[Pw_forum] pwcond.x;nz1,ewind and epsproj
Hi, In the Input File Description for pwcond.x,what does the term nz1,ewind and epsproj means and how do we choose their values in the example,I have seen that for a 7 unit cells, the nz1 value taken is 11 and for aluminum chain nz=1.My system contains 282 atoms with 7 unit cell,how shall I choose nz,ewind and epsproj values? Thanks and regards DImpy Dimpy Sharma ETG-Group Tyndall National Institute Cork -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100914/02809650/attachment.htm
[Pw_forum] segmentation fault in PWcond calcuation
Hi there, I was trying to calculate transmisson using pwcond,The system contains 282 atoms,my scf calculation for both the lead and scattering run successfully but while running the Pwcond,the calculation stops without giving CRASH file.The output file crashes with the following 6_656: (392.304688) net_send: could not write to fd=5, errno = 32 Segmentation fault segmentation fault. Any advice welcome. Thanks and regards Dimpy Dimpy Sharma ETG-Group Tyndall National Institute Cork -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100909/6cb041e8/attachment.htm
[Pw_forum] How to choose the energy0 value while doing a Ballistic conductance using the code pwcond.x
Hi there, My warm greetings to all of you. I would like to know how do we choose the energy0 (inital energy ) while doing a ballistic conductance using pwcond.x.As from the example and manual it mentions as the inital energy,which energy does it refer to?is this the total energy of the system ?I could not follow the term nenergy as well.Any advice would be appreciated. Thanks and regards Dimpy Dimpy Sharma ETG-Group Tyndall National Institute Cork -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100907/53c073ac/attachment-0001.htm
[Pw_forum] Giving shift in K points
Hi Quantum espresso user, I have to run plane wave calcuation on a periodic stucture to predict the band gap,as my system has 200 atoms (which has 5 unit cells),thus for scf I prefer to choose the k point as K_POINTS automatic 1 1 1 0 0 0 where I gave the shift as 0.I would like to ask is it possible to give shift in K_Points for periodic system?as the concept is not clear to me ,can anyone please suggest me some papers or book ?and I would be very greatfull if my question is answered. Thanks a lot in advance Dimpy. Dimpy Sharma ETG-Group Tyndall National Institute Cork -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100823/a98b5d63/attachment.htm
[Pw_forum] Predicting the cpu time usage for bigger system withour doing the simulation
Hi Quantum espresso users. I would like to predict an approximate CPU time usage to finish one scf calculation in quantum espresso for a system with 5 supercells. I have the CPU time usage for the same sytem with one supercell.So are there any possible ways to predict the time needed for more number of supercell (for the same system) required in quantum espresso,without doing the simulations.Can I calcuate it from the following method Tscf= NiterTiter + Tinit Thanks and Regards. Dimpy Dimpy Sharma ETG-Group Tyndall National Institute Cork -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100720/ec120694/attachment.htm
[Pw_forum] Calculation Crashes by running at different processors fort he same system.
