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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -51.487751 0.0000000) to (36.407338 51.487751 5.7208612) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7420996 6.9921637 5.7208612 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.487751 0.0000000) to (36.407338 51.487751 5.7208612) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7420996 6.9921637 5.7208612 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.487751 0.0000000) to (36.407338 51.487751 5.7208612) create_atoms CPU = 0.002 seconds 650 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4313.233 0 -4313.233 17831.295 52 0 -4419.2829 0 -4419.2829 4281.2607 Loop time of 1.75519 on 1 procs for 52 steps with 1298 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4313.23301968607 -4419.27888699387 -4419.28285462256 Force two-norm initial, final = 153.44535 0.14662765 Force max component initial, final = 45.975947 0.028605550 Final line search alpha, max atom move = 1.0000000 0.028605550 Iterations, force evaluations = 52 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.735 | 1.735 | 1.735 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01069 | 0.01069 | 0.01069 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009501 | | | 0.54 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7582.00 ave 7582 max 7582 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: 183588.0 ave 183588 max 183588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183588 Ave neighs/atom = 141.43914 Neighbor list builds = 0 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4419.2829 0 -4419.2829 4281.2607 21447.875 58 0 -4419.516 0 -4419.516 -3.3477035 21561.021 Loop time of 0.201674 on 1 procs for 6 steps with 1298 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 = -4419.28285462255 -4419.51509394533 -4419.51599352436 Force two-norm initial, final = 106.87340 0.43111259 Force max component initial, final = 88.740476 0.26006481 Final line search alpha, max atom move = 0.00013479724 3.5056018e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19602 | 0.19602 | 0.19602 | 0.0 | 97.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010209 | 0.0010209 | 0.0010209 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004634 | | | 2.30 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7542.00 ave 7542 max 7542 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: 185704.0 ave 185704 max 185704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185704 Ave neighs/atom = 143.06934 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4419.516 0 -4419.516 -3.3477035 Loop time of 3.197e-06 on 1 procs for 0 steps with 1298 atoms 156.4% 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 | | 3.197e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7542.00 ave 7542 max 7542 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: 184612.0 ave 184612 max 184612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184612 Ave neighs/atom = 142.22804 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.215 | 5.215 | 5.215 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 -4419.516 -4419.516 36.43774 103.50465 5.7168663 -3.3477035 -3.3477035 18.825982 -9.5574482 -19.311644 2.6618397 580.04257 Loop time of 3.264e-06 on 1 procs for 0 steps with 1298 atoms 183.8% 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 | | 3.264e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7542.00 ave 7542 max 7542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92306.0 ave 92306 max 92306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184612.0 ave 184612 max 184612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184612 Ave neighs/atom = 142.22804 Neighbor list builds = 0 Dangerous builds = 0 1298 -4419.51599352436 eV 2.66183968519192 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02