Dear Dr. Nguyën The following setup of the SCF (pw.x) calculation is also available.
################################# occupations = "fixed", tot_magnetization = 0d0, ################################# In this case, the phonons at Gamma point can be computed in the ph.x computation. Best regards, Mitsuaki Kawamura -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Mitsuaki Kawamura Sent: Thursday, April 6, 2017 5:57 PM To: 'PWSCF Forum' <[email protected]> Subject: Re: [Pw_forum] calculating frequencies in Co3O4 causing a segmentation fault 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 : [email protected] ------------------------------------------------------ -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Mitsuaki Kawamura Sent: Thursday, April 6, 2017 4:33 PM To: 'PWSCF Forum' <[email protected]> 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 : [email protected] ------------------------------------------------------ From: [email protected] [mailto:[email protected]] On Behalf Of Md. Masud Rana Sent: Thursday, April 6, 2017 11:27 AM To: PWSCF Forum <[email protected]> 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 <[email protected]> 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 [email protected]<mailto:[email protected]> - www.iciq.es<http://www.iciq.es/> _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
