LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.05001024902 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 region whole block 0 16.698620041543542 -50.09991013487964 50.09991013487964 0 4.05001024902 units box create_box 2 whole Created orthogonal box = (0 -50.0999 0) to (16.6986 50.0999 4.05001) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 50.09991013487964 INF INF units box lattice fcc 4.05001024902 orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.91136 4.91136 4.05001 create_atoms 1 region upper Created 206 atoms group upper type 1 206 atoms in group upper mass 1 26.981538 displace_atoms upper move 1.8553975315279474 0 0.3333333333333333 region lower block INF INF -50.09991013487964 0.0 INF INF units box lattice fcc 4.05001024902 orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.91136 4.91136 4.05001 create_atoms 2 region lower Created 206 atoms group lower type 2 206 atoms in group lower displace_atoms lower move -1.8553975315279474 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Sturgeon_Laird_Al__MO_120808805541_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02500512451 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 2 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 8 atoms, new total = 404 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 2 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) = 4.4 | 4.4 | 4.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1355.9618 0 -1355.9618 4803.0179 214 0 -1364.7744 0 -1364.7744 -3051.1923 Loop time of 0.395658 on 1 procs for 214 steps with 404 atoms 99.1% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1355.96184658 -1364.77439002 -1364.77439002 Force two-norm initial, final = 21.0214 2.14206e-06 Force max component initial, final = 6.93579 3.07944e-07 Final line search alpha, max atom move = 1 3.07944e-07 Iterations, force evaluations = 214 424 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38484 | 0.38484 | 0.38484 | 0.0 | 97.26 Neigh | 0.001267 | 0.001267 | 0.001267 | 0.0 | 0.32 Comm | 0.0059795 | 0.0059795 | 0.0059795 | 0.0 | 1.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003576 | | | 0.90 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016 ave 4016 max 4016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38723 ave 38723 max 38723 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38723 Ave neighs/atom = 95.849 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) = 4.4 | 4.4 | 4.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 214 0 -1364.7744 0 -1364.7744 -3051.1923 6776.472 1214 0 -1364.7988 0 -1364.7988 -224.96215 6750.9166 Loop time of 1.92576 on 1 procs for 1000 steps with 404 atoms 99.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1364.77439002 -1364.79877853 -1364.79877855 Force two-norm initial, final = 18.0829 0.00812392 Force max component initial, final = 13.3528 0.00348116 Final line search alpha, max atom move = 0.108982 0.000379383 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7873 | 1.7873 | 1.7873 | 0.0 | 92.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026551 | 0.026551 | 0.026551 | 0.0 | 1.38 Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1119 | | | 5.81 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38894 ave 38894 max 38894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38894 Ave neighs/atom = 96.2723 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 2 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) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1364.7988 0 -1364.7988 -224.96215 Loop time of 0 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41162 ave 41162 max 41162 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 = 41162 Ave neighs/atom = 101.886 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) = 4.538 | 4.538 | 4.538 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -1364.7988 16.659303 100.19982 4.0442592 -224.96215 0.82422943 -676.41842 0.70773057 -1364.7988 2.6203469 238.81938 Loop time of 0 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41162 ave 41162 max 41162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47504 ave 47504 max 47504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47504 Ave neighs/atom = 117.584 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_028.0725/energy.out -1364.79877855407 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_028.0725/numatoms.out 404 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_028.0725/mindistance.out 2.62034687274432 write_dump all cfg output/dump_028.0725/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_028.0725/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02