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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -47.920247 0.0000000) to (58.690077 47.920247 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074374 6.1611746 6.6136224 Created 1667 atoms using lattice units in orthogonal box = (0.0000000 -47.920247 0.0000000) to (58.690077 47.920247 9.9204336) create_atoms CPU = 0.003 seconds 1667 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074374 6.1611746 6.6136224 Created 1691 atoms using lattice units in orthogonal box = (0.0000000 -47.920247 0.0000000) to (58.690077 47.920247 9.9204336) create_atoms CPU = 0.002 seconds 1691 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3358 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_751354403791_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.550 | 6.550 | 6.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11105.495 0 -11105.495 5961.6396 108 0 -11247.292 0 -11247.292 3119.8453 Loop time of 4.06433 on 1 procs for 108 steps with 3358 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 = -11105.4945156163 -11247.2819640368 -11247.2919650699 Force two-norm initial, final = 48.888788 0.26185604 Force max component initial, final = 3.8282371 0.084234428 Final line search alpha, max atom move = 0.79390260 0.066873932 Iterations, force evaluations = 108 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8141 | 3.8141 | 3.8141 | 0.0 | 93.84 Neigh | 0.19819 | 0.19819 | 0.19819 | 0.0 | 4.88 Comm | 0.020659 | 0.020659 | 0.020659 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03138 | | | 0.77 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10268.0 ave 10268 max 10268 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: 468664.0 ave 468664 max 468664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468664 Ave neighs/atom = 139.56641 Neighbor list builds = 6 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.551 | 6.551 | 6.551 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -11247.292 0 -11247.292 3119.8453 55801.308 115 0 -11247.943 0 -11247.943 13.139384 56022.078 Loop time of 0.201779 on 1 procs for 7 steps with 3358 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 = -11247.29196507 -11247.9384803002 -11247.9431933873 Force two-norm initial, final = 231.65483 0.94361149 Force max component initial, final = 217.10202 0.51783975 Final line search alpha, max atom move = 9.0258801e-05 4.6739595e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19558 | 0.19558 | 0.19558 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005403 | | | 2.68 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10269.0 ave 10269 max 10269 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: 468666.0 ave 468666 max 468666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468666 Ave neighs/atom = 139.56700 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.690 | 6.690 | 6.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11247.943 0 -11247.943 13.139384 Loop time of 2.104e-06 on 1 procs for 0 steps with 3358 atoms 190.1% 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 | | 2.104e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10347.0 ave 10347 max 10347 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: 468490.0 ave 468490 max 468490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468490 Ave neighs/atom = 139.51459 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.690 | 6.690 | 6.690 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 -11247.943 -11247.943 58.664429 96.46727 9.8992977 13.139384 13.139384 11.367339 13.272656 14.778156 2.587397 2186.5513 Loop time of 2.708e-06 on 1 procs for 0 steps with 3358 atoms 258.5% 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 | | 2.708e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10347.0 ave 10347 max 10347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234245.0 ave 234245 max 234245 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 468490.0 ave 468490 max 468490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468490 Ave neighs/atom = 139.51459 Neighbor list builds = 0 Dangerous builds = 0 3358 -11247.9431932403 eV 2.58739697065594 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04