LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6063 3.6063 3.6063 Created orthogonal box = (0 -41.7496 0) to (29.5189 41.7496 5.10008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.72754 6.23074 5.10008 Created 538 atoms create_atoms CPU = 0.00117993 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.72754 6.23074 5.10008 Created 538 atoms create_atoms CPU = 0.00101709 secs 538 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 14 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: full, newton off, cut 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1058 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 7.086 | 7.086 | 7.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4372.7479 0 -4372.7479 5961.48 87 0 -4435.8253 0 -4435.8253 -19039.788 Loop time of 3.70112 on 1 procs for 87 steps with 1058 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4372.74793471 -4435.82116126 -4435.82525475 Force two-norm initial, final = 45.9891 0.27968 Force max component initial, final = 15.6699 0.0362691 Final line search alpha, max atom move = 1 0.0362691 Iterations, force evaluations = 87 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.656 | 3.656 | 3.656 | 0.0 | 98.78 Neigh | 0.021899 | 0.021899 | 0.021899 | 0.0 | 0.59 Comm | 0.016725 | 0.016725 | 0.016725 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006541 | | | 0.18 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12494 ave 12494 max 12494 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: 646480 ave 646480 max 646480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 646480 Ave neighs/atom = 611.04 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.087 | 7.087 | 7.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -4435.8253 0 -4435.8253 -19039.788 12570.681 100 0 -4437.7379 0 -4437.7379 3230.7951 12403.269 Loop time of 0.404325 on 1 procs for 13 steps with 1058 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4435.82525475 -4437.73791373 -4437.73794737 Force two-norm initial, final = 330.835 0.494515 Force max component initial, final = 301.861 0.136237 Final line search alpha, max atom move = 0.000896587 0.000122148 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39768 | 0.39768 | 0.39768 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001657 | 0.001657 | 0.001657 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004989 | | | 1.23 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12626 ave 12626 max 12626 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: 644808 ave 644808 max 644808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644808 Ave neighs/atom = 609.459 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 7.225 | 7.225 | 7.225 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.7379 0 -4437.7379 3230.7951 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1058 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12659 ave 12659 max 12659 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: 651300 ave 651300 max 651300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651300 Ave neighs/atom = 615.595 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) = 7.225 | 7.225 | 7.225 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 -4437.7379 -4437.7379 29.170811 83.499154 5.0922016 3230.7951 3230.7951 -12.059203 9722.0156 -17.571004 2.3527302 1078.5868 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1058 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12659 ave 12659 max 12659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325650 ave 325650 max 325650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 651300 ave 651300 max 651300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651300 Ave neighs/atom = 615.595 Neighbor list builds = 0 Dangerous builds = 0 1058 -4437.73794737314 eV 2.35273015305564 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04