers) Any hint? Am I doing something very wrong? I'm not using for now polarization for Ti for now in order to make things simpler. I'm planning to include it soon. Also, I'm using a large ecut but I figured out that for graphene and for this pseudo 35-40Ry might work fine. title = 'Graphene mono layer' calculation = "neb" , restart_mode = 'from_scratch' , outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , etot_conv_thr = 1.0E-3 , forc_conv_thr = 1.0D-4 , nstep=10, prefix='1MLG_Ti_NEB', / &SYSTEM ibrav = 0., ntyp = 2 , nat = 33 , ecutwfc = 50.0 , ecutrho = 400.0, occupations = 'smearing' , degauss = 0.02, smearing = 'mv' , / &ELECTRONS conv_thr = 1.0d-7 , mixing_beta = 0.4 , / &IONS num_of_images = 4, opt_scheme = "broyden", path_thr = 0.03D0, / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF Ti 47.8670 Ti.pbe-sp-van_ak.UPF CELL_PARAMETERS 16.12131954 9.383047808 0.0000000 0.00000000 18.658162370 0.0000000 0.0000000 0.000000000 56.6893424 ATOMIC_POSITIONS angstrom first_image ... last image ....... K_POINTS {automatic} 6.0 6.0 1.0 1.0 1.0 1.0 Thanks a lot and best regards ************************************************************************ Dr. Ettore Baldini-Neto, Researcher at Wernher von Braun Center of Advanced Research Campinas, Brazil *********************************************************************** From eyvaz_isaev at yahoo.com Fri Dec 17 23:50:48 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 17 Dec 2010 14:50:48 -0800 (PST) Subject: [Pw_forum] NEB Calculation with Ti and Graphene In-Reply-To: References: Message-ID: <728558.7250.qm@web65705.mail.ac4.yahoo.com> Dear Ettore, The best hints are 1) Searching the forum archive, as the same question was submitted just few days ago. 2) Read User's Guide, page 54 (for QE 4.2) Hope this will help you to find the answer to fix your problem. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Ettore Baldini Neto To: PWSCF Forum Sent: Fri, December 17, 2010 11:15:58 PM Subject: [Pw_forum] NEB Calculation with Ti and Graphene Dear users, I'm playing with a NEB calculation involving one Ti atom in a graphene monolayer. The calculation crashes due to diagonalization problems according to the message below. ******************************************* task # 8 from cdiaghg : error # 434 diagonalization (ZHEGV*) failed ******************************************** In what follows I copied my input file (without the atomic positions in order to make it small for the readers) Any hint? Am I doing something very wrong? I'm not using for now polarization for Ti for now in order to make things simpler. I'm planning to include it soon. Also, I'm using a large ecut but I figured out that for graphene and for this pseudo 35-40Ry might work fine. title = 'Graphene mono layer' calculation = "neb" , restart_mode = 'from_scratch' , outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , etot_conv_thr = 1.0E-3 , forc_conv_thr = 1.0D-4 , nstep=10, prefix='1MLG_Ti_NEB', / &SYSTEM ibrav = 0., ntyp = 2 , nat = 33 , ecutwfc = 50.0 , ecutrho = 400.0, occupations = 'smearing' , degauss = 0.02, smearing = 'mv' , / &ELECTRONS conv_thr = 1.0d-7 , mixing_beta = 0.4 , / &IONS num_of_images = 4, opt_scheme = "broyden", path_thr = 0.03D0, / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF Ti 47.8670 Ti.pbe-sp-van_ak.UPF CELL_PARAMETERS 16.12131954 9.383047808 0.0000000 0.00000000 18.658162370 0.0000000 0.0000000 0.000000000 56.6893424 ATOMIC_POSITIONS angstrom first_image ... last image ....... K_POINTS {automatic} 6.0 6.0 1.0 1.0 1.0 1.0 Thanks a lot and best regards ************************************************************************ Dr. Ettore Baldini-Neto, Researcher at Wernher von Braun Center of Advanced Research Campinas, Brazil *********************************************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From kirtinandan07 at gmail.com Sat Dec 18 02:55:31 2010 From: kirtinandan07 at gmail.com (vicky singh) Date: Sat, 18 Dec 2010 07:25:31 +0530 Subject: [Pw_forum] cohesive energy of tungsten In-Reply-To: <4D0B6D9E.3080808@democritos.it> References: <403EBE1B-3835-4765-BE5D-908DC615BB6C@sissa.it> <4D0B2962.8050806@sissa.it> <4D0B6D9E.3080808@democritos.it> Message-ID: Thanks for your suggestion. with regards vicky singh On Fri, Dec 17, 2010 at 7:33 PM, Paolo Giannozzi wrote: > vicky singh wrote: > > > > > I need to calculate the cohesive energy of W, Ni, Al and Ta and not Fe. > > this is an inappropriate answer. You need to LEARN to calculate the > cohesive energy. Gabriele has suggested to start from a simple and > well-known case, and you should take his suggestion seriously. > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101218/3a8b9ccd/attachment.htm From w2agz at w2agz.com Sat Dec 18 04:38:42 2010 From: w2agz at w2agz.com (W2AGZ) Date: Fri, 17 Dec 2010 19:38:42 -0800 Subject: [Pw_forum] nelec Message-ID: <05c101cb9e65$12a26830$37e73890$@w2agz.com> This question may have already been addressed on the Forum, but what happened to nelec in namelist &system in 4.2.1? It appears to now be defaulted to the number/occupation values of the valence orbitals within the particular pseudopotentials chosen. How do I overide this default and create some "jellum"...through tot_charge? To All, have a happy and joyous winter solstice break. -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101217/c2df266c/attachment.htm From giannozz at democritos.it Sat Dec 18 09:22:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Dec 2010 09:22:06 +0100 Subject: [Pw_forum] nelec In-Reply-To: <05c101cb9e65$12a26830$37e73890$@w2agz.com> References: <05c101cb9e65$12a26830$37e73890$@w2agz.com> Message-ID: <4A5BAF76-807A-44B2-ABE8-0C94FD33B9A5@democritos.it> On Dec 18, 2010, at 4:38 , W2AGZ wrote: > what happened to nelec in namelist &system in 4.2.1? > From file Doc/release-notes: Incompatible changes in version 4.2: [...] * nelec, nelup, neldw, multiplicity variables removed from input: use tot_charge and tot_magnetization instead So tot_charge is the variable to be used > To All, have a happy and joyous winter solstice break. > thank you! Here (Udine and Trieste) we just received the once-traditional snow delivery, in rather large amount Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sohailphysics at yahoo.co.in Sun Dec 19 09:34:23 2010 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Sun, 19 Dec 2010 14:04:23 +0530 (IST) Subject: [Pw_forum] potential parameter Message-ID: <35771.79304.qm@web137320.mail.in.yahoo.com> Dear pwscf users ? Is there anyone who is also interested in Classical Molecular Dynamics Simulation ? Pls explain how to optimise the potential parameters,lets say Tersoff Potential for ZnS Any code (using C/C++) or link explaining this ? Thanks in advance ? Sohail --------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101219/93279212/attachment.htm From tkaloni at gmail.com Sun Dec 19 09:51:23 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Sun, 19 Dec 2010 14:21:23 +0530 Subject: [Pw_forum] Request Message-ID: Dear All, I am doping Indium on graphene having 8 atom per unit cell. When i am running scf, I am getting error as follows. Can anyone tell me the reason how I can correct it ? Yours Sincerely Thaneshwor Kaloni S N Bose kolkata India total energy = -84.77491243 Ry Harris-Foulkes estimate = -84.77418035 Ry estimated scf accuracy < 0.00256499 Ry total magnetization = 0.36 Bohr mag/cell absolute magnetization = 0.38 Bohr mag/cell iteration # 7 ecut= 40.00 Ry beta=0.30 Davidson diagonalization with overlap ethr = 8.27E-06, avg # of iterations = 3.5 negative rho (up, down): 0.441E-04 0.632E-04 total cpu time spent up to now is 129.30 secs total energy = -84.77550699 Ry Harris-Foulkes estimate = -84.77522190 Ry estimated scf accuracy < 0.00184899 Ry total magnetization = 0.30 Bohr mag/cell absolute magnetization = 0.32 Bohr mag/cell iteration # 8 ecut= 40.00 Ry beta=0.30 Davidson diagonalization with overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 102 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -- Thaneshwor P Kaloni -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101219/e5af686c/attachment.htm From eyvaz_isaev at yahoo.com Sun Dec 19 12:35:42 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 19 Dec 2010 03:35:42 -0800 (PST) Subject: [Pw_forum] Request In-Reply-To: References: Message-ID: <668760.65882.qm@web65714.mail.ac4.yahoo.com> Dear Kaloni, You can correct it if you read an answer given ONLY yesterday. Please also use correct subject name , as "Request" or "NEB calculations", etc. does not reflect a real problem. This one requested many times, but ... Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Thaneshwor Kaloni To: pw_forum at pwscf.org Sent: Sun, December 19, 2010 9:51:23 AM Subject: [Pw_forum] Request Dear All, I am doping Indium on graphene having 8 atom per unit cell. When i am running scf, I am getting error as follows. Can anyone tell me the reason how I can correct it ? Yours Sincerely Thaneshwor Kaloni S N Bose kolkata India total energy = -84.77491243 Ry Harris-Foulkes estimate = -84.77418035 Ry estimated scf accuracy < 0.00256499 Ry total magnetization = 0.36 Bohr mag/cell absolute magnetization = 0.38 Bohr mag/cell iteration # 7 ecut= 40.00 Ry beta=0.30 Davidson diagonalization with overlap ethr = 8.27E-06, avg # of iterations = 3.5 negative rho (up, down): 0.441E-04 0.632E-04 total cpu time spent up to now is 129.30 secs total energy = -84.77550699 Ry Harris-Foulkes estimate = -84.77522190 Ry estimated scf accuracy < 0.00184899 Ry total magnetization = 0.30 Bohr mag/cell absolute magnetization = 0.32 Bohr mag/cell iteration # 8 ecut= 40.00 Ry beta=0.30 Davidson diagonalization with overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 102 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -- Thaneshwor P Kaloni -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101219/1ae67ded/attachment.htm From sama at ns.dcci.unipi.it Sun Dec 19 14:43:46 2010 From: sama at ns.dcci.unipi.it (sama at ns.dcci.unipi.it) Date: Sun, 19 Dec 2010 14:43:46 +0100 Subject: [Pw_forum] Measure units in electron-phonon interaction In-Reply-To: <3630533F-B1D9-4DE0-A7AB-77DAB5D5391F@democritos.it> References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> <0fed6dd8dc471ff301dfaa71e1c377bc.squirrel@www.dcci.unipi.it> <3630533F-B1D9-4DE0-A7AB-77DAB5D5391F@democritos.it> Message-ID: <1dbd765b61792cb643ae68733b958b60.squirrel@www.dcci.unipi.it> Thank you for the answer. I am trying to obtain the electron-phonon coupling matrix el_ph_mat from the subroutine elphel. My question at the moment is: el_ph_mat is the coupling with respect to the displacement patterns used in the dynamical matrix generation? In this case, in order to obtain the coupling with respect to the phonon mode, it is sufficient to perform the following operation (do cycles are implicit): 1. g1(ik,ii,jj)=conjg(el_ph_mat(jbnd,ibnd,ik,ii))* & el_ph_mat(jbnd,ibnd,ik,jj) 2. g2(ik,ll) = g2(ik,ll) + DBLE(conjg(dyn(mu,ll)) * & g1(ik,mu,vu) * dyn(vu,ll)) Thank you in advance, Samantha Bruzzone Dipartimento di ingegneria informatica, elettronica e delle telecomunicazioni Univerista' di Pisa > > On Dec 3, 2010, at 18:13 , sama at ns.dcci.unipi.it wrote: > >> I'm not able to understand the measure unit of the transition matrix >> element, as it is calculated from elphel subroutine. > > in the absence of different explicit specifications: everything > should be in atomic units (Rydberg: e^2=2, \hbar=1, m=1/2) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 > From yabraham2 at gmail.com Sun Dec 19 19:43:54 2010 From: yabraham2 at gmail.com (yabraham2 at gmail.com) Date: Sun, 19 Dec 2010 12:43:54 -0600 Subject: [Pw_forum] Request Message-ID: Sent from my LG phone Eyvaz Isaev wrote: >Dear Kaloni, > >You can correct it if you read an answer given ONLY yesterday. > >Please also use correct subject name , as "Request" or "NEB calculations", etc. >does not reflect a real problem. This one requested many times, but ... > >Bests, >Eyvaz. >------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > >________________________________ >From: Thaneshwor Kaloni >To: pw_forum at pwscf.org >Sent: Sun, December 19, 2010 9:51:23 AM >Subject: [Pw_forum] Request > >Dear All, > >I am doping Indium on graphene having 8 atom per unit cell. >When i am running scf, I am getting error as follows. >Can anyone tell me the reason how I can correct it ? > >Yours Sincerely > >Thaneshwor Kaloni >S N Bose kolkata >India > > > total energy = -84.77491243 Ry > Harris-Foulkes estimate = -84.77418035 Ry > estimated scf accuracy < 0.00256499 Ry > > total magnetization = 0.36 Bohr mag/cell > absolute magnetization = 0.38 Bohr mag/cell > > iteration # 7 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 8.27E-06, avg # of iterations = 3.5 > > negative rho (up, down): 0.441E-04 0.632E-04 > > total cpu time spent up to now is 129.30 secs > > total energy = -84.77550699 Ry > Harris-Foulkes estimate = -84.77522190 Ry > estimated scf accuracy < 0.00184899 Ry > > total magnetization = 0.30 Bohr mag/cell > absolute magnetization = 0.32 Bohr mag/cell > > iteration # 8 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 102 > diagonalization (ZHEGV*) failed > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > >-- >Thaneshwor P Kaloni > > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum From mahdi_fn109 at yahoo.com Sun Dec 19 20:11:57 2010 From: mahdi_fn109 at yahoo.com (مهدی) Date: Sun, 19 Dec 2010 11:11:57 -0800 (PST) Subject: [Pw_forum] Oxygen adsorption on graphene Message-ID: <607758.39373.qm@web43138.mail.sp1.yahoo.com> Dear all, how to define a unit cell for oxygen adsorbed on graphene in input file? Mahdi, Faqiehnasiri, MSC, Guilan, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101219/666e711e/attachment.htm From masoudnahali at gmail.com Mon Dec 20 10:44:05 2010 From: masoudnahali at gmail.com (Masoud Nahali) Date: Mon, 20 Dec 2010 13:14:05 +0330 Subject: [Pw_forum] Oxygen adsorption on graphene In-Reply-To: References: Message-ID: Dear Mahdi You need to define a vacuum (about 10 Angstrom) in the z-direction where the oxygen adsorbs. It means that you should select a large value for C (the lattice parameter in z-direction) in your slab model. Would you please modify the typo (*مهدی) *which was appeared as your name* *in the forum page. Many Thanks ** ** Best Wishes * Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * Mahdi Wrote : > > Dear all, > how to define a unit cell for oxygen adsorbed on graphene in input file? > Mahdi, Faqiehnasiri, MSC, Guilan, Iran > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101219/666e711e/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 42, Issue 32 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101220/c10e9e1c/attachment.htm From zhaohscas at yahoo.com.cn Mon Dec 20 14:07:50 2010 From: zhaohscas at yahoo.com.cn (=?gb2312?B?uuzJ+iDV1A==?=) Date: Mon, 20 Dec 2010 21:07:50 +0800 (CST) Subject: [Pw_forum] About the method to obtain the common tangent for determing the phase transition pressure. Message-ID: <32260.15043.qm@web15608.mail.cnb.yahoo.com> Dear all, For the first-order phase transitions, the following criteria should be met: Pressures of the two phases are equal, i.e., P_{eq} = - \frac{{d{E_1}}}{{d{V_1}}} = - \frac{{d{E_2}}}{{d{V_2}}} In other words, the P_{eq} is gradient of common tangent of the two phases E-V curves obtained from EOS fitting. This is a mathematical problem, but for the plot of this common tangent, can someone please give me some hints? What tools/softwares should I use for this purpose? Thanks in advance. Best regards. Hongsheng Zhao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101220/5c6aa29a/attachment.htm From baroni at sissa.it Mon Dec 20 15:52:13 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Dec 2010 15:52:13 +0100 Subject: [Pw_forum] About the method to obtain the common tangent for determing the phase transition pressure. In-Reply-To: <32260.15043.qm@web15608.mail.cnb.yahoo.com> References: <32260.15043.qm@web15608.mail.cnb.yahoo.com> Message-ID: On Dec 20, 2010, at 2:07 PM, ?? ? wrote: > Dear all, Dear Hongsheng, > > For the first-order phase transitions, the following criteria should be met: Pressures of the two phases are equal, i.e., > P_{eq} = - \frac{{d{E_1}}}{{d{V_1}}} = - \frac{{d{E_2}}}{{d{V_2}}} > > In other words, the P_{eq} is gradient of common tangent of the two phases E-V curves obtained from EOS fitting. > This is a mathematical problem, but for the plot of this common tangent, can someone please give me some hints? What tools/softwares should I use for this purpose? Thanks in advance. 