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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678310 0.0000000) to (37.339155 74.678310 4.0500000) create_atoms CPU = 0.002 seconds 682 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_664470114311_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.508 | 5.508 | 5.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4522.0124 0 -4522.0124 5307.1479 71 0 -4570.8355 0 -4570.8355 2949.506 Loop time of 3.80919 on 1 procs for 71 steps with 1362 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 = -4522.01236958895 -4570.831686495 -4570.83545409273 Force two-norm initial, final = 28.050668 0.13823040 Force max component initial, final = 4.3256221 0.010453864 Final line search alpha, max atom move = 1.0000000 0.010453864 Iterations, force evaluations = 71 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7187 | 3.7187 | 3.7187 | 0.0 | 97.63 Neigh | 0.0327 | 0.0327 | 0.0327 | 0.0 | 0.86 Comm | 0.035362 | 0.035362 | 0.035362 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0224 | | | 0.59 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10445.0 ave 10445 max 10445 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: 237152.0 ave 237152 max 237152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237152 Ave neighs/atom = 174.12041 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4570.8355 0 -4570.8355 2949.506 22586.243 76 0 -4570.9976 0 -4570.9976 -180.84463 22675.368 Loop time of 0.210224 on 1 procs for 5 steps with 1362 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 = -4570.83545409274 -4570.99315234966 -4570.99760553843 Force two-norm initial, final = 81.751239 4.5363683 Force max component initial, final = 73.149587 3.2714011 Final line search alpha, max atom move = 0.00012168247 0.00039807217 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20341 | 0.20341 | 0.20341 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016179 | 0.0016179 | 0.0016179 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005194 | | | 2.47 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9793.00 ave 9793 max 9793 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: 237604.0 ave 237604 max 237604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237604 Ave neighs/atom = 174.45228 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.638 | 5.638 | 5.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4570.9976 0 -4570.9976 -180.84463 Loop time of 6.044e-06 on 1 procs for 0 steps with 1362 atoms 198.5% 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 | | 6.044e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9778.00 ave 9778 max 9778 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: 237216.0 ave 237216 max 237216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237216 Ave neighs/atom = 174.16740 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.638 | 5.638 | 5.638 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 -4570.9976 -4570.9976 37.330216 150.08697 4.0471647 -180.84463 -180.84463 -176.14095 -135.40696 -230.98599 2.5582199 197.8895 Loop time of 7.227e-06 on 1 procs for 0 steps with 1362 atoms 249.1% 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 | | 7.227e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9778.00 ave 9778 max 9778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118608.0 ave 118608 max 118608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237216.0 ave 237216 max 237216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237216 Ave neighs/atom = 174.16740 Neighbor list builds = 0 Dangerous builds = 0 1362 -4562.71744285981 eV 2.55821986892723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04