Hello all, I was running some test calcuations to predict the CPU-time usage at different number of processors, however for the same system I can see that for certain number of processors (like at 4,8,16) the calculations run and finish properly however it crashes at different number of processors by saying the Cholesky decompostion as error message.Can anybodody give me some suggestions? Thanks in advance. Dimpy Dimpy Sharma ETG-Group Tyndall National Institute Cork Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100713/26831b47/attachment.htm
[Pw_forum] Plane waves parallelization
Hi Quantum espresso users, I was trying to run a scf calculation for my system (518 atoms), I used 100 nodes to simulate the system however it crashed after 3 iterations without any error message (consumed 883MB).I used K_Points 2x1x1. From the user guide , I was reading the parallelism in quantum espresso,I could not follow "pools" and plane wave parallelization, and how to do the K_Point sampling in mpi parallelization for my system. Thanks and regards! Dimpy Msc(Nanotechnology) PhD UCC,Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100404/6d587d56/attachment.htm
[Pw_forum] nscf calculations
Hi there, I have submitted my input file for nscf calcuation with 22 kpoints ( for the first brilloiun zone from kpoint from k=0 to 0.47) however in the output file of nscf , it calcuates the eigenvalues at k points 0,0.148,0.2960..3.1076 .Thus while plotting the band diagram my kvectir range becomes upto 3.1076. May I know why it happen? and to calculate the eigenvalues only on the given kpoints in th input file? Thanks Dimpy Dimpy Sharma(Msc Nanotechnology PhD) UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100324/499560d6/attachment.htm
[Pw_forum] simulations at 100 nodes
Hi everyone, I have to run my nscf calculation at 100 nodes for just 5 k points, I have tired running at 80 nodes.but in that case it crashes without any error message.I cannot increase my k points more than 5.And I want to plot the band structure so,I need atleast 25 kpoints. Can anyone give me some advice ? Thanks a million ! Dimpy (PhD) UCC,Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100308/0210683c/attachment.htm
[Pw_forum] spilling parameter
Hi Friends, The term spilling parameter is not much clear to me, though I read in forum.It would be great if anyone can help me. Also I would like to know is there any standard value for spilling paramter for Si-H system. Thanks and regards Dimpy (PhD) UCC,Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100302/b4451b36/attachment.htm
[Pw_forum] summation of total PDOS does not matches the Total DOS
Hi quantum espresso users, The summation of all the projected density of states is not matching the total density of states at higher energy.I repeated my calculationby reducing the number of bands. I got a spiiling parameter of 0.0174. My system is Si and H.Can anyone please tell me , where can I get some refrences about the spilling parameter .I used the following parameters etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 wf_collect = .true ecutwfc = 40 ecutrho = 160.0 diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.3 Thanks and regards Dimpy UCC,Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100224/bf66a434/attachment.htm
[Pw_forum] difference in DOS nad total projected density of states
Hi everybody, Thanks a lot for replying my previous question! I would like to ask one more question.Its about the projected density of states. I calculated the projected density of states ,and upon plotting the datas of output file pdosout_tot ,I found that my total density of states is higher than my total projected density of states.As the summation of all the PDOS must be same as total density of states.Is it because of some error in my input file? Thanks a million! Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100218/9eea80f4/attachment.htm
[Pw_forum] scf calculation for isolated hydrogen atoms
Hi there, I tried to calculate the ground state energy for isolated hydrogen atom with the following input,however I got the fermi energy level at -3.5661eV, while it should be -13.6eV. &CONTROL. calculation ='scf' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/eigenvaluesSi/wf_H/' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'H' tstress = .true. tprnfor = .true. wf_collect =.true. / &SYSTEM ibrav = 1 celldm(1) = 15 nat = 1 ntyp = 1 ecutwfc = 40 ecutrho = 160.0 nbnd = 2, nspin=2, starting_magnetization(1)=0.5 nosym=.true., occupations='smearing', smearing='mp', degauss=0.01, / &ELECTRONS diagonalization ='cg' mixing_mode = 'local-TF' conv_thr = 1.0d-6 mixing_beta = 0.7 / ATOMIC_SPECIES H 1.00794 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms H 0. 0. 0. K_POINTS automatic 1 1 1 0 0 0 Thanks Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100211/e6357167/attachment.htm
[Pw_forum] davico error in calculating projected density of states.
