LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.05000464022 Lattice spacing in x,y,z = 4.05 4.05 4.05 region whole block 0 53.26949410632704 -53.27354411096726 53.27354411096726 0 4.05000464022 units box create_box 2 whole Created orthogonal box = (0 -53.2735 0) to (53.2695 53.2735 4.05) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 53.27354411096726 INF INF units box lattice fcc 4.05000464022 orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.61874 4.61874 4.05 create_atoms 1 region upper Created 694 atoms group upper type 1 694 atoms in group upper mass 1 26.981538 displace_atoms upper move 5.918825897084657 0 0.3333333333333333 region lower block INF INF -53.27354411096726 0.0 INF INF units box lattice fcc 4.05000464022 orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.61874 4.61874 4.05 create_atoms 2 region lower Created 694 atoms group lower type 2 694 atoms in group lower displace_atoms lower move -5.918825897084657 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Mishin_Farkas_Al__MO_651801486679_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02500232011 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 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 = 1364 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 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) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4555.2887 0 -4555.2887 -1886.4435 258 0 -4567.9068 0 -4567.9068 -7215.3717 Loop time of 2.36947 on 1 procs for 258 steps with 1364 atoms 73.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4555.28867549 -4567.90684001 -4567.90684001 Force two-norm initial, final = 11.3606 1.33703e-07 Force max component initial, final = 3.01227 1.34542e-08 Final line search alpha, max atom move = 1 1.34542e-08 Iterations, force evaluations = 258 506 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.328 | 2.328 | 2.328 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015737 | 0.015737 | 0.015737 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02577 | | | 1.09 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8916 ave 8916 max 8916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159055 ave 159055 max 159055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159055 Ave neighs/atom = 116.609 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) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press Volume 258 0 -4567.9068 0 -4567.9068 -7215.3717 22986.65 1258 0 -4568.2283 0 -4568.2283 -1801.9623 22822.873 Loop time of 12.2931 on 1 procs for 1000 steps with 1364 atoms 63.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4567.90684001 -4568.2283073 -4568.22830733 Force two-norm initial, final = 122.843 0.0322322 Force max component initial, final = 88.234 0.0293785 Final line search alpha, max atom move = 0.175291 0.00514977 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.765 | 11.765 | 11.765 | 0.0 | 95.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.072668 | 0.072668 | 0.072668 | 0.0 | 0.59 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4555 | | | 3.71 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8988 ave 8988 max 8988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160446 ave 160446 max 160446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160446 Ave neighs/atom = 117.629 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 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) = 5.17 | 5.17 | 5.17 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4568.2283 0 -4568.2283 -1801.9623 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9031 ave 9031 max 9031 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160592 ave 160592 max 160592 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 = 160592 Ave neighs/atom = 117.736 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) = 5.17 | 5.17 | 5.17 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -4568.2283 53.094323 106.54709 4.0344156 -1801.9623 2.0556014 -5408.8639 0.92153095 -4568.2283 2.5314377 696.24626 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9031 ave 9031 max 9031 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160592 ave 160592 max 160592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190088 ave 190088 max 190088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190088 Ave neighs/atom = 139.361 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_017.4923/energy.out -4568.22830732524 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_017.4923/numatoms.out 1364 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_017.4923/mindistance.out 2.53143770629881 write_dump all cfg output/dump_017.4923/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_017.4923/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:14