LAMMPS (30 Aug 2013) log schrodinger-poisson2d_Jconstraint.log # physical parameters =========================== variable T equal 300 variable n0 equal 0.00007 variable J0 equal 40.0 variable Vs equal 1.0 # geometric parameters =========================== #variable Vg equal 1.0 variable iter1 equal 4 variable iter2 equal 25 variable r equal 10 # run variable nx equal 12 # elements in x variable ny equal 12 # elements in y variable nz equal 1 # elements in z variable mx equal 4 # wire elements in x variable my equal 3 # wire elements in y variable n1 equal floor(${nx}/4) # number of elements in lower vaccuum variable n1 equal floor(12/4) variable n2 equal 3*${n1} # number of elements in lower vaccuum + wire variable n2 equal 3*3 variable hx equal 1.0 # mesh size in x variable hy equal ${hx} # mesh size in y variable hy equal 1 variable l equal -${hx}*${nx} # box lower bound variable l equal -1*${nx} variable l equal -1*12 variable u equal ${hx}*${nx} # box upper bound variable u equal 1*${nx} variable u equal 1*12 variable w equal ${hy}*${my} variable w equal 1*${my} variable w equal 1*3 variable q equal ${hx}*${mx} variable q equal 1*${mx} variable q equal 1*4 variable y equal ${nx}+1-${mx} variable y equal 12+1-${mx} variable y equal 12+1-4 variable w1 equal (-$w-$l)/($u-$l) variable w1 equal (-3-$l)/($u-$l) variable w1 equal (-3--12)/($u-$l) variable w1 equal (-3--12)/(12-$l) variable w1 equal (-3--12)/(12--12) variable w2 equal 1-${w1} variable w2 equal 1-0.375 variable tol equal 0.01 #================================================ atom_style atomic timestep 0.001 boundary f f f lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region BOX block ${l} ${u} ${l} ${u} 0 1 region BOX block -12 ${u} ${l} ${u} 0 1 region BOX block -12 12 ${l} ${u} 0 1 region BOX block -12 12 -12 ${u} 0 1 region BOX block -12 12 -12 12 0 1 create_box 1 BOX Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874) 2 by 2 by 1 MPI processor grid mass * 12.01 atom_modify sort 0 1 fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat ATC: creating drift_diffusion extrinsic model ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps [pharsalus:03148] *** Process received signal *** ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e ATC: WARNING: material units metal do not match lammps ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat 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 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 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 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 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 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 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 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 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 [pharsalus:03148] Signal: Segmentation fault (11) [pharsalus:03148] Signal code: Address not mapped (1) [pharsalus:03148] Failing at address: (nil) [pharsalus:03149] *** Process received signal *** [pharsalus:03149] Signal: Segmentation fault (11) [pharsalus:03149] Signal code: Address not mapped (1) [pharsalus:03149] Failing at address: (nil) [pharsalus:03151] *** Process received signal *** [pharsalus:03150] *** Process received signal *** [pharsalus:03150] Signal: Segmentation fault (11) [pharsalus:03150] Signal code: Address not mapped (1) [pharsalus:03150] Failing at address: (nil) [pharsalus:03151] Signal: Segmentation fault (11) [pharsalus:03151] Signal code: Address not mapped (1) [pharsalus:03151] Failing at address: (nil) [pharsalus:03148] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] [pharsalus:03148] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f] [pharsalus:03148] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036] [pharsalus:03148] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d] [pharsalus:03148] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631] [pharsalus:03148] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad] [pharsalus:03148] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659] [pharsalus:03148] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b] [pharsalus:03148] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c] [pharsalus:03148] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929] [pharsalus:03148] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] [pharsalus:03148] [11] ../../../lmp_openmpi() [0x53b429] [pharsalus:03148] *** End of error message *** [pharsalus:03149] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] [pharsalus:03150] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] [pharsalus:03150] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f] [pharsalus:03150] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036] [pharsalus:03150] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d] [pharsalus:03150] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631] [pharsalus:03150] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad] [pharsalus:03150] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659] [pharsalus:03150] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b] [pharsalus:03150] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c] [pharsalus:03150] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929] [pharsalus:03150] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] [pharsalus:03150] [11] ../../../lmp_openmpi() [0x53b429] [pharsalus:03150] *** End of error message *** [pharsalus:03151] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] [pharsalus:03149] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f] [pharsalus:03149] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036] [pharsalus:03149] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d] [pharsalus:03149] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631] [pharsalus:03149] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad] [pharsalus:03149] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659] [pharsalus:03149] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b] [pharsalus:03149] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c] [pharsalus:03149] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929] [pharsalus:03149] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] [pharsalus:03149] [11] ../../../lmp_openmpi() [0x53b429] [pharsalus:03149] *** End of error message *** [pharsalus:03151] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f] [pharsalus:03151] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036] [pharsalus:03151] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d] [pharsalus:03151] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631] [pharsalus:03151] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad] [pharsalus:03151] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659] [pharsalus:03151] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b] [pharsalus:03151] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c] [pharsalus:03151] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929] [pharsalus:03151] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] [pharsalus:03151] [11] ../../../lmp_openmpi() [0x53b429] [pharsalus:03151] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 3149 on node pharsalus exited on signal 11 (Segmentation fault). --------------------------------------------------------------------------