1) plot the curves and find the tangent by hand 2) solve the equation E1(V1(p))+pV1(p)=E2(V2(p))+pV2(p), as a function of the pressure p. V12 is here the volume of the two phases as a function of the pressure. hope this helps Stefano PS: in the future, please do not forget to include your affiliation with your signature > > Best regards. > Hongsheng Zhao > > _______________________________________________ > 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/20101220/859343d9/attachment.htm From wumindt2 at zju.edu.cn Mon Dec 20 22:24:21 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 21 Dec 2010 05:24:21 +0800 Subject: [Pw_forum] wannier calculation Message-ID: Dear All, In the seedname.win file of wannier function calculation, the number of K points has to be equal to the product of n1*n2*n3, where n1, n2 and n3 are the component of the mp_grid= n1 n2 n3. However, in the nscf calculation, the number of Kpoints is always smaller than the product of n1*n2*n3. For instance, if the mp_grid = 4*4*4 in the nscf calculation, but we may have only 36 Kpoints. In this case, we can not move on to the wannier calculation. So, in order to do wannier calculation, how to get the number of Kpoints equals to the product of mp_grid n1*n2*n3 ? Thanks for any help. With regards, Min Wu 2010-12-20 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101221/a169cc42/attachment.htm From asubedi at gmail.com Tue Dec 21 00:45:19 2010 From: asubedi at gmail.com (Alaska Subedi) Date: Tue, 21 Dec 2010 00:45:19 +0100 Subject: [Pw_forum] set_irr sets incorrect npert when trans=.false. and elph=.true. Message-ID: Dear All, I would like to calculate lambda using different sets of dense k points for double delta integration. In order to do so I calculate dvscf using the following ph.in file: -- &inputph tr2_ph = 1.0d-16 prefix='Al-ep2', fildvscf='dvscf' amass(1) = 26.98 outdir = './tmp/' fildyn = 'Al-ep0.dyn2' / -0.250000000000000E+00 0.250000000000000E+00 -0.250000000000000E+00 I now want to use dvscf and dyn files generated from this run to calculate lambda. For this, I use the following input file: -- &inputph tr2_ph = 1.0d-16 prefix='Al-ep2', fildvscf='dvscf' amass(1) = 26.98 outdir = './tmp/' fildyn = 'Al-ep0.dyn2' elph=.true. trans=.false. / -0.250000000000000E+00 0.250000000000000E+00 -0.250000000000000E+00 However, the code crashes with the error: forrtl: severe (41): insufficient virtual memory After some debugging, I noticed that npertx is very large and the error happens when matrices of dimension npertx is being allocated in allocate_pert(). npertx is calculated as: DO irr = 1, nirr npertx = max (npertx, npert (irr) ) ENDDO The error occurs because npert has incorrect values assigned in the subroutine set_irr. This error does not occur when I calculate phonon and lambda in the same run (using trans=.true. and elph=.true.). Any pointer to fix this error would be greatly appreciated. Thanks, Alaska The scf file is:&control calculation='scf' restart_mode='from_scratch', tprnfor = .true. prefix='Al-ep2', pseudo_dir = './pseudo/', outdir='./tmp/' / &system ibrav= 2, celldm(1) =7.5, nat= 1, ntyp= 1, ecutwfc =45.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.05 / &electrons conv_thr = 1.0d-10 ! diagonalization = 'cg' ! mixing_mode = 'local-TF' mixing_beta = 0.3d0 / ATOMIC_SPECIES Al 26.98 Al.vbc.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 K_POINTS {automatic} 8 8 8 0 0 0 From spakinform at gmail.com Tue Dec 21 05:23:43 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Tue, 21 Dec 2010 13:23:43 +0900 Subject: [Pw_forum] wannier calculation In-Reply-To: References: Message-ID: Dear Wu, This problem is usually due to the shift of kpoints enforced by the symmetry of your unitcell. To avoid it, turn of symmetry in your calculations by adding nosym = .true. to your &system namelist. Good luck Soroush 2010/12/21 wumindt2 > Dear All, > > In the seedname.win file of wannier function calculation, the number of K > points has to > be equal to the product of n1*n2*n3, where n1, n2 and n3 are the component > of > the mp_grid= n1 n2 n3. > However, in the nscf calculation, the number of Kpoints is always smaller > than the product of n1*n2*n3. > For instance, if the mp_grid = 4*4*4 in the nscf calculation, but we may > have only 36 Kpoints. > In this case, we can not move on to the wannier calculation. > > So, in order to do wannier calculation, how to get the number of Kpoints > equals to the product of mp_grid n1*n2*n3 ? > > Thanks for any help. > > With regards, > Min Wu > 2010-12-20 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101221/50d6891a/attachment.htm From dalcorso at sissa.it Tue Dec 21 10:31:28 2010 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 21 Dec 2010 10:31:28 +0100 Subject: [Pw_forum] set_irr sets incorrect npert when trans=.false. and elph=.true. In-Reply-To: References: Message-ID: <1292923888.17626.1.camel@ulisse.cm.sissa.it> Please check the following: http://www.democritos.it/pipermail/pw_forum/2010-November/018732.html HTH, Andrea On Tue, 2010-12-21 at 00:45 +0100, Alaska Subedi wrote: > Dear All, > > I would like to calculate lambda using different sets of dense k > points for double delta integration. In order to do so I calculate > dvscf using the following ph.in file: > > -- > &inputph > tr2_ph = 1.0d-16 > prefix='Al-ep2', > fildvscf='dvscf' > amass(1) = 26.98 > outdir = './tmp/' > fildyn = 'Al-ep0.dyn2' > / > -0.250000000000000E+00 0.250000000000000E+00 -0.250000000000000E+00 > > I now want to use dvscf and dyn files generated from this run to > calculate lambda. For this, I use the following input file: > > -- > &inputph > tr2_ph = 1.0d-16 > prefix='Al-ep2', > fildvscf='dvscf' > amass(1) = 26.98 > outdir = './tmp/' > fildyn = 'Al-ep0.dyn2' > elph=.true. > trans=.false. > / > -0.250000000000000E+00 0.250000000000000E+00 -0.250000000000000E+00 > > > However, the code crashes with the error: > forrtl: severe (41): insufficient virtual memory > > After some debugging, I noticed that npertx is very large and the > error happens when matrices of dimension npertx is being allocated in > allocate_pert(). npertx is calculated as: > > DO irr = 1, nirr > npertx = max (npertx, npert (irr) ) > ENDDO > > The error occurs because npert has incorrect values assigned in the > subroutine set_irr. > > This error does not occur when I calculate phonon and lambda in the > same run (using trans=.true. and elph=.true.). > > Any pointer to fix this error would be greatly appreciated. > > Thanks, > Alaska > > The scf file is:&control > calculation='scf' > restart_mode='from_scratch', > tprnfor = .true. > prefix='Al-ep2', > pseudo_dir = './pseudo/', > outdir='./tmp/' > / > > &system > ibrav= 2, > celldm(1) =7.5, > nat= 1, ntyp= 1, > ecutwfc =45.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.05 > / > > &electrons > conv_thr = 1.0d-10 > ! diagonalization = 'cg' > ! mixing_mode = 'local-TF' > mixing_beta = 0.3d0 > / > > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > ATOMIC_POSITIONS > Al 0.00 0.00 0.00 > K_POINTS {automatic} > 8 8 8 0 0 0 > _______________________________________________ > 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 asubedi at gmail.com Tue Dec 21 15:25:16 2010 From: asubedi at gmail.com (Alaska Subedi) Date: Tue, 21 Dec 2010 15:25:16 +0100 Subject: [Pw_forum] set_irr sets incorrect npert when trans=.false. and elph=.true. In-Reply-To: <1292923888.17626.1.camel@ulisse.cm.sissa.it> References: <1292923888.17626.1.camel@ulisse.cm.sissa.it> Message-ID: On Tue, Dec 21, 2010 at 10:31 AM, Andrea Dal Corso wrote: > Please check the following: > > http://www.democritos.it/pipermail/pw_forum/2010-November/018732.html Thanks a lot! Alaska From neto.baldini at gmail.com Wed Dec 22 12:18:33 2010 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Wed, 22 Dec 2010 09:18:33 -0200 Subject: [Pw_forum] NEB Calculation with Ti and Graphene In-Reply-To: <728558.7250.qm@web65705.mail.ac4.yahoo.com> References: <728558.7250.qm@web65705.mail.ac4.yahoo.com> Message-ID: <70DAD684-7CAE-46B5-B41A-2D2A8A4574AB@gmail.com> Dear Eyvaz, Thanks for the answer. Although, I could not find the similar topic in the forum archives. Maybe I'm not searching well. The system relaxed very well. Reading the tutorial I thought it could be the pseudopotential but since the structure is fine I do not think so. Cheers, Ettore *************************************************************************** Dr. Ettore Baldini-Neto Researcher. Wernher von Braun Center for Advanced Research, Campinas, Brazil **************************************************************************** On Dec 17, 2010, at 8:50 PM, Eyvaz Isaev wrote: > Dear Ettore, > > > The best hints are > > 1) Searching the forum archive, as the same question was submitted just few > days ago. > 2) Read User's Guide, page 54 (for QE 4.2) > > Hope this will help you to find the answer to fix your problem. > > Bests, > Eyvaz. > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Ettore Baldini Neto > To: PWSCF Forum > Sent: Fri, December 17, 2010 11:15:58 PM > Subject: [Pw_forum] NEB Calculation with Ti and Graphene > > Dear users, > > I'm playing with a NEB calculation involving one Ti atom in a graphene > monolayer. > The calculation crashes due to diagonalization problems according to the message > below. > ******************************************* > task # 8 > from cdiaghg : error # 434 > diagonalization (ZHEGV*) failed > ******************************************** > > In what follows I copied my input file (without the atomic positions in order to > make it small for the readers) > Any hint? Am I doing something very wrong? > I'm not using for now polarization for Ti for now in order to make things > simpler. I'm planning to include it soon. > Also, I'm using a large ecut but I figured out that for graphene and for this > pseudo 35-40Ry might work fine. > > title = 'Graphene mono layer' > calculation = "neb" , > restart_mode = 'from_scratch' , > outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , > pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , > etot_conv_thr = 1.0E-3 , > forc_conv_thr = 1.0D-4 , > nstep=10, > prefix='1MLG_Ti_NEB', > / > &SYSTEM > ibrav = 0., > ntyp = 2 , > nat = 33 , > ecutwfc = 50.0 , > ecutrho = 400.0, > occupations = 'smearing' , > degauss = 0.02, > smearing = 'mv' , > / > &ELECTRONS > conv_thr = 1.0d-7 , > mixing_beta = 0.4 , > / > &IONS > num_of_images = 4, > opt_scheme = "broyden", > path_thr = 0.03D0, > / > ATOMIC_SPECIES > C 12.0107 C.pbe-van_ak.UPF > Ti 47.8670 Ti.pbe-sp-van_ak.UPF > CELL_PARAMETERS > 16.12131954 9.383047808 0.0000000 > 0.00000000 18.658162370 0.0000000 > 0.0000000 0.000000000 56.6893424 > ATOMIC_POSITIONS angstrom > first_image > ... > last image > ....... > K_POINTS {automatic} > 6.0 6.0 1.0 1.0 1.0 1.0 > > > Thanks a lot and best regards > > ************************************************************************ > Dr. Ettore Baldini-Neto, > Researcher at Wernher von Braun Center of Advanced Research > Campinas, Brazil > *********************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Wed Dec 22 12:34:29 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 03:34:29 -0800 (PST) Subject: [Pw_forum] NEB Calculation with Ti and Graphene In-Reply-To: <70DAD684-7CAE-46B5-B41A-2D2A8A4574AB@gmail.com> References: <728558.7250.qm@web65705.mail.ac4.yahoo.com> <70DAD684-7CAE-46B5-B41A-2D2A8A4574AB@gmail.com> Message-ID: <731625.97077.qm@web65715.mail.ac4.yahoo.com> Dear Ettore, Of course, I meant the error message, not NEB calculations for Ti and Graphene. > ******************************************* > from cdiaghg : error # 434 > diagonalization (ZHEGV*) failed > ******************************************** If you look at page 54 of User's Guide then you can find that this can be fixed using another diagonalization procedure ('cg' or "conjugated gradient" instead of davidson), but there might be another reason. Hope this helps. Bests, Eyvaz. ----- Original Message ---- From: Ettore Baldini Neto To: PWSCF Forum Sent: Wed, December 22, 2010 12:18:33 PM Subject: Re: [Pw_forum] NEB Calculation with Ti and Graphene Dear Eyvaz, Thanks for the answer. Although, I could not find the similar topic in the forum archives. Maybe I'm not searching well. The system relaxed very well. Reading the tutorial I thought it could be the pseudopotential but since the structure is fine I do not think so. Cheers, Ettore *************************************************************************** Dr. Ettore Baldini-Neto Researcher. Wernher von Braun Center for Advanced Research, Campinas, Brazil **************************************************************************** On Dec 17, 2010, at 8:50 PM, Eyvaz Isaev wrote: > Dear Ettore, > > > The best hints are > > 1) Searching the forum archive, as the same question was submitted just few > days ago. > 2) Read User's Guide, page 54 (for QE 4.2) > > Hope this will help you to find the answer to fix your problem. > > Bests, > Eyvaz. > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Ettore Baldini Neto > To: PWSCF Forum > Sent: Fri, December 17, 2010 11:15:58 PM > Subject: [Pw_forum] NEB Calculation with Ti and Graphene > > Dear users, > > I'm playing with a NEB calculation involving one Ti atom in a graphene > monolayer. > The calculation crashes due to diagonalization problems according to the >message > > below. > ******************************************* > task # 8 > from cdiaghg : error # 434 > diagonalization (ZHEGV*) failed > ******************************************** > > In what follows I copied my input file (without the atomic positions in order >to > > make it small for the readers) > Any hint? Am I doing something very wrong? > I'm not using for now polarization for Ti for now in order to make things > simpler. I'm planning to include it soon. > Also, I'm using a large ecut but I figured out that for graphene and for this > pseudo 35-40Ry might work fine. > > title = 'Graphene mono layer' > calculation = "neb" , > restart_mode = 'from_scratch' , > outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , > pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , > etot_conv_thr = 1.0E-3 , > forc_conv_thr = 1.0D-4 , > nstep=10, > prefix='1MLG_Ti_NEB', > / > &SYSTEM > ibrav = 0., > ntyp = 2 , > nat = 33 , > ecutwfc = 50.0 , > ecutrho = 400.0, > occupations = 'smearing' , > degauss = 0.02, > smearing = 'mv' , > / > &ELECTRONS > conv_thr = 1.0d-7 , > mixing_beta = 0.4 , > / > &IONS > num_of_images = 4, > opt_scheme = "broyden", > path_thr = 0.03D0, > / > ATOMIC_SPECIES > C 12.0107 C.pbe-van_ak.UPF > Ti 47.8670 Ti.pbe-sp-van_ak.UPF > CELL_PARAMETERS > 16.12131954 9.383047808 0.0000000 > 0.00000000 18.658162370 0.0000000 > 0.0000000 0.000000000 56.6893424 > ATOMIC_POSITIONS angstrom > first_image > ... > last image > ....... > K_POINTS {automatic} > 6.0 6.0 1.0 1.0 1.0 1.0 > > > Thanks a lot and best regards > > ************************************************************************ > Dr. Ettore Baldini-Neto, > Researcher at Wernher von Braun Center of Advanced Research > Campinas, Brazil > *********************************************************************** > > > _______________________________________________ > 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 neto.baldini at gmail.com Wed Dec 22 13:09:26 2010 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Wed, 22 Dec 2010 10:09:26 -0200 Subject: [Pw_forum] NEB Calculation with Ti and Graphene In-Reply-To: <731625.97077.qm@web65715.mail.ac4.yahoo.com> References: <728558.7250.qm@web65705.mail.ac4.yahoo.com> <70DAD684-7CAE-46B5-B41A-2D2A8A4574AB@gmail.com> <731625.97077.qm@web65715.mail.ac4.yahoo.com> Message-ID: Dear Evyaz, I understood that but since you mentioned another diagonalisation procedure I have a naive question (I'm sorry I'm not a native from solid state physics and all these codes are new to me). Before I used the atomic positions for my NEB calculation I performed a vc-relax calculation using the cg scheme and all went well. So the question is, by default the NEB option uses what scheme? Does it matter or could it be the error cause, I mean different diagonalisations schemes?To my experience it depends on the calculation. Sometimes a given algorithm is more suitable than others for a given problem. I read the NEB tutorials, saw some examples, but although they are good starting points, they do not mention these particular issues. Many thanks again. Regards Ettore On Dec 22, 2010, at 9:34 AM, Eyvaz Isaev wrote: > Dear Ettore, > > Of course, I meant the error message, not NEB calculations for Ti and Graphene. > > >> ******************************************* >> from cdiaghg : error # 434 >> diagonalization (ZHEGV*) failed >> ******************************************** > > > If you look at page 54 of User's Guide then you can find that this can be fixed > using another > > diagonalization procedure ('cg' or "conjugated gradient" instead of davidson), > but there might be another reason. > > Hope this helps. > > Bests, > Eyvaz. > > > > ----- Original Message ---- > From: Ettore Baldini Neto > To: PWSCF Forum > Sent: Wed, December 22, 2010 12:18:33 PM > Subject: Re: [Pw_forum] NEB Calculation with Ti and Graphene > > Dear Eyvaz, > > Thanks for the answer. Although, I could not find the similar topic in the forum > archives. Maybe I'm not searching well. > The system relaxed very well. Reading the tutorial I thought it could be the > pseudopotential but since the structure is fine I do not think so. > > Cheers, > > Ettore > > > *************************************************************************** > Dr. Ettore Baldini-Neto > Researcher. Wernher von Braun Center for Advanced Research, > Campinas, Brazil > **************************************************************************** > > > > On Dec 17, 2010, at 8:50 PM, Eyvaz Isaev wrote: > >> Dear Ettore, >> >> >> The best hints are >> >> 1) Searching the forum archive, as the same question was submitted just few >> days ago. >> 2) Read User's Guide, page 54 (for QE 4.2) >> >> Hope