Hi there, I wanted to calculate the projected density of states and thats why I performed scf, then nscf calculation which run successfully, however while calculating the Projectede density of states I found the following error davico error #10 from the previous discussion on this error, what I understood is sometimes that some wavefunction files are being corrupted. Thus I just kept one file filename.save and tried to rerun the calculation, this time it is showing me error in the file. shall I start my calculation from the beginning? I mean from scf? Kindly help! Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100210/71afdb05/attachment.htm
[Pw_forum] Cholesky decompsition in nscf calculation
Hi there, My scf calculation runs sucessfully hwoever the calculation is crashing if I perform the nscf calculation.Only changes I have made is I have taken 15 k points in my nscf calculation.The error message shows as follows : task #15 from pzpotrf : error #30 problems computing cholesky decomposition Suggestions welcome! Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100210/ad9a6c65/attachment-0001.htm
[Pw_forum] Calculation is crashing without any error message
i there, I have tried to run my scf calculation in 80 cpu, howeevr it is crashing without giving me any error message.It finished 17 iterations.Can anybody give any advice. I have checked it in Forum earlier and modified my input still I am getting similar error. Here is my input file is &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'Input2' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-8 forc_conv_thr = 1.D-8 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =14.5152 nat = 518 ntyp = 3 ecutwfc = 35 ecutrho = 120 nbnd = 1618 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.00.00.0 0.07.00.0 0.00.07.0 ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPF O15.9994 O.pz-rrkjus.UPF H1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 1.3859 18.2956 15.1401 . .. K_POINTS automatic 2 1 1 0 0 0 My file is too big. I am sorry for this ! Thanks and regards! Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091227/2ce39f30/attachment.htm
[Pw_forum] too many bands are not converging
Hi there, I have been trying to run a nscf calculation, after finishing my scsf calculation, howvever I am getting the following error 'too many bands are not converged', what I can get from previous question that 'changing mixing beta or diagonalisation ' will run it.I have tried that but it wonnt work.I have even number of electrons , so I ignored occupation. Also due to memory problem I have decided to take less number of k points, I mean I will break my kpoints in parts and will continue my calculations. Can anybody please help me! &CONTROL calculation ='nscf' restart_mode ='from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'Kpoint4' tstress = .true. tprnfor = .true. forc_conv_thr=2.D-4 etot_conv_thr=1.D-8 nstep=600 / &SYSTEM ibrav = 0 celldm(1) =14.5152 nat = 321 ntyp = 3 ecutwfc = 35 ecutrho = 120 nbnd = 742 nosym=.true. smearing='gaussian' / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-8 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.00.00.0 0.05.80.0 0.00.05.8 ATOMIC_SPECIES Si 28.0855 Si.pz-vbc.UPF O15.9994 O.pz-rrkjus.UPF H1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 7.4734 12.9443 16.0594 Si 0.9063 12.9082 11.9628 K_POINTS crystal 2 -0.5 -0.5 -0.5 1. -0.46000 -0.5 -0.5 1. Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091222/c12c1f68/attachment.htm
[Pw_forum] too few bands or 'charge is wrong
Hi there, I would like to ask one thing,as I face this problem almost in every calculation, it is about 'nbnd ' in quantum espresso input. Actually I use to calculate the nbn as per the rule given in manual i.e I use to take 20% more number of valence bands( actually I calculate total number of electrons and then divide them by 2 and take 20% extra electrons ), but since my last few calculations, if I take this value in nbn, I always get 'too few bands', thus now I am giving a random value in nbn when I get either 'charge is wrong'. My apologise, is it because of nbnd value or is there chance of any other error in my input file?I am running a scf calculation with K_points '2 1 1 0 0 0'. Actually I have tried varying other parameters like mixing beta, but I get the same output? Thanks and regards! Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091220/57121359/attachment.htm
