LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.04999995232 Lattice spacing in x,y,z = 4.05 4.05 4.05 region whole block 0 67.40543296367426 -67.40948296362657 67.40948296362657 0 4.04999995232 units box create_box 2 whole Created orthogonal box = (0 -67.4095 0) to (67.4054 67.4095 4.05) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 67.40948296362657 INF INF units box lattice fcc 4.04999995232 orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59684 5.59684 4.05 create_atoms 1 region upper Created 1109 atoms group upper type 1 1109 atoms in group upper mass 1 26.981538 displace_atoms upper move 7.489492639691956 0 0.3333333333333333 region lower block INF INF -67.40948296362657 0.0 INF INF units box lattice fcc 4.04999995232 orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59684 5.59684 4.05 create_atoms 2 region lower Created 1109 atoms group lower type 2 1109 atoms in group lower displace_atoms lower move -7.489492639691956 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Zope_Mishin_Al__MO_664470114311_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02499997616 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 16 31 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 26 atoms, new total = 2192 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 16 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Per MPI rank memory allocation (min/avg/max) = 6.003 | 6.003 | 6.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7333.4717 0 -7333.4717 -1998.8557 222 0 -7350.1017 0 -7350.1017 -5168.6322 Loop time of 2.58636 on 1 procs for 222 steps with 2192 atoms 99.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7333.4717465 -7350.1017409 -7350.1017409 Force two-norm initial, final = 10.7714 1.2964e-05 Force max component initial, final = 1.94279 1.35545e-06 Final line search alpha, max atom move = 1 1.35545e-06 Iterations, force evaluations = 222 420 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5349 | 2.5349 | 2.5349 | 0.0 | 98.01 Neigh | 0.017281 | 0.017281 | 0.017281 | 0.0 | 0.67 Comm | 0.015591 | 0.015591 | 0.015591 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01856 | | | 0.72 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13358 ave 13358 max 13358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321643 ave 321643 max 321643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321643 Ave neighs/atom = 146.735 Neighbor list builds = 3 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 6.003 | 6.003 | 6.003 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -7350.1017 0 -7350.1017 -5168.6322 36804.499 1222 0 -7350.3999 0 -7350.3999 -951.44252 36606.5 Loop time of 12.5027 on 1 procs for 1000 steps with 2192 atoms 99.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -7350.1017409 -7350.39991247 -7350.39991247 Force two-norm initial, final = 154.38 0.00664932 Force max component initial, final = 115.111 0.00490874 Final line search alpha, max atom move = 0.273634 0.0013432 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.114 | 12.114 | 12.114 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06934 | 0.06934 | 0.06934 | 0.0 | 0.55 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3197 | | | 2.56 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13348 ave 13348 max 13348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321750 ave 321750 max 321750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321750 Ave neighs/atom = 146.784 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 compute csym all centro/atom fcc compute csymsum all reduce sum c_csym compute eng all pe/atom compute eatoms all reduce sum c_eng compute distance all pair/local dist compute mindist all reduce min c_distance reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 16 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 6.141 | 6.141 | 6.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7350.3999 0 -7350.3999 -951.44252 Loop time of 0 on 1 procs for 0 steps with 2192 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0 | | | 0.00 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13348 ave 13348 max 13348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321884 ave 321884 max 321884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321884 Ave neighs/atom = 146.845 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms c_mindist c_csymsum run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 6.141 | 6.141 | 6.141 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -7350.3999 67.260486 134.81897 4.0368928 -951.44252 -0.2143813 -2854.0614 -0.051744969 -7350.3999 2.5378844 1034.0568 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2192 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13348 ave 13348 max 13348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321884 ave 321884 max 321884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 381512 ave 381512 max 381512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381512 Ave neighs/atom = 174.047 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_065.4705/energy.out -7350.39991247038 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_065.4705/numatoms.out 2192 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_065.4705/mindistance.out 2.53788438756611 write_dump all cfg output/dump_065.4705/dump_post.cfg mass type xs ys zs id type xs ys zs c_csym c_eng modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_065.4705/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15