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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -29.946897 0.0000000) to (36.677309 29.946897 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6680211 4.3559123 4.6627256 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -29.946897 0.0000000) to (36.677309 29.946897 6.9940884) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6680211 4.3559123 4.6627256 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -29.946897 0.0000000) to (36.677309 29.946897 6.9940884) create_atoms CPU = 0.001 seconds 662 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1318 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2927.4865 0 -2927.4865 369978.05 85 0 -5392.3936 0 -5392.3936 4718.7124 Loop time of 1.40856 on 1 procs for 85 steps with 1318 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 = -2927.48650648389 -5392.38887217208 -5392.39358555334 Force two-norm initial, final = 3806.9005 0.27960543 Force max component initial, final = 534.92999 0.097881367 Final line search alpha, max atom move = 1.0000000 0.097881367 Iterations, force evaluations = 85 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3675 | 1.3675 | 1.3675 | 0.0 | 97.08 Neigh | 0.025265 | 0.025265 | 0.025265 | 0.0 | 1.79 Comm | 0.0074819 | 0.0074819 | 0.0074819 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008348 | | | 0.59 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6066.00 ave 6066 max 6066 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: 217584.0 ave 217584 max 217584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217584 Ave neighs/atom = 165.08649 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -5392.3936 0 -5392.3936 4718.7124 15364.216 90 0 -5392.6256 0 -5392.6256 -109.80381 15408.472 Loop time of 0.0643959 on 1 procs for 5 steps with 1318 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 = -5392.39358555335 -5392.62518354219 -5392.62564547302 Force two-norm initial, final = 108.72222 2.7052644 Force max component initial, final = 96.716222 1.9532652 Final line search alpha, max atom move = 0.00018472050 0.00036080814 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062526 | 0.062526 | 0.062526 | 0.0 | 97.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030474 | 0.00030474 | 0.00030474 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001566 | | | 2.43 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6115.00 ave 6115 max 6115 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: 217616.0 ave 217616 max 217616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217616 Ave neighs/atom = 165.11077 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.604 | 5.604 | 5.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5392.6256 0 -5392.6256 -109.80381 Loop time of 1.758e-06 on 1 procs for 0 steps with 1318 atoms 170.6% 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 | | 1.758e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6174.00 ave 6174 max 6174 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: 217340.0 ave 217340 max 217340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217340 Ave neighs/atom = 164.90137 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.604 | 5.604 | 5.604 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 -5392.6256 -5392.6256 36.712464 60.136896 6.9791903 -109.80381 -109.80381 -183.0061 56.263008 -202.66834 2.2359063 1496.5157 Loop time of 1.976e-06 on 1 procs for 0 steps with 1318 atoms 202.4% 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 | | 1.976e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6174.00 ave 6174 max 6174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108670.0 ave 108670 max 108670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217340.0 ave 217340 max 217340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217340 Ave neighs/atom = 164.90137 Neighbor list builds = 0 Dangerous builds = 0 1318 -5392.62564547302 eV 2.23590633646625 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01