Re: [Pw_forum] running OpenMPI pw.x error
On Wed, Apr 13, 2016 at 3:19 AM, K.M. Mohsin wrote: Error in routine read_input (2): opening input file > the input file is not there (or it is not readable anyway) Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] running OpenMPI pw.x error
Dear all, I am trying to calculate SCF for graphene (2D bulk) using 16 processors. I am having following errors. I am attaching Input and PBS file at the bottom of email. Thanks. *Error : * -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. *Inside output file: * Program PWSCF v.5.1 starts on 9Apr2016 at 12:38:21 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org";, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Parallel version (MPI), running on16 processors R & G space division: proc/nbgrp/npool/nimage = 16 %% Error in routine read_input (2): opening input file %%% stopping ... This error message is repeated 16 times from each processors. *My input file:* &CONTROL calculation = 'scf' restart_mode='from_scratch', prefix='graphene', pseudo_dir = '/home/kmohsi1/QE/', outdir='./', / &SYSTEM ibrav= 0, celldm(1) =4.7375, nat= 2, ntyp= 1, ecutwfc =70.0, ecutrho=560.0, occupations='smearing', nbnd = 8, degauss=0.1, exxdiv_treatment = 'gygi-baldereschi' , / &ELECTRONS diagonalization='david', electron_maxstep = 100, mixing_mode = 'plain', mixing_beta = 0.7, conv_thr = 1.0d-2, / CELL_PARAMETERS alat 1.00.00.0 0.50.8660254000.0 0.00.0 12.0 ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS alat C 0.00.0.00 C 0.00.5773503 0.00 K_POINTS tpiba_b 4 0.000 0.000 0.000 10 1.000 0.000 0.000 10 1.000 0.5773503 0.000 10 0.000 0.000 0.000 10 *For job submission I used following PBS file, * #!/bin/bash #PBS -l nodes=1:ppn=16 #PBS -l walltime=00:05:00 #PBS -q workq #PBS -A hpc_graphene01 BIN_DIR=$ESPRESSO_ROOT/bin mpirun -np 16 $BIN_DIR/pw.x -i gr.in I appreciate any help, suggestion or comments. If I am missing any necessary postfix or prefix in PBS command, please remind me. Thanks. -- K. M. MOHSIN PhD candidate Dept. of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA. U.S.A. Phone : +1 (832) 868 8371 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Regarding Absolute band-edges
Dear Vipul, This is an old problem in semiconductor physics. In summary you need 2 set of calculations. One for a surface (interface) and another one for bulk. Key papers to review are: http://journals.aps.org/prb/abstract/10.1103/PhysRevB.35.8154 http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.61.734 There are many modern examples as well. In my opinion absolute alignment to vacuum is more difficult than aliment of material 1 to material 2. Best Regards, Mostafa ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Segmentation Fault when using pw2casino on moderately sized system?
On Tuesday, April 12, 2016 10:58:32 AM Henry J Seeley wrote: > Thank you very much Paolo! > > While I have your attention, could you answer another quick question for > me? > I'm able to obtain the wavefunctions of my system in k-space with > 'pw_export' instead of 'pw2casino', but I would like to transform this > into real space. Is there a utility in Quantum Espresso that can do this > for me? I found 'wfck2r.x', but this gave me a binary file. Perhaps > there is an option to convert this to a text file? There is no such option, but you can trivially change the line if(ionode) call davcio (dist_evc_r, lrwfcr, iuwfcr, (ik-1)*nbnd+ibnd, +1) to do formatted output. The dimension of the real-space wavefunction (a comple quantity, of course) is stated just a few lines above: ALLOCATE ( dist_evc_r(dffts%nr1x*dffts%nr2x*dffts%nr3x,nspin_mag) ) and the ouptut line is repeated for every k-point and band (counters ik and ibnd), so you can just change it to whatever formatted output you want taking care of the filenames if you wish. However, keep in mind, that real space wavefunction in text format will take up a lot of disk space! -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Université Paris 6 +33 (0)1 44 275 084 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ 23-24/4é16 Boîte courrier 115 4 place Jussieu 75252 Paris Cédex 05 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Segmentation Fault when using pw2casino on moderately sized system?