[Pw_forum] calculating eigenenergy of single atom using QE
Hi there, I have tried to calculate the eigen energy of an isolated Hydrogen atom using quantum espresso, however in the output file it is showing me 'charge is wrong'. I guess my input file is correct. I used 1 node to run the calculation. My input file is as given below! &CONTROL calculation ='scf' restart_mode = 'from_scratch' outdir = '/' pseudo_dir = '/' prefix = 'H' tstress = .true. tprnfor = .true. wf_collect =.true. / &SYSTEM ibrav = 0 celldm(1) = 1 nat = 1 ntyp = 1 ecutwfc = 40 ecutrho = 160.0 nbnd = 2 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.00.00.0 0.02.00.0 0.00.02.0 ATOMIC_SPECIES H 1.00794 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms H 0. 0. 0. K_POINTS automatic 1 1 1 0 0 0 suggestions welcome! Thanks and regards Dimpy UCC Ireland -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091219/8b34bc38/attachment.htm
[Pw_forum] Relax calculation not converging
Hi Quantum espresso users, I have been trying to perform a relax calculation in my system with 99 atoms (semiconductor system) and I am running my calculation in 48 processors. The calculation has finished 3 scf steps and finished 100 iterations, but after this it stops and it is showing me the following message . ' convergence NOT achieved after 100 iterations: stopping' I have restart my calculation, still I got the same error message after 100 iteration steps. Can any body give me any suggestion? Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091009/1191e362/attachment.htm
[Pw_forum] Energy convergence in a scf calculation
Hello there, One of my scf calculation is running ( not yet finished), it has completed almost 10 iterations, however what I have found is in iteration #8, it is showing me as CG style diagonalization c_bands: 3 eigenvalues not converged c_bands: 5 eigenvalues not converged ethr = 1.00E-02, avg # of iterations = 8.6 After that it is still running and moved to iteration #10. Also I have seen that in some of the iteration steps the energy is either increasing or decreasing in the successive steps;i.e it is not converging .My thresold values are as follows etot_thr= 1.D-8 forc_thr values =1.D-8Ry conv_thr = 1.0D-8Ry . ecutwfc=35Ry ecutrho=120Ry So can anybody tell me why is it happening so? Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/ebb42a7f/attachment.htm
[Pw_forum] Band structure calculation
Hi Quantum espresso user, I have been trying to perfom a band structute calculation in my system which is running in 32 processors, it is still running, however in the output I got the following information. Band Structure Calculation CG style diagonalization c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalues not converged I used 15 k points for my calculations. Can anybody give any suggesstion ? Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/8509c051/attachment.htm
[Pw_forum] Request for Pseudopotentials for Si and H
Hi There, Thanks for your help, however I did not need these Pseudopotentials as I already have these ( Si.pz-vbc.UPF and H.pz-vbc.UPF ). I need the following or else if I use these values my calculations did not run. The one which I need are as follows. Si 28.08600 Si.vbc.UPF and H1.00800 H.vbc.UPF Thanks Shapta. -Original Message- From: pw_forum-bounces at pwscf.org on behalf of pw_forum-requ...@pwscf.org Sent: Sat 8/15/2009 7:35 AM To: pw_forum at pwscf.org Subject: Pw_forum Digest, Vol 26, Issue 44 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: matdyn error (Mikiyas Tsegaye) 2. Re: matdyn error (Paolo Giannozzi) 3. Re: line crossing Valance bands (VB) & CB (Paolo Giannozzi) 4. Request for Pseudopotentials Si and H (Shaptrishi Sharma) 5. Re: Request for Pseudopotentials Si and H (Manoj Srivastava) 6. Re: Request for Pseudopotentials Si and H (Stefano Baroni) -- Message: 1 Date: Fri, 14 Aug 2009 10:13:46 -0400 From: Mikiyas Tsegaye Subject: Re: [Pw_forum] matdyn error To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="us-ascii" Dear Rakshit, I'm just copy pasting from a previous answer in the forum to the same question: it might help, it might not. Hello, Assuming that there are no problems of numerical inaccuracy or inadequate convergence thresholds, negative frequencies at gamma point in a geometry-relaxed system