this will help you to find the answer to fix your problem. >> >> Bests, >> Eyvaz. >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Ettore Baldini Neto >> To: PWSCF Forum >> Sent: Fri, December 17, 2010 11:15:58 PM >> Subject: [Pw_forum] NEB Calculation with Ti and Graphene >> >> Dear users, >> >> I'm playing with a NEB calculation involving one Ti atom in a graphene >> monolayer. >> The calculation crashes due to diagonalization problems according to the >> message >> >> below. >> ******************************************* >> task # 8 >> from cdiaghg : error # 434 >> diagonalization (ZHEGV*) failed >> ******************************************** >> >> In what follows I copied my input file (without the atomic positions in order >> to >> >> make it small for the readers) >> Any hint? Am I doing something very wrong? >> I'm not using for now polarization for Ti for now in order to make things >> simpler. I'm planning to include it soon. >> Also, I'm using a large ecut but I figured out that for graphene and for this >> pseudo 35-40Ry might work fine. >> >> title = 'Graphene mono layer' >> calculation = "neb" , >> restart_mode = 'from_scratch' , >> outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , >> pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , >> etot_conv_thr = 1.0E-3 , >> forc_conv_thr = 1.0D-4 , >> nstep=10, >> prefix='1MLG_Ti_NEB', >> / >> &SYSTEM >> ibrav = 0., >> ntyp = 2 , >> nat = 33 , >> ecutwfc = 50.0 , >> ecutrho = 400.0, >> occupations = 'smearing' , >> degauss = 0.02, >> smearing = 'mv' , >> / >> &ELECTRONS >> conv_thr = 1.0d-7 , >> mixing_beta = 0.4 , >> / >> &IONS >> num_of_images = 4, >> opt_scheme = "broyden", >> path_thr = 0.03D0, >> / >> ATOMIC_SPECIES >> C 12.0107 C.pbe-van_ak.UPF >> Ti 47.8670 Ti.pbe-sp-van_ak.UPF >> CELL_PARAMETERS >> 16.12131954 9.383047808 0.0000000 >> 0.00000000 18.658162370 0.0000000 >> 0.0000000 0.000000000 56.6893424 >> ATOMIC_POSITIONS angstrom >> first_image >> ... >> last image >> ....... >> K_POINTS {automatic} >> 6.0 6.0 1.0 1.0 1.0 1.0 >> >> >> Thanks a lot and best regards >> >> ************************************************************************ >> Dr. Ettore Baldini-Neto, >> Researcher at Wernher von Braun Center of Advanced Research >> Campinas, Brazil >> *********************************************************************** >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mohnish.iitk at gmail.com Wed Dec 22 13:30:07 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 22 Dec 2010 18:00:07 +0530 Subject: [Pw_forum] calculation for system having number of different species greater than 10 Message-ID: Dear QE users, I want to do some calculations having number of different species greater than 10. I want to know is it possible to increase the dimension of QE for more than 10 different species. -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/5f7c1d83/attachment.htm From eyvaz_isaev at yahoo.com Wed Dec 22 13:36:59 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 04:36:59 -0800 (PST) Subject: [Pw_forum] calculation for system having number of different species greater than 10 In-Reply-To: References: Message-ID: <47448.35737.qm@web65712.mail.ac4.yahoo.com> Hi, Just go to /Modules/parameters.f90, and change ntypx=10 to that you want to. Then make clean and make pw (or whatever you want to re-compile). Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: mohnish pandey To: PWSCF Forum Sent: Wed, December 22, 2010 1:30:07 PM Subject: [Pw_forum] calculation for system having number of different species greater than 10 Dear QE users, I want to do some calculations having number of different species greater than 10. I want to know is it possible to increase the dimension of QE for more than 10 different species. -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/e1ceb522/attachment-0001.htm From mohnish.iitk at gmail.com Wed Dec 22 14:15:01 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 22 Dec 2010 18:45:01 +0530 Subject: [Pw_forum] calculation for system having number of different species greater than 10 In-Reply-To: <47448.35737.qm@web65712.mail.ac4.yahoo.com> References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> Message-ID: Thanks a lot Dr. Eyvaz. On Wed, Dec 22, 2010 at 6:06 PM, Eyvaz Isaev wrote: > Hi, > > Just go to /Modules/parameters.f90, and change ntypx=10 to that you want > to. > Then make clean and make pw (or whatever you want to re-compile). > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* mohnish pandey > *To:* PWSCF Forum > *Sent:* Wed, December 22, 2010 1:30:07 PM > *Subject:* [Pw_forum] calculation for system having number of different > species greater than 10 > > Dear QE users, > I want to do some calculations having number of > different species greater than 10. I want to know is it possible to increase > the dimension of QE for more than 10 different species. > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/8b00df99/attachment.htm From nazari at iasbs.ac.ir Wed Dec 22 14:31:41 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 22 Dec 2010 17:01:41 +0330 (IRST) Subject: [Pw_forum] topological analysis(critic) In-Reply-To: References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> Message-ID: <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir>
Dear All, Critic is a program for the topological analysis of electron density for solid state. How I can start to produce an interface with?QES. It has interface with win2k.? regards Fariba Nazari -- 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/20101222/4b529be7/attachment.htm From eyvaz_isaev at yahoo.com Wed Dec 22 14:41:55 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 05:41:55 -0800 (PST) Subject: [Pw_forum] NEB Calculation with Ti and Graphene In-Reply-To: References: <728558.7250.qm@web65705.mail.ac4.yahoo.com> <70DAD684-7CAE-46B5-B41A-2D2A8A4574AB@gmail.com> <731625.97077.qm@web65715.mail.ac4.yahoo.com> Message-ID: <411494.11767.qm@web65702.mail.ac4.yahoo.com> Dear Ettore, > From: Ettore Baldini Neto >I understood that but since you mentioned another diagonalisation procedure I >have a naive >question (I'm sorry I'm not a native from solid state physics and >all these codes are new to me). >Before I used the atomic positions for my NEB calculation I performed a vc-relax >calculation using >the cg scheme and all went well. So the question is, by >default the NEB option uses what >scheme? > I suppose, the diagonalization procedure is not related to the NEB or other structure optimization scheme, as always we have to solve an eigenvalue problem Hx=\lambda*x to find eigenvalues and eigenvectors. The default diagonalization procedure is "david", i.e. Davidson scheme. >Does it matter or could it be the error cause, I mean different diagonalisations >schemes? No. >To my experience it depends on the calculation. Sometimes a given algorithm is >more suitable >than others for a given problem. I read the NEB tutorials, saw >some examples, but although they >are good starting points, they do not mention >these particular issues. > Results should not depend on the diagonalization procedure used, though, sometime it might fail. But this depends on libraries used, numerical errors, etc. In fact, the error means that diagonalization of a matrix failed within specific machine precision (that depends on a computer). If you suppose "david" or "cg" gives you different results, please provide your script to test. Bests, Eyvaz. On Dec 22, 2010, at 9:34 AM, Eyvaz Isaev wrote: > Dear Ettore, > > Of course, I meant the error message, not NEB calculations for Ti and >Graphene. > > > >> ******************************************* >> from cdiaghg : error # 434 >> diagonalization (ZHEGV*) failed >> ******************************************** > > > If you look at page 54 of User's Guide then you can find that this can be fixed > > using another > > diagonalization procedure ('cg' or "conjugated gradient" instead of davidson), > but there might be another reason. > > Hope this helps. > > Bests, > Eyvaz. > > > > ----- Original Message ---- > From: Ettore Baldini Neto > To: PWSCF Forum > Sent: Wed, December 22, 2010 12:18:33 PM > Subject: Re: [Pw_forum] NEB Calculation with Ti and Graphene > > Dear Eyvaz, > > Thanks for the answer. Although, I could not find the similar topic in the >forum > > archives. Maybe I'm not searching well. > The system relaxed very well. Reading the tutorial I thought it could be the > pseudopotential but since the structure is fine I do not think so. > > Cheers, > > Ettore > > > *************************************************************************** > Dr. Ettore Baldini-Neto > Researcher. Wernher von Braun Center for Advanced Research, > Campinas, Brazil > **************************************************************************** > > > > On Dec 17, 2010, at 8:50 PM, Eyvaz Isaev wrote: > >> Dear Ettore, >> >> >> The best hints are >> >> 1) Searching the forum archive, as the same question was submitted just few >> days ago. >> 2) Read User's Guide, page 54 (for QE 4.2) >> >> Hope this will help you to find the answer to fix your problem. >> >> Bests, >> Eyvaz. >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Ettore Baldini Neto >> To: PWSCF Forum >> Sent: Fri, December 17, 2010 11:15:58 PM >> Subject: [Pw_forum] NEB Calculation with Ti and Graphene >> >> Dear users, >> >> I'm playing with a NEB calculation involving one Ti atom in a graphene >> monolayer. >> The calculation crashes due to diagonalization problems according to the >> message >> >> below. >> ******************************************* >> task # 8 >> from cdiaghg : error # 434 >> diagonalization (ZHEGV*) failed >> ******************************************** >> >> In what follows I copied my input file (without the atomic positions in order >> to >> >> make it small for the readers) >> Any hint? Am I doing something very wrong? >> I'm not using for now polarization for Ti for now in order to make things >> simpler. I'm planning to include it soon. >> Also, I'm using a large ecut but I figured out that for graphene and for this >> pseudo 35-40Ry might work fine. >> >> title = 'Graphene mono layer' >> calculation = "neb" , >> restart_mode = 'from_scratch' , >> outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , >> pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , >> etot_conv_thr = 1.0E-3 , >> forc_conv_thr = 1.0D-4 , >> nstep=10, >> prefix='1MLG_Ti_NEB', >> / >> &SYSTEM >> ibrav = 0., >> ntyp = 2 , >> nat = 33 , >> ecutwfc = 50.0 , >> ecutrho = 400.0, >> occupations = 'smearing' , >> degauss = 0.02, >> smearing = 'mv' , >> / >> &ELECTRONS >> conv_thr = 1.0d-7 , >> mixing_beta = 0.4 , >> / >> &IONS >> num_of_images = 4, >> opt_scheme = "broyden", >> path_thr = 0.03D0, >> / >> ATOMIC_SPECIES >> C 12.0107 C.pbe-van_ak.UPF >> Ti 47.8670 Ti.pbe-sp-van_ak.UPF >> CELL_PARAMETERS >> 16.12131954 9.383047808 0.0000000 >> 0.00000000 18.658162370 0.0000000 >> 0.0000000 0.000000000 56.6893424 >> ATOMIC_POSITIONS angstrom >> first_image >> ... >> last image >> ....... >> K_POINTS {automatic} >> 6.0 6.0 1.0 1.0 1.0 1.0 >> >> >> Thanks a lot and best regards >> >> ************************************************************************ >> Dr. Ettore Baldini-Neto, >> Researcher at Wernher von Braun Center of Advanced Research >> Campinas, Brazil >> *********************************************************************** >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Wed Dec 22 14:47:58 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 05:47:58 -0800 (PST) Subject: [Pw_forum] topological analysis(critic) In-Reply-To: <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir> References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir> Message-ID: <258181.73116.qm@web65712.mail.ac4.yahoo.com> Dear Nazari, > How I can start to produce an interface with QES It is quite simple and standard. First, understand how it works for WIEN2k, then implement it for QE. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: "nazari at iasbs.ac.ir" To: PWSCF Forum Sent: Wed, December 22, 2010 2:31:41 PM Subject: [Pw_forum] topological analysis(critic) Dear All,Critic is a program for the topological analysis of electron density for solid state. How I can start to produce an interface with QES. It has interface with win2k. regards Fariba Nazari -- 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/20101222/36ec1d72/attachment.htm From nazari at iasbs.ac.ir Wed Dec 22 15:47:16 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 22 Dec 2010 18:17:16 +0330 (IRST) Subject: [Pw_forum] topological analysis(critic) In-Reply-To: <258181.73116.qm@web65712.mail.ac4.yahoo.com> References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir> <258181.73116.qm@web65712.mail.ac4.yahoo.com> Message-ID: <24518.85.185.211.90.1293029236.squirrel@mail.iasbs.ac.ir>
Dear Eyvaz, ?I know the ciritic needs 2 files . one for charge density and the othe for structure and has the following format. But I am not famileir with wien2k. How I can produce the following file in pwscf. Some of the are clear but I don 't know for exaple: MODE OF CALC=RELA and symmetry in pwscf. runwien.awk lapw calculation, v.1.0.5 F?? LATTICE,NONEQUIV.ATOMS:? 1 225 Fm-3m MODE OF CALC=RELA ? 6.787710? 6.787710? 6.787710 90.000000 90.000000 90.000000 ATOM?? 1: X=0.00000000 Y=0.00000000 Z=0.00000000 ????????? MULT= 1????????? ISPLIT= 2 Fe1??????? NPT=? 781? R0=0.00010000 RMT=?? 2.39000?? Z:26.00 LOCAL ROT MATRIX:??? 1.0000000 0.0000000 0.0000000 ???????????????????? 0.0000000 1.0000000 0.0000000 ???????????????????? 0.0000000 0.0000000 1.0000000 ? 48????? NUMBER OF SYMMETRY OPERATIONS ?1 0 0 0.00000000 ?0 1 0 0.00000000 ?0 0 1 0.00000000 ?????? 1 -1 0 0 0.00000000 ?0-1 0 0.00000000 ?0 0 1 0.00000000 ?????? 2 -1 0 0 0.00000000 ?0 1 0 0.00000000 ?0 0-1 0.00000000 ?????? 3 ?1 0 0 0.00000000 ?0-1 0 0.00000000 ?0 0-1 0.00000000 ?????? 4 ?0 0 1 0.00000000 ?1 0 0 0.00000000 ?0 1 0 0.00000000 ?????? 5 ?0 0 1 0.00000000 -1 0 0 0.00000000 ?0-1 0 0.00000000 ?????? 6 ?0 0-1 0.00000000 -1 0 0 0.00000000 ?0 1 0 0.00000000 ?????? 7 ?0 0-1 0.00000000 ?1 0 0 0.00000000 ?0-1 0 0.00000000 ?????? 48 regards Fariba nazari > Dear Nazari, > >> How I can start to produce an interface with QES > > It is quite simple and standard. > First, understand how it works for WIEN2k, then implement it for QE. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ > From: "nazari at iasbs.ac.ir" > To: PWSCF Forum > Sent: Wed, December 22, 2010 2:31:41 PM > Subject: [Pw_forum] topological analysis(critic) > > > Dear All,Critic is a program for the topological analysis of electron > density > for solid state. How I can start to produce an interface with QES. It has > interface with win2k. > regards > Fariba Nazari > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20101222/0c2a5a92/attachment-0001.htm From eyvaz_isaev at yahoo.com Wed Dec 22 16:13:24 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 07:13:24 -0800 (PST) Subject: [Pw_forum] topological analysis(critic) In-Reply-To: <24518.85.185.211.90.1293029236.squirrel@mail.iasbs.ac.ir> References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir> <258181.73116.qm@web65712.mail.ac4.yahoo.com> <24518.85.185.211.90.1293029236.squirrel@mail.iasbs.ac.ir> Message-ID: <896845.66753.qm@web65702.mail.ac4.yahoo.com> Hi agian, Well, can you please give me a link for Critic? Then we can discuss it separately, until we manage it working for QE. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: "nazari at iasbs.ac.ir" To: PWSCF Forum Sent: Wed, December 22, 2010 3:47:16 PM Subject: Re: [Pw_forum] topological analysis(critic) Dear Eyvaz, I know the ciritic needs 2 files . one for charge density and the othe for structure and has the following format. But I am not famileir with wien2k. How I can produce the following file in pwscf. Some of the are clear but I don 't know for exaple: MODE OF CALC=RELA and symmetry in pwscf. runwien.awk lapw calculation, v.1.0.5 F LATTICE,NONEQUIV.ATOMS: 1 225 Fm-3m MODE OF CALC=RELA 6.787710 6.787710 6.787710 90.000000 90.000000 90.000000 ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000 MULT= 1 ISPLIT= 2 Fe1 NPT= 781 R0=0.00010000 RMT= 2.39000 Z:26.00 LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 48 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0.00000000 0 1 0 0.00000000 0 0 1 0.00000000 1 -1 0 0 0.00000000 0-1 0 0.00000000 0 0 1 0.00000000 2 -1 0 0 0.00000000 0 1 0 0.00000000 0 0-1 0.00000000 3 1 0 0 0.00000000 0-1 0 0.00000000 0 0-1 0.00000000 4 0 0 1 0.00000000 1 0 0 0.00000000 0 1 0 0.00000000 5 0 0 1 0.00000000 -1 0 0 0.00000000 0-1 0 0.00000000 6 0 0-1 0.00000000 -1 0 0 0.00000000 0 1 0 0.00000000 7 0 0-1 0.00000000 1 0 0 0.00000000 0-1 0 0.00000000 48 regards Fariba nazari > Dear Nazari, > >> How I can start to produce an interface with QES > > It is quite simple and standard. > First, understand how it works for WIEN2k, then implement it for QE. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ > From: "nazari at iasbs.ac.ir" > To: PWSCF Forum > Sent: Wed, December 22, 2010 2:31:41 PM > Subject: [Pw_forum] topological analysis(critic) > > > Dear All,Critic is a program for the topological analysis of electron > density > for solid state. How I can start to produce an interface with QES. It has > interface with win2k. > regards > Fariba Nazari > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20101222/78473e86/attachment.htm From elcortogm at googlemail.com Wed Dec 22 17:08:09 2010 From: elcortogm at googlemail.com (Steve Schmerler) Date: Wed, 22 Dec 2010 17:08:09 +0100 Subject: [Pw_forum] cluster*.in tests fail with PAW and ifort -xHost Message-ID: <20101222160809.GE25842@cartman.physik.tu-freiberg.de> Hello I'm compiling QE 4.2.1 (pw.x) with ifort 11.1.046 MKL 10.2.1.017 fftw 3.2.2 on Xeon E5530 CPUs. I found that the 4 tests espresso-4.2.1/tests/cluster*.in [1] segfault with "ifort -O3 -xHost", but only when using PAW datasets. Using normal pseudos works, as does using less optimization (no -xHost). I recompiled the files, which I thought might have been miscompiled, with less optimization PW/martyna_tuckerman.f90 PW/makov_payne.f90 PW/paw_onecenter.f90 PW/paw_init.f90 Modules/paw_variables.f90 but to no avail. Which other files should I recompile? Thanks. best, Steve [1] http://qe-forge.org/frs/download.php/115/espresso-4.2.1-examples.tar.gz -- Steve Schmerler Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany From eyvaz_isaev at yahoo.com Wed Dec 22 17:44:34 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 22 Dec 2010 08:44:34 -0800 (PST) Subject: [Pw_forum] topological analysis(critic) In-Reply-To: <896845.66753.qm@web65702.mail.ac4.yahoo.com> References: <47448.35737.qm@web65712.mail.ac4.yahoo.com> <20765.85.185.211.90.1293024701.squirrel@mail.iasbs.ac.ir> <258181.73116.qm@web65712.mail.ac4.yahoo.com> <24518.85.185.211.90.1293029236.squirrel@mail.iasbs.ac.ir> <896845.66753.qm@web65702.mail.ac4.yahoo.com> Message-ID: <871668.80636.qm@web65706.mail.ac4.yahoo.com> Well, I have found it. According to User's Guide: >>Right now, only the atomic volumes and atomic charges are calculated in all >>versions This is a tool to calculate and visualize atomic charges like the Bader analysis that requires the knowledge of all - electron charge density (or details of wave-function inside cutoff radii for PAW, not US, potentials). It seems, there is an option in PP (plot_num= 17) to deal with such kind a problem. You can try this one (in conjunction with XCrysDen to visualize, hopefully output file supports XCrysDen). So, in fact, I do not see a strong argument to be worried about this code. Bests, Eyvaz. ________________________________ From: Eyvaz Isaev To: PWSCF Forum Sent: Wed, December 22, 2010 4:13:24 PM Subject: Re: [Pw_forum] topological analysis(critic) Hi agian, Well, can you please give me a link for Critic? Then we can discuss it separately, until we manage it working for QE. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: "nazari at iasbs.ac.ir" To: PWSCF Forum Sent: Wed, December 22, 2010 3:47:16 PM Subject: Re: [Pw_forum] topological analysis(critic) Dear Eyvaz, I know the ciritic needs 2 files . one for charge density and the othe for structure and has the following format. But I am not famileir with wien2k. How I can produce the following file in pwscf. Some of the are clear but I don 't know for exaple: MODE OF CALC=RELA and symmetry in pwscf. runwien.awk lapw calculation, v.1.0.5 F LATTICE,NONEQUIV.ATOMS: 1 225 Fm-3m MODE OF CALC=RELA 6.787710 6.787710 6.787710 90.000000 90.000000 90.000000 ATOM 1: X=0.00000000 Y=0.00000000 Z=0.00000000 MULT= 1 ISPLIT= 2 Fe1 NPT= 781 R0=0.00010000 RMT= 2.39000 Z:26.00 LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 48 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0.00000000 0 1 0 0.00000000 0 0 1 0.00000000 1 -1 0 0 0.00000000 0-1 0 0.00000000 0 0 1 0.00000000 2 -1 0 0 0.00000000 0 1 0 0.00000000 0 0-1 0.00000000 3 1 0 0 0.00000000 0-1 0 0.00000000 0 0-1 0.00000000 4 0 0 1 0.00000000 1 0 0 0.00000000 0 1 0 0.00000000 5 0 0 1 0.00000000 -1 0 0 0.00000000 0-1 0 0.00000000 6 0 0-1 0.00000000 -1 0 0 0.00000000 0 1 0 0.00000000 7 0 0-1 0.00000000 1 0 0 0.00000000 0-1 0 0.00000000 48 regards Fariba nazari > Dear Nazari, > >> How I can start to produce an interface with QES > > It is quite simple and standard. > First, understand how it works for WIEN2k, then implement it for QE. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ > From: "nazari at iasbs.ac.ir" > To: PWSCF Forum > Sent: Wed, December 22, 2010 2:31:41 PM > Subject: [Pw_forum] topological analysis(critic) > > > Dear All,Critic is a program for the topological analysis of electron > density > for solid state. How I can start to produce an interface with QES. It has > interface with win2k. > regards > Fariba Nazari > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20101222/894dcffc/attachment.htm From ranjit.phy at gmail.com Wed Dec 22 19:11:00 2010 From: ranjit.phy at gmail.com (Ranjit Thapa) Date: Wed, 22 Dec 2010 23:41:00 +0530 Subject: [Pw_forum] installation problem Message-ID: Dear all I want to install the Graphical interface i.e pwgui in my computer ( Intel(R) Pentium(R) Dual CPU E2140 @ 1.60GHz, OS= CENTOS-5.0,)but i am unable to do that. I download the .tar.gz file and extract it in the folder espresso-4.2. than type ./pwgui it shows. [root at ranjit PWgui-4.2]# ./pwgui ================================================== This is PWgui version: 4.2 -------------------------------------------------- PWgui: using the system default "tclsh" interpreter PWGUI : /home/espresso-4.2/PWgui-4.2 GUIB engine : /home/espresso-4.2/PWgui-4.2/lib/Guib-0.5 can't find package Itk while executing "package require Itk " (file "/home/espresso-4.2/PWgui-4.2/lib/Guib-0.5/init.tcl" line 11) invoked from within "source /home/espresso-4.2/PWgui-4.2/lib/Guib-0.5/init.tcl" ("package ifneeded" script) invoked from within "package require Guib 0.5" (file "/home/espresso-4.2/PWgui-4.2/init.tcl" line 5) invoked from within "source [file join $env(PWGUI) init.tcl]" (file "/home/espresso-4.2/PWgui-4.2/pwgui.tcl" line 62) Please tell me what to do for solving the problem Thanks in advance -- Ranjit Thapa Research Associate Materials Simulation Lab. Department of Materials Science Indian Association for the Cultivation of Science KOL-700032 Mobile No: +91 9593936060, +91 9804101030 http://sites.google.com/site/ranjitphy/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/38baf5a4/attachment-0001.htm From mirnezhad.mm at gmail.com Wed Dec 22 20:08:32 2010 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Wed, 22 Dec 2010 11:08:32 -0800 Subject: [Pw_forum] mechanical properties Message-ID: Dear all, in Quantum ESPRESSO How can we calculate Elastic bending modulus of graphene ? mahdi,guilan,iran From metokal at gmail.com Wed Dec 22 21:06:25 2010 From: metokal at gmail.com (Mehmet Topsakal) Date: Wed, 22 Dec 2010 22:06:25 +0200 Subject: [Pw_forum] mechanical properties In-Reply-To: References: Message-ID: Dear Mahdi, I think this is the best paper on the elastic properties of graphene http://prb.aps.org/abstract/PRB/v71/i20/e205214 You can also examine this: http://apl.aip.org/resource/1/applab/v96/i9/p091912_s1 On Wed, Dec 22, 2010 at 9:08 PM, Mahdi Mirnezhad wrote: > Dear all, > in Quantum ESPRESSO ?How can we calculate Elastic bending modulus of graphene ? > mahdi,guilan,iran > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Mehmet Topsakal? (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/T?rkiye Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 From giannozz at democritos.it Wed Dec 22 21:16:05 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Dec 2010 21:16:05 +0100 Subject: [Pw_forum] installation problem In-Reply-To: References: Message-ID: <60722D52-800E-40E6-AD0A-D09AC50A1AE1@democritos.it> On Dec 22, 2010, at 19:11 , Ranjit Thapa wrote: > can't find package Itk pwgui uses a version of Tcl/Tk called "IncrTcl" or something like this. On some Linux distributions it is not installed by default. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Dec 22 23:04:46 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Dec 2010 23:04:46 +0100 Subject: [Pw_forum] Band structure of non-metallic antiferromagnet In-Reply-To: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> References: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> Message-ID: <1D209BB4-9BDE-4581-954F-8634A9464CE0@democritos.it> On Dec 17, 2010, at 15:06 , Silvia Bahmann wrote: > In v. 4.2.1 of QE one has to define antiferromagnetism in > an insulator like this: > > starting_magnetization(1) = 1, > starting_magnetization(2) = -1, > tot_magnetization = 0 actually the input documentation says If you fix the magnetization with "tot_magnetization", you should not specify starting_magnetization. Setting starting_magnetization should be sufficient to produce an AFM state (if the systems wants to go there) > Is there another way to define the antiferromagnetism since nelup and > neldw are not available anymore? tot_magnetization does exactly the same as nelup, neldw. Too many ways to specify the same thing are a source of confusion. > And why is the bands code not working? maybe it is just an overzealous check (always preferrable to insufficient checks allowing to produce meaningless results). You may try to locate the error message and to disable it if you think that there is no good reason P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ranjit.phy at gmail.com Thu Dec 23 12:47:04 2010 From: ranjit.phy at gmail.com (Ranjit Thapa) Date: Thu, 23 Dec 2010 17:17:04 +0530 Subject: [Pw_forum] not running in node Message-ID: dear all, i have installed MPICH2-1.3.1. The program in example of mpich2-1.3.1 run successfully in master and node parrallely. But the program in examples of espresso-4.2 only run in master. What is the problem? Please help me Thanks in advance -- Ranjit Thapa Research Associate Materials Simulation Lab. Department of Materials Science Indian Association for the Cultivation of Science KOL-700032 Mobile No: +91 9593936060, +91 9804101030 http://sites.google.com/site/ranjitphy/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101223/2f1f0275/attachment.htm From giannozz at democritos.it Thu Dec 23 14:39:04 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Dec 2010 14:39:04 +0100 Subject: [Pw_forum] not running in node In-Reply-To: References: Message-ID: <5DB8F76F-5D76-4EE2-BBDC-10C3DE57A739@democritos.it> On Dec 23, 2010, at 12:47 , Ranjit Thapa wrote: > What is the problem? most likely the problem is in your software configuration. Look at what the final message of "configure" looks like. If it says "parallel environment non detected", consult the documentation in the user guide P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lfhuang at theory.issp.ac.cn Thu Dec 23 11:36:25 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 23 Dec 2010 18:36:25 +0800 Subject: [Pw_forum] =?utf-8?q?mechanical_properties?= Message-ID: <20101223103625.16926.qmail@ms.hfcas.ac.cn> Dear M. Mirnezhad: This is a quite interesting topic, which I have considered before. To calculate the bending modulus of graphene, certain approach is needed to bend the carbon plane. Probably, supercells should be needed in simulation. You can refer to one example below to see how the authors (my collegues and supervisor) made the carbon plane bended (folded): http://apl.aip.org/resource/1/applab/v97/i15/p153129_s1 May this can be helpful to you. Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101223/37aa01b6/attachment.htm From zucco at dipteris.unige.it Thu Dec 23 15:49:36 2010 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Thu, 23 Dec 2010 15:49:36 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 Message-ID: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> Hello to all, I would like to propose to your attention an apparent inconsistency in the matrix of the CELL_PARAMETERS section that I noticed during a relaxation of a crystal with trigonal symmetry (ibrav=5, in attach). These inconsistency arise writing few lines in output_tau.f90 to enable the code to print the crystal parameters celldm() for each optimization step. This is the output of these few lines of code with a simple explanation ... New celldm() values 1) celldm(1) = 10.118244326 5.354344288 # new cell edge in bohr and angstrom 2) celldm(4) = 0.647279099 # cos(alpha) solved respect to c in tx 3) |tx| = 0.419952914 0.419952914 # value of tx as reported in INPUT.PW and in the code compared with the element of the matrix at(1,1) 4) |ty| = 0.242459928 0.242459928 # value of tx as reported in INPUT.PW and in the code compared with the element of the matrix at(2,1) 5) |tz| = 0.874558593 >0.911266395< # value of tx as reported in INPUT.PW and in the code compared with the element of the matrix at(3,1) 6) c_tx = 0.647279099 # cos(alpha) solved respect to c in tx - redundant with 2) 7) c_ty = 0.647279099 # cos(alpha) solved respect to c in ty 8) c_tz = >0.745609664< # cos(alpha) solved respect to c in tz ... Points 5) and 8) seem to be not consistent as expected at least by me :) Please, can someone explain where probably I'm going wrong? Many thanks to all m. -------------- next part -------------- A non-text attachment was scrubbed... Name: calcite.in Type: application/octet-stream Size: 1584 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101223/a6955407/attachment.obj -------------- next part -------------- ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From degironc at sissa.it Thu Dec 23 16:23:05 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Dec 2010 16:23:05 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> Message-ID: <4D136959.1020107@sissa.it> sorry but I fail to understand what you are printing ... what is your definition for c, tx,ty,tz ... ? stefano Marino Vetuschi Zuccolini wrote: > Hello to all, > > I would like to propose to your attention an apparent inconsistency in the matrix of the CELL_PARAMETERS section that I noticed during a relaxation of a crystal with trigonal symmetry (ibrav=5, in attach). > These inconsistency arise writing few lines in output_tau.f90 to enable the code to print the crystal parameters celldm() for each optimization step. > > This is the output of these few lines of code with a simple explanation > > ... > New celldm() values > > 1) celldm(1) = 10.118244326 5.354344288 # new cell edge in bohr and angstrom > 2) celldm(4) = 0.647279099 # cos(alpha) solved respect to c in tx > 3) |tx| = 0.419952914 0.419952914 # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(1,1) > 4) |ty| = 0.242459928 0.242459928 # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(2,1) > 5) |tz| = 0.874558593 >0.911266395< # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(3,1) > 6) c_tx = 0.647279099 # cos(alpha) solved respect to c in tx - redundant with 2) > 7) c_ty = 0.647279099 # cos(alpha) solved respect to c in ty > 8) c_tz = >0.745609664< # cos(alpha) solved respect to c in tz > ... > > Points 5) and 8) seem to be not consistent as expected at least by me :) > > Please, can someone explain where probably I'm going wrong? > > Many thanks to all > > m. > > > ------------------------------------------------------------------------ > > > > ******************************************************* > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > Researcher / Geochemist > Laboratory of Geochemistry > > DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Dec 23 16:28:38 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Dec 2010 16:28:38 +0100 Subject: [Pw_forum] Band structure of non-metallic antiferromagnet In-Reply-To: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> References: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> Message-ID: <69E22B61-FBC4-43A1-A2EA-1BC8A87F1AC4@democritos.it> On Dec 17, 2010, at 15:06 , Silvia Bahmann wrote: > starting_magnetization(1) = 1, > starting_magnetization(2) = -1, > tot_magnetization = 0 > > This is considered as constrained magnetization which is not allowed > to use with the bands code. the bands code should simply ignore these variables because they are never used in band structure calculations. If it complains, just remove those variables from the input of the band structure calculation P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From seoman at yandex.ru Thu Dec 23 16:33:55 2010 From: seoman at yandex.ru (Oleg Sergeev) Date: Thu, 23 Dec 2010 18:33:55 +0300 Subject: [Pw_forum] not running in node In-Reply-To: References: Message-ID: <920581293118435@web131.yandex.ru> dear Ranjit, maybe you should check your PARA_PREFIX and PARA_POSTFIX in environment_variables. By default, they are configured to run examples on a single node. best, Oleg Sergeev, Moscow Institute of Physics and Technology. 