[Pw_forum] set_irr error during phonon calculation
Hi, Eyvaz I have modified "npert > 6" to "> 9" in set_irr.f90 file and recompiled the ph.x program. The calculation runs without error message any more. Thank you! Bests, Kun 2010/11/1 Eyvaz Isaev : > Hi, > > So, you got two different set of q-points with different symmetry. > In fact, this is very famous error ?and you should find the solution if search > QE forum archive). > > Just have a look at set_irr.f90, find line with "npert > 6" (line 192 in QE > 4.2) > and then take more neprt (number of irreducible presentations). Do not forget > recompile the phonon code. > > 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: Kun Yin > To: pw_forum at pwscf.org > Sent: Mon, November 1, 2010 4:01:46 AM > Subject: [Pw_forum] set_irr error during phonon calculation > > Dear Users, > > I did two similar phonon runs after a same scf calculation. The only > difference between the two phonon calculations is the dimension of > q-point mesh. > > ? ?nq1=2,nq2=2,nq3=2 (in 1st ph.x run) > ? ?nq1=2,nq2=2,nq3=1 (in 2nd ph.x run) > > The first calculation was successful to finish, while the second one > met the following error and stopped. > > ? ?from set_irr: error# 2 > ? ?npert > 6 > > This problem seems different from someone have asked before which > could be solved by increasing max_irr_dim value in phcom.f90 file. > Actually I didn't find max_irr_dim in this file in QE version 4.2 > which I used. > > Any suggestions or help will be appreciated. > > Kun Yin > Nanjing University,China > > Input of scf run: > > &CONTROL > ? calculation ? ? ? ? ?= ?'scf', > ? outdir ? ? ? ? ? ? ? = ?'/state/partition1/kyin', > ? prefix ? ? ? ? ? ? ? = ?'qe', > ? pseudo_dir ? ? ? ? ? = ?'/share/apps/qe_pseudo', > ? restart_mode ? ? ? ? = ?'from_scratch', > ? title ? ? ? ? ? ? ? ?= ?'qe', > ? verbosity ? ? ? ? ? ?= ?'high', > / > > &SYSTEM > ? celldm(1) ? ? ? ? ? ?= ?1, > ? ecutrho ? ? ? ? ? ? ?= ?400, > ? ecutwfc ? ? ? ? ? ? ?= ?40, > ? ibrav ? ? ? ? ? ? ? ?= ?0, > ? nat ? ? ? ? ? ? ? ? ?= ?20, > ? ntyp ? ? ? ? ? ? ? ? = ?3, > ? nr1=60,nr2=60,nr3=90 > / > > &ELECTRONS > ? conv_thr ? ? ? ? ? ? = ?1.0d-9, > ? mixing_mode ? ? ? ? ?= ?'plain', > / > > ATOMIC_SPECIES > ?Mg ? 24.305 ? Mg.pw91-np-van.UPF > ?Si ? 28.0855 ? Si.pw91-n-van.UPF > ?O ? 15.9994 ? O.pw91-van_ak.UPF > > K_POINTS automatic > ?4 ? 4 ? 2 ? 0 ? 0 ? 0 > > CELL_PARAMETERS (alat= ?1.) > ? 7.646348501 ? 0.0 ? 0.0 > ? 0.0 ? 8.393090445 ? 0.0 > ? 0.0 ? 0.0 ?11.365238746 > > ATOMIC_POSITIONS (crystal) > Mg ? ? ? 0.533728470 ? 0.589922896 ? 0.25000 > Mg ? ? ? 0.466271530 ? 0.410077104 ? 0.75000 > Mg ? ? ? 0.033728470 ? 0.910077104 ? 0.75000 > Mg ? ? ? 0.966271530 ? 0.089922896 ? 0.25000 > Si ? ? ? 0.5 ? 0.0 ? 0.5 > > Si ? ? ? 0.5 ? 0.0 ? 0.0 > Si ? ? ? 0.0 ? 0.5 ? 0.5 > Si ? ? ? 0.0 ? 0.5 ? 0.0 > O ? ? ? ?0.125931013 ? 0.465888786 ? 0.25000 > O ? ? ? ?0.874068987 ? 0.534111214 ? 0.75000 > O ? ? ? ?0.625931013 ? 0.034111214 ? 0.75000 > O ? ? ? ?0.374068987 ? 0.965888786 ? 0.25000 > O ? ? ? ?0.171733094 ? 0.187375245 ? 0.559982148 > O ? ? ? ?0.828266906 ? 0.812624755 ? 0.440017852 > O ? ? ? ?0.828266906 ? 0.812624755 ? 0.059982148 > O ? ? ? ?0.171733094 ? 0.187375245 ? 0.940017852 > O ? ? ? ?0.671733094 ? 0.312624755 ? 0.440017852 > O ? ? ? ?0.328266906 ? 0.687375245 ? 0.559982148 > O ? ? ? ?0.328266906 ? 0.687375245 ? 0.940017852 > O ? ? ? ?0.671733094 ? 0.312624755 ? 0.059982148 > > Input of phonon run: > Phonons > &inputph > ?amass(1)=24.3050, > ?amass(2)=28.0855, > ?amass(3)=15.9994, > ?prefix='qe', > ?outdir='/state/partition1/kyin' > ?fildyn='qe.dyn', > ?tr2_ph=1.0d-14, > ?ldisp=.true. > ?nq1=2,nq2=2,nq3=2 > / > ___ > 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] set_irr error during phonon calculation
