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core dumped in the exchange coupling calculation (Jx) for cluster system Date: 2022/10/25 15:14 Name: HEMANT ARORA   <harora@ph.iitr.ac.in> Dear Prof. Ozaki and developers, I have been recently using exchange coupling calculator jx that comes with openmx 3.9 to test several materials and all seem to work well. when I am trying to test this on the input file (given below), I am getting core dumped error - ******************************************************************** ******************************************************************** jx: code for calculating an effective exchange coupling constant J Copyright (C), 2003, Myung Joon Han, Jaejun Yu, and Taisuke Ozaki 2019, Asako Terasawa and Taisuke Ozaki This is free software, and you are welcome to redistribute it under the constitution of the GNU-GPL. ******************************************************************** ******************************************************************** Read the scfout file (Mn2-100-FM.scfout) [root1-HP-Z8-G4-Workstation:09724] *** Process received signal *** [root1-HP-Z8-G4-Workstation:09724] Signal: Segmentation fault (11) [root1-HP-Z8-G4-Workstation:09724] Signal code: Address not mapped (1) [root1-HP-Z8-G4-Workstation:09724] Failing at address: 0x491 [root1-HP-Z8-G4-Workstation:09724] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef10)[0x7f6efbe61f10] [root1-HP-Z8-G4-Workstation:09724] [ 1] ./jx(+0x13f60)[0x5637fae09f60] [root1-HP-Z8-G4-Workstation:09724] [ 2] ./jx(+0x202f)[0x5637fadf802f] [root1-HP-Z8-G4-Workstation:09724] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f6efbe44c87] [root1-HP-Z8-G4-Workstation:09724] [ 4] ./jx(+0x218a)[0x5637fadf818a] [root1-HP-Z8-G4-Workstation:09724] *** End of error message *** This is the input file - # # File Name # System.CurrrentDirectory ./ # default=./ System.Name Mn2-100-FM level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (1-3) HS.fileout on # on|off, default=off # # Definition of Atomic Species # Species.Number 3 <Definition.of.Atomic.Species Si Si7.0-s2p2d1 Si_PBE19 Mn Mn8.0-s3p2d1 Mn_PBE19 H H5.0-s2p1 H_PBE19 Definition.of.Atomic.Species> # # Atoms # Atoms.Number 144 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates # Unit=Ang. 1 Si 11.79767 11.71864 1.935350 2 2 2 Si 11.79767 11.71864 7.365950 2 2 3 Si 11.79767 11.71864 12.79656 2 2 4 Si 10.42071 15.84950 0.543140 2 2 5 Si 10.42071 15.84950 5.973750 2 2 6 Si 10.42071 15.84950 11.40434 2 2 7 Si 11.80174 17.16745 1.950910 2 2 8 Si 11.80174 17.16745 7.381510 2 2 9 Si 11.80174 17.16745 12.81210 2 2 10 Si 10.41983 13.04424 3.342050 2 2 11 Si 10.41983 13.04424 8.772660 2 2 12 Si 10.41983 13.04424 14.20326 2 2 13 Si 11.80107 14.44392 4.662030 2 2 14 Si 11.80107 14.44392 10.09262 2 2 15 Si 11.80107 14.44392 15.52323 2 2 16 Si 15.92853 10.34168 0.543140 2 2 17 Si 15.92853 10.34168 5.973750 2 2 18 Si 15.92853 10.34168 11.40434 2 2 19 Si 17.24648 11.72271 1.950910 2 2 20 Si 17.24648 11.72271 7.381510 2 2 21 Si 17.24648 11.72271 12.81210 2 2 22 Si 13.12327 10.34080 3.342050 2 2 23 Si 13.12327 10.34080 8.772660 2 2 24 Si 13.12327 10.34080 14.20326 2 2 25 Si 14.52296 11.72204 4.662030 2 2 26 Si 14.52296 11.72204 10.09262 2 2 27 Si 14.52296 11.72204 15.52323 2 2 28 Si 13.16808 13.08905 0.589070 2 2 29 Si 13.16808 13.08905 6.019670 2 2 30 Si 13.16808 13.08905 11.45027 2 2 31 Si 14.52739 14.44835 1.948890 2 2 32 Mn 14.52739 14.44835 12.81010 9 6 33 Si 15.89079 15.81176 0.594820 2 2 34 Si 15.89079 15.81176 6.025410 2 2 35 Si 15.89079 15.81176 11.45602 2 2 36 Si 17.25009 17.17106 1.954640 2 2 37 Si 17.25009 17.17106 7.385240 2 2 38 Si 17.25009 17.17106 12.81583 2 2 39 Si 15.88330 13.08875 3.311620 2 2 40 Si 15.88330 13.08875 8.742210 2 2 41 Mn 15.88330 13.08875 14.17281 9 6 42 Si 17.25040 14.45585 4.662700 2 2 43 Si 17.25040 14.45585 10.09329 2 2 44 Si 17.25040 14.45585 15.52390 2 2 45 Si 13.16778 15.80426 3.311620 2 2 46 Si 13.16778 15.80426 8.742210 2 2 47 Si 13.16778 15.80426 14.17281 2 2 48 Si 14.53488 17.17136 4.662700 2 2 49 Si 14.53488 17.17136 10.09329 2 2 50 Si 14.53488 17.17136 15.52390 2 2 51 Si 13.17169 18.53740 0.592800 2 2 52 Si 13.17169 18.53740 6.023400 2 2 53 Si 13.17169 18.53740 11.45400 2 2 54 Si 14.48965 19.91843 2.000570 2 2 55 Si 14.48965 19.91843 7.431160 2 2 56 Si 14.48965 19.91843 12.86176 2 2 57 Si 15.89522 18.53807 3.312290 2 2 58 Si 15.89522 18.53807 8.742880 2 2 59 Si 15.89522 18.53807 14.17347 2 2 60 Si 17.29491 19.91931 4.632250 2 2 61 Si 17.29491 19.91931 10.06284 2 2 62 Si 17.29491 19.91931 15.49345 2 2 63 Si 18.61644 13.09266 0.592800 2 2 64 Si 18.61644 13.09266 6.023400 2 2 65 Si 18.61644 13.09266 11.45400 2 2 66 Si 19.99747 14.41061 2.000570 2 2 67 Si 19.99747 14.41061 7.431160 2 2 68 Si 19.99747 14.41061 12.86176 2 2 69 Si 18.61711 15.81619 3.312290 2 2 70 Si 18.61711 15.81619 8.742880 2 2 71 Si 18.61711 15.81619 14.17347 2 2 72 Si 19.99835 17.21587 4.632250 2 2 73 Si 19.99835 17.21587 10.06284 2 2 74 Si 19.99835 17.21587 15.49345 2 2 75 Si 18.62047 18.54147 0.608360 2 2 76 Si 18.62047 18.54147 6.038960 2 2 77 Si 18.62047 18.54147 11.46956 2 2 78 Si 14.52739 14.44835 7.379480 2 2 79 H 10.95150 10.87247 1.072890 0.5 0.5 80 H 10.95150 10.87247 6.503490 0.5 0.5 81 H 10.95150 10.87247 11.93410 0.5 0.5 82 H 9.636980 16.73265 15.95056 0.5 0.5 83 H 9.636980 16.73265 5.089360 0.5 0.5 84 H 9.636980 16.73265 10.51996 0.5 0.5 85 H 9.496840 15.03901 1.354740 0.5 0.5 86 H 9.496840 15.03901 6.785340 0.5 0.5 87 H 9.496840 15.03901 12.21593 0.5 0.5 88 H 10.95360 18.01757 2.807650 0.5 0.5 89 H 10.95360 18.01757 8.238260 0.5 0.5 90 H 10.95360 18.01757 13.66885 0.5 0.5 91 H 9.501970 13.85943 2.528410 0.5 0.5 92 H 9.501970 13.85943 7.959020 0.5 0.5 93 H 9.501970 13.85943 13.38961 0.5 0.5 94 H 9.629270 12.16384 4.223160 0.5 0.5 95 H 9.629270 12.16384 9.653760 0.5 0.5 96 H 9.629270 12.16384 15.08437 0.5 0.5 97 H 15.11804 9.417840 1.354740 0.5 0.5 98 H 15.11804 9.417840 6.785340 0.5 0.5 99 H 15.11804 9.417840 12.21593 0.5 0.5 100 H 16.81169 9.557940 15.95056 0.5 0.5 101 H 16.81169 9.557940 5.089360 0.5 0.5 102 H 16.81169 9.557940 10.51996 0.5 0.5 103 H 18.09660 10.87456 2.807650 0.5 0.5 104 H 18.09660 10.87456 8.238260 0.5 0.5 105 H 18.09660 10.87456 13.66885 0.5 0.5 106 H 12.24288 9.550240 4.223160 0.5 0.5 107 H 12.24288 9.550240 9.653760 0.5 0.5 108 H 12.24288 9.550240 15.08437 0.5 0.5 109 H 13.93847 9.422930 2.528410 0.5 0.5 110 H 13.93847 9.422930 7.959020 0.5 0.5 111 H 13.93847 9.422930 13.38961 0.5 0.5 112 H 12.32155 19.38555 16.02785 0.5 0.5 113 H 12.32155 19.38555 5.166650 0.5 0.5 114 H 12.32155 19.38555 10.59725 0.5 0.5 115 H 15.30014 20.84227 1.188970 0.5 0.5 116 H 15.30014 20.84227 6.619570 0.5 0.5 117 H 15.30014 20.84227 12.05016 0.5 0.5 118 H 13.60649 20.70217 2.884950 0.5 0.5 119 H 13.60649 20.70217 8.315550 0.5 0.5 120 H 13.60649 20.70217 13.74614 0.5 0.5 121 H 18.17530 20.70987 3.751140 0.5 0.5 122 H 18.17530 20.70987 9.181750 0.5 0.5 123 H 18.17530 20.70987 14.61234 0.5 0.5 124 H 16.47971 20.83718 5.445890 0.5 0.5 125 H 16.47971 20.83718 10.87650 0.5 0.5 126 H 16.47971 20.83718 0.015310 0.5 0.5 127 H 19.46458 12.24254 16.02785 0.5 0.5 128 H 19.46458 12.24254 5.166650 0.5 0.5 129 H 19.46458 12.24254 10.59725 0.5 0.5 130 H 20.78120 13.52746 2.884950 0.5 0.5 131 H 20.78120 13.52746 8.315550 0.5 0.5 132 H 20.78120 13.52746 13.74614 0.5 0.5 133 H 20.92131 15.22110 1.188970 0.5 0.5 134 H 20.92131 15.22110 6.619570 0.5 0.5 135 H 20.92131 15.22110 12.05016 0.5 0.5 136 H 20.91621 16.40068 5.445890 0.5 0.5 137 H 20.91621 16.40068 10.87650 0.5 0.5 138 H 20.91621 16.40068 0.015310 0.5 0.5 139 H 20.78891 18.09627 3.751140 0.5 0.5 140 H 20.78891 18.09627 9.181750 0.5 0.5 141 H 20.78891 18.09627 14.61234 0.5 0.5 142 H 19.46668 19.38764 1.470810 0.5 0.5 143 H 19.46668 19.38764 6.901420 0.5 0.5 144 H 19.46668 19.38764 12.33201 0.5 0.5 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors # unit=Ang. 30.33960000000 0.000000000000 0.000000000000 0.000000000000 30.33960000000 0.000000000000 0.000000000000 0.000000000000 16.29180000000 Atoms.UnitVectors> # # SCF or Electronic System # scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization On # On|Off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 160.