LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -39.6035 0) to (8.0833 39.6035 8.85481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.84998 5.27999 5.90321 Created 242 atoms create_atoms CPU = 0.000243187 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.84998 5.27999 5.90321 Created 242 atoms create_atoms CPU = 0.000125885 secs 242 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 2 19 3 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: full, newton off, cut 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1657.2317 0 -1657.2317 -4007.4627 19 0 -1664.475 0 -1664.475 -10145.593 Loop time of 0.0690608 on 1 procs for 19 steps with 472 atoms 101.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1657.23169831 -1664.47355409 -1664.47503937 Force two-norm initial, final = 13.4939 0.123995 Force max component initial, final = 4.63708 0.0333404 Final line search alpha, max atom move = 1 0.0333404 Iterations, force evaluations = 19 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067805 | 0.067805 | 0.067805 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080109 | 0.00080109 | 0.00080109 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004544 | | | 0.66 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93320 ave 93320 max 93320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93320 Ave neighs/atom = 197.712 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -1664.475 0 -1664.475 -10145.593 5669.3261 24 0 -1664.6182 0 -1664.6182 -154.17946 5628.5401 Loop time of 0.020117 on 1 procs for 5 steps with 472 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1664.47503937 -1664.61805941 -1664.61823924 Force two-norm initial, final = 55.7033 0.214163 Force max component initial, final = 39.7815 0.0655295 Final line search alpha, max atom move = 0.00113393 7.43057e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019263 | 0.019263 | 0.019263 | 0.0 | 95.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021195 | 0.00021195 | 0.00021195 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006421 | | | 3.19 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93964 ave 93964 max 93964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93964 Ave neighs/atom = 199.076 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d 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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1664.6182 0 -1664.6182 -154.17946 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 atoms 0.0% CPU use with 1 MPI tasks x 1 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94176 ave 94176 max 94176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94176 Ave neighs/atom = 199.525 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1664.6182 -1664.6182 8.0511165 79.207039 8.826243 -154.17946 -154.17946 5.5871561 -458.64721 -9.4783325 2.3006569 319.29158 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 atoms 0.0% CPU use with 1 MPI tasks x 1 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47088 ave 47088 max 47088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94176 ave 94176 max 94176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94176 Ave neighs/atom = 199.525 Neighbor list builds = 0 Dangerous builds = 0 472 -1664.61823924273 eV 2.30065686810226 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00