LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 3.32812592387 Lattice spacing in x,y,z = 3.32813 3.32813 3.32813 region whole block 0 38.95471520398486 -38.95804332990873 38.95804332990873 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -38.958 0) to (38.9547 38.958 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 38.95804332990873 INF INF units box lattice fcc 3.32812592387 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.26511 4.26511 3.32813 create_atoms 1 region upper Created 550 atoms group upper type 1 550 atoms in group upper mass 1 26.981538 displace_atoms upper move 5.267114959823831 0 0.0 region lower block INF INF -38.95804332990873 0.0 INF INF units box lattice fcc 3.32812592387 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.26511 4.26511 3.32813 create_atoms 2 region lower Created 550 atoms group lower type 2 550 atoms in group lower displace_atoms lower move -5.267114959823831 0 -0.0 mass 2 26.981538 pair_style kim LAMMPSvirial LennardJones612_UniversalShifted__MO_959249795837_002 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 1.66406296194 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 8 15 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 24 atoms, new total = 1076 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 8 15 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) = 6.619 | 6.619 | 6.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23090.204 0 -23090.204 466236.65 338 0 -23757.917 0 -23757.917 -102325.5 Loop time of 3.7315 on 1 procs for 338 steps with 1076 atoms 93.2% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -23090.2037398 -23757.917216 -23757.917216 Force two-norm initial, final = 2887.59 0.000165101 Force max component initial, final = 892.171 5.08037e-05 Final line search alpha, max atom move = 1 5.08037e-05 Iterations, force evaluations = 338 671 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6257 | 3.6257 | 3.6257 | 0.0 | 97.17 Neigh | 0.025408 | 0.025408 | 0.025408 | 0.0 | 0.68 Comm | 0.045753 | 0.045753 | 0.045753 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03462 | | | 0.93 Nlocal: 1076 ave 1076 max 1076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14732 ave 14732 max 14732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 529297 ave 529297 max 529297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 529297 Ave neighs/atom = 491.912 Neighbor list builds = 1 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) = 6.619 | 6.619 | 6.619 Mbytes Step Temp E_pair E_mol TotEng Press Volume 338 0 -23757.917 0 -23757.917 -102325.5 10101.524 1338 0 -23758.545 0 -23758.545 -31107.43 10077.551 Loop time of 10.8355 on 1 procs for 1000 steps with 1076 atoms 99.4% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -23757.917216 -23758.5451535 -23758.545154 Force two-norm initial, final = 728.338 0.235699 Force max component initial, final = 565.571 0.147615 Final line search alpha, max atom move = 0.00783724 0.0011569 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.379 | 10.379 | 10.379 | 0.0 | 95.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10496 | 0.10496 | 0.10496 | 0.0 | 0.97 Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3516 | | | 3.24 Nlocal: 1076 ave 1076 max 1076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14746 ave 14746 max 14746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 529384 ave 529384 max 529384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 529384 Ave neighs/atom = 491.993 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 8 15 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) = 6.757 | 6.757 | 6.757 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23758.545 0 -23758.545 -31107.43 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1076 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: 1076 ave 1076 max 1076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14753 ave 14753 max 14753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 529628 ave 529628 max 529628 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 = 529628 Ave neighs/atom = 492.219 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) = 6.757 | 6.757 | 6.757 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -23758.545 38.893928 77.916087 3.3254167 -31107.43 -14.802484 -93284.037 -23.449459 -23758.545 2.1418225 668.89514 Loop time of 0.000638008 on 1 procs for 0 steps with 1076 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 | | 0.000638 | | |100.00 Nlocal: 1076 ave 1076 max 1076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14753 ave 14753 max 14753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 529628 ave 529628 max 529628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 586004 ave 586004 max 586004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586004 Ave neighs/atom = 544.613 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_039.9662/energy.out -23758.5451540174 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.9662/numatoms.out 1076 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_039.9662/mindistance.out 2.14182246980313 write_dump all cfg output/dump_039.9662/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_039.9662/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:14