Thank you very much Paolo! While I have your attention, could you answer another quick question for me? I'm able to obtain the wavefunctions of my system in k-space with 'pw_export' instead of 'pw2casino', but I would like to transform this into real space. Is there a utility in Quantum Espresso that can do this for me? I found 'wfck2r.x', but this gave me a binary file. Perhaps there is an option to convert this to a text file? Thank you very much, Hank Seeley On 2016/04/12 09:25, Paolo Giannozzi wrote: > Answering myself: it doesn't, since pw2casino is not implemented for > noncollinear magnetization. I think that the CASINO code works only > for norm-conserving PP, by the way, so you shouldn't use it with > either USPP or PAW. > > Paolo > > On Tue, Apr 12, 2016 at 8:05 AM, Paolo Giannozzi > wrote: > >> Does it work for a simple 2-atom PbS cell? Paolo >> >> Il 11/apr/2016 08:07 PM, "Henry J Seeley" ha >> scritto: >> >>> Hello all, >>> >>> I keep getting a mysterious error when trying to use the option >>> '-pw2casino' on my nscf calculations in an attempt to obtain the >>> wavefunctions for my system. All other calculations run smoothly, >>> it's only when I use pw2casino that I get this error, which occurs >>> immediately after all band energies have been solved: >>> >>> 'Program received signal SIGSEGV: Segmentation fault - invalid >>> memory reference.' >>> >>> I've tried using '-pw2casino' for two simple test systems: a >>> primitive cell of bulk Si and a Si monolayer (pbe-mt_fhi >>> psuedopotential). When I do these calculations everything runs >>> smoothly; I get no error and obtain my wavefunctions. >>> >>> Attached is one of the input files that DOES give me the error >>> (PbS supercell). I'm guessing this error arises from either the >>> size of the system or the psuedopotentials I'm using. >>> >>> Does anyone know what the issue may be? >>> >>> Thank you, >>> Hank Seeley >>> Chemistry Department, University of Oregon >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum > > -- > > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Segmentation Fault when using pw2casino on moderately sized system?
Answering myself: it doesn't, since pw2casino is not implemented for noncollinear magnetization. I think that the CASINO code works only for norm-conserving PP, by the way, so you shouldn't use it with either USPP or PAW. Paolo On Tue, Apr 12, 2016 at 8:05 AM, Paolo Giannozzi wrote: > Does it work for a simple 2-atom PbS cell? Paolo > Il 11/apr/2016 08:07 PM, "Henry J Seeley" ha > scritto: > >> Hello all, >> >> I keep getting a mysterious error when trying to use the option >> '-pw2casino' on my nscf calculations in an attempt to obtain the >> wavefunctions for my system. All other calculations run smoothly, it's only >> when I use pw2casino that I get this error, which occurs immediately after >> all band energies have been solved: >> >> 'Program received signal SIGSEGV: Segmentation fault - invalid memory >> reference.' >> >> I've tried using '-pw2casino' for two simple test systems: a primitive >> cell of bulk Si and a Si monolayer (pbe-mt_fhi psuedopotential). When I do >> these calculations everything runs smoothly; I get no error and obtain my >> wavefunctions. >> >> Attached is one of the input files that DOES give me the error (PbS >> supercell). I'm guessing this error arises from either the size of the >> system or the psuedopotentials I'm using. >> >> Does anyone know what the issue may be? >> >> Thank you, >> Hank Seeley >> Chemistry Department, University of Oregon >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] tb09 functional with libxc
Thanks so much! It works now. Best, Xiaoming Postdoc Rutgers University -Original Message- From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Lorenzo Paulatto Sent: Tuesday, April 12, 2016 4:05 AM To: PWSCF Forum Subject: Re: [Pw_forum] tb09 functional with libxc On Monday, 11 April 2016 18:07:48 CEST Xiaoming Wang wrote: > DFLAGS = -D_LIBXC -D__INTEL -D__FFTW3 -D__MPI -D__PARA I think you need two underscores before LIBXC in DFLAGS, i.e. DFLAGS = -D__LIBXC -D__INTEL -D__FFTW3 -D__MPI -D__PARA (spot the difference!) hth -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Université Paris 6 +33 (0)1 44 275 084 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] how to obtain exchange energy and correlation energy separately?
