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 -41.302058 0.0000000) to (35.768632 41.302058 7.0148058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4200108 6.3541628 7.0148058 Created 620 atoms using lattice units in orthogonal box = (0.0000000 -41.302058 0.0000000) to (35.768632 41.302058 7.0148058) create_atoms CPU = 0.004 seconds 620 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4200108 6.3541628 7.0148058 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -41.302058 0.0000000) to (35.768632 41.302058 7.0148058) create_atoms CPU = 0.004 seconds 627 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 19 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1247 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 19 2 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) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4108.9305 0 -4108.9305 6908.1764 134 0 -4172.9208 0 -4172.9208 5661.1821 Loop time of 5.85431 on 1 procs for 134 steps with 1247 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 = -4108.93045691082 -4172.91663148403 -4172.92076607033 Force two-norm initial, final = 43.317305 0.15507692 Force max component initial, final = 10.802871 0.016926009 Final line search alpha, max atom move = 1.0000000 0.016926009 Iterations, force evaluations = 134 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6406 | 5.6406 | 5.6406 | 0.0 | 96.35 Neigh | 0.14212 | 0.14212 | 0.14212 | 0.0 | 2.43 Comm | 0.036107 | 0.036107 | 0.036107 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03554 | | | 0.61 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6220.00 ave 6220 max 6220 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: 215792.0 ave 215792 max 215792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215792 Ave neighs/atom = 173.04892 Neighbor list builds = 5 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 19 2 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 : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -4172.9208 0 -4172.9208 5661.1821 20726.199 145 0 -4173.5411 0 -4173.5411 30.502265 20872.361 Loop time of 0.335781 on 1 procs for 11 steps with 1247 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 = -4172.92076607033 -4173.54107481999 -4173.54111844334 Force two-norm initial, final = 148.53799 0.77776505 Force max component initial, final = 135.07172 0.44342292 Final line search alpha, max atom move = 0.0019402796 0.00086036443 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32717 | 0.32717 | 0.32717 | 0.0 | 97.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016988 | 0.0016988 | 0.0016988 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006912 | | | 2.06 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6216.00 ave 6216 max 6216 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: 216030.0 ave 216030 max 216030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216030 Ave neighs/atom = 173.23978 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 20 2 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) = 5.583 | 5.583 | 5.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4173.5411 0 -4173.5411 30.502265 Loop time of 6.415e-06 on 1 procs for 0 steps with 1247 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6216.00 ave 6216 max 6216 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: 215548.0 ave 215548 max 215548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215548 Ave neighs/atom = 172.85325 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 20 2 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) = 5.583 | 5.583 | 5.583 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 -4173.5411 -4173.5411 35.759899 83.434577 6.9956687 30.502265 30.502265 27.433635 34.379637 29.693522 2.5073501 1156.298 Loop time of 7.247e-06 on 1 procs for 0 steps with 1247 atoms 262.2% 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 | | 7.247e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6216.00 ave 6216 max 6216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107774.0 ave 107774 max 107774 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215548.0 ave 215548 max 215548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215548 Ave neighs/atom = 172.85325 Neighbor list builds = 0 Dangerous builds = 0 1247 -4165.96008844317 eV 2.50735006063881 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06