Dear Users, I did two similar phonon runs after a same scf calculation. The only difference between the two phonon calculations is the dimension of q-point mesh. nq1=2,nq2=2,nq3=2 (in 1st ph.x run) nq1=2,nq2=2,nq3=1 (in 2nd ph.x run) The first calculation was successful to finish, while the second one met the following error and stopped. from set_irr: error# 2 npert > 6 This problem seems different from someone have asked before which could be solved by increasing max_irr_dim value in phcom.f90 file. Actually I didn't find max_irr_dim in this file in QE version 4.2 which I used. Any suggestions or help will be appreciated. Kun Yin Nanjing University,China Input of scf run: &CONTROL calculation = 'scf', outdir = '/state/partition1/kyin', prefix = 'qe', pseudo_dir = '/share/apps/qe_pseudo', restart_mode = 'from_scratch', title= 'qe', verbosity= 'high', / &SYSTEM celldm(1)= 1, ecutrho = 400, ecutwfc = 40, ibrav= 0, nat = 20, ntyp = 3, nr1=60,nr2=60,nr3=90 / &ELECTRONS conv_thr = 1.0d-9, mixing_mode = 'plain', / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF Si 28.0855 Si.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF K_POINTS automatic 4 4 2 0 0 0 CELL_PARAMETERS (alat= 1.) 7.646348501 0.0 0.0 0.0 8.393090445 0.0 0.0 0.0 11.365238746 ATOMIC_POSITIONS (crystal) Mg 0.533728470 0.589922896 0.25000 Mg 0.466271530 0.410077104 0.75000 Mg 0.033728470 0.910077104 0.75000 Mg 0.966271530 0.089922896 0.25000 Si 0.5 0.0 0.5 Si 0.5 0.0 0.0 Si 0.0 0.5 0.5 Si 0.0 0.5 0.0 O0.125931013 0.465888786 0.25000 O0.874068987 0.534111214 0.75000 O0.625931013 0.034111214 0.75000 O0.374068987 0.965888786 0.25000 O0.171733094 0.187375245 0.559982148 O0.828266906 0.812624755 0.440017852 O0.828266906 0.812624755 0.059982148 O0.171733094 0.187375245 0.940017852 O0.671733094 0.312624755 0.440017852 O0.328266906 0.687375245 0.559982148 O0.328266906 0.687375245 0.940017852 O0.671733094 0.312624755 0.059982148 Input of phonon run: Phonons &inputph amass(1)=24.3050, amass(2)=28.0855, amass(3)=15.9994, prefix='qe', outdir='/state/partition1/kyin' fildyn='qe.dyn', tr2_ph=1.0d-14, ldisp=.true. nq1=2,nq2=2,nq3=2 /
[Pw_forum] how to do fixed volume optimization
Hi, Han It is well known that GGA functionals tend to overestimate lattice parameters, while LDAs underestimate. When performing phonon calculations, using the experimental volume of a crystal will give more accurate frequencies with experimental data than using theoretically predicted volume. So I need this functionality when doing "the volume scaling" computations. But I have a new idea. Maybe this could be done by replacement of "the volume scaling" by "pressure scaling" through an equation of state. -- Kun Yin 2010-06-01 Hello Kun Yin, I'd appreciate if you would let me know why constant-volume vc-relax is "very useful" in high-pressure physics. Here is my response to your question. Do you really need to perform vc-relax at a "constant" volume, or do you just need the final volume to be very close to the initial volume? If the latter, you can do so by properly setting the target pressure (press), usually through good guessing, in your input file. Han > I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement > functionality, doing 'vc-relax' at constant volume, will be done by some > enthusiastic guy, since it is very useful in some research such as the > study of high-pressure materials. > Kun Yin > 2010-05-31 > > > > short answer: no. It should be relatively easy to implement but > it has never been done, to the best of my knowledge. You can > use 'vc-relax' at costant pressure, though, and vary the > pressure, if I remember correctly > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy *** Han Hsu, Ph.D. Postdoctoral Associate Department of Chemical Engineering & Materials Science University of Minnesota http://www.cems.umn.edu/~hsuhan *** ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] how to do fixed volume optimization
I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement functionality, doing 'vc-relax' at constant volume, will be done by some enthusiastic guy, since it is very useful in some research such as the study of high-pressure materials. -- Kun Yin 2010-05-31 Kun Yin wrote: > I want to optimize the both the cell parameters and atomic > positions while keeping the symmetry and volume constant. > I don't know if QE has the options in input to do this easily. short answer: no. It should be relatively easy to implement but it has never been done, to the best of my knowledge. You can use 'vc-relax' at costant pressure, though, and vary the pressure, if I remember correctly 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
[Pw_forum] how to do fixed volume optimization
