[Pw_forum] vc-relax, GGA
> > Dear Santos Using vc-relax variable, all cell parameters ( distances and angles) are optimized so one may obtain some parameters lower than expected. Did you consider symmetry in your job or not? this would affect the resuls. I think that your obtained value is plausible. vc-relaxed calculation in quantum espresso works very well and effective. Best Wishes Masoud Nahali SUT > Hello PWscf users. I optimize a triclinic cell using the vc-relax, GGA > functional. My expectation was that all values of the calculated parameters > were > slightly higher than the respective experimental values. But, the angle > alpha > showed a value slightly lower. The experimental value is in degree, 103.32, > the > calculated value is 102.6. There is some inconsistency in this result? > > Sincerely, > A. S. Santos > > Univesidade Federal Fluminense > Niter?i-Rio de Janeiro-Brasil > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/19c8ccef/attachment.htm
[Pw_forum] Surface simulation....
Dear QE users I have some doubts, not exactly related to QE but i need to solve these problems to continue using the QE to finish my calculations on adsorption of some molecules in MgO surface.. I want to simulate an MgO surface (slab) with 7x7 atoms in XxY axes and 6 atoms in Z axis I need the positions of the atoms to have my input file, than i can make a "relax" calculation os this surface... I tryed to get the MgO.cif file and make a supercell from it, but i had no success... If you can help me with this i really appreciate And i need to know the multiplicity of this surface, how could i know it? Sorry because i have basic questions, and thank you a lot - Thiago Guerra Mestrando - Programa de P?s Gradua??o em Engenharia de Defesa Instituto Militar de Engenharia (IME) Pra?a General Tib?rcio, 80 Praia Vermelha - Rio de Janeiro - RJ CEP: 22290-270 Brazil Mobile: (21) 8444-9186 E-mail: guerrathiago at gmail.com -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/8db084f0/attachment.htm
[Pw_forum] error in pseudopotential generation
Dear users, I have faced this error while trying to generate a pseudopotential for Ti. %% from ld1_readin : error # 1 Two wavefunctions for the same l %% Can any one tell me what's wrong? Thanks in advance. This is my input file: title='Ti', zed=22.0, rel=1, iswitch=3, rlderiv=2.50, eminld=-4.0, emaxld=4.0, deld=0.02, nld=5, config='[Ne] 3s2 3p6 3d2 4s2 4p0', dft='PBE' / pseudotype=1 lloc=0, file_pseudopw='Ti.ncpp', ! nlcc=.true., ! rcore=0.8, / 5 3D 5 2 2.00 0.00 1.0 1.0 3P 4 1 6.00 0.00 2.7 2.7 4P 3 1 0.00 0.00 2.7 2.7 3S 2 0 2.00 -0.00 2.2 2.2 4S 1 0 2.00 -0.00 2.2 2.2 -- - Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/99af169d/attachment.htm
[Pw_forum] error in pseudopotential generation
On Tue, 24 Aug 2010 15:14:23 +0200, mohaddeseh abbasnejad wrote: > Two wavefunctions for the same l > [...] > file_pseudopw='Ti.ncpp', Dear Mohaddeseh, the old ncpp format only supports one wavefunctions per angular momentum, which is incompatible with your semi-core configuration. You will have to use the UPF format: just change the pseudopotential file name to something ending in .UPF, i.e. Ti.ncpp.UPF. 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] ambiguous results with vc-relax
sorry for interrupting you guys, I didn't follow the whole post before. Pressure calculations need very high ecutoff. And,according to my experience, vc-relax is supposed to be slow. So, I usually avoid vc-relax if possible... Last but not least, I am a student, maybe very wrong. Have a good day. -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/28af1bbb/attachment-0001.htm
[Pw_forum] Problem about applying US-PP in Au
Dear Pwscf users
I use pwscf for simulation of Au cluster (RAM = 8 GIGABYTE , PROCESSOR =
QUADCORE 2.8 , OPERATION SYSTEM =
UBUNTU 9.10) . With employing all of (ultrasoft) pseudopotentials*** *in
espresso site, I face to the segmentation
fault error but with employing a non-US pseudopotential this error
disappeares.