23.12.2010, 14:47, "Ranjit Thapa" : > dear all, > > i have installed MPICH2-1.3.1. The program in example of mpich2-1.3.1 run successfully in master and node parrallely. > But the program in examples of espresso-4.2 only run in master. > What is the problem? From degironc at sissa.it Thu Dec 23 16:44:06 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Dec 2010 16:44:06 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> Message-ID: <4D136E46.6000707@sissa.it> dear Marino Vetuschi Zuccolini, the input you give in attachment does not correspond to the situation you are describing below... can you post a consistent set of input and output ? stefano Marino Vetuschi Zuccolini wrote: > Hello to all, > > I would like to propose to your attention an apparent inconsistency in the matrix of the CELL_PARAMETERS section that I noticed during a relaxation of a crystal with trigonal symmetry (ibrav=5, in attach). > These inconsistency arise writing few lines in output_tau.f90 to enable the code to print the crystal parameters celldm() for each optimization step. > > This is the output of these few lines of code with a simple explanation > > ... > New celldm() values > > 1) celldm(1) = 10.118244326 5.354344288 # new cell edge in bohr and angstrom > 2) celldm(4) = 0.647279099 # cos(alpha) solved respect to c in tx > 3) |tx| = 0.419952914 0.419952914 # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(1,1) > 4) |ty| = 0.242459928 0.242459928 # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(2,1) > 5) |tz| = 0.874558593 >0.911266395< # value of tx as reported in INPUT.PW and in the code > compared with the element of the matrix at(3,1) > 6) c_tx = 0.647279099 # cos(alpha) solved respect to c in tx - redundant with 2) > 7) c_ty = 0.647279099 # cos(alpha) solved respect to c in ty > 8) c_tz = >0.745609664< # cos(alpha) solved respect to c in tz > ... > > Points 5) and 8) seem to be not consistent as expected at least by me :) > > Please, can someone explain where probably I'm going wrong? > > Many thanks to all > > m. > > > ------------------------------------------------------------------------ > > > > ******************************************************* > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > Researcher / Geochemist > Laboratory of Geochemistry > > DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zucco at dipteris.unige.it Thu Dec 23 16:46:52 2010 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Thu, 23 Dec 2010 16:46:52 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <4D136959.1020107@sissa.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> <4D136959.1020107@sissa.it> Message-ID: Stefano, On 23 Dec 2010, at 16:23, Stefano de Gironcoli wrote: > sorry but I fail to understand what you are printing ... what is your > definition for c, tx,ty,tz ... ? > stefano > right...the definition of c, tx, ty, tz are those of PW documentation trigonal(r) =================== for these groups, the z-axis is chosen as the 3-fold axis, but the crystallographic vectors form a three-fold star around the z-axis, and the primitive cell is a simple rhombohedron. The crystallographic vectors are: v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). where c=cos(alpha) is the cosine of the angle alpha between any pair of crystallographic vectors, tc, ty, tz are defined as tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3) and here you can find the file I modified -------------- next part -------------- A non-text attachment was scrubbed... Name: output_tau.f90 Type: application/octet-stream Size: 7287 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101223/c311f2b2/attachment-0001.obj -------------- next part -------------- m. > Marino Vetuschi Zuccolini wrote: >> Hello to all, >> >> I would like to propose to your attention an apparent inconsistency in the matrix of the CELL_PARAMETERS section that I noticed during a relaxation of a crystal with trigonal symmetry (ibrav=5, in attach). >> These inconsistency arise writing few lines in output_tau.f90 to enable the code to print the crystal parameters celldm() for each optimization step. >> >> This is the output of these few lines of code with a simple explanation >> >> ... >> New celldm() values >> >> 1) celldm(1) = 10.118244326 5.354344288 # new cell edge in bohr and angstrom >> 2) celldm(4) = 0.647279099 # cos(alpha) solved respect to c in tx >> 3) |tx| = 0.419952914 0.419952914 # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(1,1) >> 4) |ty| = 0.242459928 0.242459928 # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(2,1) >> 5) |tz| = 0.874558593 >0.911266395< # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(3,1) >> 6) c_tx = 0.647279099 # cos(alpha) solved respect to c in tx - redundant with 2) >> 7) c_ty = 0.647279099 # cos(alpha) solved respect to c in ty >> 8) c_tz = >0.745609664< # cos(alpha) solved respect to c in tz >> ... >> >> Points 5) and 8) seem to be not consistent as expected at least by me :) >> >> Please, can someone explain where probably I'm going wrong? >> >> Many thanks to all >> >> m. >> >> >> ------------------------------------------------------------------------ >> >> >> >> ******************************************************* >> Marino Vetuschi Zuccolini >> zucco at dipteris.unige.it >> Researcher / Geochemist >> Laboratory of Geochemistry >> >> DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova >> Tel. ++39 010 3538136 Fax. ++39 010 352169 >> Corso Europa 26, 16132 - Genova - Italy >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From zucco at dipteris.unige.it Thu Dec 23 17:00:01 2010 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Thu, 23 Dec 2010 17:00:01 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <4D136E46.6000707@sissa.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> <4D136E46.6000707@sissa.it> Message-ID: <43CEBCC6-CFFA-470E-AAB2-48228BF4BEC2@dipteris.unige.it> stefano On 23 Dec 2010, at 16:44, Stefano de Gironcoli wrote: > dear Marino Vetuschi Zuccolini, > the input you give in attachment does not correspond to the situation > you are describing below... > can you post a consistent set of input and output ? > stefano > -------------- next part -------------- A non-text attachment was scrubbed... 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Name: i_R_5 Type: application/octet-stream Size: 1580 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101223/c38bdcbb/attachment-0003.obj -------------- next part -------------- input > Marino Vetuschi Zuccolini wrote: >> Hello to all, >> >> I would like to propose to your attention an apparent inconsistency in the matrix of the CELL_PARAMETERS section that I noticed during a relaxation of a crystal with trigonal symmetry (ibrav=5, in attach). >> These inconsistency arise writing few lines in output_tau.f90 to enable the code to print the crystal parameters celldm() for each optimization step. >> >> This is the output of these few lines of code with a simple explanation >> >> ... >> New celldm() values >> >> 1) celldm(1) = 10.118244326 5.354344288 # new cell edge in bohr and angstrom >> 2) celldm(4) = 0.647279099 # cos(alpha) solved respect to c in tx >> 3) |tx| = 0.419952914 0.419952914 # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(1,1) >> 4) |ty| = 0.242459928 0.242459928 # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(2,1) >> 5) |tz| = 0.874558593 >0.911266395< # value of tx as reported in INPUT.PW and in the code >> compared with the element of the matrix at(3,1) >> 6) c_tx = 0.647279099 # cos(alpha) solved respect to c in tx - redundant with 2) >> 7) c_ty = 0.647279099 # cos(alpha) solved respect to c in ty >> 8) c_tz = >0.745609664< # cos(alpha) solved respect to c in tz >> ... >> >> Points 5) and 8) seem to be not consistent as expected at least by me :) >> >> Please, can someone explain where probably I'm going wrong? >> >> Many thanks to all >> >> m. >> >> >> ------------------------------------------------------------------------ >> >> >> >> ******************************************************* >> Marino Vetuschi Zuccolini >> zucco at dipteris.unige.it >> Researcher / Geochemist >> Laboratory of Geochemistry >> >> DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova >> Tel. ++39 010 3538136 Fax. ++39 010 352169 >> Corso Europa 26, 16132 - Genova - Italy >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From degironc at sissa.it Thu Dec 23 17:28:15 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Dec 2010 17:28:15 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> <4D136959.1020107@sissa.it> Message-ID: <4D13789F.5030701@sissa.it> Dear Marino Vetuschi Zuccolini wrote: > trigonal(r) > =================== > for these groups, the z-axis is chosen as the 3-fold axis, but the > crystallographic vectors form a three-fold star around the z-axis, > and the primitive cell is a simple rhombohedron. The crystallographic > vectors are: > v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). > where c=cos(alpha) is the cosine of the angle alpha between any pair > of crystallographic vectors, tc, ty, tz are defined as > tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3) > in order to extract c you are forgetting to divide v1 by a=|v1|. stefano From zucco at dipteris.unige.it Thu Dec 23 19:43:13 2010 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Thu, 23 Dec 2010 19:43:13 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <4D13789F.5030701@sissa.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> <4D136959.1020107@sissa.it> <4D13789F.5030701@sissa.it> Message-ID: <83A6AC03-DAFB-4679-8818-3711AA2D2C4F@dipteris.unige.it> stefano, thanks but can you explain a little bit more exhaustively, because I do not understand. It seems that tx and ty and the cos(alpha) derived from them are numerically exact and I suppose the algorithm are right. ... v_1=sqrt(at(1,1)**2+at(2,1)**2+at(3,1)**2) cell_edge=alat*v_1 c_tx=(1-2*(at(1,1))**2) c_ty=(-6*at(2,1)**2)+1 c_tz=((3*at(3,1)**2-1)/(2)) .... tx=sqrt((1-c)/2) ty=sqrt((1-c)/6) tz=sqrt((1+2*c)/3) ... m. On 23 Dec 2010, at 17:28, Stefano de Gironcoli wrote: > Dear Marino Vetuschi Zuccolini wrote: >> trigonal(r) >> =================== >> for these groups, the z-axis is chosen as the 3-fold axis, but the >> crystallographic vectors form a three-fold star around the z-axis, >> and the primitive cell is a simple rhombohedron. The crystallographic >> vectors are: >> v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). >> where c=cos(alpha) is the cosine of the angle alpha between any pair >> of crystallographic vectors, tc, ty, tz are defined as >> tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3) >> > > in order to extract c you are forgetting to divide v1 by a=|v1|. > > stefano > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From degironc at sissa.it Thu Dec 23 19:49:13 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Dec 2010 19:49:13 +0100 Subject: [Pw_forum] Inconsistencies in the CELL_PARAMETERS - ibrav=5 In-Reply-To: <83A6AC03-DAFB-4679-8818-3711AA2D2C4F@dipteris.unige.it> References: <6C88F240-136D-4A44-A50B-6BF6E1FD0DAB@dipteris.unige.it> <4D136959.1020107@sissa.it> <4D13789F.5030701@sissa.it> <83A6AC03-DAFB-4679-8818-3711AA2D2C4F@dipteris.unige.it> Message-ID: <4D1399A9.6030505@sissa.it> if you are interested in comparing with the definition of in INPUT.PW you should apply the definition in INPUT.PW... which is not the one you are using. There is a value of "a" missing in your definition. stefano Marino Vetuschi Zuccolini wrote: > stefano, > thanks but can you explain a little bit more exhaustively, because I do not understand. It seems that tx and ty and the cos(alpha) derived from them are numerically exact and I suppose the algorithm are right. > > ... > v_1=sqrt(at(1,1)**2+at(2,1)**2+at(3,1)**2) > cell_edge=alat*v_1 > c_tx=(1-2*(at(1,1))**2) > c_ty=(-6*at(2,1)**2)+1 > c_tz=((3*at(3,1)**2-1)/(2)) > .... > > tx=sqrt((1-c)/2) > ty=sqrt((1-c)/6) > tz=sqrt((1+2*c)/3) > ... > > m. > > > On 23 Dec 2010, at 17:28, Stefano de Gironcoli wrote: > > >> Dear Marino Vetuschi Zuccolini wrote: >> >>> trigonal(r) >>> =================== >>> for these groups, the z-axis is chosen as the 3-fold axis, but the >>> crystallographic vectors form a three-fold star around the z-axis, >>> and the primitive cell is a simple rhombohedron. The crystallographic >>> vectors are: >>> v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). >>> where c=cos(alpha) is the cosine of the angle alpha between any pair >>> of crystallographic vectors, tc, ty, tz are defined as >>> tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3) >>> >>> >> in order to extract c you are forgetting to divide v1 by a=|v1|. >> >> stefano >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ******************************************************* > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > Researcher / Geochemist > Laboratory of Geochemistry > > DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From wang.riping.81 at gmail.com Fri Dec 24 07:56:51 2010 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 24 Dec 2010 15:56:51 +0900 Subject: [Pw_forum] ion_radius Message-ID: Dear Forum, I am using espresso-4.2.1. In example18, for cp.x practice. I found the " ion_radius(1) and ion_radius(2) " in the input file. Could you please tell me something about this input parameter, and how to set? as following: &ions ion_dynamics='verlet' , ion_temperature='nose' , tempw = .2 , fnosep = 250 , ion_radius(1) = 1.0 , ion_radius(2) = 1.0 , I can not find any explanation about ion_radius from espresso manual. Thanks very much. WANG Riping 2010.12.24 -- ****************************************************************************** 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), 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/20101224/f278e2a2/attachment.htm From giannozz at democritos.it Fri Dec 24 09:56:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Dec 2010 09:56:00 +0100 Subject: [Pw_forum] ion_radius In-Reply-To: References: Message-ID: <5B32AABF-A8DA-4C29-8850-9250578A7450@democritos.it> On Dec 24, 2010, at 7:56 , Riping WANG wrote: > In example18, for cp.x practice. I found the " ion_radius(1) > and ion_radius(2) " in the input file. > Could you please tell me something about this input parameter, and > how to set? usuallly you do not need to set it: the default value should be fine. ion_radius is the width of a gaussian distribution of charge replacing the point charge of the (pseudo-)nucleus. It should be big enough to ensure convergence of the total energy in G-space, small enough to yield negligible overlap between gaussians. Valus around 0.8 are usually fine. The total energy and forces should not change if ion_radius changes. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mohnish.iitk at gmail.com Fri Dec 24 10:42:19 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 24 Dec 2010 15:12:19 +0530 Subject: [Pw_forum] how does the calculation scales with number of processors Message-ID: Dear QE users, I am trying to see how the runtime scales with number of processors. I did the same calculation using one node with eight processors on one cluster and 8 nodes with total 56 processors on other cluster but the time does not seem to scale linearly with the number of processors. Can anybody give me an idea how does the time scale with number of processors. Thanks a lot in advance. -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101224/094c0e6d/attachment.htm From degironc at sissa.it Fri Dec 24 11:20:34 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 24 Dec 2010 11:20:34 +0100 Subject: [Pw_forum] how does the calculation scales with number of processors In-Reply-To: References: Message-ID: <4D1473F2.9090302@sissa.it> It strongly depends on the particular calculation and on the parallelization strategy you choose. Linear scaling would be the ideal scaling which you never get. The things to keep in mind are load balancing and communication overhead. This last is affected by your communication network latency and bandwidth ... As a general rule the bigger the calculation the easier is to scale. It may be useful to have a look at the final timing summary of a calculation to see the fraction of time spent in communication (FFT scatter/gather and reduce operations) compared with the total wall clock time for your system and how this changes for different settings. Another factor to keep in mind is RAM memory as with certain parallelization strategies you can trade some speed with increased memory. stefano mohnish pandey wrote: > Dear QE users, > I am trying to see how the runtime scales with > number of processors. I did the same calculation using one node with eight > processors on one cluster and 8 nodes with total 56 processors on other > cluster but the time does not seem to scale linearly with the number of > processors. Can anybody give me an idea how does the time scale with number > of processors. > Thanks a lot in advance. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mohnish.iitk at gmail.com Fri Dec 24 11:26:41 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 24 Dec 2010 15:56:41 +0530 Subject: [Pw_forum] how does the calculation scales with number of processors In-Reply-To: <4D1473F2.9090302@sissa.it> References: <4D1473F2.9090302@sissa.it> Message-ID: Thanks a lot Dr. Stefano for your reply. On Fri, Dec 24, 2010 at 3:50 PM, Stefano de Gironcoli wrote: > It strongly depends on the particular calculation and on the > parallelization strategy you choose. Linear scaling would be the ideal > scaling which you never get. > The things to keep in mind are load balancing and communication > overhead. This last is affected by your communication network latency > and bandwidth ... As a general rule the bigger the calculation the > easier is to scale. > It may be useful to have a look at the final timing summary of a > calculation to see the fraction of time spent in communication (FFT > scatter/gather and reduce operations) compared with the total wall clock > time for your system and how this changes for different settings. > Another factor to keep in mind is RAM memory as with certain > parallelization strategies you can trade some speed with increased memory. > > stefano > > mohnish pandey wrote: > > Dear QE users, > > I am trying to see how the runtime scales with > > number of processors. I did the same calculation using one node with > eight > > processors on one cluster and 8 nodes with total 56 processors on other > > cluster but the time does not seem to scale linearly with the number of > > processors. Can anybody give me an idea how does the time scale with > number > > of processors. > > Thanks a lot in advance. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101224/e6654593/attachment.htm From giannozz at democritos.it Fri Dec 24 11:28:22 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Dec 2010 11:28:22 +0100 Subject: [Pw_forum] how does the calculation scales with number of processors In-Reply-To: References: Message-ID: On Dec 24, 2010, at 10:42 , mohnish pandey wrote: > Can anybody give me an idea how does the time scale with number of > processors. please see the user guide in particular chapter 3: http://www.quantum-espresso.org/user_guide/node15.html and this, in particular the "(Too) Frequently Asked Question" http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From daijiayu at nudt.edu.cn Fri Dec 24 13:07:29 2010 From: daijiayu at nudt.edu.cn (jiayudai) Date: Fri, 24 Dec 2010 20:07:29 +0800 Subject: [Pw_forum] Merry Christmas Message-ID: Mearry Christmas to every body. Good luck for us! From zhaohscas at yahoo.com.cn Fri Dec 24 15:30:44 2010 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 24 Dec 2010 22:30:44 +0800 Subject: [Pw_forum] About the difference between the energy obtained from geometry optimization and single energy calculation. Message-ID: <232357947.20101224223044@yahoo.com.cn> Dear PWSCF users, The geometry optimization can give the minimal energy of our system. What's the difference between the energy obtained from geometry optimization and the single energy calculation? Best regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2010-12-24 __________________________________________________ ????????????????????????????? http://cn.mail.yahoo.com From zhaohscas at yahoo.com.cn Sat Dec 25 02:50:43 2010 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 25 Dec 2010 09:50:43 +0800 Subject: [Pw_forum] About the relationship between enthalpy and pressure. Message-ID: <1504855182.20101225095043@yahoo.com.cn> Dear PWSCF users, We all know that, the pressure-Volume, and energy--Volume curve can be obtained by fitting of EOS. But what's the relationship between enthalpy and pressure? Best regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2010-12-25 __________________________________________________ ????????????????????????????? http://cn.mail.yahoo.com From degironc at sissa.it Sat Dec 25 03:10:52 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 25 Dec 2010 03:10:52 +0100 Subject: [Pw_forum] About the relationship between enthalpy and pressure. In-Reply-To: <1504855182.20101225095043@yahoo.com.cn> References: <1504855182.20101225095043@yahoo.com.cn> Message-ID: <4D1552AC.1090207@sissa.it> Pressure is the thermodynamical variable upon which enthalpy depends If you know E(V) you can define H(P) = min_V ( E(V) + P V ) Have a look in a book of thermodynamics. stefano Hongsheng Zhao wrote: > Dear PWSCF users, > > We all know that, the pressure-Volume, and energy--Volume curve can be obtained by fitting of EOS. But what's the relationship between enthalpy and pressure? > > Best regards. > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From prasenjit.jnc at gmail.com Sat Dec 25 04:36:09 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Sat, 25 Dec 2010 09:06:09 +0530 Subject: [Pw_forum] About the difference between the energy obtained from geometry optimization and single energy calculation. In-Reply-To: <232357947.20101224223044@yahoo.com.cn> References: <232357947.20101224223044@yahoo.com.cn> Message-ID: In geometry optimization you relax both the ionic coordinates and the electronic coordinates to obtain the minimum energy configuration. In a single energy calculation, you minimize only the electronic coordinates for a given fixed ionic position. Prasenjit On 24 December 2010 20:00, Hongsheng Zhao wrote: > Dear PWSCF users, > > The geometry optimization can give the minimal energy of our system. What's the difference between the energy obtained from geometry optimization and the single energy calculation? > > Best regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2010-12-24 > > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com > > _______________________________________________ > 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 From zhaohscas at yahoo.com.cn Sat Dec 25 04:42:47 2010 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 25 Dec 2010 11:42:47 +0800 Subject: [Pw_forum] On the doping modeling. Message-ID: <1576482102.20101225114247@yahoo.com.cn> Dear PWSCF users, I've 2*2*2 supercell of hcp Mg and want doping Al into it. Suppose 2 atoms will be substituted by Al in this supercell, I want to know which 2 atoms should I selected to do the substitution. Any hints will be highly appreciated. Best regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2010-12-25 __________________________________________________ ????????????????????????????? http://cn.mail.yahoo.com From georgeamolo862 at gmail.com Sat Dec 25 18:02:16 2010 From: georgeamolo862 at gmail.com (George Amolo) Date: Sat, 25 Dec 2010 18:02:16 +0100 Subject: [Pw_forum] Ghost States In-Reply-To: References: Message-ID: Hello Phillip, Greetings in the name of our Lord Jesus Christ. Merry Christmas although I do not know how you are celebrating it. Itedo kuon gi rech? Kose? I have done the marking and can spare some time to do the work again. I already send some jobs to CHPC where I see tens of jobs that are yours which have huge wall times. Please update me on how your work is going on: Exactly what defects are you looking at? What is the size of your cell? Still 96 atoms? Have you checked to see that whatever values you have calculated do no change with a larger cell? Hoping to hear from you soon george On Fri, Dec 10, 2010 at 11:54 AM, Phillip Nyawere wrote: > Dear pwscf > I am doing a "relax" calculation by shifting the position of an atom in a > supercell. Some sites appear unfavorable and one of them is hear below > showing the presence of a ghost state. Could anyone give me an idear of how > to remove the ghost sites (energy) in a calculation? Part of the output is > here: > > k = 0.0000 0.0000 0.0000 ( 36612 PWs) bands (ev): > -30.6867 -19.5462 -19.4947 -19.4037 -19.3662 -19.3332 -19.2705 -19.2304 > -19.1717 -19.1681 -19.1466 -19.1386 -19.1164 -19.1036 -19.0976 -19.0943 > -19.0939 -19.0851 -19.0845 -19.0825 -19.0527 -19.0276 -19.0078 -18.9858 > -18.9681 -18.9567 -18.9032 -18.8883 -18.8418 -18.8179 -18.8140 -18.7612 > -16.0244 -16.0133 -15.9881 -15.9532 -15.9512 -15.9385 -15.9291 -15.9228 > -15.9189 -15.9102 -15.9075 -15.8753 -15.8739 -15.8689 -15.8610 -15.8544 > -15.8478 -15.8397 -15.8373 -15.8212 -15.8090 -15.8056 -15.8013 -15.8011 > -15.7823 -15.7817 -15.7715 -15.7649 -15.7627 -15.7584 -15.7468 -15.7436 > -15.7351 -15.7292 -15.7268 -15.7206 -15.7142 -15.7116 -15.6975 -15.6971 > -15.6943 -15.6870 -15.6812 -15.6688 -15.6646 -15.6594 -15.6557 -15.6490 > -15.6428 -15.6409 -15.6229 -15.6099 -15.6036 -15.6026 -15.5933 -15.5905 > -15.5677 -15.4540 -15.2097 -15.0390 -14.9480 -14.9457 -13.8970 -8.5916 > -8.4985 -6.7400 -4.8562 -4.8507 -4.7891 -4.7626 -4.7525 -4.7343 > -4.6927 -4.6912 -4.6645 -4.6403 -4.6237 -4.6234 -4.6209 -4.6134 > -4.6053 -4.5858 -4.5672 -4.5576 -4.5273 -4.5016 -4.4944 -4.4676 > -4.4578 -4.4492 -4.4396 -4.4155 -4.4061 -4.3838 -4.3792 -4.3767 > -4.3725 -4.3714 -4.3711 -4.3593 -4.3566 -4.3515 -4.3489 -4.3463 > -4.3440 -4.3399 -4.3383 -4.3366 -4.3351 -4.3343 -4.3326 -4.3321 > -4.3299 -4.3266 -4.3264 -4.3241 -4.3239 -4.3229 -4.3224 -4.3206 > -4.3189 -4.3165 -4.3158 -4.3152 -4.3045 -4.3029 -4.2829 -4.2798 > > > -- > Phillip W. Otieno Nyawere, > International Center for Theoretical Physics, ICTP, > Strada Costiera, 11 - 34014217, > Leonardo Building, > Office 305, > Trieste, > Italy. > Tel +393382213805 office +39 040 2240 217 > pnyawere at gmail.com, potieno at kabarak.ac.ke > > God raises the meek from the ground and sits them with Kings. > > > > _______________________________________________ > 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/20101225/8f8f86ac/attachment.htm From wang.riping.81 at gmail.com Mon Dec 27 01:07:25 2010 From: wang.riping.81 at gmail.com (Riping WANG) Date: Mon, 27 Dec 2010 09:07:25 +0900 Subject: [Pw_forum] Pw_forum Digest, Vol 42, Issue 43 In-Reply-To: References: Message-ID: Der prof. Paolo, Thanks very much to your reply. 1. Re: ion_radius (Paolo Giannozzi) WANG Riping 2010.12.27 On 25 December 2010 12:36, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: ion_radius (Paolo Giannozzi) > 2. how does the calculation scales with number of processors > (mohnish pandey) > 3. Re: how does the calculation scales with number of processors > (Stefano de Gironcoli) > 4. Re: how does the calculation scales with number of processors > (mohnish pandey) > 5. Re: how does the calculation scales with number of processors > (Paolo Giannozzi) > 6. Merry Christmas (jiayudai) > 7. About the difference between the energy obtained from > geometry optimization and single energy calculation. (Hongsheng Zhao) > 8. About the relationship between enthalpy and pressure. > (Hongsheng Zhao) > 9. Re: About the relationship between enthalpy and pressure. > (Stefano de Gironcoli) > 10. Re: About the difference between the energy obtained from > geometry optimization and single energy calculation. (Prasenjit Ghosh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Dec 2010 09:56:00 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] ion_radius > To: PWSCF Forum > Message-ID: <5B32AABF-A8DA-4C29-8850-9250578A7450 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Dec 24, 2010, at 7:56 , Riping WANG wrote: > > > In example18, for cp.x practice. I found the " ion_radius(1) > > and ion_radius(2) " in the input file. > > Could you please tell me something about this input parameter, and > > how to set? > > usuallly you do not need to set it: the default value should be fine. > ion_radius is the width of a gaussian distribution of charge replacing > the point charge of the (pseudo-)nucleus. It should be big enough > to ensure convergence of the total energy in G-space, small enough > to yield negligible overlap between gaussians. Valus around 0.8 are > usually fine. The total energy and forces should not change if > ion_radius changes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Dec 2010 15:12:19 +0530 > From: mohnish pandey > Subject: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear QE users, > I am trying to see how the runtime scales with > number of processors. I did the same calculation using one node with eight > processors on one cluster and 8 nodes with total 56 processors on other > cluster but the time does not seem to scale linearly with the number of > processors. Can anybody give me an idea how does the time scale with number > of processors. > Thanks a lot in advance. > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101224/094c0e6d/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Fri, 24 Dec 2010 11:20:34 +0100 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum > Message-ID: <4D1473F2.9090302 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > It strongly depends on the particular calculation and on the > parallelization strategy you choose. Linear scaling would be the ideal > scaling which you never get. > The things to keep in mind are load balancing and communication > overhead. This last is affected by your communication network latency > and bandwidth ... As a general rule the bigger the calculation the > easier is to scale. > It may be useful to have a look at the final timing summary of a > calculation to see the fraction of time spent in communication (FFT > scatter/gather and reduce operations) compared with the total wall clock > time for your system and how this changes for different settings. > Another factor to keep in mind is RAM memory as with certain > parallelization strategies you can trade some speed with increased memory. > > stefano > > mohnish pandey wrote: > > Dear QE users, > > I am trying to see how the runtime scales with > > number of processors. I did the same calculation using one node with > eight > > processors on one cluster and 8 nodes with total 56 processors on other > > cluster but the time does not seem to scale linearly with the number of > > processors. Can anybody give me an idea how does the time scale with > number > > of processors. > > Thanks a lot in advance. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 24 Dec 2010 15:56:41 +0530 > From: mohnish pandey > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > Thanks a lot Dr. Stefano for your reply. > > On Fri, Dec 24, 2010 at 3:50 PM, Stefano de Gironcoli >wrote: > > > It strongly depends on the particular calculation and on the > > parallelization strategy you choose. Linear scaling would be the ideal > > scaling which you never get. > > The things to keep in mind are load balancing and communication > > overhead. This last is affected by your communication network latency > > and bandwidth ... As a general rule the bigger the calculation the > > easier is to scale. > > It may be useful to have a look at the final timing summary of a > > calculation to see the fraction of time spent in communication (FFT > > scatter/gather and reduce operations) compared with the total wall clock > > time for your system and how this changes for different settings. > > Another factor to keep in mind is RAM memory as with certain > > parallelization strategies you can trade some speed with increased > memory. > > > > stefano > > > > mohnish pandey wrote: > > > Dear QE users, > > > I am trying to see how the runtime scales with > > > number of processors. I did the same calculation using one node with > > eight > > > processors on one cluster and 8 nodes with total 56 processors on other > > > cluster but the time does not seem to scale linearly with the number of > > > processors. Can anybody give me an idea how does the time scale with > > number > > > of processors. > > > Thanks a lot in advance. > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101224/e6654593/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Fri, 24 Dec 2010 11:28:22 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Dec 24, 2010, at 10:42 , mohnish pandey wrote: > > > Can anybody give me an idea how does the time scale with number of > > processors. > > please see the user guide in particular chapter 3: > http://www.quantum-espresso.org/user_guide/node15.html > and this, in particular the "(Too) Frequently Asked Question" > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 6 > Date: Fri, 24 Dec 2010 20:07:29 +0800 > From: "jiayudai" > Subject: [Pw_forum] Merry Christmas > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Mearry Christmas to every body. > > Good luck for us! > > > > ------------------------------ > > Message: 7 > Date: Fri, 24 Dec 2010 22:30:44 +0800 > From: Hongsheng Zhao > Subject: [Pw_forum] About the difference between the energy obtained > from geometry optimization and single energy calculation. > To: PWSCF Forum > Message-ID: <232357947.20101224223044 at yahoo.com.cn> > Content-Type: text/plain; charset=us-ascii > > Dear PWSCF users, > > The geometry optimization can give the minimal energy of our system. What's > the difference between the energy obtained from geometry optimization and > the single energy calculation? > > Best regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2010-12-24 > > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com > > > ------------------------------ > > Message: 8 > Date: Sat, 25 Dec 2010 09:50:43 +0800 > From: Hongsheng Zhao > Subject: [Pw_forum] About the relationship between enthalpy and > pressure. > To: PWSCF Forum > Message-ID: <1504855182.20101225095043 at yahoo.com.cn> > Content-Type: text/plain; charset=us-ascii > > Dear PWSCF users, > > We all know that, the pressure-Volume, and energy--Volume curve can be > obtained by fitting of EOS. But what's the relationship between enthalpy > and pressure? > > Best regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2010-12-25 > > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com > > > ------------------------------ > > Message: 9 > Date: Sat, 25 Dec 2010 03:10:52 +0100 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] About the relationship between enthalpy and > pressure. > To: PWSCF Forum > Message-ID: <4D1552AC.1090207 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Pressure is the thermodynamical variable upon which enthalpy depends > > If you know E(V) you can define H(P) = min_V ( E(V) + P V ) > > Have a look in a book of thermodynamics. > > stefano > > > > Hongsheng Zhao wrote: > > Dear PWSCF users, > > > > We all know that, the pressure-Volume, and energy--Volume curve can be > obtained by fitting of EOS. But what's the relationship between enthalpy > and pressure? > > > > Best regards. > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 10 > Date: Sat, 25 