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 -49.063408 0.0000000) to (24.531704 49.063408 3.1409628) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4237499 4.4237499 3.1409628 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -49.063408 0.0000000) to (24.531704 49.063408 3.1409628) create_atoms CPU = 0.001 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4237499 4.4237499 3.1409628 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.063408 0.0000000) to (24.531704 49.063408 3.1409628) create_atoms CPU = 0.000 seconds 245 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 = 5 18 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 3 atoms, new total = 486 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 = 5 18 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) = 5.339 | 5.339 | 5.339 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1861.4224 0 -1861.4224 291148.91 117 0 -3272.5383 0 -3272.5383 -3259.7768 Loop time of 2.19089 on 1 procs for 117 steps with 486 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 = -1861.42236809603 -3272.53545238327 -3272.53832840444 Force two-norm initial, final = 3391.0839 0.27867577 Force max component initial, final = 1625.3903 0.028675244 Final line search alpha, max atom move = 0.88146992 0.025276365 Iterations, force evaluations = 117 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1406 | 2.1406 | 2.1406 | 0.0 | 97.71 Neigh | 0.022598 | 0.022598 | 0.022598 | 0.0 | 1.03 Comm | 0.018811 | 0.018811 | 0.018811 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008848 | | | 0.40 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9339.00 ave 9339 max 9339 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: 197766.0 ave 197766 max 197766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197766 Ave neighs/atom = 406.92593 Neighbor list builds = 2 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 = 5 18 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 : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.339 | 5.339 | 5.339 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -3272.5383 0 -3272.5383 -3259.7768 7560.9821 178 0 -3281.0253 0 -3281.0253 252.76789 7542.9086 Loop time of 0.845219 on 1 procs for 61 steps with 486 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3272.53832840444 -3281.02464679058 -3281.02531728124 Force two-norm initial, final = 204.59313 4.2557112 Force max component initial, final = 175.68409 2.0511523 Final line search alpha, max atom move = 0.00023896309 0.00049014968 Iterations, force evaluations = 61 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79265 | 0.79265 | 0.79265 | 0.0 | 93.78 Neigh | 0.022642 | 0.022642 | 0.022642 | 0.0 | 2.68 Comm | 0.0062849 | 0.0062849 | 0.0062849 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02365 | | | 2.80 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9238.00 ave 9238 max 9238 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: 198224.0 ave 198224 max 198224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198224 Ave neighs/atom = 407.86831 Neighbor list builds = 2 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 = 5 18 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) = 5.476 | 5.476 | 5.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3281.0253 0 -3281.0253 252.76789 Loop time of 3.22e-06 on 1 procs for 0 steps with 486 atoms 155.3% 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 | | 3.22e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9204.00 ave 9204 max 9204 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: 199278.0 ave 199278 max 199278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199278 Ave neighs/atom = 410.03704 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 = 5 18 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) = 5.476 | 5.476 | 5.476 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 -3281.0253 -3281.0253 25.21471 100.62629 2.9728528 252.76789 252.76789 -21.322763 446.77944 332.84698 2.6109512 157.26927 Loop time of 4.154e-06 on 1 procs for 0 steps with 486 atoms 216.7% 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 | | 4.154e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9204.00 ave 9204 max 9204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99639.0 ave 99639 max 99639 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199278.0 ave 199278 max 199278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199278 Ave neighs/atom = 410.03704 Neighbor list builds = 0 Dangerous builds = 0 486 -3281.02531728126 eV 2.61095120890468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03