forked from lijiext/lammps
164 lines
9.8 KiB
Plaintext
164 lines
9.8 KiB
Plaintext
LAMMPS (30 Aug 2013)
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log schrodinger-poisson2d_Jconstraint.log
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# physical parameters ===========================
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variable T equal 300
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variable n0 equal 0.00007
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variable J0 equal 40.0
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variable Vs equal 1.0
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# geometric parameters ===========================
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#variable Vg equal 1.0
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variable iter1 equal 4
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variable iter2 equal 25
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variable r equal 10 # run
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variable nx equal 12 # elements in x
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variable ny equal 12 # elements in y
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variable nz equal 1 # elements in z
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variable mx equal 4 # wire elements in x
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variable my equal 3 # wire elements in y
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variable n1 equal floor(${nx}/4) # number of elements in lower vaccuum
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variable n1 equal floor(12/4)
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variable n2 equal 3*${n1} # number of elements in lower vaccuum + wire
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variable n2 equal 3*3
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variable hx equal 1.0 # mesh size in x
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variable hy equal ${hx} # mesh size in y
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variable hy equal 1
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variable l equal -${hx}*${nx} # box lower bound
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variable l equal -1*${nx}
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variable l equal -1*12
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variable u equal ${hx}*${nx} # box upper bound
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variable u equal 1*${nx}
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variable u equal 1*12
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variable w equal ${hy}*${my}
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variable w equal 1*${my}
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variable w equal 1*3
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variable q equal ${hx}*${mx}
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variable q equal 1*${mx}
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variable q equal 1*4
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variable y equal ${nx}+1-${mx}
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variable y equal 12+1-${mx}
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variable y equal 12+1-4
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variable w1 equal (-$w-$l)/($u-$l)
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variable w1 equal (-3-$l)/($u-$l)
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variable w1 equal (-3--12)/($u-$l)
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variable w1 equal (-3--12)/(12-$l)
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variable w1 equal (-3--12)/(12--12)
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variable w2 equal 1-${w1}
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variable w2 equal 1-0.375
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variable tol equal 0.01
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#================================================
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atom_style atomic
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timestep 0.001
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boundary f f f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
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region BOX block ${l} ${u} ${l} ${u} 0 1
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region BOX block -12 ${u} ${l} ${u} 0 1
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region BOX block -12 12 ${l} ${u} 0 1
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region BOX block -12 12 -12 ${u} 0 1
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region BOX block -12 12 -12 12 0 1
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create_box 1 BOX
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Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874)
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2 by 2 by 1 MPI processor grid
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mass * 12.01
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atom_modify sort 0 1
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fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
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Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.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: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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ATC: creating drift_diffusion extrinsic model
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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[pharsalus:03148] *** Process received signal ***
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 9 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 9 1. 1 12 4.0
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[pharsalus:03148] Signal: Segmentation fault (11)
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[pharsalus:03148] Signal code: Address not mapped (1)
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[pharsalus:03148] Failing at address: (nil)
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[pharsalus:03149] *** Process received signal ***
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[pharsalus:03149] Signal: Segmentation fault (11)
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[pharsalus:03149] Signal code: Address not mapped (1)
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[pharsalus:03149] Failing at address: (nil)
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[pharsalus:03151] *** Process received signal ***
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[pharsalus:03150] *** Process received signal ***
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[pharsalus:03150] Signal: Segmentation fault (11)
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[pharsalus:03150] Signal code: Address not mapped (1)
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[pharsalus:03150] Failing at address: (nil)
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[pharsalus:03151] Signal: Segmentation fault (11)
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[pharsalus:03151] Signal code: Address not mapped (1)
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[pharsalus:03151] Failing at address: (nil)
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[pharsalus:03148] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03148] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03148] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03148] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03148] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03148] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03148] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:03148] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:03148] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:03148] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:03148] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:03148] [11] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:03148] *** End of error message ***
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[pharsalus:03149] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03150] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03150] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03150] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03150] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03150] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03150] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03150] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:03150] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:03150] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:03150] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:03150] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:03150] [11] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:03150] *** End of error message ***
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[pharsalus:03151] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03149] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03149] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03149] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03149] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03149] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03149] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:03149] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:03149] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:03149] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:03149] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:03149] [11] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:03149] *** End of error message ***
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[pharsalus:03151] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03151] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03151] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03151] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03151] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03151] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:03151] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:03151] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:03151] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:03151] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:03151] [11] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:03151] *** End of error message ***
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--------------------------------------------------------------------------
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mpirun noticed that process rank 1 with PID 3149 on node pharsalus exited on signal 11 (Segmentation fault).
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--------------------------------------------------------------------------
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