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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -71.537243 0.0000000) to (41.302047 71.537243 7.0148038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3541610 6.4200090 7.0148038 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -71.537243 0.0000000) to (41.302047 71.537243 7.0148038) create_atoms CPU = 0.008 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3541610 6.4200090 7.0148038 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.537243 0.0000000) to (41.302047 71.537243 7.0148038) create_atoms CPU = 0.008 seconds 1249 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 = 12 41 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 5 atoms, new total = 2489 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_315820974149_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 = 12 41 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) = 5.251 | 5.251 | 5.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7487.4669 0 -7487.4669 31942.521 122 0 -8340.3092 0 -8340.3092 2419.2604 Loop time of 35.5281 on 1 procs for 122 steps with 2489 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 = -7487.46694401935 -8340.30153245957 -8340.30920113308 Force two-norm initial, final = 828.51366 0.36103081 Force max component initial, final = 138.40241 0.044333764 Final line search alpha, max atom move = 1.0000000 0.044333764 Iterations, force evaluations = 122 230 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.357 | 35.357 | 35.357 | 0.0 | 99.52 Neigh | 0.070849 | 0.070849 | 0.070849 | 0.0 | 0.20 Comm | 0.041443 | 0.041443 | 0.041443 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05889 | | | 0.17 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7432.00 ave 7432 max 7432 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: 197926.0 ave 197926 max 197926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197926 Ave neighs/atom = 79.520289 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 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 : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -8340.3092 0 -8340.3092 2419.2604 41452.364 127 0 -8340.623 0 -8340.623 44.180331 41579.739 Loop time of 1.02157 on 1 procs for 5 steps with 2489 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8340.30920113303 -8340.61648969893 -8340.62302558861 Force two-norm initial, final = 145.47755 2.3496693 Force max component initial, final = 138.63894 1.8900606 Final line search alpha, max atom move = 7.7384787e-05 0.00014626194 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0147 | 1.0147 | 1.0147 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001243 | 0.001243 | 0.001243 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005654 | | | 0.55 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8330.00 ave 8330 max 8330 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: 199932.0 ave 199932 max 199932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199932 Ave neighs/atom = 80.326235 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 = 12 42 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) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8340.623 0 -8340.623 44.180331 Loop time of 8.69e-06 on 1 procs for 0 steps with 2489 atoms 184.1% 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 | | 8.69e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416.00 ave 8416 max 8416 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: 194714.0 ave 194714 max 194714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194714 Ave neighs/atom = 78.229811 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 = 12 42 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) = 5.412 | 5.412 | 5.412 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 -8340.623 -8340.623 41.299616 143.73517 7.0044286 44.180331 44.180331 9.3724355 50.447276 72.721281 2.527403 1110.5342 Loop time of 3.3027e-05 on 1 procs for 0 steps with 2489 atoms 130.2% 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 | | 3.303e-05 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416.00 ave 8416 max 8416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97357.0 ave 97357 max 97357 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194714.0 ave 194714 max 194714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194714 Ave neighs/atom = 78.229811 Neighbor list builds = 0 Dangerous builds = 0 2489 -8340.62302558861 eV 2.52740297038841 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37