[Pw_forum] calculating frequencies in Co3O4 causing a segmentation fault

Mitsuaki Kawamura mkawamura at issp.u-tokyo.ac.jp
Thu Apr 6 10:56:59 CEST 2017


Dear Dr. Nguyën

As Dr. Masud says, it is available to compute phonons at q-points other than the Gamma point. E.g.

#################################
Phonons of Co3O4 at R
&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,
/
0.5 0.5 0.5
#################################

Best regards,
Mitsuaki Kawamura

--
------------------------------------------------------
Dr. Mitsuaki Kawamura
Software Advancement Team
Supercomputer Section
Materials Design and Characterization Laboratory The Institute for Solid State Physics, Kashiwa, Japan e-mail : mkawamura at issp.u-tokyo.ac.jp
------------------------------------------------------



-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Mitsuaki Kawamura
Sent: Thursday, April 6, 2017 4:33 PM
To: 'PWSCF Forum' <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] calculating frequencies in Co3O4 causing a segmentation fault

Dear Dr. Nguyën

Hello,

The tetrahedron method for the DFPT calculation does not work together with the old XML I/O (Sorry!).
Please build QE 6.1 with activating new XML routines. i.e., $ ./configure --enable-xml $ make pw ph

The tetrahedron method has no advantage in the single-k electronic structure calculation.
I did not check the situation of DFPT + tetrahedron + single-k, and I found NaN (Bug?) during the reproduction of your calculation (together with the new XML).

############################################################
     Representation #  1 mode #   1

     Self-consistent Calculation

     Pert. #  1: Fermi energy shift (Ry) =       Infinity       Infinity

      iter #   1 total cpu time :   373.5 secs   av.it.:   8.5
      thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =        NaN

     kpoint   1 ibnd 265 solve_linter: root not converged        NaN
     kpoint   2 ibnd 265 solve_linter: root not converged        NaN

     Pert. #  1: Fermi energy shift (Ry) =            NaN            NaN
############################################################

So, please use the smearing method for the single-k calculation.

Best regards,
Mitsuaki Kawamura

--
------------------------------------------------------
Dr. Mitsuaki Kawamura
Software Advancement Team
Supercomputer Section
Materials Design and Characterization Laboratory The Institute for Solid State Physics, Kashiwa, Japan e-mail : mkawamura at issp.u-tokyo.ac.jp
------------------------------------------------------

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Md. Masud Rana
Sent: Thursday, April 6, 2017 11:27 AM
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] calculating frequencies in Co3O4 causing a segmentation fault

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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