[Pw_forum] calculating frequencies in Co3O4 causing a segmentation fault
Md. Masud Rana
masud at eee.kuet.ac.bd
Thu Apr 6 04:26:58 CEST 2017
dear Dr. Huu Chuong Nguyën (Bob)
plz set ldisp=.true in ph.x code and gamma point should be changed some
value by other point
prefix = 'PAWlocal_Co3O4_mag_revPBE450_323' ,
fildyn = 'Co3O4.dynG' ,
trans = .true.,
ldisp=.true,
amass(1) = 15.99990,
amass(2) = 15.99990,
amass(3) = 58.93320,
amass(4) = 58.93320,
nq1=1,
nq2=1,
nq3=1,
/
On Wed, Apr 5, 2017 at 11:37 PM, Huu Chuong Nguyën <hnguyen at iciq.es> wrote:
> Hello,
>
>
> I am trying to compute vibrational frequencies for a bulk
> anti-ferromagnetic Co3O4 with QE 6.1 to know its Zero-point energy. After a
> geometry optimisation, I have run a scf calculation with pw.x:
>
>
> &CONTROL
> calculation = 'scf' ,
> restart_mode = 'restart' ,
> wf_collect = .true. ,
> prefix = 'PAWlocal_Co3O4_mag_revPBE450_323' ,
> verbosity = 'high' ,
> tstress = .true. ,
> tprnfor = .true. ,
> /
> &SYSTEM
> ibrav = 1,
> A = 8.1585360148 ,
> nat = 56,
> ntyp = 4,
> ecutwfc = 34.0 ,
> ecutrho = 323.0 ,
> input_dft = 'revPBE' ,
> occupations = 'tetrahedra_opt' ,
> nspin = 2 ,
> starting_magnetization(1) = 0.4,
> starting_magnetization(2) = -0.4,
> starting_magnetization(3) = 0.9,
> starting_magnetization(4) = -0.9,
> report = 1 ,
> /
> &ELECTRONS
> electron_maxstep = 300,
> conv_thr = 1e-9 ,
> startingpot = 'file' ,
> startingwfc = 'random' ,
> adaptive_thr = .true. ,
> conv_thr_init = 1e-4 ,
> mixing_beta = 0.15 ,
> diagonalization = 'cg' ,
> /
> ATOMIC_SPECIES
> O1 15.99990 O.revpbe-n-kjpaw_psl.1.0.0.UPF
> O2 15.99990 O.revpbe-n-kjpaw_psl.1.0.0.UPF
> Co1 58.93320 Co.revpbe-n-kjpaw_psl.0.2.3.UPF
> Co2 58.93320 Co.revpbe-n-kjpaw_psl.0.2.3.UPF
> ATOMIC_POSITIONS alat
> Co1 0.624889370 0.874845281 0.374933343
> Co2 0.624888554 0.624890765 0.124977843
> Co1 0.374931369 0.874845108 0.624891800
> Co2 0.874843981 0.624889689 0.374933687
> Co1 0.749865119 0.749868048 0.749869202
> Co2 -0.000000291 0.499912268 -0.000000091
> Co1 0.624889318 0.374933355 0.874845725
> Co2 0.624888564 0.124979485 0.624890990
> Co1 0.374931352 0.374933292 0.124978809
> Co2 0.874843684 0.124978234 0.874845862
> Co1 0.749865073 0.249956415 0.249955786
> Co2 -0.000000324 0.000001049 0.499913121
> Co1 0.124978436 0.874844840 0.874845829
> Co2 0.124977608 0.624890806 0.624891029
> Co1 0.874842254 0.874845160 0.124978832
> Co2 0.374932939 0.624889719 0.874845984
> Co1 0.249953483 0.749868488 0.249955574
> Co2 0.499910977 0.499912018 0.499913335
> Co1 0.124978075 0.374933191 0.374933226
> Co2 0.124977578 0.124979225 0.124977923
> Co1 0.874842311 0.374933324 0.624891763
> Co2 0.374933102 0.124978043 0.374933595
> Co1 0.249953867 0.249956453 0.749869251
> Co2 0.499910660 0.000000860 -0.000000039
> O1 0.137098969 0.362813056 0.137098481
> O2 0.112856608 0.612769174 0.387054264
> O1 0.886963277 0.612768289 0.612770221
> O2 0.886962961 0.387054004 0.387054223
> O1 0.862725253 0.637010238 0.137097538
> O2 0.862725063 0.862723604 0.362814259
> O1 0.612767890 0.886965586 0.612769342
> O2 0.637010640 0.637009824 0.362812520
> O1 0.137098734 0.862724980 0.637011103
> O2 0.112856856 0.112857670 0.886966422
> O1 0.886963309 0.112856456 0.112857687
> O2 0.886963380 0.886965697 0.886966315
> O1 0.862724620 0.137098426 0.637010098
> O2 0.862725043 0.362812354 0.862726595
> O1 0.612767462 0.387053886 0.112857183
> O2 0.637009979 0.137098292 0.862725069
> O1 0.637009807 0.362813598 0.637011423
> O2 0.612767649 0.612769353 0.886966165
> O1 0.387052357 0.612768175 0.112857886
> O2 0.387052541 0.387054258 0.886966096
> O1 0.362814027 0.637010101 0.637010154
> O2 0.362813976 0.862723773 0.862726808
> O1 0.112856528 0.886965790 0.112857424
> O2 0.137099117 0.637009666 0.862724849
> O1 0.637010175 0.862725061 0.137098283
> O2 0.612767456 0.112858199 0.387054320
> O1 0.387052625 0.112856614 0.612770175
> O2 0.387052565 0.886965924 0.387054098
> O1 0.362813927 0.137098374 0.137097310
> O2 0.362813993 0.362811469 0.362814300
> O1 0.112856944 0.387053608 0.612769183
> O2 0.137099468 0.137098115 0.362812356
> K_POINTS automatic
> 1 1 1 0 0 0
>
>
> which ended successfully.