Would you please helping me about solving this error ?
input file :
calculation='scf'
title='Au_ Pd_surface'
restart_mode='from_scratch'
outdir='./tmp'
prefix='Au_Pd'
etot_conv_thr=1.0D-4
pseudo_dir = '/home/reza/pseudo/'
/
ibrav= 6, celldm(1) = 23.137,celldm(3)=2,nat= 72, ntyp= 1,
ecutwfc =40.0, ecutrho=400.0,
occupations='smearing',smearing='mp',degauss= 0.01,
nspin=1
/
electron_maxstep=100,
conv_thr=1.0D-6,
mixing_beta=0.5,
/
/
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
Au 00 0
Au 2.042.04 0
Au 02.04 2.04
Au 2.040 2.04
Au 4.080 0
Au 6.122.04 0
Au 4.082.04 2.04
Au 6.120 2.04
Au 8.160 0
Au 10.22.04 0
Au 8.162.04 2.04
Au 10.20 2.04
Au 04.08 0
Au 2.046.12 0
Au 06.12 2.04
Au 2.044.08 2.04
Au 4.084.08 0
Au 6.126.12 0
Au 4.086.12 2.04
Au 6.124.08 2.04
Au 8.164.08 0
Au 10.26.12 0
Au 8.166.12 2.04
Au 10.24.08 2.04
Au 08.16 0
Au 2.0410.2 0
Au 010.2 2.04
Au 2.048.16 2.04
Au 4.088.16 0
Au 6.1210.2 0
Au 4.0810.2 2.04
Au 6.128.16 2.04
Au 8.168.16 0
Au 10.210.2 0
Au 8.1610.2 2.04
Au 10.28.16 2.04
Au 00 4.08
Au 2.042.04 4.08
Au 02.04 6.12
Au 2.040 6.12
Au 4.080 4.08
Au 6.122.04 4.08
Au 4.082.04 6.12
Au 6.120 6.12
Au 8.160 4.08
Au 10.22.04 4.08
Au 8.162.04 6.12
Au 10.20 6.12
Au 04.08 4.08
Au 2.046.12 4.08
Au 06.12 6.12
Au 2.044.08 6.12
Au 4.084.08 4.08
Au 6.126.12 4.08
Au 4.086.12 6.12
Au 6.124.08 6.12
Au 8.164.08 4.08
Au 10.26.12 4.08
Au 8.166.12 6.12
Au 10.24.08 6.12
Au 08.16 4.08
Au 2.0410.2 4.08
Au 010.2 6.12
Au 2.048.16 6.12
Au 4.088.16 4.08
Au 6.1210.2 4.08
Au 4.0810.2 6.12
Au 6.128.16 6.12
Au 8.168.16 4.08
Au 10.210.2 4.08
Au 8.1610.2 6.12
Au 10.28.16 6.12
K_POINTS {automatic}
2 2 1 1 1 1
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[Pw_forum] Res: vc-relax, GGA
Dear Nahali Is there any reference in which I get more information about vc-relax? Sincerely, A. S. Santos Univesidade Federal Fluminense Niter?i-Rio de Janeiro-Brasil De: Masoud Nahali Para: pw_forum at pwscf.org Enviadas: Ter?a-feira, 24 de Agosto de 2010 15:14:41 Assunto: Re: [Pw_forum] vc-relax, GGA Dear Santos Using vc-relax variable, all cell parameters ( distances and angles) are optimized so one may obtain some parameters lower than expected. Did you consider symmetry in your job or not? this would affect the resuls. I think that your obtained value is plausible. vc-relaxed calculation in quantum espresso works very well and effective. Best Wishes Masoud Nahali SUT Hello PWscf users. I optimize a triclinic cell using the vc-relax, GGA >functional. My expectation was that all values of the calculated parameters were >slightly higher than the respective experimental values. But, the angle alpha >showed a value slightly lower. The experimental value is in degree, 103.32, the >calculated value is 102.6. There is some inconsistency in this result? > >Sincerely, >A. S. Santos > >Univesidade Federal Fluminense >Niter?i-Rio de Janeiro-Brasil > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/cf117dcb/attachment.htm
[Pw_forum] ambiguous results with vc-relax
Hi, Can you please elaborate on how you selected your ecutwfc? regards, On Mon, Aug 23, 2010 at 10:48 AM, jia chen wrote: > I did similar thing before, total energy doesn't need to converge... > > On Mon, Aug 23, 2010 at 2:22 AM, Guda Karthik > wrote: > > Hi, > > > > The total energy doesn't converge till 80 Ryd of ecutwfc. I am using > Ni > > and Ti USPPs (Ti.pbe-sp-van_ak.UPF, Ni.pbe-nd-rrkjus.UPF). My > calculations > > become very slow while using such a large kinetic energy cutoff. am I > doing > > something wrong here? > > > > regards, > > Karthik > > > > On Tue, Aug 17, 2010 at 4:46 PM, Stefano de Gironcoli > > > wrote: > >> > >> please note that the two outputs that you submitted ARE NOT examples of > >> vc-relaxation but of structural relaxation of the internal coordinates > >> only. Your question is anyway legittimate... > >> Are you sure to have converged the total energy of your system with > >> respect to cutoff to a sufficient level ? > >> when comparing different volumes one is using different basis sets in > >> the two cases. If convergence w.r.t. cutoff is not sufficient this can > >> lead to sudden decreases of the energy when increasing the volume. > >> > >> stefano > >> SISSA and DEMOCRITOS > >> > >> Guda Karthik wrote: > >> > Hi, > >> > > >> > Here are the input and output files. > >> > > >> > b19_Acklatpos_new.* - original structure > >> > > >> > b19_pwscf.