usually mean that (within the system and the calculation method used) there is some distortion (decreasing the symmetry of the system) which leads to lower energy, i.e. you are at a saddle point in the energy hypersurface. You must move some atom out of the initial symmetry and optimize geometry again starting from that modified situation. If you can obtain the vector coordinates for the normal mode of vibration corresponding to the negative frequency, a displacement of the involved atoms, proportional to that normal mode, by e.g. a maximum of 0.2 angstrom will give to you a starting displaced geometry closer to the true energy minimum. Sometimes you need to do this several times if not all of the negative frequencies disappear after the first attempt. If, after obtaining a new geometry with no negative frequencies at the gamma point, you still have negative frequencies at other BZ points, this means that your system is unstable against some atomic displacements that multiply some of the primitive cell vectors by e.g. 2 or 3, leading to a supercell. Curing this situation may be more tedious. Good luck, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 > > > Message: 3 > Date: Fri, 14 Aug 2009 11:25:23 +0530 > From: Bipul Rakshit > Subject: [Pw_forum] matdyn error > To: PWSCF Forum > Message-ID: > <3a749910908132255x13311317j4eb55858c46affe0 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear pwscf users, > > I am doing Gamma point phonon analysis for LaMnO3, after running > matdyn.x i > am getting the following, error. > > Norm of the difference between old and new effective charges: > 0. > Norm of the difference between old and new force-constants: > 0.20461738165775616993 > 0.833 > > % > % > from frc_blk : error # 1 > wrong total_weight > % > % > > stopping ... > 2 > > Since at gamma point i am getting some -ve freq. the sum rule i want > to > apply. And to see the final frequencies after applying sum rule. > > Kindly guide me and suggest for the possible reason for this error. > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0001.htm > -- next part -- > A non-text attachment was scrubbed... > Name: lamno3.ph.in > Type: application/octet-stream > Size: 316 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20090814/9aeba1c4/attachment-0003.obj > --
[Pw_forum] Calculation of spin polarisation from PWscf
Hi there, I want to know how do we perform calculation for spin polarisation in PWscf, as I have odd number of electrons in my system. However I have one more thing to ask, in my previous system as I already wrote charge is wrong apperedin the output, but in that system there are even number of electrons, so is their any other probable reason? Can anybody help? Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090814/fab6c3db/attachment.htm
[Pw_forum] Charge is wrong ...in the output file
Hi QEs users, I got an error in my output file as follows %% from electrons : error # 1 charge is wrong %% However from my previous survey in PW_forum, I have found that this problem may be due to not doing spin polarized calculation with an odd number of electrons, what does it mean? My input file is &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/sfihome/dsharma/Pscf/test' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'Pscf1' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =20.40066 nat = 94 ntyp = 3 ecutwfc = 30 ecutrho = 120 nbnd = 220 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.00.00.0 0.01.00.0 0.00.05.0 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H1.00800 H.pz-vbc.UPF O 15.9994O.pz-rrkjus.UPF ATOMIC_POSITIONS angstroms O 7.07816.9497 27.1761 O 4.39526.9992 27.2391 H 7.45996.0212 27.1358 H 5.39217.0051 27.1349 H 1.56154.4933 27.1304 Si 3.42770.5123 26.6794 Si 7.26343.3235 26.6750 Si 0.44700.4413 26.6627 K_POINTS automatic 2 2 1 0 0 0 Can anyboy please help? DS. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/8208bef7/attachment.htm
[Pw_forum] (no subject)
