[QE-users] DFT-1/2 method
Mohammad Moaddeli
mohammad.moaddeli at gmail.com
Wed Sep 16 09:47:41 CEST 2020
Thank you for taking the time.
with best regards,
Mohammad
On Wed, Sep 16, 2020 at 11:11 AM <pdelugas at sissa.it> wrote:
> Good that at least one of the options worked :-)
>
> Greetings and best regards
> Pietro
>
> Il 16 set 2020 8:19 AM, Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
> ha scritto:
>
> Dear Pietro,
>
> Yes, I had changed both of them. I also tried by changing the second one.
> but it caused the following error :
>
> ================================================
> .
> .
> .
> .
> Parallelization info
> --------------------
> sticks: dense smooth PW G-vecs: dense smooth PW
> Min 214 114 32 9544 3716 568
> Max 215 115 33 9546 3719 571
> Sum 3433 1829 517 152719 59479 9111
>
> *** Error in `*** Error in `projwfc.x': *** Error in `projwfc.x': ***
> Error in `projwfc.x': malloc(): memory corruption: 0x00000000042f2480 ***
> *** Error in `projwfc.x': malloc(): memory corruption: 0x0000000003466830
> ***
> *** Error in `projwfc.x*** Error in `*** Error in `projwfc.x*** Error in
> `projwfc.x': malloc(): memory corruption: 0x000000000538c590 ***
> ======= Backtrace: =========
> /lib64/libc.so.6(+0x82e86)[0x7f966777fe86]
>
> Gaussian broadening (read from input): ngauss,degauss= 1 0.020000
>
>
> Calling projwave ....
> projwfc.x[0xa41cff]
> projwfc.x[0x44739b]
> projwfc.x[0x406a9e]
> /lib64/libc.so.6======= Memory map: ========
> /lib64/libc.so.6(+0x82e86)[0x7f1ae5cd5e86]
> /lib64/libc.so.6(__libc_malloc+0x4c)[0x7f1ae5cd8adc]
> projwfc.x[0xbb24ee]
> projwfc.x[0xb7d601]
> projwfc.x[0xbb7173]
> projwfc.x[0xa41cff]
> projwfc.x[0x44739b]
> projwfc.x[0x40b3f7]
> projwfc.x[0x407143]
> projwfc.x[0x406a9e]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f1ae5c75505]
> projwfc.x[0x4069a9]
> ======= Memory map: ========
> 00400000-00e30000 r-xp 00000000 fd:00 15202532
> /codes/qe_6.6/qe-6.6/PP/src/projwfc.x
> 0102f000-01032000 r--p 00a2f000 fd:00 15202532
> /codes/qe_6.6/qe-6.6/PP/src/projwfc.x
> 01032000-01152000 rw-p 00a32000 fd:00 15202532
> /codes/qe_6.6/qe-6.6/PP/src/projwfc.x
> 01152000-0259f000 rw-p 00000000 00:00 0
> 03e3d000-059b5000 rw-p 00000000 00:00 0
> [heap]
> 7f1ad0000000-7f1ad0021000 rw-p 00000000 00:00 0
> 7f1ad0021000-7f1ad4000000 ---p 00000000 00:00 0
> 7f1ad7fd9000-7f1adb77d000 r-xp 00000000 fd:00 3512522
> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so
> 7f1adb77d000-7f1adb97c000 ---p 037a4000 fd:00 3512522
> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so
> 7f1adb97c000-7f1adb983000 r--p 037a3000 fd:00 3512522
> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so
> 7f1adb983000-7f1adb990000 rw-p 037aa000 fd:00 3512522
> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so
> .
> .
> .
> ================================================
>
> I tried to copy the non-zero PP_PSWFC from the original file before
> running SCF and finally got the job done.
>
> Best,
>
> Mohammad
>
> ShirazU
>
> On Tue, Sep 15, 2020 at 10:00 AM <pdelugas at sissa.it> wrote:
>
> Hi
> Before or after does not make difference that info is used only for doing
> the projections.
> The pseudo names are written in two places. The one read by the program is
> the second. Have you changed that one?
> Regards
> Pietro
>
> Il 14 set 2020 10:24 PM, Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
> ha scritto:
>
> Dear Pietro,
>
> Thank you for technical advice.
> Should I copy the non-zero PP_PSWFC from the original file before running
> SCF?
>
> Replacing the pseudo file name in data-file-schema.xml before running
> projwfc.x results in:
>
> %%%%%
> Error in routine projwave (1):
> Cannot project on zero atomic wavefunctions!
> %%%%%
>
> Best,
>
> Mohammad
>
> On Sun, Sep 13, 2020 at 7:23 PM Pietro Delugas <pdelugas at sissa.it> wrote:
>
>
>
> Hello
>
>
>
> Try to copy the PP_PSWFC from the original file 'Si.pbe-nl-rrkjus_psl.1.0.0.UPF'
> replacing the all 0s one contained in Si.PBE.0.25.UPF.
>
>
>
> Other thing you can do is to replace the pseudo file name in
> data-file-schema.xml before running projwfc.x.