Thanks Linh. I doubt that if I don't break the crystal symmetry, the 'relax' optimization of a supercell will have the same effect as the primitive cell. Even if not, there are two side effects of this idea: (1) more time to spend for computing a supercell, (2) difficulty to extract a primitive cell back from the supercell and appreciate its symmetry. The 'vc-relax' calculation optimzes both the shape of the cell and atomic positions while keeping the symmetry at a target pressure. It takes the pressure as convergence criterion. The 'relax' calculation optimizes the atomic positions while keeping the shape of the cell. It takes the force on atoms as convergence criterion. I want to optimize the both the cell parameters and atomic positions while keeping the symmetry and volume constant. It will take energy as convergence criterion. I don't know if QE has the options in input to do this easily. This can be done by performing a series of 'relax' calculation to optimize all degrees of freedom in cell parameters and find the minimum value. But this is labrious especially for low symmetry structure such as monoclinic cell. ---------- Kun Yin 2010-05-31 Kun Yin wrote: > Thanks for your reply, Mohnish. > The 'relax' calculation will keep the volume constant but it will fix the > cell parameters, too. For example, if I optimize a tetragonal cell, I want > the c and a axis to change but the volume unchanged. I know this could be > done by varing c/a ratio manually with a series of relax calculation. My > question is, can this be done automatically in QE > Why don't you build a supercell that stores the considering structure. When you do optimization, the volume of supercell will be fixed , but the structure is still optimized. Hope this help. Linh > -- > Kun Yin > 2010-05-30 > > Dear Yin 'vc-relax' calculation optimizes the structures by the lattice > parameters also but if you set the calculation 'relax' then it optimizes the > geometry within the given fixed volume constraints. This calculation moves > the atom keeping the volume constant within the given symmetry constraint. > hope this helps :) > > On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > > >> Dear All, >> >> Does anyone have the experience to do volume fixed optimization with QE, >> which means the structure is optimized allowing all cell parameters and >> atomic positions to vary while keeping the volume fixed? >> >> Kun Yin >> Najing University, China >> 2010-05-30 >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- - Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys - "The physics is theoretical but the fun is real" ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] how to do fixed volume optimization
Thanks for your reply, Mohnish. The 'relax' calculation will keep the volume constant but it will fix the cell parameters, too. For example, if I optimize a tetragonal cell, I want the c and a axis to change but the volume unchanged. I know this could be done by varing c/a ratio manually with a series of relax calculation. My question is, can this be done automatically in QE? -- Kun Yin 2010-05-30 Dear Yin 'vc-relax' calculation optimizes the structures by the lattice parameters also but if you set the calculation 'relax' then it optimizes the geometry within the given fixed volume constraints. This calculation moves the atom keeping the volume constant within the given symmetry constraint. hope this helps :) On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > Dear All, > > Does anyone have the experience to do volume fixed optimization with QE, > which means the structure is optimized allowing all cell parameters and > atomic positions to vary while keeping the volume fixed? > > Kun Yin > Najing University, China > 2010-05-30 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] how to do fixed volume optimization
Dear All, Does anyone have the experience to do volume fixed optimization with QE, which means the structure is optimized allowing all cell parameters and atomic positions to vary while keeping the volume fixed? Kun Yin Najing University, China 2010-05-30
[Pw_forum] Questions about Thermal properties calculation