* - scf calculation with a structure obtained after > >> > vc-relax > >> > > >> > Please have a look if they are of help. > >> > > >> > regards, > >> > Karthik > >> > > >> > On Sat, Aug 14, 2010 at 6:27 AM, Paolo Giannozzi > >> > wrote: > >> > > >> > > >> >> On Aug 4, 2010, at 4:41 , Guda Karthik wrote: > >> >> > >> >> > >> >>> I am trying to relax an orthorhombic structure using vc-relax > >> >>> (celldofree - xyz). I start with a structure which is at a Pressure > >> >>> of -20.5 Kbar and at the end of the vc-relax I get a structure > >> >>> which is at a pressure of -0.21 Kbar. Surprisingly, the structure > >> >>> at pressure closer to zero is higher in energy than the original > >> >>> structure by 8 * 10^-4 eV/formula unit. All the symmetry elements > >> >>> have been conserved during relaxation and the initial and final > >> >>> structures are the same. I am not able to make sense of this > >> >>> result. I observe this inconsistency in my B2 structure as well. > >> >>> Please help regarding this. > >> >>> > >> >> hard to help without input and output > >> >> > >> >> P. > >> >> --- > >> >> 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 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 > > > > > > > > -- > > Karthik Guda > > Graduate Student > > Materials Engineering > > Purdue University > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Jia Chen > > Dept of Chemistry > Princeton University > Princeton, NJ 08544 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Karthik Guda Graduate Student Materials Engineering Purdue University -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/7afbeb4a/attachment.htm
[Pw_forum] vc-relax, GGA
GGA results tend to overestimate the lattice parameters where as LDA results tend to underestimate the lattice parameters. Check how much is the error% in your DFT calculations. regards, On Tue, Aug 24, 2010 at 12:35 PM, ?lvaro Alves wrote: > Hello PWscf users. I optimize a triclinic cell using the vc-relax, GGA > functional. My expectation was that all values of the calculated > parameters were slightly higher than the respective experimental values. But, > the angle alpha showed a value slightly lower. The experimental value is > in degree, 103.32, the calculated value is 102.6. There is some > inconsistency in this result? > > Sincerely, > A. S. Santos > Univesidade Federal Fluminense > Niter?i-Rio de Janeiro-Brasil > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Karthik Guda Graduate Student Materials Engineering Purdue University -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/c2e706b0/attachment.htm
[Pw_forum] Constraints of the distance between centers of mass in CP.x
Dear PWSCF users and developers. We want to calculate the reactive system and in order to calculate such a system, I knew the constrained dynamics is useful for the treatment of rare events. Now, I want to set the distance between target atom and the center of mass of molecule as a reactive coordinate. Can we set the constraint of the center of mass of some atoms ? Or Can I use "dummy atom" in the calculation of Car-Parrinello method in PW.x or CP.x ? (If we can set dummy atom, I want to set dummy atom on the center of mass of molecule.) Sincerely. Yukihiro Okuno.
[Pw_forum] error in pseudopotential generation
With "pseudotype=1" you can use just one projector for each "L", and you used 2 "P"s and 2 "S"s. Leonardo Jorge Nanomol group Universidade de S?o Paulo, Brazil On Tue, Aug 24, 2010 at 10:14, mohaddeseh abbasnejad wrote: > > Dear users, > > I have faced this error while trying to generate a pseudopotential for Ti. > > ?%% > from ld1_readin : error # 1 > Two wavefunctions for the same l > ?%% > > Can any one tell me what's wrong? > > Thanks in advance. > > This is my input file: > > ? > ??? title='Ti', > ??? zed=22.0, > ??? rel=1, > ??? iswitch=3, > ??? rlderiv=2.50, > ??? eminld=-4.0, > ??? emaxld=4.0, > ??? deld=0.02, > ??? nld=5, > ??? config='[Ne] 3s2 3p6 3d2 4s2 4p0', > ??? dft='PBE' > ?/ > ? > ??? pseudotype=1 > ??? lloc=0, > ??? file_pseudopw='Ti.ncpp', > ?? ! nlcc=.true., > ?? ! rcore=0.8, > ?/ > 5 > 3D? 5? 2? 2.00? 0.00? 1.0 1.0 > 3P? 4? 1? 6.00? 0.00? 2.7 2.7 > 4P? 3? 1? 0.00? 0.00? 2.7 2.7 > 3S? 2? 0? 2.00 -0.00? 2.2 2.2 > 4S? 1? 0? 2.00 -0.00? 2.2 2.2 > > > > -- > - > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634? & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail:? ?? m.abbasnejad at gmail.com > Website:? http://physics.ut.ac.ir > > - > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >
[Pw_forum] Parallel bandstructure calculations
