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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -72.584395 0.0000000) to (41.904530 72.584395 6.2700240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6289667 5.7775742 6.2700240 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584395 0.0000000) to (41.904530 72.584395 6.2700240) create_atoms CPU = 0.004 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6289667 5.7775742 6.2700240 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584395 0.0000000) to (41.904530 72.584395 6.2700240) create_atoms CPU = 0.004 seconds 1610 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11240.52 0 -11240.52 -657.51204 30 0 -11273.769 0 -11273.769 -4843.2653 Loop time of 1.532 on 1 procs for 30 steps with 3192 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11240.5197347143 -11273.7591040032 -11273.7691818473 Force two-norm initial, final = 28.051503 0.36322449 Force max component initial, final = 4.7324531 0.064528822 Final line search alpha, max atom move = 0.72280706 0.046641888 Iterations, force evaluations = 30 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4804 | 1.4804 | 1.4804 | 0.0 | 96.63 Neigh | 0.031836 | 0.031836 | 0.031836 | 0.0 | 2.08 Comm | 0.010197 | 0.010197 | 0.010197 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009551 | | | 0.62 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14519.0 ave 14519 max 14519 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: 556124.0 ave 556124 max 556124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556124 Ave neighs/atom = 174.22431 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -11273.769 0 -11273.769 -4843.2653 38141.998 33 0 -11273.909 0 -11273.909 -1185.0211 38038.545 Loop time of 0.17684 on 1 procs for 3 steps with 3192 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 = -11273.7691818472 -11273.9090301359 -11273.909198319 Force two-norm initial, final = 143.77969 0.37303899 Force max component initial, final = 112.13409 0.061726978 Final line search alpha, max atom move = 0.00038424520 2.3718295e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17219 | 0.17219 | 0.17219 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076756 | 0.00076756 | 0.00076756 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003881 | | | 2.19 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14534.0 ave 14534 max 14534 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: 556604.0 ave 556604 max 556604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556604 Ave neighs/atom = 174.37469 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.46 | 10.46 | 10.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11273.909 0 -11273.909 -1185.0211 Loop time of 2.266e-06 on 1 procs for 0 steps with 3192 atoms 176.5% 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 | | 2.266e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545.0 ave 14545 max 14545 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: 556744.0 ave 556744 max 556744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556744 Ave neighs/atom = 174.41855 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.46 | 10.46 | 10.46 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 -11273.909 -11273.909 41.858145 145.16879 6.259947 -1185.0211 -1185.0211 -0.83251752 -3556.342 2.1111269 2.3129402 1064.301 Loop time of 2.67e-06 on 1 procs for 0 steps with 3192 atoms 224.7% 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 | | 2.67e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545.0 ave 14545 max 14545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278372.0 ave 278372 max 278372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556744.0 ave 556744 max 556744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556744 Ave neighs/atom = 174.41855 Neighbor list builds = 0 Dangerous builds = 0 3192 -11273.909198319 eV 2.3129402049007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02