Dear Zhou: > > Dear Yin: > > > Thank you for your answers. Sorry, I didn't make myself clear. > > For A1: > > QHA is what I want. Thank you. > > For A2: > The soft modes are not from numerical error. It is high temperature > phase. > > For A3: > It is not what I want. The discontinuity happens when two phonon > bands cross. The phonon eigenvalues in the output file xxx.freq are > always arranged ascendingly. When ploting with gnuplot, the cross two > bands turn to two ugly separate lines. I don't understand what you want. > Another represention, how do you plot just a single phonon band among > the phonon dispersion ? > The frequency is stored in a nband*nks array. xxx.freq file always starts with a line such as, &plot nbnd=??, nks=?? /. Then output loop each qpoint, at each qpoint, loop each band. > Zhou Bo Your affiliation? > 2009.8.9 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Questions about Thermal properties calculation
Dear Zhou Bo: Please add your affiliation when you post email next time. > Q1: Does pwscf have tools to calculate internal energe, specific heat, > entropy? Though I find fqha.x. Should I modify it to calculate the > other properties myself? > > Yes for internal energy. No for specific heat, entropy at present. As I know fqha.x has bug until version 4.0.5. (Maybe fixed at version 4.1, you should check it by yourself). We modified matdyn.f90 to calculate thermal properties as we need. I think it is not so difficult if you know how to do numerical integration. Alternatively, you can try qha package provided by Eyvaz Isaev. Download at https://qe-forge.org/projects/qha/ > Q2: I have a system with soft mode (negative phonon freq) in phonon > dispersion. Is it meaningful to calculate these thermal properties. If > it still have physical meaning, how to deal with the DOS below zero, > abandon it or just add into the integration? > If you don't provide us what your system is, we can not answer negative frequency is meaningful or not. Generally, negative frequency has two reasons: numerical errors or unstable structure at your calculated condition. For the former case, the negative value should not far from zero, and you can add acoustic sum rule (asr=.crystal.) to eliminate it. For the latter case, negative frequency is meaningful. It shows the structure you calculated is unstable at some direction. You should analyze this 'soft mode' carefully. For both cases, when you do integration, I THINK negative value should be abandoned. > Q3: Using matdyn.x to get the full phonon dispersion, there are some > discontiguous in phonon bands. Is there a convenient way to get > continual phonon dispersion? > Calculate different path once a time, then connect them together when you plot. Or modify the matdyn.f90 to meet your need as I did. See matdyn2.f90 at attachment. The original qpoint list in matdyn input file is replaced by connected qpoint list of qpath. More details and sample input see HowTo.pdf. Example output graph as pdc-pdos.eps. Because the attachment size in this mailing list can not exceed 200 KB. So if you want other files, send me a personal email for request. Cheers, Kun Yin School of Earth Sciences and Engineering Nanjing University China email: kyin.cn at gmail.com -- next part -- A non-text attachment was scrubbed... Name: matdyn2.f90 Type: text/x-fortran Size: 67333 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090809/947fc64f/attachment-0001.bin
[Pw_forum] temperature dependent density functional theory
On Sat, 2009-06-06 at 00:09 +0800, Hongsheng Zhao wrote: > By what means/parameters can I apply a finite temperature to my > system? > Dear Zhao, You can extend to finite temperature by two means depending your specific system: (1) ab-initio molecular dynamics (e.g. CPMD) This method usually is applied to molecular systems or liquid systems or surface, interface. It takes more time to compute such calculations and system size can not be very large. (2) phonon calculations (e.g. DFPT or frozen phonon method) This method usually is applied to solid system which is far from melting. The DFPT is implemented in Quantum-ESPRESSO, see examples related ph.x In a word, if you want to consider "temperature", you should have some method to calculate the contribution of nuclei motions. Cheers, Kun YIN, PhD candidate Nanjing University, China
[Pw_forum] how can I create a supercell in PWSCF?