>
>
> I then tried to run this script with ph.x:
>
>
> Phonons of Co3O4 at Gamma
> &INPUTPH
> prefix = 'PAWlocal_Co3O4_mag_revPBE450_323' ,
> fildyn = 'Co3O4.dynG' ,
> trans = .true.,
> amass(1) = 15.99990,
> amass(2) = 15.99990,
> amass(3) = 58.93320,
> amass(4) = 58.93320,
> /
> 0.0 0.0 0.0
>
>
> But I got this error message:
>
>
> Program PHONON v.6.1 (svn rev. 13369) starts on 5Apr2017 at 19:11:52
>
> 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 on 1 processors
>
> Reading data from directory:
> /home/hnguyen/Desktop/shared/espresso_tmp/PAWlocal_Co3O4_
> mag_revPBE450_323.save
>
> Info: using nr1, nr2, nr3 values from input
>
> Info: using nr1, nr2, nr3 values from input
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> ph.x 0000000000974B65 qexml_module_mp_q 3753
> qexml.f90
> ph.x 000000000072D3B4 pw_restart_mp_rea 2101
> pw_restart.f90
> ph.x 0000000000729F54 pw_restart_mp_pw_ 1057
> pw_restart.f90
> ph.x 0000000000735796 read_file_ 55
> read_file.f90
> ph.x 00000000004D0F9E phq_readin_ 641
> phq_readin.f90
> ph.x 0000000000455AB9 MAIN__ 66
> phonon.f90
> ph.x 0000000000455A3C Unknown Unknown Unknown
> libc.so.6 00007FD126C127ED Unknown Unknown Unknown
> ph.x 0000000000455939 Unknown Unknown Unknown
>
> phcg.x gave me the same error message:
>
> Program PHCG v.6.1 (svn rev. 13369) starts on 5Apr2017 at 19:34:21
>
> 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 on 1 processors
>
> Reading data from directory:
> /home/hnguyen/Desktop/shared/espresso_tmp/PAWlocal_Co3O4_
> mag_revPBE450_323.save
>
> Info: using nr1, nr2, nr3 values from input
>
> Info: using nr1, nr2, nr3 values from input
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> phcg.x 00000000007D1335 qexml_module_mp_q 3753
> qexml.f90
> phcg.x 00000000006BBDD4 pw_restart_mp_rea 2101
> pw_restart.f90
> phcg.x 00000000006B8974 pw_restart_mp_pw_ 1057
> pw_restart.f90
> phcg.x 00000000005B6836 read_file_ 55
> read_file.f90
> phcg.x 0000000000447088 cg_readin_ 88
> cg_readin.f90
> phcg.x 00000000004605F2 MAIN__ 41
> phcg.f90
> phcg.x 00000000004452DC Unknown Unknown Unknown
> libc.so.6 00007F1CDBC357ED Unknown Unknown Unknown
> phcg.x 00000000004451D9 Unknown Unknown Unknown
>
>
> Which is the worst kind of error, the segmentation fault. Does anyone has
> a clue on what could cause such error? Maybe something terribly wrong in my
> input that I missed?
>
>
>
> Dr. Huu Chuong Nguyën (Bob)
>
> Postdoc Researcher - Group of Prof. Núria López
>
> Institute of Chemical Research of Catalonia (ICIQ)
> The Barcelona Institute of Science and Technology
>
> Av. Països Catalans 16 - 43007 Tarragona (Spain)
>
> PB-11 Huu Chuong Nguyën - PERSONAL
>
> hnguyen at iciq.es<mailto:user at iciq.es> - www.iciq.es<http://www.iciq.es/>
>
>
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