Hi there, I have tried to perform scf alculation in my system, however the result is not converged,It stopped after first few iterations. Instead the output shows following error p4_16508: p4_error: interrupt SIGx: 13 rm_l_23_24807: (392.835938) net_send: could not write to fd=5, errno = 32 rm_l_5_16527: (398.265625) net_send: could not write to fd=5, errno = 32 mpirun: got sig, my pid is 17869 childs pid is 18462 mpirun My input file is as follows &CONTROL calculation ='scf' restart_mode ='from_scratch' outdir = '/sfiwork/dsharma/test/ pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'dsh' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =14.895468 nat = 780 ntyp = 2 ecutwfc = 35 ecutrho = 120 nbnd =1700 / &ELECTRONS diagonalization ='cg' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 / CELL_PARAMETERS cubic 1.00.00.0 0.01.00.0 0.00.06.0 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si4.4286589228.103176805 29.794371687 Si4.336832871 18.551141820 20.425720839 Si3.983248480 19.970914222 26.328297321 .. Kindly advice me! Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/126ed455/attachment.htm
[Pw_forum] Pw_forum Digest, Vol 26, Issue 34
Thanks for your advice, however as per the information given in the output, %% from read_cards : error # 691 species H in ATOMIC_POSITIONS is nonexistent % At this position the Hydrogen atom has got coordiantes a 0.00 in all the three axes. Thus any other suggestions?? Thanks Dimpy -Original Message- From: pw_forum-bounces at pwscf.org on behalf of pw_forum-requ...@pwscf.org Sent: Tue 8/11/2009 1:48 PM To: pw_forum at pwscf.org Subject: Pw_forum Digest, Vol 26, Issue 34 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: generating k point weights (Stefano Baroni) 2. Re: generating k point weights (xirainbow) 3. Error in output file (Dimpy Sharma) 4. Re: Error in output file (Lorenzo Paulatto) 5. Re: Error in output file (lan haiping) 6. Re: TDDFT and GW (Geoffrey Stenuit) 7. Doubt in Phonon calculations (Bipul Rakshit) -- Message: 1 Date: Tue, 11 Aug 2009 10:10:52 +0200 From: Stefano Baroni Subject: Re: [Pw_forum] generating k point weights To: PWSCF Forum Message-ID: <5E60B11C-C950-48FA-A781-FC117B3EED06 at sissa.it> Content-Type: text/plain; charset="utf-8" YOU have written the answer to your question "If .true. the bands are classified according to the irreducible representations of the small group of k" (which is the only sensible thing to do) Stefano Baroni - SISSA Trieste --- swift text written and sent on the go On 11/ago/2009, at 04.02, xirainbow wrote: > Dear Stefano Baroni and Gabriele Sclauzero: > > First of all, thank you very much for your detailed explanation :? > I think I fully undertand it. > First, the "kpoints.x" reduces the number of k-points according to > parameter "ibrav". That means kpoints.x chooses the symmetry among > 14 Bravais lattices. > Second, the "pw.x" checkes all symmetry operations within a given > Bravais lattice determined by kpoints.x. That means pw.x determines > the symmetry among 7 crystal systems. > > But, now I have a another question about bands.x. > In the instruction of bands.x, it says: > Presently it can calculate: >(a) The expectation value of the spin operator on each spinor > wave-function. >(b) The symmetry properties of each wavefunction. > The instruction of parameter "lsym" says: > If .true. the bands are classified according to the irreducible > representations of the small group of k. A file "filband".rap with > the same format of "filband" is written. > > I want to know the symmetry properties obatained by "band.x" is > based on 7 crystal systems, 14 Bravais lattices or 32 point groups. > > Once again, thank you very much ?? > > > Hui Wang > School of physics, Nankai University, Tianjin, China > ___ > 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/20090811/444e9e73/attachment-0001.htm -- Message: 2 Date: Tue, 11 Aug 2009 16:28:06 +0800 From: xirainbow Subject: Re: [Pw_forum] generating k point weights To: PWSCF Forum Message-ID: <21fbc4790908110128m1407479h86629f33ca9be122 at mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Stefano Baroni: >YOU have written the answer to your question >"If .true. the bands are classified according to the irreducible representations of the small group >of k" (which is the only sensible thing to do) Sorry, I almost forgot the definition of "small group". I refered to text book and found the answer ?? Thank you for your concise reply ?? Hui Wang School of physics, Nankai University, Tianjin, China ------ next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/f9c371a6/attachment-0001.htm -- Message: 3 Date: Tue, 1
[Pw_forum] Error in output file