Dear all: Share my solutions. (1) Make supercell, primitive cell and conventional unit-cell positions -- "spacegroup" program in EXCITING package (http://exciting.sourceforge.net, seems changing name). I edited very little code of "spacegroup" program, recompiled to make it output file format of PWSCF alike and POSCAR (for VASP and fropho). Usage: after program compiled, make a file containing lattice parameters, wyckoff positions, supercell size,etc called spacegroup.in and then execute command: spacegroup spacegroup.in (2) Check symmetry -- I use "fropho" (http://fropho.sourceforge.net), something like PHON, but I think newer and better. Usage: after program compiled, just execute command: echo 'find_symmetry' | fropho or echo 'find_symmetry = xxx' | fropho (xxx is the precision, e.g., 1.0d-6) Hope helpful. -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com - Original Message - From: "Eyvaz Isaev" To: "PWSCF Forum" Sent: Friday, April 24, 2009 11:55 PM Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? Dear all, Let me add (again!!!) my 5 cent words to this issue: If you need to create a supercell (and too lazy to create a small program to translate atoms), use Dario's PHON code. http://chianti.geol.ucl.ac.uk/~dario/ As Dario and QE have the same origin, Triest, they are compatible. Bests, Eyvaz. --- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 4/24/09, Pieremanuele Canepa wrote: > From: Pieremanuele Canepa > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > To: "PWSCF Forum" > Date: Friday, April 24, 2009, 7:27 PM > You are right man ! > Cheers, Piero > > On Fri, Apr 24, 2009 at 5:13 PM, Axel Kohlmeyer > > wrote: > > > On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk > wrote: > > > I know Thanks. I thought there was by far a > simpler way already > > > prepared! > > > > as with almost any open source project, people > primarily > > focus on what they personally think to be the most > important. > > > > i consider the method i outlined quite simple and it > > allows for very large flexibility. if you think > differently, > > then this is _your_ chance. write it and contribute > it. > > this is the best way to pay back the developers of Q-E > > for all their efforts. > > > > cheers, > > axel. > > > > > > > > - Original Message - > > > From: Axel Kohlmeyer > > > > Date: Friday, April 24, 2009 4:49 pm > > > Subject: Re: [Pw_forum] how can I create a > supercell in PWSCF? > > > To: PWSCF Forum > > > > > > > On Fri, 2009-04-24 at 16:41 +0200, > pc229 at kent.ac.uk wrote: > > > > > It doesn't. Xcrysden let me only > visualize the output structure > > > > > without manipulate it. I can create > the supercell using > > > > the command > > > > > unit repetition but I can export the > final structure. > > > > Should I do it > > > > > by hand? > > > > > > > > what is so difficult about it?? > > > > > > > > you can just write a little script using > awk/perl/python/tcl/... > > > > to do one translation/scaling operation and > then cut and paste > > > > the final (or initial) alat based > coordinates from a previous > > > > run into this and piece the different > translations together and > > > > make one input from it. this needs to be > adjusted most of the > > > > time anyways. > > > > > > > > cheers, > > > >axel. > > > > > > > > > Best Regards, Piero > > > > > > > > > > Nobody knows any shortcut to avoid to > write it by hand? > > > > > > > > > > - Original Message - > > > > > From: Stefano Baroni > > > > > > Date: Friday, April 24, 2009 4:31 pm > > > > > Subject: Re: [Pw_forum] how can I > create a supercell in PWSCF? > > >
[Pw_forum] improper symmetry analysis
Thank you for your answers, Paolo and Lorenzo. First time to know using nr1,nr2,nr3 and nr1s,nr2s,nr3s keywords.^_^ Lorenzo wrote: > "just make sure that the dimensions of the grids are multiple of the > numbers of replicas in the fractional traslation." I don't quite understand this sentence. Just try to increase and decrease default nr and nrs values as suggested. There are total 9 calculations, 1-3 and 8-0 find symmetry right, 4-7 find symmetry wrong. [kyin at geohpclab results]$ grep 'FFT grid:' *.out temp-1.out: G cutoff = 744.8786 ( 170271 G-vectors) FFT grid: ( 80, 80, 80) temp-2.out: G cutoff = 722.7847 ( 162825 G-vectors) FFT grid: ( 80, 80, 80) temp-3.out: G cutoff = 704.6276 ( 156325 G-vectors) FFT grid: ( 80, 80, 80) temp-4.out: G cutoff = 689.2743 ( 151669 G-vectors) FFT grid: ( 75, 75, 75) temp-5.out: G cutoff = 676.0151 ( 147349 G-vectors) FFT grid: ( 75, 75, 75) temp-6.out: G cutoff = 