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 10.52445825928135 -42.10116116304927 42.10116116304927 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -42.1012 0) to (10.5245 42.1012 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 42.10116116304927 INF INF units box lattice fcc 3.32812592387 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.20978 4.20978 3.32813 create_atoms 1 region upper Created 162 atoms group upper type 1 162 atoms in group upper mass 1 26.981538 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 region lower block INF INF -42.10116116304927 0.0 INF INF units box lattice fcc 3.32812592387 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.20978 4.20978 3.32813 create_atoms 2 region lower Created 162 atoms group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 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 = 2 16 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 6 atoms, new total = 318 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 = 2 16 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) = 4.896 | 4.896 | 4.896 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5821.3844 0 -5821.3844 3078427.1 371 0 -7049.8036 0 -7049.8036 151788.02 Loop time of 2.49268 on 1 procs for 371 steps with 318 atoms 49.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5821.38441744 -7049.80364734 -7049.80364734 Force two-norm initial, final = 5060.92 0.000225675 Force max component initial, final = 1321 4.81994e-05 Final line search alpha, max atom move = 1 4.81994e-05 Iterations, force evaluations = 371 738 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4405 | 2.4405 | 2.4405 | 0.0 | 97.91 Neigh | 0.012483 | 0.012483 | 0.012483 | 0.0 | 0.50 Comm | 0.032098 | 0.032098 | 0.032098 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007572 | | | 0.30 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8352 ave 8352 max 8352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163320 ave 163320 max 163320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163320 Ave neighs/atom = 513.585 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) = 4.896 | 4.896 | 4.896 Mbytes Step Temp E_pair E_mol TotEng Press Volume 371 0 -7049.8036 0 -7049.8036 151788.02 2949.3314 1371 0 -7050.0644 0 -7050.0644 75812.145 2956.4399 Loop time of 5.09455 on 1 procs for 1000 steps with 318 atoms 78.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -7049.80364734 -7050.06439356 -7050.06439356 Force two-norm initial, final = 226.474 0.000858283 Force max component initial, final = 204.056 0.000439975 Final line search alpha, max atom move = 0.576558 0.000253671 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.755 | 4.755 | 4.755 | 0.0 | 93.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.094387 | 0.094387 | 0.094387 | 0.0 | 1.85 Output | 1.3828e-05 | 1.3828e-05 | 1.3828e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2452 | | | 4.81 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8442 ave 8442 max 8442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163441 ave 163441 max 163441 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163441 Ave neighs/atom = 513.965 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 = 2 16 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) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7050.0644 0 -7050.0644 75812.145 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8406 ave 8406 max 8406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163353 ave 163353 max 163353 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 = 163353 Ave neighs/atom = 513.689 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) = 5.032 | 5.032 | 5.032 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -7050.0644 10.521344 84.202322 3.337135 75812.145 -0.045716179 227436.24 0.23908016 -7050.0644 2.2085307 149.1057 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8406 ave 8406 max 8406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163353 ave 163353 max 163353 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174132 ave 174132 max 174132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174132 Ave neighs/atom = 547.585 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_036.8699/energy.out -7050.06439355934 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_036.8699/mindistance.out 2.20853072657434 write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:07