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 49.476148783984335 -49.47947690990821 49.47947690990821 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -49.4795 0) to (49.4761 49.4795 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 49.47947690990821 INF INF units box lattice fcc 3.32812592387 orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.25361 4.25361 3.32813 create_atoms 1 region upper Created 885 atoms group upper type 1 885 atoms in group upper mass 1 26.981538 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 region lower block INF INF -49.47947690990821 0.0 INF INF units box lattice fcc 3.32812592387 orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.25361 4.25361 3.32813 create_atoms 2 region lower Created 885 atoms group lower type 2 885 atoms in group lower displace_atoms lower move -6.689730936293327 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 = 10 19 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 22 atoms, new total = 1748 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 = 10 19 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) = 11.78 | 11.78 | 11.78 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -37185.948 0 -37185.948 735199.95 809 0 -38813.689 0 -38813.689 -35052.85 Loop time of 22.9835 on 1 procs for 809 steps with 1748 atoms 61.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -37185.9483079 -38813.6888546 -38813.6888546 Force two-norm initial, final = 4101.53 6.09487e-05 Force max component initial, final = 930.378 1.27585e-05 Final line search alpha, max atom move = 1 1.27585e-05 Iterations, force evaluations = 809 1609 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.608 | 22.608 | 22.608 | 0.0 | 98.37 Neigh | 0.070251 | 0.070251 | 0.070251 | 0.0 | 0.31 Comm | 0.211 | 0.211 | 0.211 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09412 | | | 0.41 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19434 ave 19434 max 19434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 860651 ave 860651 max 860651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 860651 Ave neighs/atom = 492.363 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) = 11.78 | 11.78 | 11.78 Mbytes Step Temp E_pair E_mol TotEng Press Volume 809 0 -38813.689 0 -38813.689 -35052.85 16294.864 1809 0 -38813.961 0 -38813.961 2315.7596 16275.029 Loop time of 31.6255 on 1 procs for 1000 steps with 1748 atoms 60.3% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -38813.6888546 -38813.9611886 -38813.9611889 Force two-norm initial, final = 612.974 0.451607 Force max component initial, final = 483.929 0.297045 Final line search alpha, max atom move = 0.00529673 0.00157337 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.451 | 30.451 | 30.451 | 0.0 | 96.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.26653 | 0.26653 | 0.26653 | 0.0 | 0.84 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.9083 | | | 2.87 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19434 ave 19434 max 19434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 860749 ave 860749 max 860749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 860749 Ave neighs/atom = 492.419 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 = 10 19 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) = 11.28 | 11.28 | 11.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38813.961 0 -38813.961 2315.7596 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19434 ave 19434 max 19434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 860907 ave 860907 max 860907 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 = 860907 Ave neighs/atom = 492.51 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) = 11.28 | 11.28 | 11.28 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -38813.961 49.434149 98.958954 3.3268991 2315.7596 28.25054 6889.7968 29.231469 -38813.961 2.1529822 789.9596 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19434 ave 19434 max 19434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 860907 ave 860907 max 860907 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 956932 ave 956932 max 956932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 956932 Ave neighs/atom = 547.444 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_039.3076/energy.out -38813.9611888875 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.3076/numatoms.out 1748 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_039.3076/mindistance.out 2.15298222163032 write_dump all cfg output/dump_039.3076/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_039.3076/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:54