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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -29.268373 0.0000000) to (25.347154 29.268373 4.9709860) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5494892 4.5028266 4.9709860 Created 311 atoms using lattice units in orthogonal box = (0.0000000 -29.268373 0.0000000) to (25.347154 29.268373 4.9709860) create_atoms CPU = 0.003 seconds 311 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5494892 4.5028266 4.9709860 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -29.268373 0.0000000) to (25.347154 29.268373 4.9709860) create_atoms CPU = 0.003 seconds 316 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 624 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_024705128470_000#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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2482.4019 0 -2482.4019 48277.39 96 0 -2650.3063 0 -2650.3063 12827.022 Loop time of 0.94672 on 1 procs for 96 steps with 624 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2482.40192279241 -2650.3037669628 -2650.30631056234 Force two-norm initial, final = 183.91913 0.17435724 Force max component initial, final = 43.758123 0.040423311 Final line search alpha, max atom move = 1.0000000 0.040423311 Iterations, force evaluations = 96 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90652 | 0.90652 | 0.90652 | 0.0 | 95.75 Neigh | 0.0081085 | 0.0081085 | 0.0081085 | 0.0 | 0.86 Comm | 0.016 | 0.016 | 0.016 | 0.0 | 1.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01609 | | | 1.70 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3287.00 ave 3287 max 3287 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: 42314.0 ave 42314 max 42314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42314 Ave neighs/atom = 67.810897 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -2650.3063 0 -2650.3063 12827.022 7375.6503 100 0 -2650.5361 0 -2650.5361 -2.0423025 7432.8545 Loop time of 0.0354997 on 1 procs for 4 steps with 624 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2650.30631056234 -2650.53575554502 -2650.53607671563 Force two-norm initial, final = 102.53582 0.30678557 Force max component initial, final = 63.246355 0.16784058 Final line search alpha, max atom move = 0.00049001737 8.2244801e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033173 | 0.033173 | 0.033173 | 0.0 | 93.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050217 | 0.00050217 | 0.00050217 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001824 | | | 5.14 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3286.00 ave 3286 max 3286 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: 41860.0 ave 41860 max 41860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41860 Ave neighs/atom = 67.083333 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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 -2650.5361 0 -2650.5361 -2.0423025 Loop time of 6.124e-06 on 1 procs for 0 steps with 624 atoms 179.6% 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 | | 6.124e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3243.00 ave 3243 max 3243 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: 41624.0 ave 41624 max 41624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41624 Ave neighs/atom = 66.705128 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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 -2650.5361 -2650.5361 25.398392 58.694786 4.9859727 -2.0423025 -2.0423025 -12.346027 36.276272 -30.057152 2.3204869 687.80532 Loop time of 7.167e-06 on 1 procs for 0 steps with 624 atoms 251.2% 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 | | 7.167e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3243.00 ave 3243 max 3243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20812.0 ave 20812 max 20812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41624.0 ave 41624 max 41624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41624 Ave neighs/atom = 66.705128 Neighbor list builds = 0 Dangerous builds = 0 624 -2650.53601431563 eV 2.32048687499676 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01