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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -38.882951 0.0000000) to (12.960984 38.882951 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8120540 3.8120540 3.1435003 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -38.882951 0.0000000) to (12.960984 38.882951 3.1435003) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8120540 3.8120540 3.1435003 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.882951 0.0000000) to (12.960984 38.882951 3.1435003) create_atoms CPU = 0.000 seconds 103 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 16 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 204 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -891.54131 0 -891.54131 294292.16 98 0 -1354.565 0 -1354.565 17827.767 Loop time of 0.544036 on 1 procs for 98 steps with 204 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -891.541312760598 -1354.56364535331 -1354.56498748278 Force two-norm initial, final = 1326.5527 0.20760472 Force max component initial, final = 469.51630 0.043047963 Final line search alpha, max atom move = 0.93999604 0.040464915 Iterations, force evaluations = 98 184 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5267 | 0.5267 | 0.5267 | 0.0 | 96.81 Neigh | 0.0070861 | 0.0070861 | 0.0070861 | 0.0 | 1.30 Comm | 0.0069177 | 0.0069177 | 0.0069177 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003332 | | | 0.61 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4367.00 ave 4367 max 4367 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: 56454.0 ave 56454 max 56454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56454 Ave neighs/atom = 276.73529 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -1354.565 0 -1354.565 17827.767 3168.405 852 0 -1375.5283 0 -1375.5283 -799.76442 3167.0055 Loop time of 3.15471 on 1 procs for 754 steps with 204 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1354.56498748278 -1375.52698566533 -1375.52829011328 Force two-norm initial, final = 108.53246 4.2500863 Force max component initial, final = 84.194097 1.7588266 Final line search alpha, max atom move = 0.00028098514 0.00049420415 Iterations, force evaluations = 754 916 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9028 | 2.9028 | 2.9028 | 0.0 | 92.02 Neigh | 0.025285 | 0.025285 | 0.025285 | 0.0 | 0.80 Comm | 0.05478 | 0.05478 | 0.05478 | 0.0 | 1.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1718 | | | 5.45 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 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: 55968.0 ave 55968 max 55968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55968 Ave neighs/atom = 274.35294 Neighbor list builds = 7 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1375.5283 0 -1375.5283 -799.76442 Loop time of 3.774e-06 on 1 procs for 0 steps with 204 atoms 159.0% 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 | | 3.774e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4844.00 ave 4844 max 4844 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: 55952.0 ave 55952 max 55952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55952 Ave neighs/atom = 274.27451 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.591 | 4.591 | 4.591 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 -1375.5283 -1375.5283 13.132893 85.32258 2.8263403 -799.76442 -799.76442 -705.88121 -893.4019 -800.01016 2.631085 904.03795 Loop time of 4.412e-06 on 1 procs for 0 steps with 204 atoms 226.7% 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 | | 4.412e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4844.00 ave 4844 max 4844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27976.0 ave 27976 max 27976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55952.0 ave 55952 max 55952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55952 Ave neighs/atom = 274.27451 Neighbor list builds = 0 Dangerous builds = 0 204 -1375.52829011328 eV 2.63108501488234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03