LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.02484538406 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 region whole block 0 32.449340883341385 -64.90270661206684 64.90270661206684 0 4.02484538406 units box create_box 2 whole Created orthogonal box = (0 -64.9027 0) to (32.4493 64.9027 4.02485) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 64.90270661206684 INF INF units box lattice fcc 4.02484538406 orient x 8 -1 0 orient y 1 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.49299 4.49299 4.02485 create_atoms 1 region upper Created 522 atoms group upper type 1 522 atoms in group upper mass 1 26.981538 displace_atoms upper move 3.628015986734347 0 0.3333333333333333 region lower block INF INF -64.90270661206684 0.0 INF INF units box lattice fcc 4.02484538406 orient x 8 1 0 orient y -1 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.49299 4.49299 4.02485 create_atoms 2 region lower Created 522 atoms group lower type 2 522 atoms in group lower displace_atoms lower move -3.628015986734347 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Winey_Kubota_Al__MO_149316865608_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.01242269203 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 32 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 12 atoms, new total = 1032 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 32 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) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2713.4858 0 -2713.4858 -226.83933 521 0 -2723.8778 0 -2723.8778 -2285.6657 Loop time of 2.96954 on 1 procs for 521 steps with 1032 atoms 99.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2713.48578206 -2723.8778256 -2723.8778256 Force two-norm initial, final = 12.933 7.04447e-06 Force max component initial, final = 3.12382 1.09497e-06 Final line search alpha, max atom move = 1 1.09497e-06 Iterations, force evaluations = 521 1040 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9211 | 2.9211 | 2.9211 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.027288 | 0.027288 | 0.027288 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02114 | | | 0.71 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7773 ave 7773 max 7773 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122338 ave 122338 max 122338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122338 Ave neighs/atom = 118.545 Neighbor list builds = 0 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) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press Volume 521 0 -2723.8778 0 -2723.8778 -2285.6657 16953.052 1521 0 -2723.9185 0 -2723.9185 -53.246582 16904.975 Loop time of 6.14792 on 1 procs for 1000 steps with 1032 atoms 98.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2723.8778256 -2723.9185034 -2723.9185034 Force two-norm initial, final = 37.5786 0.000407819 Force max component initial, final = 30.4096 0.000329161 Final line search alpha, max atom move = 1 0.000329161 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8942 | 5.8942 | 5.8942 | 0.0 | 95.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04735 | 0.04735 | 0.04735 | 0.0 | 0.77 Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2063 | | | 3.36 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7788 ave 7788 max 7788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122629 ave 122629 max 122629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122629 Ave neighs/atom = 118.827 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 32 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) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2723.9185 0 -2723.9185 -53.246582 Loop time of 0 on 1 procs for 0 steps with 1032 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: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7788 ave 7788 max 7788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122701 ave 122701 max 122701 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 = 122701 Ave neighs/atom = 118.896 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) = 5.112 | 5.112 | 5.112 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -2723.9185 32.42905 129.80541 4.0159428 -53.246582 -0.031176844 -159.7064 -0.0021730137 -2723.9185 2.5031323 477.24063 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1032 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 | | 1.192e-06 | | |100.00 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7788 ave 7788 max 7788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122701 ave 122701 max 122701 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 144280 ave 144280 max 144280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144280 Ave neighs/atom = 139.806 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_014.2500/energy.out -2723.91850339719 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_014.2500/numatoms.out 1032 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_014.2500/mindistance.out 2.50313229644357 write_dump all cfg output/dump_014.2500/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_014.2500/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09