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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7941953 5.5194308 5.9005197 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7941953 5.5194308 5.9005197 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 507 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 29 3 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_122936827583_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.991 | 4.991 | 4.991 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2999.8725 0 -2999.8725 175824.26 104 0 -3555.3081 0 -3555.3081 4872.8921 Loop time of 11.9978 on 1 procs for 104 steps with 1008 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2999.8724691259 -3555.30487745755 -3555.3081167428 Force two-norm initial, final = 1303.7224 0.18313011 Force max component initial, final = 243.66065 0.038307930 Final line search alpha, max atom move = 1.0000000 0.038307930 Iterations, force evaluations = 104 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.946 | 11.946 | 11.946 | 0.0 | 99.57 Neigh | 0.029148 | 0.029148 | 0.029148 | 0.0 | 0.24 Comm | 0.010609 | 0.010609 | 0.010609 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01181 | | | 0.10 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5025.00 ave 5025 max 5025 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: 133718.0 ave 133718 max 133718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133718 Ave neighs/atom = 132.65675 Neighbor list builds = 3 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.991 | 4.991 | 4.991 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -3555.3081 0 -3555.3081 4872.8921 11888.259 108 0 -3555.4152 0 -3555.4152 14.004188 11934.653 Loop time of 0.76756 on 1 procs for 4 steps with 1008 atoms 49.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3555.30811674279 -3555.41495779515 -3555.41517448856 Force two-norm initial, final = 69.631886 0.67169327 Force max component initial, final = 53.657438 0.55936445 Final line search alpha, max atom move = 0.00034158211 0.00019106889 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75275 | 0.75275 | 0.75275 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029321 | 0.00029321 | 0.00029321 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01452 | | | 1.89 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5025.00 ave 5025 max 5025 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: 133726.0 ave 133726 max 133726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133726 Ave neighs/atom = 132.66468 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.129 | 5.129 | 5.129 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3555.4152 0 -3555.4152 14.004188 Loop time of 1.976e-06 on 1 procs for 0 steps with 1008 atoms 151.8% 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 | | 1.976e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5025.00 ave 5025 max 5025 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: 133676.0 ave 133676 max 133676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133676 Ave neighs/atom = 132.61508 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.129 | 5.129 | 5.129 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 -3555.4152 -3555.4152 13.555228 99.539945 8.8451581 14.004188 14.004188 -40.059325 75.236053 6.8358358 2.3057426 432.07901 Loop time of 2.237e-06 on 1 procs for 0 steps with 1008 atoms 178.8% 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 | | 2.237e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5025.00 ave 5025 max 5025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66838.0 ave 66838 max 66838 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133676.0 ave 133676 max 133676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133676 Ave neighs/atom = 132.61508 Neighbor list builds = 0 Dangerous builds = 0 1008 -3555.41517448856 eV 2.30574256447869 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13