>
>
>
> Hope it helps
>
> Greetings – Pietro
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
> *Sent: *Sunday, September 13, 2020 2:25 PM
> *To: *Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> *Subject: *Re: [QE-users] DFT-1/2 method
>
>
>
> Dear Giuseppe,
>
>
>
> A pseudopotential from PSlibrary is applied:
>
>
>
> =============================
>
> &input
> title='Si',
> zed=14.0,
> config='[Ne] 3s2 3p2 3d-1',
> iswitch=4
> dft='PBE'
> rel = 1,
> /
> &test
> file_pseudo='Si.pbe-nl-rrkjus_psl.1.0.0.UPF',
> file_pseudopw='Si.PBE.0.25.UPF',
> configts(1)='3s2 3p2 3d-1',
> configts(2)='3s2 3p1.75 3d-1',
> rcutv=1.0
> /
>
> =============================
>
> SCF input:
>
>
>
> =============================
>
> &control
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='silicon',
> tstress = .true.
> tprnfor = .true.
> pseudo_dir = './',
> outdir='tmp'
> ! disk_io = 'none'
> /
> &system
> ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
> ecutwfc =50.0,
> /
> &electrons
> diagonalization='david'
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr = 1.0d-8
> /
> ATOMIC_SPECIES
> Si 28.086 Si.PBE.0.25.UPF
> ATOMIC_POSITIONS alat
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> K_POINTS
> 10
> 0.1250000 0.1250000 0.1250000 1.00
> 0.1250000 0.1250000 0.3750000 3.00
> 0.1250000 0.1250000 0.6250000 3.00
> 0.1250000 0.1250000 0.8750000 3.00
> 0.1250000 0.3750000 0.3750000 3.00
> 0.1250000 0.3750000 0.6250000 6.00
> 0.1250000 0.3750000 0.8750000 6.00
> 0.1250000 0.6250000 0.6250000 3.00
> 0.3750000 0.3750000 0.3750000 1.00
> 0.3750000 0.3750000 0.6250000 3.00
>
> =============================
>
> To the best of my knowledge ONCVPS could not be run using ld1.x, because
> of its format.
>
>
>
>
>
> With best regards,
>
>
>
> Mohammad
>
>
>
> ShirazU
>
>
>
> On Sun, Sep 13, 2020 at 2:59 PM Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it> wrote:
>
>
> Dear Mohammad
> You are likely using a pseudopotential which does not include atomic
> pseudo-wavefunctions in the UPF file; maybe, as often reported, one of
> the ONCVPS contained in the sg15 database. Thus projwfc.x cannot find
> atomic wavefunctions suitable for performing projections of Kohn-Sham
> orbitals onto.
>
> You should look for PSP files containing the pseudowavefunctions, and
> if you are actually looking for ONCVPS files containing them, you
> should find what you need here:
>
> https://github.com/pipidog/ONCVPSP/tree/master/sg15
>
> HTH
> Giuseppe
>
> Quoting Mohammad Moaddeli <mohammad.moaddeli at gmail.com>:
>
> > Dear all,
> >
> > I am trying to run pdos for Si based on the dft-1/2 method implemented by
> > Leonardo Matheus Marion Jorge. However, the following warning in the scf
> > run is appeared:
> >
> > ==================================
> > Program PWSCF v.6.6 starts on 13Sep2020 at 11:33:39
> >
> > 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);
> > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
> > 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 on 1 processors
> >
> > MPI processes distributed on 1 nodes
> > Fft bands division: nmany = 1
> > Reading input from scf_si.in
> >
> > Current dimensions of program PWSCF are:
> > Max number of different atomic species (ntypx) = 10
> > Max number of k-points (npk) = 40000
> > Max angular momentum in pseudopotentials (lmaxx) = 3
> > WARNING: atomic wfc # 1 for atom typeSi has zero norm
> > WARNING: atomic wfc # 2 for atom typeSi has zero norm
> > WARNING: atomic wfc # 3 for atom typeSi has zero norm
> >
> > Subspace diagonalization in iterative solution of the eigenvalue
> > problem:
> > a serial algorithm will be used
> > .
> > .
> > .
> > ==================================
> >
> >
> >
> >
> > Therefore pdos could not be computed:
> >
> >
> >
> >
> > ==================================
> > Program PROJWFC v.6.6 starts on 13Sep2020 at 11:33:50
> >
> > 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);
> > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
> > 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 on 1 processors
> >
> > MPI processes distributed on 1 nodes
> > Fft bands division: nmany = 1
> >
> > Reading xml data from directory:
> >
> > tmp/silicon.save/
> > WARNING: atomic wfc # 1 for atom typeSi has zero norm
> > WARNING: atomic wfc # 2 for atom typeSi has zero norm
> > WARNING: atomic wfc # 3 for atom typeSi has zero norm
> >
> > IMPORTANT: XC functional enforced from input :
> > Exchange-correlation= PBE
> > ( 1 4 3 4 0 0 0)
> > Any further DFT definition will be discarded
> > Please, verify this is what you really want
> >
> >
> > G-vector sticks info
> > --------------------
> > sticks: dense smooth PW G-vecs: dense smooth PW
> > Sum 721 721 211 12627 12627 1989
> >
> >
> > Gaussian broadening (read from input): ngauss,degauss= 1
> 0.010000
> >
> >
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > Error in routine projwave (1):
> > Cannot project on zero atomic wavefunctions!
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > stopping ...
> > ==================================
> >
> > Is it a limitation in the DFT-1/2 method?
> >
> > Best regards,
> >
> > Mohammad
> >
> > Department of Materials Science and Engineering, School of Engineering,
> > Shiraz University
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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