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 41.69740759111658 -41.7014576013656 41.7014576013656 0 4.05001024902 units box create_box 2 whole Created orthogonal box = (0 -41.7015 0) to (41.6974 41.7015 4.05001) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 41.7014576013656 INF INF units box lattice fcc 4.05001024902 orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5072 5.5072 4.05001 create_atoms 1 region upper Created 426 atoms group upper type 1 426 atoms in group upper mass 1 26.981538 displace_atoms upper move 4.63303356344415 0 0.3333333333333333 region lower block INF INF -41.7014576013656 0.0 INF INF units box lattice fcc 4.05001024902 orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5072 5.5072 4.05001 create_atoms 2 region lower Created 426 atoms group lower type 2 426 atoms in group lower displace_atoms lower move -4.63303356344415 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 = 11 22 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 18 atoms, new total = 834 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 = 11 22 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2795.8459 0 -2795.8459 3443.6329 288 0 -2814.8216 0 -2814.8216 -6982.6682 Loop time of 0.883098 on 1 procs for 288 steps with 834 atoms 99.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2795.84585579 -2814.82161302 -2814.82161302 Force two-norm initial, final = 27.7129 6.2318e-06 Force max component initial, final = 7.40824 1.25105e-06 Final line search alpha, max atom move = 1 1.25105e-06 Iterations, force evaluations = 288 555 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85732 | 0.85732 | 0.85732 | 0.0 | 97.08 Neigh | 0.0070019 | 0.0070019 | 0.0070019 | 0.0 | 0.79 Comm | 0.010071 | 0.010071 | 0.010071 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008704 | | | 0.99 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5856 ave 5856 max 5856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72188 ave 72188 max 72188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72188 Ave neighs/atom = 86.5564 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 288 0 -2814.8216 0 -2814.8216 -6982.6682 14084.661 1288 0 -2815.0233 0 -2815.0233 -1422.0107 13980.009 Loop time of 3.23577 on 1 procs for 1000 steps with 834 atoms 99.4% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2814.82161302 -2815.02328207 -2815.02328572 Force two-norm initial, final = 76.8126 0.144829 Force max component initial, final = 56.9414 0.135409 Final line search alpha, max atom move = 0.0298313 0.00403944 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0563 | 3.0563 | 3.0563 | 0.0 | 94.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03335 | 0.03335 | 0.03335 | 0.0 | 1.03 Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1461 | | | 4.52 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5881 ave 5881 max 5881 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71700 ave 71700 max 71700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71700 Ave neighs/atom = 85.9712 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 = 11 22 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2815.0233 0 -2815.0233 -1422.0107 Loop time of 0 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5876 ave 5876 max 5876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79974 ave 79974 max 79974 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 = 79974 Ave neighs/atom = 95.8921 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) = 4.632 | 4.632 | 4.632 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -2815.0233 41.528922 83.402915 4.0362268 -1422.0107 -15.455836 -4250.0746 -0.50156302 -2815.0233 2.5576349 645.29226 Loop time of 0 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5876 ave 5876 max 5876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79974 ave 79974 max 79974 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94648 ave 94648 max 94648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94648 Ave neighs/atom = 113.487 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_058.1092/energy.out -2815.02328571781 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_058.1092/numatoms.out 834 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_058.1092/mindistance.out 2.557634908725 write_dump all cfg output/dump_058.1092/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_058.1092/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:04