LAMMPS (24 Dec 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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -58.230826 0.0000000) to (29.113607 58.230826 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9269182 4.9269182 3.6110986 Created 522 atoms create_atoms CPU = 0.001 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9269182 4.9269182 3.6110986 Created 522 atoms create_atoms CPU = 0.000 seconds 522 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 39 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: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1036 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4347.5922 0 -4347.5922 10745.183 28 0 -4380.9824 0 -4380.9824 -773.25318 Loop time of 0.770719 on 1 procs for 28 steps with 1036 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4347.59222264609 -4380.97816406621 -4380.98236832114 Force two-norm initial, final = 43.557388 0.21176346 Force max component initial, final = 11.664384 0.051623937 Final line search alpha, max atom move = 1.0000000 0.051623937 Iterations, force evaluations = 28 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76505 | 0.76505 | 0.76505 | 0.0 | 99.26 Neigh | 0.0026506 | 0.0026506 | 0.0026506 | 0.0 | 0.34 Comm | 0.0017461 | 0.0017461 | 0.0017461 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001277 | | | 0.17 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5408.00 ave 5408 max 5408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80304.0 ave 80304 max 80304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80304 Ave neighs/atom = 77.513514 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4380.9824 0 -4380.9824 -773.25318 12243.859 34 0 -4381.0886 0 -4381.0886 -2037.7632 12252.961 Loop time of 0.129708 on 1 procs for 6 steps with 1036 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4380.98236832114 -4381.08840313679 -4381.08863673754 Force two-norm initial, final = 30.554782 2.1371832 Force max component initial, final = 24.916984 2.0825649 Final line search alpha, max atom move = 0.00038308812 0.00079780589 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12855 | 0.12855 | 0.12855 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002451 | 0.0002451 | 0.0002451 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009111 | | | 0.70 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396.00 ave 5396 max 5396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80320.0 ave 80320 max 80320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80320 Ave neighs/atom = 77.528958 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.737 | 4.737 | 4.737 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4381.0886 0 -4381.0886 -2037.7632 Loop time of 2.40002e-06 on 1 procs for 0 steps with 1036 atoms 125.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396.00 ave 5396 max 5396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80332.0 ave 80332 max 80332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80332 Ave neighs/atom = 77.540541 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) = 4.737 | 4.737 | 4.737 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 -4381.0886 -4381.0886 28.989601 116.46165 3.6292415 -2037.7632 -2037.7632 42.802382 -6429.7729 273.68083 2.3131012 384.02434 Loop time of 2.50002e-06 on 1 procs for 0 steps with 1036 atoms 160.0% 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 | | 2.5e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396.00 ave 5396 max 5396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40166.0 ave 40166 max 40166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80332.0 ave 80332 max 80332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80332 Ave neighs/atom = 77.540541 Neighbor list builds = 0 Dangerous builds = 0 1036 -4381.08863673754 eV 2.31310120066283 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01