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 44.402738039383635 -44.40606616530751 44.40606616530751 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -44.4061 0) to (44.4027 44.4061 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 44.40606616530751 INF INF units box lattice fcc 3.32812592387 orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 3.99126 3.99126 3.32813 create_atoms 1 region upper Created 714 atoms group upper type 1 714 atoms in group upper mass 1 26.981538 displace_atoms upper move 6.003748828856851 0 0.3333333333333333 region lower block INF INF -44.40606616530751 0.0 INF INF units box lattice fcc 3.32812592387 orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 3.99126 3.99126 3.32813 create_atoms 2 region lower Created 714 atoms group lower type 2 714 atoms in group lower displace_atoms lower move -6.003748828856851 0 -0.3333333333333333 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 = 9 17 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 20 atoms, new total = 1408 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 = 9 17 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29759.165 0 -29759.165 828175.81 436 0 -31221.979 0 -31221.979 -4244.5375 Loop time of 10.4509 on 1 procs for 436 steps with 1408 atoms 60.1% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -29759.1649194 -31221.9786976 -31221.9786976 Force two-norm initial, final = 4573.75 4.4976e-05 Force max component initial, final = 954.125 1.12526e-05 Final line search alpha, max atom move = 1 1.12526e-05 Iterations, force evaluations = 436 866 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.204 | 10.204 | 10.204 | 0.0 | 97.64 Neigh | 0.057066 | 0.057066 | 0.057066 | 0.0 | 0.55 Comm | 0.12453 | 0.12453 | 0.12453 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06514 | | | 0.62 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16937 ave 16937 max 16937 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 694142 ave 694142 max 694142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 694142 Ave neighs/atom = 492.999 Neighbor list builds = 2 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 436 0 -31221.979 0 -31221.979 -4244.5375 13124.471 1436 0 -31222.014 0 -31222.014 11209.144 13117.887 Loop time of 26.0165 on 1 procs for 1000 steps with 1408 atoms 55.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -31221.9786976 -31222.0143708 -31222.0143709 Force two-norm initial, final = 199.368 0.0464644 Force max component initial, final = 148.872 0.0423322 Final line search alpha, max atom move = 0.0733084 0.00310331 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.951 | 24.951 | 24.951 | 0.0 | 95.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.23994 | 0.23994 | 0.23994 | 0.0 | 0.92 Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.8258 | | | 3.17 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16610 ave 16610 max 16610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 694128 ave 694128 max 694128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 694128 Ave neighs/atom = 492.989 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 = 9 17 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) = 10.81 | 10.81 | 10.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -31222.014 0 -31222.014 11209.144 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16610 ave 16610 max 16610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 694182 ave 694182 max 694182 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 = 694182 Ave neighs/atom = 493.027 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) = 10.81 | 10.81 | 10.81 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -31222.014 44.389561 88.812132 3.3274439 11209.144 5.1687883 33622.023 0.24039158 -31222.014 2.1561131 649.18011 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16610 ave 16610 max 16610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 694182 ave 694182 max 694182 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 770136 ave 770136 max 770136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 770136 Ave neighs/atom = 546.972 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_025.9892/energy.out -31222.0143708469 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.9892/numatoms.out 1408 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_025.9892/mindistance.out 2.15611306304804 write_dump all cfg output/dump_025.9892/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_025.9892/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:36