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lammps/examples/USER/atc/cauchy_born/cb_unistrain.screen
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cb_unistrain.screen
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
# create domain
lattice fcc 5.256227487 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
region BOX block -8 8 -2 2 -2 2
boundary f p p
create_box 1 BOX
Created orthogonal box = (-42.0498 -10.5125 -10.5125) to (42.0498 10.5125 10.5125)
4 by 1 by 1 MPI processor grid
# create atoms
region MD block -7 7 -2 2 -2 2
create_atoms 1 region MD
Created 896 atoms
mass 1 39.95
# specify interal/ghost atoms
region FREE block -6 6 -2 2 -2 2
group internal region FREE
768 atoms in group internal
# specify inter-atomic potential
pair_style lj/cut 13.5
pair_coeff 1 1 0.238 3.405
# specify neighbor/re-neighboring parameters
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
# setup thermal output
thermo 10
thermo_style custom step pe ke press lx ly lz
# ID group atc PhysicsType ParameterFile
fix AtC internal atc field Ar_CauchyBorn.mat
ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
ATC: peratom PE compute created with ID: 3
fix_modify AtC mesh create 8 1 1 BOX f p p
terminate called after throwing an instance of 'terminate called after throwing an instance of 'ATC::ATC_Error'
terminate called after throwing an instance of 'ATC::ATC_Error'
ATC: P1, ERROR: elastic_deformation_gradient is not a valid field
ATC: P3, ERROR: elastic_deformation_gradient is not a valid field
ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements
fix_modify AtC fields none
fix_modify AtC fields add displacement
fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify AtC gradients add displacement
fix_modify AtC fields add elastic_deformation_gradient
ATC: P0, ERROR: elastic_deformation_gradient is not a valid field
[pharsalus:35580] *** Process received signal ***
[pharsalus:35580] Signal: Aborted (6)
[pharsalus:35580] Signal code: (-6)
[pharsalus:35582] *** Process received signal ***
[pharsalus:35582] Signal: Aborted (6)
[pharsalus:35582] Signal code: (-6)
ATC::ATC_Error'
[pharsalus:35579] *** Process received signal ***
[pharsalus:35579] Signal: Aborted (6)
[pharsalus:35579] Signal code: (-6)
ATC: P2, ERROR: elastic_deformation_gradient is not a valid field
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:35581] *** Process received signal ***
[pharsalus:35581] Signal: Aborted (6)
[pharsalus:35581] Signal code: (-6)
[pharsalus:35582] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35582] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35582] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35582] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35582] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35582] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35582] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35579] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35579] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35579] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35579] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35579] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35579] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35579] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35579] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35579] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35579] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35579] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35579] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35579] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35579] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35579] *** End of error message ***
[pharsalus:35582] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35582] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35582] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35582] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35582] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35582] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35582] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35582] *** End of error message ***
[pharsalus:35581] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35581] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35581] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35581] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35581] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35581] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35581] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35581] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35581] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35581] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35581] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35581] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35581] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35581] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35581] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 35581 on node pharsalus exited on signal 6 (Aborted).
--------------------------------------------------------------------------
[pharsalus:35580] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:35580] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:35580] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:35580] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:35580] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:35580] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:35580] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:35580] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090]
[pharsalus:35580] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9]
[pharsalus:35580] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb]
[pharsalus:35580] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc]
[pharsalus:35580] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9]
[pharsalus:35580] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:35580] [13] ../../../lmp_openmpi() [0x537209]
[pharsalus:35580] *** End of error message ***
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