Hi, You have 32 CPU cores that devided into 4 pools, so you have only 8 CPU cores for each pool. 8 is not a square of any integer, and it's why it used serial algorithm. you need to run mpirun -np 32 pw.x -npool 2 -ndiag 4 BUT, you'd better make tests to determine the best combination. For my case of a 56 atom system with spin polarization, I found the best one (parallel efficiency 79%) is 16 CPU cores (Xeon 5550) for each pool, serial algorithm, 64 CPU cores in total, that is, mpirun -np 64 pw.x -npool 4 huiqun zhou @earth sciences, nanjing university, china - - ???: "Nicki Frank Hinsche" ???: "pw forum" : ???, 2010? 8 ? 23? ?? 10:32:13 ??: [Pw_forum] Parallel bandstructure calculations Hi there, I am currently doing calculations of iso-energy surfaces on doped semiconductors. Therefore I generate with an external program a quite big k-point mesh for which I want to determine the eigenvalues and later on construct the iso-energy surface with a tetrahedron method. My problem is the running time of the bandstructure calculation. The size of the unit (super)-cells is in the order of 30-50 atoms, containing 1 or 2 different atomic species. For k-points in the order of 4000-6000 the eigenvalues have to be calculated (most often around 50-100 ev's for each k-point). After the scf-calculation is done quite fast, I am running the nscf bandstructure calc. with the command mpirun -np 32 pw.x -npool 4 -diag 16 but the calculation isn't done parallel, as the output says: Parallel version (MPI), running on32 processors K-points division: npool =4 R & G space division: proc/pool =8 Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used due to this, the calculation runs much longer than 72 hours...to long for me and our cluster system So is there a possibility to parallelize the bandstructure calculation efficiently and to reduce tje calculation time? thanks in advance, Nicki - Nicki Frank Hinsche, Dipl. Phys. Institute of physics - Theoretical physics, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, Room 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525462 - Fellow of the International Max Planck Re- search School-MPI for Microstructure Physics - ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Total energy value in QE, strange value.
On Aug 23, 2010, at 17:40 , joaquin peralta wrote: > Al 26.982 Al.pbe-sp-van.UPF -sp- means "semicore states in valence". This pseudopotential should be used for special purposes only. > in a paper of Sanchez et al (Molecular Physics, 2004, vol 102, > 1045-1055), > the energies are aroung 2 to 20 eV. absolute total energies calculate with pseudopotentials are not comparable, because... > And the ouput in my case say : [...] > !total energy = -3357.65873780 Ry > ---> 2K eV by atom. they depend upon the pseudopotential. In this case, the presence of semicore states will lead to much larger energies wrt typical energies for typical Al pseudopotentials Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] vc-relax, GGA
Hello PWscf users. I optimize a triclinic cell using the vc-relax, GGA functional. My expectation was that all values of the calculated parameters were slightly higher than the respective experimental values. But, the angle alpha showed a value slightly lower. The experimental value is in degree, 103.32, the calculated value is 102.6. There is some inconsistency in this result? Sincerely, A. S. Santos Univesidade Federal Fluminense Niter?i-Rio de Janeiro-Brasil -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/f0ae27b1/attachment-0001.htm
[Pw_forum] Total energy value in QE, strange value.
> > ___ > 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 +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/5faa22f5/attachment-0001.htm
[Pw_forum] Giving shift in K points
Giving shift is moving the position from 0 0 0 to say 1 1 1. So the position you have given below is not shifted. It could be 1 1 1 1 1 1. Cheers On Mon, Aug 23, 2010 at 6:28 PM, Dimpy Sharma wrote: > > 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 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, International Center for Theoretical Physics, ICTP, Strada Costriera, 11 - 34014, Galileo Guest House, Trieste, Italy. Tel +393382213805 office +39 040 2240 234 pnyawere at gmail.com, potieno at kabarak.ac.ke The battle belongs to the Lord. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/4f20d8e2/attachment.htm
[Pw_forum] Raman cross section calculation- From basic
Dear all, I have tried to calculate the raman spectrum of graphene nanoribbon by QE. Even I can practically use the code to get the results, I can not understand the principle of calculation. From my calculation result, the intensity of radical mode (RBM mode) is negligible while some papers showed this mode was strong. Can you give me some instructions to understand how the code running ( calculation steps)? It is perfect to give me the detail steps that I should follow to understand the code. If possible, can you give some good books and references that related basic as well as the calculation steps of the code? I appreciate to all you instructions. Sincerely, --- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu