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver Cluster # Recursion|Cluster|Band scf.lapack.dste dstegr # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 1 1 9 # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 40 # default=5 scf.Mixing.StartPulay 30 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type NoMD # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH MD.maxIter 200 # default=1 MD.TimeStep 1 # default=0.5 (fs) MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr) I have also seen the previous thread - http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2565 but this is not helpful. Please tell me if there is any way to work around this issue. Thanks! Regards, Hemant Arora

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Re: core dumped in the exchange coupling calculation (Jx) for cluster system ( No.1 ) Date: 2022/10/27 17:30 Name: T. Ozaki Hi, The SCF calculation was found to be normal. After the SCF calculation, I normally finished the jx calculation with a config file: ---- Flag.PeriodicSum off # default - off Num.Poles 60 Num.Kgrid 1 1 9 Num.ij.pairs 1 #Bunch.ij.pairs 1 <ijpairs.cellid 32 41 0 0 0 ijpairs.cellid> ---- The result is as follows: ---- [ozaki@mx17 work]$ mpirun -np 28 ./jx Mn2-100-FM.scfout jx.config ******************************************************************** ******************************************************************** jx: code for calculating an effective exchange coupling constant J Copyright (C), 2003, Myung Joon Han, Jaejun Yu, and Taisuke Ozaki 2019, Asako Terasawa and Taisuke Ozaki This is free software, and you are welcome to redistribute it under the constitution of the GNU-GPL. ******************************************************************** ******************************************************************** Read the scfout file (Mn2-100-FM.scfout) *** The file format of the SCFOUT file: 3 And it supports the following functions: - jx - polB - kSpin - Z2FH - calB *** Previous eigenvalue solver = Band atomnum = 144 ChemP = -0.163059049187 (Hartree) E_Temp = 300.000000000000 (K) Jij calculation for a periodic structure Number of k-grids: 1 1 9 flag_periodic_sum = 0: coupling between site i at cell 0 and site j at cell R Number of poles of Fermi-Dirac continued fraction (PRB.75.035123): 60 i j c1 c2 c3 J [meV] J [mRy] time_eig [s] time_Jij [s] ------------------------------------------------------------------------------------------------- 32 41 0 0 0 -439.319034429601 -32.289353760194 14.51941 0.34431 Elapsed time = 15.065304 (s) ---- Regards, TO Re: core dumped in the exchange coupling calculation (Jx) for cluster system ( No.2 ) Date: 2022/10/28 16:06 Name: HEMANT ARORA  <harora@ph.iitr.ac.in> Dear Prof. T. Ozaki, Thank you so much for the help but I have a doubt that I am using eigenvalue solver Cluster but in jx.out it is showing eigenvalue solver Band. Why? Thanks and Regards Hemant Arora Re: core dumped in the exchange coupling calculation (Jx) for cluster system ( No.3 ) Date: 2022/11/01 23:42 Name: T. Ozaki Hi, Your system is an one-dimentional system which is indicated by a message in the standard output as <Check_System> The system is bulk. Also, you specified as scf.Kgrid 1 1 9 So, even if you specify the 'cluster' solver, OpenMX automatically switches the solver to 'Band' in which the periodic boundary condtion is properly taken into account with the Bloch function. Regards, TO

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