LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -29.760000 0.0000000) to (21.043498 29.760000 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6763329 3.8577778 4.0498230 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -29.760000 0.0000000) to (21.043498 29.760000 4.0498230) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6763329 3.8577778 4.0498230 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.760000 0.0000000) to (21.043498 29.760000 4.0498230) create_atoms CPU = 0.000 seconds 218 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 22 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 432 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_856956178669_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1261.5883 0 -1261.5883 178607.81 54 0 -1839.0223 0 -1839.0223 13188.484 Loop time of 0.88494 on 1 procs for 54 steps with 432 atoms 95.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1261.58833207437 -1839.02088098252 -1839.02229513762 Force two-norm initial, final = 1091.3074 0.14860689 Force max component initial, final = 275.68921 0.033724489 Final line search alpha, max atom move = 1.0000000 0.033724489 Iterations, force evaluations = 54 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87882 | 0.87882 | 0.87882 | 0.0 | 99.31 Neigh | 0.0021048 | 0.0021048 | 0.0021048 | 0.0 | 0.24 Comm | 0.0020334 | 0.0020334 | 0.0020334 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001985 | | | 0.22 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2736.00 ave 2736 max 2736 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: 25172.0 ave 25172 max 25172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25172 Ave neighs/atom = 58.268519 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1839.0223 0 -1839.0223 13188.484 5072.4398 66 0 -1839.4268 0 -1839.4268 23.592369 5110.1395 Loop time of 0.155928 on 1 procs for 12 steps with 432 atoms 87.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1839.02229513762 -1839.42585563663 -1839.42675300481 Force two-norm initial, final = 85.566207 0.59499461 Force max component initial, final = 79.082239 0.16825587 Final line search alpha, max atom move = 0.00048257127 8.1195450e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15416 | 0.15416 | 0.15416 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029632 | 0.00029632 | 0.00029632 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001474 | | | 0.95 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 25108.0 ave 25108 max 25108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25108 Ave neighs/atom = 58.120370 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1839.4268 0 -1839.4268 23.592369 Loop time of 1.958e-06 on 1 procs for 0 steps with 432 atoms 204.3% 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 | | 1.958e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2708.00 ave 2708 max 2708 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: 25080.0 ave 25080 max 25080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25080 Ave neighs/atom = 58.055556 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 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 -1839.4268 -1839.4268 21.00276 60.207067 4.0411867 23.592369 23.592369 32.457051 -7.1756753 45.495731 2.3149179 457.16864 Loop time of 2.049e-06 on 1 procs for 0 steps with 432 atoms 195.2% 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 | | 2.049e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2708.00 ave 2708 max 2708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12540.0 ave 12540 max 12540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25080.0 ave 25080 max 25080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25080 Ave neighs/atom = 58.055556 Neighbor list builds = 0 Dangerous builds = 0 432 -1839.42675300481 eV 2.31491785407198 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01