664.3728 ( 143471 G-vectors) FFT grid: ( 75, 75, 75) temp-7.out: G cutoff = 654.0170 ( 140255 G-vectors) FFT grid: ( 75, 75, 75) temp-8.out: G cutoff = 644.7053 ( 136787 G-vectors) FFT grid: ( 72, 72, 72) temp-9.out: G cutoff = 636.2575 ( 134435 G-vectors) FFT grid: ( 72, 72, 72) [kyin at geohpclab results]$ grep 'smooth grid:' *.out temp-1.out: G cutoff = 297.9514 ( 43143 G-vectors) smooth grid: ( 50, 50, 50) temp-2.out: G cutoff = 289.1139 ( 41151 G-vectors) smooth grid: ( 50, 50, 50) temp-3.out: G cutoff = 281.8510 ( 39597 G-vectors) smooth grid: ( 48, 48, 48) temp-4.out: G cutoff = 275.7097 ( 38421 G-vectors) smooth grid: ( 48, 48, 48) temp-5.out: G cutoff = 270.4060 ( 37309 G-vectors) smooth grid: ( 48, 48, 48) temp-6.out: G cutoff = 265.7491 ( 36085 G-vectors) smooth grid: ( 48, 48, 48) temp-7.out: G cutoff = 261.6068 ( 35557 G-vectors) smooth grid: ( 45, 45, 45) temp-8.out: G cutoff = 257.8821 ( 34621 G-vectors) smooth grid: ( 45, 45, 45) temp-9.out: G cutoff = 254.5030 ( 34015 G-vectors) smooth grid: ( 45, 45, 45) For No. 5 calculation, defulat value is 75 and 48. I set nr1=nr2=nr3=80, nr1s=nr2s=nr3s=50. It finds symmetry right! when I decrease to nr1=nr2=nr3=72, nr1s=nr2s=nr3s=45. It reports error and crash. %% task # 1 from fft_dlay_set : error # 8 inconsistent number of sticks %%--Kun YinPh.D. CandidateSchool of Earth Sciences and EngineeringNanjing University502 Geological Laboratory Building22 Hankou RoadNanjing 210093P.R. Chinaemail: kyin.cn at gmail.com- Original Message -From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, April 22, 2009 3:45 PMSubject: Re: [Pw_forum] improper symmetry analysis> Lorenzo Paulatto wrote:>>> You should not decrease them from their default value, but only increasethem!>> actually the default should be slightly overestimated, so one can try to> decrease it a little bit>> 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
[Pw_forum] improper symmetry analysis
Thank you, Paolo. I have read 17.22 and 17.24 sections of user guide. I think the problem of my calculations arises from "they contain a fractional translation that is incompatible with the FFT grid" since they change in unit cell volume. As a consquence, they do have different number of k points. [kyin at geohpclab results]$ grep 'number of k points=' *.out temp-1.out: number of k points= 16 temp-2.out: number of k points= 16 temp-3.out: number of k points= 16 temp-4.out: number of k points= 32 temp-5.out: number of k points= 32 temp-6.out: number of k points= 32 temp-7.out: number of k points= 32 temp-8.out: number of k points= 16 temp-9.out: number of k points= 16 I think this missing of symmetries will not affect calculation of groud state energy. But if I use this scf calculation results to do phonon calculations, can I get correct phonon band assignment? -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com - Original Message - From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, April 22, 2009 2:46 PM Subject: Re: [Pw_forum] improper symmetry analysis > > On Apr 22, 2009, at 8:33 , Kun Yin wrote: > >> I don't know how to fix this "improper symmetry analysis" problem. >> Can you help me? > > item 1.22 of the Troubleshooting section of the user guide > > --- > 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
[Pw_forum] improper symmetry analysis
Dear Users and Developers:
I met a weird phenomenon when calculating with a fcc crystal (sg. Fd-3m). I
used the same crystal structure. The only difference among the input files
is the value of parameter celldm(1). The crystal symmetries recognized by
pw.x are not consistent. There are also some warnings like "symmetry
operation # not allowed" in the head of the output files.
Below is part of my shell script including input file:
primitive_volumes="1056.5261 1009.8683 972.0540 940.4584 913.4519 889.9579
869.2306 850.7331 834.0674"
i=0;
for v in $primitive_volumes; do
a=`echo 'scale=6; e(l('$v'*0.5)/3.0)' | bc -l`
i=`expr $i + 1`
cat > temp.in << EOF
&control
calculation = 'relax'
restart_mode='from_scratch',
prefix='temp',
tprnfor = .true.
pseudo_dir = '$PSEUDO_DIR'
outdir = '$TMP_DIR'
/
&system
ibrav = 0, celldm(1)=$a,
nat = 14, ntyp = 3,
ecutwfc = 45.0, ecutrho = 450.0
/
&electrons
conv_thr = 1.0d-8
/
&ions
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
Mg 24.305 Mg.pw91-np-van.UPF
Al 26.9815 Al.pw91-n-van.UPF
O 15.9994 O.pw91-van_ak.UPF
K_POINTS automatic
6 6 6 0 0 0
CELL_PARAMETERS cubic
1.0 1.0 0.0
1.0 -1.0 0.0
1.0 0.0 1.0
ATOMIC_POSITIONS crystal
Mg0.12500.87500.2500
Mg0.87500.12500.7500
Al0.50000.50000.