Dec 2010 09:06:09 +0530 > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] About the difference between the energy > obtained from geometry optimization and single energy calculation. > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset=GB2312 > > In geometry optimization you relax both the ionic coordinates and the > electronic coordinates to obtain the minimum energy configuration. In > a single energy calculation, you minimize only the electronic > coordinates for a given fixed ionic position. > > Prasenjit > > On 24 December 2010 20:00, Hongsheng Zhao wrote: > > Dear PWSCF users, > > > > The geometry optimization can give the minimal energy of our system. > What's the difference between the energy obtained from geometry optimization > and the single energy calculation? > > > > Best regards. > > -- > > Hongsheng Zhao > > School of Physics and Electrical Information Science, > > Ningxia University, Yinchuan 750021, China > > GnuPG DSA: 0xD108493 > > 2010-12-24 > > > > __________________________________________________ > > ??????????????? > > http://cn.mail.yahoo.com > > > > _______________________________________________ > > 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 > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 42, Issue 43 > **************************************** > -- ****************************************************************************** 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), 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/20101227/3ef5bf67/attachment-0001.htm From degironc at sissa.it Mon Dec 27 01:18:49 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 27 Dec 2010 01:18:49 +0100 Subject: [Pw_forum] ion_radius ------------- WAS Re: Pw_forum Digest, Vol 42, Issue 43 In-Reply-To: References: Message-ID: <4D17DB69.2050100@sissa.it> PLEASE DO NOT REPLY TO DIGEST MESSAGES. help yourself and everybody by specifying a tread-specific subject. stefano Riping WANG wrote: > Der prof. Paolo, > > Thanks very much to your reply. > > 1. Re: ion_radius (Paolo Giannozzi) > > WANG Riping > 2010.12.27 > > > On 25 December 2010 12:36, wrote: > > >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. Re: ion_radius (Paolo Giannozzi) >> 2. how does the calculation scales with number of processors >> (mohnish pandey) >> 3. Re: how does the calculation scales with number of processors >> (Stefano de Gironcoli) >> 4. Re: how does the calculation scales with number of processors >> (mohnish pandey) >> 5. Re: how does the calculation scales with number of processors >> (Paolo Giannozzi) >> 6. Merry Christmas (jiayudai) >> 7. About the difference between the energy obtained from >> geometry optimization and single energy calculation. (Hongsheng Zhao) >> 8. About the relationship between enthalpy and pressure. >> (Hongsheng Zhao) >> 9. Re: About the relationship between enthalpy and pressure. >> (Stefano de Gironcoli) >> 10. Re: About the difference between the energy obtained from >> geometry optimization and single energy calculation. (Prasenjit Ghosh) >> >> From physolde at yahoo.fr Mon Dec 27 12:52:53 2010 From: physolde at yahoo.fr (kada galami) Date: Mon, 27 Dec 2010 11:52:53 +0000 (GMT) Subject: [Pw_forum] elastic properties Message-ID: <17542.38772.qm@web26607.mail.ukl.yahoo.com> hi? i want to do the elastic properties of cubic structure i read in the forum that i have to put 0 ibrav to do the calculation but when i do the monoclinic deformation i have a error :? from latgen : error #????? 8 wrong celldm(2)? wha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101227/779c0371/attachment.htm From eyvaz_isaev at yahoo.com Mon Dec 27 14:04:01 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 27 Dec 2010 05:04:01 -0800 (PST) Subject: [Pw_forum] elastic properties In-Reply-To: <17542.38772.qm@web26607.mail.ukl.yahoo.com> References: <17542.38772.qm@web26607.mail.ukl.yahoo.com> Message-ID: <357553.14390.qm@web65715.mail.ac4.yahoo.com> Dear Kada, > i read in the forum that i have to put 0 ibrav to do the calculation You should specify ibrav=0, if you choose basis vectors manually, i.e. you specify CELL_PARAMETERS. Nobody can help you until you submit your input file. Please do not forget about your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: kada galami To: pw_forum at pwscf.org Sent: Mon, December 27, 2010 12:52:53 PM Subject: [Pw_forum] elastic properties hi i want to do the elastic properties of cubic structure i read in the forum that i have to put 0 ibrav to do the calculation but when i do the monoclinic deformation i have a error : from latgen : error # 8 wrong celldm(2) wha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101227/7c1de96a/attachment.htm From physolde at yahoo.fr Tue Dec 28 00:04:17 2010 From: physolde at yahoo.fr (kada galami) Date: Mon, 27 Dec 2010 23:04:17 +0000 (GMT) Subject: [Pw_forum] elastic properties In-Reply-To: <357553.14390.qm@web65715.mail.ac4.yahoo.com> Message-ID: <674966.25045.qm@web26601.mail.ukl.yahoo.com> hi ?dear evayz i spoke to you earlier in the forum about the elastic properties with ibrav = 0 ( free lattice i have some questions : 1- we do the calculation of elastic propreties only with ibrav= 0 2- i read about the input ibrav= 0 we have to put only the celldm(1) and the cell parameters where i can get the cell parameter, i think have somthing with basic vectors thank you in advance for your help --------------------------------------------------- phd student departement de physique faculte de science universite de sidi bel abbes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101227/0a1522bb/attachment.htm From degironc at sissa.it Tue Dec 28 00:42:17 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 28 Dec 2010 00:42:17 +0100 Subject: [Pw_forum] elastic properties In-Reply-To: <674966.25045.qm@web26601.mail.ukl.yahoo.com> References: <674966.25045.qm@web26601.mail.ukl.yahoo.com> Message-ID: <20101228004217.9xt6vwcwows0o8os@webmail.sissa.it> Dear kada galami, what you need to do is to calculate the stress for the equilibrium geometry and for a few slightly deformed cell shapes. The way you choose to describe each of these cells is up to you. Ibrav=0 is an option that gives you the possibility to define directly the lattice vectors (in unit of celldm(1)). If you want to describe a simple cubic cell of lattice spacing 3.14 bohrs it's up to you to define ibrav=1, celldm(1)=3.14 or ibrav=0, celldm(1)=3.14 CELL_PARAMETERS 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 or ibrav=0, celldm(1)=6.28 CELL_PARAMETERS 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 hope this helps, stefano Quoting kada galami : > hi > ?dear evayz > i spoke to you earlier in the forum about the elastic properties > with ibrav = 0 ( free lattice > i have some questions : > > 1- we do the calculation of elastic propreties only with ibrav= 0 > 2- i read about the input ibrav= 0 > we have to put only the celldm(1) > and the cell parameters > where i can get the cell parameter, i think have somthing with basic vectors > > thank you in advance for your help > > > > > > > > > > --------------------------------------------------- > phd student > departement de physique > faculte de science > universite de sidi bel abbes > > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From eyvaz_isaev at yahoo.com Tue Dec 28 01:35:56 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 27 Dec 2010 16:35:56 -0800 (PST) Subject: [Pw_forum] elastic properties In-Reply-To: <674966.25045.qm@web26601.mail.ukl.yahoo.com> References: <674966.25045.qm@web26601.mail.ukl.yahoo.com> Message-ID: <908883.15284.qm@web65716.mail.ac4.yahoo.com> Dear Kada, >From: kada galami > 1- we do the calculation of elastic propreties only with ibrav= 0 Not necessarily, it may depend on system considered and a strain applied. As example, for an orthorhombic strain (for B2 structure) you can use ibrav by default. >2- i read about the input ibrav= 0 >we have to put only the celldm(1) Correct. > and the cell parameters > where i can get the cell parameter, i think have somthing with basic vectors Take your basis vectors for undistorted lattice and multiply by the strain matrix. Do not forget to transform your atomic positions in the same manner. Thanks Stegano G. for the explanation how to apply CELL_PARAMETRS with ibrav=0. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101227/10ccb376/attachment.htm From wumindt2 at zju.edu.cn Tue Dec 28 10:01:03 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 28 Dec 2010 17:01:03 +0800 Subject: [Pw_forum] wannier function Message-ID: Dear All, I met a problem with the wannier calculation. Shall the kpoint mesh in the wannier calculation input *.win file be the same with the kpoint mesh in the nscf calculation ? Thanks for any help! Min Wu 2010-12-28 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101228/e1845c33/attachment.htm From spakinform at gmail.com Tue Dec 28 12:32:56 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Tue, 28 Dec 2010 20:32:56 +0900 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: Yes it should. To be more precise, your kpoints in case.nnkp case.win and case.nscf.in should be the same. 2010/12/28 wumindt2 > Dear All, > > I met a problem with the wannier calculation. > Shall the kpoint mesh in the wannier calculation input *.win file be the > same > with the kpoint mesh in the nscf calculation ? > > Thanks for any help! > > Min Wu > 2010-12-28 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Soroush Pakseresht Advanced Science Institute (RIKEN) Saitama-Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101228/83b163fc/attachment.htm From zxf888 at 163.com Wed Dec 29 07:39:52 2010 From: zxf888 at 163.com (Xiang-FengZhou) Date: Wed, 29 Dec 2010 14:39:52 +0800 (CST) Subject: [Pw_forum] Reference of example07 (version 4.2.1) In-Reply-To: References: Message-ID: <6ccfb1cc.658a.12d30daa917.Coremail.zxf888@163.com> Dear members, which will be the best reference for the example07 (electron-phonon calculation) within the version of 4.1 or 4.2.1 ? I noticed such information from elphon.f90: ! Sum over BZ of the electron-phonon matrix elements el_ph_mat ! Original routine written by Francesco Mauri, modified by PG ! New version by Malgorzata Wierzbowska Best regards, Xiang-Feng Zhou Nankai University China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/147a7924/attachment.htm From mansourehp at gmail.com Wed Dec 29 13:32:53 2010 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Wed, 29 Dec 2010 16:02:53 +0330 Subject: [Pw_forum] WanT Message-ID: Dear all I would like to run test10 of WanT code but I have recieved following message.What dose it mean and how can I solve it? M. Pashangpour Islamic Azad University of Tehran ====================================================================== = = = *** WanT *** Wannier Transport Code = = (www.wannier-transport.org) = = Ultra Soft Pseudopotential Implem. = = = ====================================================================== Program v. 2.1.0 starts ... Date 29Dec2010 at 19:25:15 Serial run. BUILT : Mon Dec 27 22:17:47 2010 HOST : i686-pc-linux-gnu ARCH : ia32 CC : cc CPP : cpp F90 : gfortran F77 : gfortran DFLAGS : -D__FFTW -D__USE_INTERNAL_FFTW BLAS LIBS : ../libs/blas.a LAPACK LIBS : ../libs/lapack.a FFT LIBS : MASS LIBS : *** glibc detected *** /root/want/want-2.1.1/bin/conductor.x: malloc(): memory corruption (fast): 0x0ac346d0 *** ======= Backtrace: ========= /lib/libc.so.6[0xc907e4] /lib/libc.so.6[0xc93846] /lib/libc.so.6(__libc_malloc+0x95)[0xc94c55] /usr/lib/libgfortran.so.3[0x15700d] /usr/lib/libgfortran.so.3(_gfortran_string_trim+0x71)[0x1dda11] /root/want/want-2.1.1/bin/conductor.x[0x808f26c] /root/want/want-2.1.1/bin/conductor.x[0x805bcce] /root/want/want-2.1.1/bin/conductor.x[0x80572dc] /root/want/want-2.1.1/bin/conductor.x[0x8049921] /root/want/want-2.1.1/bin/conductor.x[0x820ad59] /lib/libc.so.6(__libc_start_main+0xe6)[0xc395d6] /root/want/want-2.1.1/bin/conductor.x[0x80497f1] ======= Memory map: ======== 00110000-00111000 r-xp 00110000 00:00 0 [vdso] 0012a000-00146000 r-xp 00000000 08:0a 2000193 /lib/ld-2.8.so 00146000-00147000 r--p 0001c000 08:0a 2000193 /lib/ld-2.8.so 00147000-00148000 rw-p 0001d000 08:0a 2000193 /lib/ld-2.8.so 00148000-001f5000 r-xp 00000000 08:0a 1679370 /usr/lib/libgfortran.so.3.0.0 001f5000-001f7000 rw-p 000ac000 08:0a 1679370 /usr/lib/libgfortran.so.3.0.0 00c23000-00d86000 r-xp 00000000 08:0a 2000194 /lib/libc-2.8.so 00d86000-00d88000 r--p 00163000 08:0a 2000194 /lib/libc-2.8.so 00d88000-00d89000 rw-p 00165000 08:0a 2000194 /lib/libc-2.8.so 00d89000-00d8c000 rw-p 00d89000 00:00 0 00d8e000-00db5000 r-xp 00000000 08:0a 2000207 /lib/libm-2.8.so 00db5000-00db6000 r--p 00026000 08:0a 2000207 /lib/libm-2.8.so 00db6000-00db7000 rw-p 00027000 08:0a 2000207 /lib/libm-2.8.so 059e8000-059f5000 r-xp 00000000 08:0a 2000219 /lib/libgcc_s-4.3.0-20080428.so.1 059f5000-059f6000 rw-p 0000c000 08:0a 2000219 /lib/libgcc_s-4.3.0-20080428.so.1 08048000-08215000 r-xp 00000000 08:0a 1362230 /root/want/want-2.1.1/transport/conductor.x 08215000-08219000 rw-p 001cd000 08:0a 1362230 /root/want/want-2.1.1/transport/conductor.x 08219000-08c66000 rw-p 08219000 00:00 0 0ac11000-0ac55000 rw-p 0ac11000 00:00 0 [heap] b7b9e000-b7c3d000 rw-p b7b9e000 00:00 0 b7f00000-b7f21000 rw-p b7f00000 00:00 0 b7f21000-b8000000 ---p b7f21000 00:00 0 b8005000-b807e000 rw-p b8005000 00:00 0 bfe55000-bfe91000 rw-p bffc4000 00:00 0 [stack] Aborted -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/34ff95dc/attachment.htm From eyvaz_isaev at yahoo.com Wed Dec 29 13:46:08 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 29 Dec 2010 04:46:08 -0800 (PST) Subject: [Pw_forum] Reference of example07 (version 4.2.1) In-Reply-To: <6ccfb1cc.658a.12d30daa917.Coremail.zxf888@163.com> References: <6ccfb1cc.658a.12d30daa917.Coremail.zxf888@163.com> Message-ID: <642054.81981.qm@web65713.mail.ac4.yahoo.com> Hi, >From: Xiang-FengZhou >which will be the best reference for the example07 (electron-phonon calculation) >within the >version of 4.1 or 4.2.1 ? If you mean which one 4.1 or 4.2.1 is better for \lambda calculations, you can use both, in my experience I do not see any difference between them. You can try CVS version which should give additional information (lambda.out) with \lambda and T_c). Hopefully it contains changes I have made in July. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/06804a90/attachment.htm From trambui at u.boisestate.edu Thu Dec 30 00:14:30 2010 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 29 Dec 2010 16:14:30 -0700 Subject: [Pw_forum] Oxygen molecule binding energy In-Reply-To: <4CFDECCE.2030608@ictp.it> References: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> <4CFAB250.7090401@materials.ox.ac.uk> <4CFCA2C6.1050909@sissa.it> <4CFDECCE.2030608@ictp.it> Message-ID: Dear All, Hope everyone is having a great Holiday. would you please help me out with this, I'm looking for the "ev.f" that help to calculate the bulk modulus of a material. But I couldn't find it any where, please let me know where and how I can find that and use it to calculate for the bulk modulus, B. Thank you so much, Tram Bui On Tue, Dec 7, 2010 at 1:14 AM, Sandro Scandolo wrote: > In the specific case of the O2 molecule, in a molecular orbital picture > O2 has two degenerate pi-star HOMO orbitals that need to be filled with > 2 electrons. The ground state is a triplet S=1 (up,up), > (up,down)+(down,up),(down,down), the next state is a singlet > (up,down)-(down,up). A good representation of the triplet should be > given by the ground state of a spin-polarized calculation. The ground > state should have nup-ndown=2, and the two unpaired electrons fill the > two pi-star orbitals (with the same spin). I believe you don't need to > impose any symmetry to find this ground state. If you force the system > to have total spin=0 (in a spin-polarized calculation), you should > obtain the state (up,down) (or its degenerate counterpart (down,up)). > This state does not satisfy the correct symmetry of the 2-electron wfc, > so in principle does not correspond to any of the correct many-electron > states above. However this spurious state can be expressed as a linear > combination (sum or difference) of one of the triplet states > ((up,down)+(down,up)) and the singlet state ((up,down)-(down,up)). > Perhaps its energy corresponds to the average energy of the triplet and > the singlet??!? > > Best regards > Sandro > > > On 06/12/2010 09:45, Stefano de Gironcoli wrote: > > Nicola Marzari wrote: > >> I've never managed to get from anyone, including some of the luminaries > >> in the fundamentals of DFT, a clear answer to which solution is the > >> "correct" one. Note that even with nosym=.true. you ahve the option > >> of having occupation 2.0 on 2 of the p orbitals, or occupation > >> 1.3333333 on oeach of the 3 p orbitals - the latter solution > >> would probably be similar to the symmetrized solution (but shouldn't > >> be identical). > >> > > I think there's no general consensus whether it's "more correct" to have > > the lowest possible energy giving up the known symmetry of the true GS > > or to constraint the system to the expected symmetry accepting a > > slightly higher energy... Of course the "true" xc functional would not > > put you in this dilemma, but while awaiting for it, I think the > > important thing is to be aware of the two alternatives and clearly state > > which one one chooses to conpare with. > > > > stefano > > > > > > > >> nicola > >> > >> > >> > >> On 12/3/10 5:27 PM, elbuesta at icqmail.com wrote: > >> > >>> Dear all, > >>> > >>> I recently evaluated with PW the binding energy of a O2 molecule using > >>> the regular ultra-soft PP from the webpage. I noticed that the energy > >>> obtained could be 5.7eV or 6.7eV depending if the flag "nosym=.true." > is > >>> used or not in the energy evaluation of the isolated oxygen atom. I > >>> would like to know if anyone could help me understand why such a large > >>> difference is obtained for this system, since for many other systems > >>> (such as metals) the inclusion of "nosym=.true." for the isolated atom > >>> do not affect so much (or not at all) the value of the binding/cohesive > >>> energy. > >>> > >>> > >>> Thanks very much for your time, and all best for all! > >>> > >>> Fabio Negreiros > >>> IPCF - CNR, Pisa - Italia > >>> > >> > >> > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Sandro Scandolo -- http:/www.ictp.it/~scandolo > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Tram Bui B.