hello, I wish to separate the "xc contribution" at the scf.out file into "exchange contribution" and "correlation contribution". What are you recommend? 1. to use the subroutine exxenergy2 from exx.f90 and substract the results from the "xc contribution"? 2. to do something similar to what is written in v_of_rho.f90 for each of the contributions? 3. maybe something smarter? I found similar question in the forum from 2014 with the answer that I have to modify the code. thanks in advance, Uri Argaman Materials engineering department Ben-Gurion university Israel ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] the symmetry problem in calculating phonon frequency of wurtzite AlN
Dear all, I am trying to calculate the phonon frequency of wurtzite AlN in gamma point?? i try to use the input files as PHonon/examples/example01/ in Quantum Espresso. The symmetry of wurtzite AlN is C6v, but in the output of my calculation, the symmetry is C3v so that the phonon frequency get by my work do not correspond with that get by reference. I want to know that if there is a way in quantum espresso to specify the symmetry? or some other method to get the right symmetry in phonon calculation? === pw input &SYSTEM ibrav= 4, celldm(1)= 5.8804, nat= 4, ntyp= 2, celldm(3) = 1.600724 ecutwfc = 160 / &ELECTRONS conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.982 Al.pbesol-n-kjpaw_psl.0.1.UPF N14.007 N.pbesol-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS crystal Al 0.33343 0.66687 0.0 Al 0.66627 0.33313 0.5 N 0.33343 0.66687 0.381929994 N 0.66627 0.33313 0.881929994 K_POINTS automatic 2 2 1 1 1 1 -- ph input phonons of aln at Gamma &inputph tr2_ph=1.0d-14, prefix='aln', epsil=.true., outdir='/tmp', fildyn='aln.dyn', / 0.0 0.0 0.0___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] (no subject)
Dear all, I am trying to calculate the phonon frequency of wurtzite AlN in gamma point?? i try to use the input files as PHonon/examples/example01/ in Quantum Espresso. The symmetry of wurtzite AlN is C6v, but in the output of my calculation, the symmetry is C3v so that the phonon frequency get by my work do not correspond with that get by reference. I want to know that if there is a way in quantum espresso to specify the symmetry? or some other method to get the right symmetry in phonon calculation? === pw input &SYSTEM ibrav= 4, celldm(1)= 5.8804, nat= 4, ntyp= 2, celldm(3) = 1.600724 ecutwfc = 160 / &ELECTRONS conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.982 Al.pbesol-n-kjpaw_psl.0.1.UPF N14.007 N.pbesol-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS crystal Al 0.33343 0.66687 0.0 Al 0.66627 0.33313 0.5 N 0.33343 0.66687 0.381929994 N 0.66627 0.33313 0.881929994 K_POINTS automatic 2 2 1 1 1 1 -- ph input phonons of aln at Gamma &inputph tr2_ph=1.0d-14, prefix='aln', epsil=.true., outdir='/tmp', fildyn='aln.dyn', / 0.0 0.0 0.0___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Regarding Absolute band-edges
Hi all, How can we get absolute band-edges in QE to compare with the experimental values? For quantum dots we have scissor operator to shift the homo level. But, i have got expected bandgap, but need to find absolute band-edges. What is the shift for homo and lumo. -- Vipul S. Ghemud Ph.D. student. Dept of Physics, SPPU, Ganeshkhind, Pune- 411007. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] tb09 functional with libxc
On Monday, 11 April 2016 18:07:48 CEST Xiaoming Wang wrote: > DFLAGS = -D_LIBXC -D__INTEL -D__FFTW3 -D__MPI -D__PARA I think you need two underscores before LIBXC in DFLAGS, i.e. DFLAGS = -D__LIBXC -D__INTEL -D__FFTW3 -D__MPI -D__PARA (spot the difference!) hth -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Université Paris 6 +33 (0)1 44 275 084 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