Al0.50000.0.5000
Al0.0.50000.
Al0.50000.50000.5000
O0.26230.73770.5246
O0.73770.26230.4754
O0.73770.71310.0246
O0.26230.28690.9754
O0.71310.73770.5246
O0.28690.26230.4754
O0.73770.26230.0246
O0.26230.73770.9754
EOF
Check symmetry operations in output files (grep 'Sym.Ops' *.out):
temp-1.out: 48 Sym.Ops. (with inversion)
temp-2.out: 48 Sym.Ops. (with inversion)
temp-3.out: 48 Sym.Ops. (with inversion)
temp-4.out: 12 Sym.Ops. (with inversion)
temp-5.out: 12 Sym.Ops. (with inversion)
temp-6.out: 12 Sym.Ops. (with inversion)
temp-7.out: 12 Sym.Ops. (with inversion)
temp-8.out: 48 Sym.Ops. (with inversion)
temp-9.out: 48 Sym.Ops. (with inversion)
I think the correct symmetry operations number should be 48 for this
crystal. I don't know how to fix this "improper symmetry analysis" problem.
Can you help me?
--
Kun Yin
Ph.D. Candidate
School of Earth Sciences and Engineering
Nanjing University
502 Geological Laboratory Building
22 Hankou Road
Nanjing 210093
P.R. China
email: kyin.cn at gmail.com
[Pw_forum] effective charges and USPP implementation
Dear Stefano de Gironcoli, Thank you for your reply! -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com - Original Message - From: "Stefano de Gironcoli" To: "PWSCF Forum" Sent: Sunday, April 19, 2009 5:42 PM Subject: Re: [Pw_forum] effective charges and USPP implementation > Dear Kun Yin, > the webpage http://www.pwscf.org/pseudo.htm is outdated and is not > linked anymore from the pwscf website . > effective charges and electron-phonon coefficients are implemented > with USPP. > third order derivatives are not. > > stefano de Gironcoli - SISSA and DEMOCRITOS > > Kun Yin wrote: >> Dear Users and Developers: >> >> PWscf website (http://www.pwscf.org/pseudo.htm) states that "calculations >> of >> effective charges, electron-phonon coefficients, third-order derivatives >> are >> not implemented with USPPs". Does this situation still exist? My primary >> concern is the effective chareges calculation. Please tell me if this >> feature has been implemented with USPPs now, and if yes, from which >> version >> on? Thank you in advance! >> >> -- >> Kun Yin >> Ph.D. Candidate >> School of Earth Sciences and Engineering >> Nanjing University >> 502 Geological Laboratory Building >> 22 Hankou Road >> Nanjing 210093 >> P.R. China >> >> email: kyin.cn at gmail.com >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] effective charges and USPP implementation
Dear Users and Developers: PWscf website (http://www.pwscf.org/pseudo.htm) states that "calculations of effective charges, electron-phonon coefficients, third-order derivatives are not implemented with USPPs". Does this situation still exist? My primary concern is the effective chareges calculation. Please tell me if this feature has been implemented with USPPs now, and if yes, from which version on? Thank you in advance! -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com
[Pw_forum] matdyn.x input file problem