Hi Quantum espresso users, I have tried to set up calculation in quantum espresso , however in the output file, it is showing as %% from read_cards : error # 1 wrong number of columns in ATOMIC_POSITIONS %%% I have given the coordinates directly from my structure as I got in Material studio, Can anybody please help me? Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090811/d8668080/attachment.htm
[Pw_forum] Volume in a supercell
Hi Quantum espresso user, I would like to know how do we fix the cell parameters for a supercell while running any calculation with quantum espresso as from the manual it has been mentioned about lattice vector which is not making it clear ? How shall we relate the lattice parameter with the volume added in order to avoid any overlapping? Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090731/b1dfc3e7/attachment.htm
[Pw_forum] Pw_forum Digest, Vol 25, Issue 10
Hi Paolo, I want to know about calculating strain from Q.E , howver from stress also we can calculate stress,as we can relate stress and strain . DS -Original Message- From: pw_forum-bounces at pwscf.org on behalf of pw_forum-requ...@pwscf.org Sent: Wed 7/8/2009 11:38 AM To: pw_forum at pwscf.org Subject: Pw_forum Digest, Vol 25, Issue 10 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. vc-relax (ali kazempour) 2. Re: vc-relax (Lorenzo Paulatto) 3. Errors in examples of QuantumEspresso (leila salimi) 4. Errors in examples of QuantumEspresso (leila salimi) 5. Strain calculation through quantum espresso (Dimpy Sharma) 6. Re: Strain calculation through quantum espresso (Paolo Giannozzi) 7. Re: Errors in examples of QuantumEspresso (Paolo Giannozzi) -- Message: 1 Date: Wed, 8 Jul 2009 02:03:55 -0700 (PDT) From: ali kazempour Subject: [Pw_forum] vc-relax To: pw Message-ID: <511270.21408.qm at web112502.mail.gq1.yahoo.com> Content-Type: text/plain; charset="us-ascii" Can I use vc-relax to optimize the value of lattice constant in ZnO wurtzite structure?Because the lattice constant change and also atomic positions either. After finishing the run, Which atomic position shoud be used in next calculation(relaxed position or initial positions)? How can I optimize the value of u that is ideally equal to 3/8? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran.Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090708/7b0b1a07/attachment-0001.htm -- Message: 2 Date: Wed, 8 Jul 2009 11:33:29 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] vc-relax To: "PWSCF Forum" Message-ID: <42848.78.12.162.251.1247045609.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Wed, July 8, 2009 11:03, ali kazempour wrote: > Can I use vc-relax to optimize the value of lattice constant in ZnO > wurtzite structure? Dear ali, of course you can! > Because the lattice constant change and also atomic > positions either. You can nail the atoms to their position by adding " 0 0 0" after the atomic coordinates (see manual for detail), although it only make sense for crystal and possibly alat coordinates, when you are doing vc-relax. > After finishing the run, Which atomic position shoud be > used in next calculation(relaxed position or initial positions)? The optimized ones, if not, why would you do the optimization? > How can I > optimize the value of u that is ideally equal to 3/8? Doing vc-relax, I don't see the problem )I asume you are using this notation: http://cst-www.nrl.navy.mil/lattice/struk/b4.html). If you want the Zn atoms to stay in z=0 you can fix their position as explained above; nevertheless "u" is just the difference in the z coordinate of Zn and O atoms. > thanks a lot you are welcome, best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- Message: 3 Date: Wed, 8 Jul 2009 14:29:38 +0330 (IRST) From: leila salimi Subject: [Pw_forum] Errors in examples of QuantumEspresso To: pw forum Message-ID: <2112806.51091247050778893.JavaMail.root at mta.iut.ac.ir> Content-Type: text/plain; charset="utf-8" Hi every body, I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. and I used the special make.sys which is matched with our system and then ?make pwall? was successful but now I'm getting the following error trying to run the examples. I will attach "make.sys" and "environment_variables" to this mail. Do you have any idea what is going wrong? Best Regards, Leila Salimi. Isfahan University of Technology, Isfahan, Iran. ?from ewald : error # ? ? ? ? 1 > ? ? ?optimal alpha not found running the scf calculation.
