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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -38.059334 0.0000000) to (23.306487 38.059334 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2375431 4.3249243 4.6847802 Created 527 atoms using lattice units in orthogonal box = (0.0000000 -38.059334 0.0000000) to (23.306487 38.059334 7.0271702) create_atoms CPU = 0.001 seconds 527 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2375431 4.3249243 4.6847802 Created 533 atoms using lattice units in orthogonal box = (0.0000000 -38.059334 0.0000000) to (23.306487 38.059334 7.0271702) create_atoms CPU = 0.001 seconds 533 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 15 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.275 | 6.275 | 6.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3910.027 0 -3910.027 79186.249 96 0 -4346.8146 0 -4346.8146 14321.604 Loop time of 2.82244 on 1 procs for 96 steps with 1060 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 = -3910.02702674235 -4346.81067383747 -4346.81459270529 Force two-norm initial, final = 486.23038 0.28950502 Force max component initial, final = 74.640517 0.036210791 Final line search alpha, max atom move = 0.60767442 0.022004371 Iterations, force evaluations = 96 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7726 | 2.7726 | 2.7726 | 0.0 | 98.23 Neigh | 0.022103 | 0.022103 | 0.022103 | 0.0 | 0.78 Comm | 0.016684 | 0.016684 | 0.016684 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01104 | | | 0.39 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8730.00 ave 8730 max 8730 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: 414008.0 ave 414008 max 414008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 414008 Ave neighs/atom = 390.57358 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.277 | 6.277 | 6.277 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -4346.8146 0 -4346.8146 14321.604 12466.613 108 0 -4348.0462 0 -4348.0462 24.506701 12569.488 Loop time of 0.211533 on 1 procs for 12 steps with 1060 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 = -4346.81459270527 -4348.04603387883 -4348.04617819056 Force two-norm initial, final = 239.30702 1.2874096 Force max component initial, final = 221.37212 0.69791756 Final line search alpha, max atom move = 0.00091388963 0.00063781962 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20619 | 0.20619 | 0.20619 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001068 | 0.001068 | 0.001068 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004275 | | | 2.02 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8838.00 ave 8838 max 8838 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: 412468.0 ave 412468 max 412468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412468 Ave neighs/atom = 389.12075 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.414 | 6.414 | 6.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4348.0462 0 -4348.0462 24.506701 Loop time of 1.876e-06 on 1 procs for 0 steps with 1060 atoms 213.2% 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 | | 1.876e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 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: 403044.0 ave 403044 max 403044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403044 Ave neighs/atom = 380.23019 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.414 | 6.414 | 6.414 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 -4348.0462 -4348.0462 23.559657 75.752143 7.0429351 24.506701 24.506701 37.701886 88.532075 -52.713858 2.2606072 1052.3752 Loop time of 1.852e-06 on 1 procs for 0 steps with 1060 atoms 270.0% 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 | | 1.852e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201522.0 ave 201522 max 201522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 403044.0 ave 403044 max 403044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403044 Ave neighs/atom = 380.23019 Neighbor list builds = 0 Dangerous builds = 0 1060 -4348.04617819056 eV 2.26060721139819 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03