Dear Paolo Giannozzi, You said matdyn.x is waiting for input, I don't understand what kind of 'input' you refered to. I have posted the input file of matdyn.in for the second one in last mail. Can you tell me how to modify it to make it run but wait? Best regards, Kun Yin - Original Message - From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Thursday, April 03, 2008 5:46 PM Subject: Re: [Pw_forum] matdyn.x input file problem > > On Apr 3, 2008, at 11:28 , Kun Yin wrote: > >> Does matdyn.x have a q-vector number limit? > > no > >> The followings are two matdyn.x input file. The difference is >> one has 96 q-vectors >> and the other one has 97 q-vectors, their front 96 vectors are the >> same. The first one >> runs OK with output after a while. But the second one runs without >> any output even error >> message, the CPU utilization of matdyn.x is zero. > > the second one is not running, but waiting for input > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] matdyn.x input file problem
ple', amass(1)=24.305, amass(2)=26.981, amass(3)=15.999, flfrc='mgal2o4-0.88v0_444.fc', flfrq='frequency' / 97 0.5 0.5 0.5 1.0 0.45833 0.45833 0.45833 1.0 0.52083 0.52083 0.45833 1.0 0.54167 0.5 0.45833 1.0 0.41667 0.41667 0.41667 1.0 0.47917 0.47917 0.41667 1.0 0.5 0.45833 0.41667 1.0 0.54167 0.54167 0.41667 1.0 0.56250 0.52083 0.41667 1.0 0.58333 0.5 0.41667 1.0 0.37500 0.37500 0.37500 1.0 0.43750 0.43750 0.37500 1.0 0.45833 0.41667 0.37500 1.0 0.5 0.5 0.37500 1.0 0.52083 0.47917 0.37500 1.0 0.54167 0.45833 0.37500 1.0 0.56250 0.56250 0.37500 1.0 0.58333 0.54167 0.37500 1.0 0.60417 0.52083 0.37500 1.0 0.62500 0.5 0.37500 1.0 0.3 0.3 0.3 1.0 0.39583 0.39583 0.3 1.0 0.41667 0.37500 0.3 1.0 0.45833 0.45833 0.3 1.0 0.47917 0.43750 0.3 1.0 0.5 0.41667 0.3 1.0 0.52083 0.52083 0.3 1.0 0.54167 0.5 0.3 1.0 0.56250 0.47917 0.3 1.0 0.58333 0.45833 0.3 1.0 0.58333 0.58333 0.3 1.0 0.60417 0.56250 0.3 1.0 0.62500 0.54167 0.3 1.0 0.64583 0.52083 0.3 1.0 0.7 0.5 0.3 1.0 0.29167 0.29167 0.29167 1.0 0.35417 0.35417 0.29167 1.0 0.37500 0.3 0.29167 1.0 0.41667 0.41667 0.29167 1.0 0.43750 0.39583 0.29167 1.0 0.45833 0.37500 0.29167 1.0 0.47917 0.47917 0.29167 1.0 0.5 0.45833 0.29167 1.0 0.52083 0.43750 0.29167 1.0 0.54167 0.41667 0.29167 1.0 0.54167 0.54167 0.29167 1.0 0.56250 0.52083 0.29167 1.0 0.58333 0.5 0.29167 1.0 0.60417 0.47917 0.29167 1.0 0.62500 0.45833 0.29167 1.0 0.60417 0.60417 0.29167 1.0 0.62500 0.58333 0.29167 1.0 0.64583 0.56250 0.29167 1.0 0.7 0.54167 0.29167 1.0 0.68750 0.52083 0.29167 1.0 0.70833 0.5 0.29167 1.0 0.25000 0.25000 0.25000 1.0 0.31250 0.31250 0.25000 1.0 0.3 0.29167 0.25000 1.0 0.37500 0.37500 0.25000 1.0 0.39583 0.35417 0.25000 1.0 0.41667 0.3 0.25000 1.0 0.43750 0.43750 0.25000 1.0 0.45833 0.41667 0.25000 1.0 0.47917 0.39583 0.25000 1.0 0.5 0.37500 0.25000 1.0 0.5 0.5 0.25000 1.0 0.52083 0.47917 0.25000 1.0 0.54167 0.45833 0.25000 1.0 0.56250 0.43750 0.25000 1.0 0.58333 0.41667 0.25000 1.0 0.56250 0.56250 0.25000 1.0 0.58333 0.54167 0.25000 1.0 0.60417 0.52083 0.25000 1.0 0.62500 0.5 0.25000 1.0 0.64583 0.47917 0.25000 1.0 0.7 0.45833 0.25000 1.0 0.62500 0.62500 0.25000 1.0 0.64583 0.60417 0.25000 1.0 0.7 0.58333 0.25000 1.0 0.68750 0.56250 0.25000 1.0 0.70833 0.54167 0.25000 1.0 0.72917 0.52083 0.25000 1.0 0.75000 0.5 0.25000 1.0 0.20833 0.20833 0.20833 1.0 0.27083 0.27083 0.20833 1.0 0.29167 0.25000 0.20833 1.0 0.3 0.3 0.20833 1.0 0.35417 0.31250 0.20833 1.0 0.37500 0.29167 0.20833 1.0 0.39583 0.39583 0.20833 1.0 0.41667 0.37500 0.20833 1.0 0.43750 0.35417 0.20833 1.0 0.45833 0.3 0.20833 1.0 0.45833 0.45833 0.20833 1.0 0.47917 0.43750 0.20833 1.0 0.5 0.41667 0.20833 1.0 Have you ever found this problem? Why? Please help me to analyze it, thank you! Kun Yin Department of Earth Sciences, Nanjing University, Jiangsu, Nanjing 210093, People's Republic of China. Email:kyin.cn at gmail.com