[Pw_forum] Strain calculation through quantum espresso
Hi Quantum espresso users, Could anyone please tell me how to calculate strain of a supercell through quantum espresso, as in the manual it has not been mentioned properly. Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090708/f7bb5b4b/attachment.htm
[Pw_forum] cholesky decomposition
Hi Quantum espresso user, I have tried to run a calculation on a sytem using fractional coordinates of the system, however I ahve found that while suing fractioanl coordinates the itreations are not finished and in the erro it is showing problem in computing in cholesky decomposition. However while using atomic coordiantes, I can successfullt get my output, can anybody please help me . Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090707/244699d9/attachment.htm
[Pw_forum] Error in output in calculating stress
Hi Quantum espresso users, I tried to calculate stress for a sytem by performing a scf calculation, presently I am running two diffrenet calculations by varying the lattice paarmeter of the system, howvever, I have found that at cell dimension either smaller or greater than the optimum lattice parameter, I cannot find the output, instead it is showing rm_l_6_1007: (61.828125) net_send: could not write to fd=5, errno = 32 can any body please give me a possible reason for the error, also I want to ask one more thing, will there be any difference in my output result, if instead of atomic coordinates, I use fractional coordinates? Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090707/cbf92e9b/attachment.htm
[Pw_forum] Stress calculation in SCF
Hi Quantum espresso user, I want to calculate stress and my calculation is a scf calculation,howevr it is not converged, in the output it is showing that problme in cholesky decomposition. can anybody please help me in giving an explanation to this? as in the manual it is written that stress can only be calculated if calculation is either vc-md or vc-relax. Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090706/c012f123/attachment.htm
[Pw_forum] Stress calculation in quantum espresso
Hi Quantum espresso users I want to calculate stress for a system using quantum espresso, I know that setting tstress=true in the first namelist $ control, but that one is for vc-md. I want to calculate stress using a relax and scf calculation, Can anyone help me. Thanks Dimpy -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090629/e628cb04/attachment.htm
[Pw_forum] (no subject)
Hi Can anybody please tell me the difference meaning of ecut_conv_thr and forc_conv_thr -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/9a849e2a/attachment.htm
[Pw_forum] Hi
Hi everybody, Can anybody please tell me how to recognise whether the input values for DFT calculations involve norm conserving pseudopotentials. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/edbdf42e/attachment.htm
[Pw_forum] (no subject)
Hi everybody, can anybody please tell me why my the following program get crashed. &CONTROL calculation ='relax' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/silane/wfc5' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = '1' tstress = .false. tprnfor = .true. etot_conv_thr = 1.D-3 forc_conv_thr = 1.D-4 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =6.9371 nat = 6 ntyp = 2 ecutwfc = 35.0 ecutrho = 100 nbnd = 10 / &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-8 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.00.00.0 0.02.00.0 0.00.02.0 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 2.95020 -0.66592 -0.12341 Si 4.909390.617490.11358 H5.117461.46255 -1.09398 H4.698231.559151.25968 H2.84169 -1.617791.02344 H3.00948 -1.48841 -1.36525 K_POINTS automatic 4 1 1 0 0 0 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/6ac39bbb/attachment.htm
[Pw_forum] (no subject)
Hi, Can anyone please explain me the significance of ecutwfc and ecutrho in quantum espresso input file. And what is the diffeence between these two values. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/24f1be34/attachment.htm
[Pw_forum] Queries
Hi, I am not getting my output . My input file is given below. I have kept the kinetic energy cut of for the wavefunction (ecutwfc) as 35Ry. Can you please tell me. &CONTROL calculation ='relax' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/silane/wfc4' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = '5' tstress = .false. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =7.1516 nat = 6 ntyp = 2 ecutwfc = 35.0 ecutrho = 100.0 nbnd = 10 / &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-1 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.00.00.0 0.02.00.0 0.00.02.0 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 2.95020 -0.66592 -0.12341 Si 4.909390.617490.11358 H5.117461.46255 -1.09398 H4.698231.559151.25968 H2.84169 -1.617791.02344 H3.00948 -1.48841 -1.36525 K_POINTS automatic 4 1 1 0 0 0 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/a62334da/attachment.htm