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/3ccbbb5c/attachment-0001.htm From trambui at u.boisestate.edu Thu Dec 30 00:16:48 2010 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 29 Dec 2010 16:16:48 -0700 Subject: [Pw_forum] Bulk Modulus calculation Message-ID: Dear All, Hope everyone is having a great Holiday. would you please help me out with this, I'm looking for the "ev.f" that help to calculate the bulk modulus of a material. But I couldn't find it any where, please let me know where and how I can find that and use it to calculate for the bulk modulus, B. Thank you so much, Tram Bui B.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/542f0d3f/attachment.htm From ttduyle at gmail.com Thu Dec 30 00:25:44 2010 From: ttduyle at gmail.com (Duy Le) Date: Wed, 29 Dec 2010 18:25:44 -0500 Subject: [Pw_forum] Bulk Modulus calculation In-Reply-To: References: Message-ID: ev.f90 and ev.x should be in [WHEREEVER IT IS]espressso-X/pwtools/ ev.x can be also found in [WHEREEVER IT IS]espressso-X/bin If you can not find executable file of ev.x, you should make it with: $ cd [WHEREEVER IT IS]espressso-X/ $ make tools -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Dec 29, 2010 at 6:16 PM, Tram Bui wrote: > Dear All, > ??? Hope everyone is having a great Holiday. would you please help me out > with this, I'm looking for the "ev.f" that help to calculate the bulk > modulus of a material. But I couldn't find it any where, please let me know > where and how I can find that and use it to calculate for the bulk modulus, > B. > > Thank you so much, > > Tram Bui > > B.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From eyvaz_isaev at yahoo.com Thu Dec 30 00:39:06 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 29 Dec 2010 15:39:06 -0800 (PST) Subject: [Pw_forum] Oxygen molecule binding energy In-Reply-To: References: <8CD61268854008A-1924-6CA8@webmail-d071.sysops.aol.com> <4CFAB250.7090401@materials.ox.ac.uk> <4CFCA2C6.1050909@sissa.it> <4CFDECCE.2030608@ictp.it> Message-ID: <571796.70875.qm@web65705.mail.ac4.yahoo.com> Dear Tram Bui, Please do not duplicate your message and choose correct Subject name. What you request and the subject are absolutely different. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Tram Bui To: PWSCF Forum Sent: Thu, December 30, 2010 12:14:30 AM Subject: Re: [Pw_forum] Oxygen molecule binding energy Dear All, Hope everyone is having a great Holiday. would you please help me out with this, I'm looking for the "ev.f" that help to calculate the bulk modulus of a material. But I couldn't find it any where, please let me know where and how I can find that and use it to calculate for the bulk modulus, B. Thank you so much, Tram Bui -- Tram Bui B.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101229/f4c7ef12/attachment.htm From ferretti at mit.edu Thu Dec 30 14:21:55 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Thu, 30 Dec 2010 13:21:55 +0000 (GMT) Subject: [Pw_forum] WanT (fwd) Message-ID: Dear M. Pashangpour, please note want-2.1.0 is obsolete now. A number of problems have been fixed since then, so I strongly recommend to use a newer version of the code, such as want-2.3.0 (the one that comes with quantum-espresso): http://qe-forge.org/frs/download.php/99/want-2.3.0.tar.gz let me know if the problem you've observed is still there. all the best andrea -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612792; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > Dear all > I would like to run test10 of WanT code but I have recieved following > message.What dose it mean and how can I solve it? > M. Pashangpour > Islamic Azad University of Tehran > ? > ? > ?====================================================================== > ????????????? =??????????????????????????????????????????? = > ????????????? =???? *** WanT *** Wannier Transport Code??? = > ????????????? =??????? (www.wannier-transport.org)???????? = > ????????????? =????? Ultra Soft Pseudopotential Implem.??? = > ????????????? =??????????????????????????????????????????? = > ? ====================================================================== > > > ? Program ? v. 2.1.0? starts ... > ? Date 29Dec2010 at 19:25:15 > > ???? Serial run. > > ????????? BUILT :??? Mon Dec 27 22:17:47 2010 > ?????????? HOST :??? i686-pc-linux-gnu > ?????????? ARCH :??? ia32 > ???????????? CC :??? cc > ??????????? CPP :??? cpp > ??????????? F90 :??? gfortran > ??????????? F77 :??? gfortran > ?? ??????DFLAGS :??? -D__FFTW -D__USE_INTERNAL_FFTW > ????? BLAS LIBS :??? ../libs/blas.a > ??? LAPACK LIBS :??? ../libs/lapack.a > ?????? FFT LIBS :??? > ????? MASS LIBS :??? > > > *** glibc detected *** /root/want/want-2.1.1/bin/conductor.x: malloc(): > memory corruption (fast): 0x0ac346d0 *** > ======= Backtrace: ========= > /lib/libc.so.6[0xc907e4] > /lib/libc.so.6[0xc93846] > /lib/libc.so.6(__libc_malloc+0x95)[0xc94c55] > /usr/lib/libgfortran.so.3[0x15700d] > /usr/lib/libgfortran.so.3(_gfortran_string_trim+0x71)[0x1dda11] > /root/want/want-2.1.1/bin/conductor.x[0x808f26c] > /root/want/want-2.1.1/bin/conductor.x[0x805bcce] > /root/want/want-2.1.1/bin/conductor.x[0x80572dc] > /root/want/want-2.1.1/bin/conductor.x[0x8049921] > /root/want/want-2.1.1/bin/conductor.x[0x820ad59] > /lib/libc.so.6(__libc_start_main+0xe6)[0xc395d6] > /root/want/want-2.1.1/bin/conductor.x[0x80497f1] > ======= Memory map: ======== > 00110000-00111000 r-xp 00110000 00:00 0????????? [vdso] > 0012a000-00146000 r-xp 00000000 08:0a 2000193??? /lib/ld-2.8.so > 00146000-00147000 r--p 0001c000 08:0a 2000193??? /lib/ld-2.8.so > 00147000-00148000 rw-p 0001d000 08:0a 2000193??? /lib/ld-2.8.so > 00148000-001f5000 r-xp 00000000 08:0a 1679370??? > /usr/lib/libgfortran.so.3.0.0 > 001f5000-001f7000 rw-p 000ac000 08:0a 1679370??? > /usr/lib/libgfortran.so.3.0.0 > 00c23000-00d86000 r-xp 00000000 08:0a 2000194??? /lib/libc-2.8.so > 00d86000-00d88000 r--p 00163000 08:0a 2000194??? /lib/libc-2.8.so > 00d88000-00d89000 rw-p 00165000 08:0a 2000194??? /lib/libc-2.8.so > 00d89000-00d8c000 rw-p 00d89000 00:00 0 > 00d8e000-00db5000 r-xp 00000000 08:0a 2000207??? /lib/libm-2.8.so > 00db5000-00db6000 r--p 00026000 08:0a 2000207??? /lib/libm-2.8.so > 00db6000-00db7000 rw-p 00027000 08:0a 2000207??? /lib/libm-2.8.so > 059e8000-059f5000 r-xp 00000000 08:0a 2000219??? > /lib/libgcc_s-4.3.0-20080428.so.1 > 059f5000-059f6000 rw-p 0000c000 08:0a 2000219??? > /lib/libgcc_s-4.3.0-20080428.so.1 > 08048000-08215000 r-xp 00000000 08:0a 1362230??? > /root/want/want-2.1.1/transport/conductor.x > 08215000-08219000 rw-p 001cd000 08:0a 1362230??? > /root/want/want-2.1.1/transport/conductor.x > 08219000-08c66000 rw-p 08219000 00:00 0 > 0ac11000-0ac55000 rw-p 0ac11000 00:00 0????????? [heap] > b7b9e000-b7c3d000 rw-p b7b9e000 00:00 0 > b7f00000-b7f21000 rw-p b7f00000 00:00 0 > b7f21000-b8000000 ---p b7f21000 00:00 0 > b8005000-b807e000 rw-p b8005000 00:00 0 > bfe55000-bfe91000 rw-p bffc4000 00:00 0????????? [stack] > Aborted > > From zxf888 at 163.com Thu Dec 30 14:58:20 2010 From: zxf888 at 163.com (Xiang-FengZhou) Date: Thu, 30 Dec 2010 21:58:20 +0800 (CST) Subject: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) In-Reply-To: References: Message-ID: <14f2e7.18b6c.12d3792714c.Coremail.zxf888@163.com> Dear Eyvaz, Thanks a lot for such quick response. I want to know the current method which is just implemented in espresso-4.2.1. I guess it may bearXiv:cond-mat/0504077v2 with the title "Origins of low- and high-pressure discontinuities of Tc in niobium". But I am not very sure about it. Best regards, Xiang-Feng Zhou Nankai University >Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) >To: PWSCF Forum >Message-ID: <642054.81981.qm at web65713.mail.ac4.yahoo.com> >Content-Type: text/plain; charset="us-ascii" > >Hi, > >>From: Xiang-FengZhou > >>which will be the best reference for the example07 (electron-phonon calculation) >>within the >version of 4.1 or 4.2.1 ? >If you mean which one 4.1 or 4.2.1 is better for \lambda calculations, you can >use both, in my experience I do not see any difference between them. > > >You can try CVS version which should give additional information (lambda.out) >with \lambda and T_c). Hopefully it contains changes I have made in July. > > >Bests, >Eyvaz. > ------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101230/32d7f4ec/attachment.htm From eyvaz_isaev at yahoo.com Thu Dec 30 17:37:10 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 30 Dec 2010 08:37:10 -0800 (PST) Subject: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) In-Reply-To: <14f2e7.18b6c.12d3792714c.Coremail.zxf888@163.com> References: <14f2e7.18b6c.12d3792714c.Coremail.zxf888@163.com> Message-ID: <22908.81035.qm@web65715.mail.ac4.yahoo.com> Dear Zhou, It is a good idea citing the paper as it contains all formulas used to calculate \lambda. Bests, Eyvaz. ________________________________ From: Xiang-FengZhou To: pw_forum at pwscf.org Sent: Thu, December 30, 2010 2:58:20 PM Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) Dear Eyvaz, Thanks a lot for such quick response. I want to know the current method which is just implemented in espresso-4.2.1. I guess it may be arXiv:cond-mat/0504077v2 with the title "Origins of low- and high-pressure discontinuities of Tc in niobium". But I am not very sure about it. Best regards, Xiang-Feng Zhou Nankai University >Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) >To: PWSCF Forum >Message-ID: <642054.81981.qm at web65713.mail.ac4.yahoo.com> >Content-Type: text/plain; charset="us-ascii" > >Hi, > >>From: Xiang-FengZhou > >>which will be the best reference for the example07 (electron-phonon calculation) >> >>within the >version of 4.1 or 4.2.1 ? >If you mean which one 4.1 or 4.2.1 is better for \lambda calculations, you can >use both, in my experience I do not see any difference between them. > > >You can try CVS version which should give additional information (lambda.out) >with \lambda and T_c). Hopefully it contains changes I have made in July. > > >Bests, >Eyvaz. > ------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101230/db9923c0/attachment.htm From Trinh.Vo at jpl.nasa.gov Thu Dec 30 21:48:33 2010 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Thu, 30 Dec 2010 12:48:33 -0800 Subject: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) In-Reply-To: <22908.81035.qm@web65715.mail.ac4.yahoo.com> Message-ID: Dear Paul, How are you? I hope you are fine and enjoying the holidays. I filled out the tie card today. I saw one of the funding is not there: the TE funding. The ABSCO, I think, will be out in the next week. If you don?t mind, could you renew these 2 funding if possible. You don?t have to do it now, since it is holiday time now, and you probably have your own plan in the holidays. I just let you know in advance since the week after New Year, I will need them for charging the time card. I emailed you the data last week of the nscf run using the scf 9x9x9. I am waiting for your calculation of Seebeck coefficient, so that I can decide whether I should run the scf 9x9x9 for the one atom case. I don?t mean to ask you to do it now since it is your holidays, and you need to enjoy too. I will fly back on Jan. 3, and from Jan 4 to Jan 6, I have class. I am not sure if I can do anything much after the class. I will try to work if I am not very tired. See you after Jan. 6. HAPPY NEW YEAR! Trinh On 12/30/10 8:37 AM, "Eyvaz Isaev" wrote: Dear Zhou, It is a good idea citing the paper as it contains all formulas used to calculate \lambda. Bests, Eyvaz. ________________________________ From: Xiang-FengZhou To: pw_forum at pwscf.org Sent: Thu, December 30, 2010 2:58:20 PM Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) Dear Eyvaz, Thanks a lot for such quick response. I want to know the current method which is just implemented in espresso-4.2.1. I guess it may be arXiv:cond-mat/0504077v2 with the title "Origins of low- and high-pressure discontinuities of Tc in niobium". But I am not very sure about it. Best regards, Xiang-Feng Zhou Nankai University >Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) >To: PWSCF Forum >Message-ID: <642054.81981.qm at web65713.mail.ac4.yahoo.com> >Content-Type: text/plain; charset="us-ascii" > >Hi, > >>From: Xiang-FengZhou > >>which will be the best reference for the example07 (electron-phonon calculation) >>within the >version of 4.1 or 4.2.1 ? >If you mean which one 4.1 or 4.2.1 is better for \lambda calculations, you can >use both, in my experience I do not see any difference between&n bsp;them. > > >You can try CVS version which should give additional information (lambda.out) >with \lambda and T_c). Hopefully it contains changes I have made in July. > > >Bests, >Eyvaz. > ------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101230/22e146a8/attachment-0001.htm From Trinh.Vo at jpl.nasa.gov Thu Dec 30 22:19:21 2010 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Thu, 30 Dec 2010 13:19:21 -0800 Subject: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) In-Reply-To: Message-ID: Dear All, I am sorry for the mistake of sending the wrong email. I remember I typed different email address, but, I don?t know why it ended up like this. I apologize for the inconvenience. Trinh On 12/30/10 12:48 PM, "Vo, Trinh (388C)" wrote: Dear Paul, How are you? I hope you are fine and enjoying the holidays. I filled out the tie card today. I saw one of the funding is not there: the TE funding. The ABSCO, I think, will be out in the next week. If you don?t mind, could you renew these 2 funding if possible. You don?t have to do it now, since it is holiday time now, and you probably have your own plan in the holidays. I just let you know in advance since the week after New Year, I will need them for charging the time card. I emailed you the data last week of the nscf run using the scf 9x9x9. I am waiting for your calculation of Seebeck coefficient, so that I can decide whether I should run the scf 9x9x9 for the one atom case. I don?t mean to ask you to do it now since it is your holidays, and you need to enjoy too. I will fly back on Jan. 3, and from Jan 4 to Jan 6, I have class. I am not sure if I can do anything much after the class. I will try to work if I am not very tired. See you after Jan. 6. HAPPY NEW YEAR! Trinh On 12/30/10 8:37 AM, "Eyvaz Isaev" wrote: Dear Zhou, It is a good idea citing the paper as it contains all formulas used to calculate \lambda. Bests, Eyvaz. ________________________________ From: Xiang-FengZhou To: pw_forum at pwscf.org Sent: Thu, December 30, 2010 2:58:20 PM Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) (Eyvaz Isaev) Dear Eyvaz, Thanks a lot for such quick response. I want to know the current method which is just implemented in espresso-4.2.1. I guess it may be arXiv:cond-mat/0504077v2 with the title "Origins of low- and high-pressure discontinuities of Tc in niobium". But I am not very sure about it. Best regards, Xiang-Feng Zhou Nankai University >Subject: Re: [Pw_forum] Reference of example07 (version 4.2.1) >To: PWSCF Forum >Message-ID: <642054.81981.qm at web65713.mail.ac4.yahoo.com> >Content-Type: text/plain; charset="us-ascii" > >Hi, > >>From: Xiang-FengZhou > >>which will be the best reference for the example07 (electron-phonon calculation) >>within the >version of 4.1 or 4.2.1 ? >If you mean which one 4.1 or 4.2.1 is better for \lambda calculations, you can >use both, in my experience I do not see any difference between&n bsp;them. > > >You can try CVS version which should give additional information (lambda.out) >with \lambda and T_c). Hopefully it contains changes I have made in July. > > >Bests, >Eyvaz. > ------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101230/f20fb940/attachment.htm From baroni at sissa.it Fri Dec 31 17:50:27 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 31 Dec 2010 17:50:27 +0100 Subject: [Pw_forum] Happy New Year Message-ID: Dear Quantum Espressionists, two lines just to wish all of you a successful and most happy New Year. May peace, freedom, and tolerance be with all of us! All the best to all Stefano B --- 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/20101231/c55c5d1b/attachment.htm