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 68.96909380210113 -68.97314380674135 68.97314380674135 0 4.05000464022 units box create_box 2 whole Created orthogonal box = (0 -68.9731 0) to (68.9691 68.9731 4.05) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 68.97314380674135 INF INF units box lattice fcc 4.05000464022 orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70779 5.70779 4.05 create_atoms 1 region upper Created 1161 atoms group upper type 1 1161 atoms in group upper mass 1 26.981538 displace_atoms upper move 7.663223864666881 0 0.3333333333333333 region lower block INF INF -68.97314380674135 0.0 INF INF units box lattice fcc 4.05000464022 orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70779 5.70779 4.05 create_atoms 2 region lower Created 1161 atoms group lower type 2 1161 atoms in group lower displace_atoms lower move -7.663223864666881 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 = 17 34 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 31 atoms, new total = 2291 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 = 17 34 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) = 5.636 | 5.636 | 5.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7660.5329 0 -7660.5329 -1975.3809 304 0 -7680.4362 0 -7680.4362 -7155.1112 Loop time of 3.35694 on 1 procs for 304 steps with 2291 atoms 100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7660.53293135 -7680.43619314 -7680.43619314 Force two-norm initial, final = 12.4132 1.72559e-05 Force max component initial, final = 2.33139 4.7036e-06 Final line search alpha, max atom move = 1 4.7036e-06 Iterations, force evaluations = 304 599 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2926 | 3.2926 | 3.2926 | 0.0 | 98.08 Neigh | 0.0083911 | 0.0083911 | 0.0083911 | 0.0 | 0.25 Comm | 0.030143 | 0.030143 | 0.030143 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02577 | | | 0.77 Nlocal: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13564 ave 13564 max 13564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268523 ave 268523 max 268523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268523 Ave neighs/atom = 117.208 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) = 5.636 | 5.636 | 5.636 Mbytes Step Temp E_pair E_mol TotEng Press Volume 304 0 -7680.4362 0 -7680.4362 -7155.1112 38531.867 1304 0 -7680.9362 0 -7680.9362 -1817.911 38268.428 Loop time of 11.7114 on 1 procs for 1000 steps with 2291 atoms 99.2% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -7680.43619314 -7680.93616229 -7680.93616229 Force two-norm initial, final = 205.483 0.00268479 Force max component initial, final = 148.071 0.00148004 Final line search alpha, max atom move = 0.256888 0.000380205 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.235 | 11.235 | 11.235 | 0.0 | 95.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.087298 | 0.087298 | 0.087298 | 0.0 | 0.75 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.389 | | | 3.32 Nlocal: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13579 ave 13579 max 13579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268627 ave 268627 max 268627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268627 Ave neighs/atom = 117.253 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 = 17 34 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) = 5.774 | 5.774 | 5.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7680.9362 0 -7680.9362 -1817.911 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2291 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: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13579 ave 13579 max 13579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268710 ave 268710 max 268710 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 = 268710 Ave neighs/atom = 117.289 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) = 5.774 | 5.774 | 5.774 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -7680.9362 68.75846 137.94629 4.034637 -1817.911 -0.061775316 -5453.719 0.047679973 -7680.9362 2.4846597 767.82 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2291 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: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13579 ave 13579 max 13579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268710 ave 268710 max 268710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 319404 ave 319404 max 319404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319404 Ave neighs/atom = 139.417 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_080.4727/energy.out -7680.93616229103 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_080.4727/numatoms.out 2291 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_080.4727/mindistance.out 2.48465972992648 write_dump all cfg output/dump_080.4727/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_080.4727/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15