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 45.26740660287571 -45.27073472879958 45.27073472879958 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -45.2707 0) to (45.2674 45.2707 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 45.27073472879958 INF INF units box lattice fcc 3.32812592387 orient x 13 -4 0 orient y 4 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.15971 4.15971 3.32813 create_atoms 1 region upper Created 742 atoms group upper type 1 742 atoms in group upper mass 1 26.981538 displace_atoms upper move 6.1206617289309495 0 0.3333333333333333 region lower block INF INF -45.27073472879958 0.0 INF INF units box lattice fcc 3.32812592387 orient x 13 4 0 orient y -4 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.15971 4.15971 3.32813 create_atoms 2 region lower Created 742 atoms group lower type 2 742 atoms in group lower displace_atoms lower move -6.1206617289309495 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 = 9 18 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 = 1460 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 = 9 18 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -31554.333 0 -31554.333 426204.63 560 0 -32364.695 0 -32364.695 -68736.448 Loop time of 11.8094 on 1 procs for 560 steps with 1460 atoms 76.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -31554.3332098 -32364.6953116 -32364.6953116 Force two-norm initial, final = 2722.02 0.000359897 Force max component initial, final = 702.648 6.15806e-05 Final line search alpha, max atom move = 1 6.15806e-05 Iterations, force evaluations = 560 1118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.673 | 11.673 | 11.673 | 0.0 | 98.84 Neigh | 0.014155 | 0.014155 | 0.014155 | 0.0 | 0.12 Comm | 0.084269 | 0.084269 | 0.084269 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03811 | | | 0.32 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18155 ave 18155 max 18155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 718309 ave 718309 max 718309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718309 Ave neighs/atom = 491.992 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 560 0 -32364.695 0 -32364.695 -68736.448 13640.582 1560 0 -32365.22 0 -32365.22 -11581.957 13615.091 Loop time of 20.0659 on 1 procs for 1000 steps with 1460 atoms 76.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -32364.6953116 -32365.2201581 -32365.2201582 Force two-norm initial, final = 771.209 0.107431 Force max component initial, final = 587.684 0.0774922 Final line search alpha, max atom move = 0.00459919 0.000356401 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.306 | 19.306 | 19.306 | 0.0 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18785 | 0.18785 | 0.18785 | 0.0 | 0.94 Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5721 | | | 2.85 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17013 ave 17013 max 17013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 718962 ave 718962 max 718962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718962 Ave neighs/atom = 492.44 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 = 9 18 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -32365.22 0 -32365.22 -11581.957 Loop time of 0 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17020 ave 17020 max 17020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 719203 ave 719203 max 719203 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 = 719203 Ave neighs/atom = 492.605 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) = 10.83 | 10.83 | 10.83 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -32365.22 45.240898 90.541469 3.323853 -11581.957 -5.8148148 -34749.163 9.1073074 -32365.22 2.1532118 725.14727 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17020 ave 17020 max 17020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 719203 ave 719203 max 719203 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 798176 ave 798176 max 798176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 798176 Ave neighs/atom = 546.696 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_034.2055/energy.out -32365.220158181 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_034.2055/numatoms.out 1460 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_034.2055/mindistance.out 2.15321181684626 write_dump all cfg output/dump_034.2055/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_034.2055/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:32