5302074b3f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
125 lines
7.3 KiB
Plaintext
125 lines
7.3 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style atomic
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# create domain
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lattice fcc 5.256227487 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
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region BOX block -8 8 -2 2 -2 2
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boundary f p p
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create_box 1 BOX
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Created orthogonal box = (-42.0498 -10.5125 -10.5125) to (42.0498 10.5125 10.5125)
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4 by 1 by 1 MPI processor grid
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# create atoms
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region MD block -7 7 -2 2 -2 2
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create_atoms 1 region MD
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Created 896 atoms
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mass 1 39.95
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# specify interal/ghost atoms
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region FREE block -6 6 -2 2 -2 2
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group internal region FREE
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768 atoms in group internal
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# specify inter-atomic potential
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pair_style lj/cut 13.5
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pair_coeff 1 1 0.238 3.405
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# specify neighbor/re-neighboring parameters
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neighbor 0.3 bin
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neigh_modify every 10 delay 0 check no
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# setup thermal output
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thermo 10
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thermo_style custom step pe ke press lx ly lz
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc field Ar_CauchyBorn.mat
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ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: P1, ERROR: elastic_deformation_gradient is not a valid field
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ATC: P3, ERROR: elastic_deformation_gradient is not a valid field
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fix_modify AtC mesh create 8 1 1 BOX f p p
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ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
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fix_modify AtC fields none
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fix_modify AtC fields add displacement
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fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
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fix_modify AtC gradients add displacement
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fix_modify AtC fields add elastic_deformation_gradient
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ATC: P0, ERROR: elastic_deformation_gradient is not a valid field
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terminate called after throwing an instance of 'ATC::ATC_Error'
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[pharsalus:01453] *** Process received signal ***
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[pharsalus:01453] Signal: Aborted (6)
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[pharsalus:01453] Signal code: (-6)
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terminate called after throwing an instance of 'ATC::ATC_Error'
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[pharsalus:01450] *** Process received signal ***
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terminate called after throwing an instance of 'ATC::ATC_Error'
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[pharsalus:01451] *** Process received signal ***
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[pharsalus:01450] Signal: Aborted (6)
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[pharsalus:01450] Signal code: (-6)
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[pharsalus:01451] Signal: Aborted (6)
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[pharsalus:01451] Signal code: (-6)
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ATC: P2, ERROR: elastic_deformation_gradient is not a valid field
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terminate called after throwing an instance of 'ATC::ATC_Error'
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[pharsalus:01452] *** Process received signal ***
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[pharsalus:01452] Signal: Aborted (6)
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[pharsalus:01452] Signal code: (-6)
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[pharsalus:01453] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:01453] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
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[pharsalus:01453] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
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[pharsalus:01453] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
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[pharsalus:01453] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
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[pharsalus:01453] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
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[pharsalus:01453] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
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[pharsalus:01453] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x697000]
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[pharsalus:01453] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:01453] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:01453] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:01453] [11] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:01453] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:01453] [13] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:01453] *** End of error message ***
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[pharsalus:01450] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:01450] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
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[pharsalus:01450] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
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[pharsalus:01450] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
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[pharsalus:01450] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
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[pharsalus:01450] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
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[pharsalus:01450] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
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[pharsalus:01450] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x697000]
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[pharsalus:01450] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:01450] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:01450] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:01450] [11] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:01450] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:01450] [13] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:01450] *** End of error message ***
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[pharsalus:01451] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:01451] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
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[pharsalus:01451] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
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[pharsalus:01451] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
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[pharsalus:01451] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
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[pharsalus:01451] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
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[pharsalus:01451] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
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[pharsalus:01451] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x697000]
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[pharsalus:01451] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:01451] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:01451] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:01451] [11] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:01451] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:01451] [13] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:01451] *** End of error message ***
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[pharsalus:01452] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:01452] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
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[pharsalus:01452] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
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[pharsalus:01452] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
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[pharsalus:01452] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
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[pharsalus:01452] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
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[pharsalus:01452] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
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[pharsalus:01452] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x697000]
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[pharsalus:01452] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:01452] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:01452] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:01452] [11] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:01452] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:01452] [13] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:01452] *** End of error message ***
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--------------------------------------------------------------------------
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mpirun noticed that process rank 3 with PID 1453 on node pharsalus exited on signal 6 (Aborted).
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--------------------------------------------------------------------------
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