Thank you for taking the time. with best regards,
Mohammad On Wed, Sep 16, 2020 at 11:11 AM <[email protected]> wrote: > Good that at least one of the options worked :-) > > Greetings and best regards > Pietro > > Il 16 set 2020 8:19 AM, Mohammad Moaddeli <[email protected]> > 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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> > *Sent: *Sunday, September 13, 2020 2:25 PM > *To: *Quantum ESPRESSO users Forum <[email protected]> > *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 < > [email protected]> 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 <[email protected]>: > > > 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: <[email protected]> > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users
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