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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -39.977930 0.0000000) to (9.4228884 39.977930 4.4419922) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2349380 4.4419922 4.4419922 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -39.977930 0.0000000) to (9.4228884 39.977930 4.4419922) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2349380 4.4419922 4.4419922 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -39.977930 0.0000000) to (9.4228884 39.977930 4.4419922) create_atoms CPU = 0.000 seconds 110 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 216 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1231.4993 0 -1231.4993 166029.13 63 0 -1446.84 0 -1446.84 16765.244 Loop time of 0.641454 on 1 procs for 63 steps with 216 atoms 91.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1231.49925661566 -1446.83854164517 -1446.83996579078 Force two-norm initial, final = 534.34186 0.23140052 Force max component initial, final = 188.07408 0.044984779 Final line search alpha, max atom move = 1.0000000 0.044984779 Iterations, force evaluations = 63 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62636 | 0.62636 | 0.62636 | 0.0 | 97.65 Neigh | 0.0056631 | 0.0056631 | 0.0056631 | 0.0 | 0.88 Comm | 0.0066589 | 0.0066589 | 0.0066589 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002769 | | | 0.43 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5613.00 ave 5613 max 5613 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: 89024.0 ave 89024 max 89024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89024 Ave neighs/atom = 412.14815 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1446.84 0 -1446.84 16765.244 3346.6642 660 0 -1463.807 0 -1463.807 -717.63126 3351.9345 Loop time of 3.85237 on 1 procs for 597 steps with 216 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 = -1446.83996579078 -1463.80580478542 -1463.80699162504 Force two-norm initial, final = 192.16233 3.8161414 Force max component initial, final = 174.07256 1.9339664 Final line search alpha, max atom move = 0.00032655929 0.00063155470 Iterations, force evaluations = 597 743 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6436 | 3.6436 | 3.6436 | 0.0 | 94.58 Neigh | 0.032049 | 0.032049 | 0.032049 | 0.0 | 0.83 Comm | 0.03506 | 0.03506 | 0.03506 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1417 | | | 3.68 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5470.00 ave 5470 max 5470 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: 89472.0 ave 89472 max 89472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89472 Ave neighs/atom = 414.22222 Neighbor list builds = 6 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1463.807 0 -1463.807 -717.63126 Loop time of 2.188e-06 on 1 procs for 0 steps with 216 atoms 137.1% 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 | | 2.188e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 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: 90088.0 ave 90088 max 90088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90088 Ave neighs/atom = 417.07407 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.633 | 4.633 | 4.633 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 -1463.807 -1463.807 9.5899985 72.971338 4.7898804 -717.63126 -717.63126 -688.0749 -843.65672 -621.16215 2.6148987 1170.173 Loop time of 2.164e-06 on 1 procs for 0 steps with 216 atoms 184.8% 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 | | 2.164e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45044.0 ave 45044 max 45044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90088.0 ave 90088 max 90088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90088 Ave neighs/atom = 417.07407 Neighbor list builds = 0 Dangerous builds = 0 216 -1463.80699162504 eV 2.61489874543784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04