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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -72.431928 0.0000000) to (44.355316 72.431928 8.9611271) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1295264 5.1737092 5.9740848 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -72.431928 0.0000000) to (44.355316 72.431928 8.9611271) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1295264 5.1737092 5.9740848 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -72.431928 0.0000000) to (44.355316 72.431928 8.9611271) create_atoms CPU = 0.002 seconds 2358 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 11.46 | 11.46 | 11.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18316.177 0 -18316.177 35197.904 1306 0 -19084.675 0 -19084.675 -49539.795 Loop time of 77.7352 on 1 procs for 1306 steps with 4710 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 = -18316.1774342947 -19084.6573309383 -19084.6748392291 Force two-norm initial, final = 431.70718 0.43938339 Force max component initial, final = 59.517301 0.040309301 Final line search alpha, max atom move = 1.0000000 0.040309301 Iterations, force evaluations = 1306 2575 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 75.969 | 75.969 | 75.969 | 0.0 | 97.73 Neigh | 0.90075 | 0.90075 | 0.90075 | 0.0 | 1.16 Comm | 0.3418 | 0.3418 | 0.3418 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5239 | | | 0.67 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13296.0 ave 13296 max 13296 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: 660616.0 ave 660616 max 660616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660616 Ave neighs/atom = 140.25817 Neighbor list builds = 22 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1306 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.46 | 11.46 | 11.46 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1306 0 -19084.675 0 -19084.675 -49539.795 57579.563 1359 0 -19204.069 0 -19204.069 -9.8689714 55895.145 Loop time of 1.81505 on 1 procs for 53 steps with 4710 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 = -19084.6748392287 -19204.0656479186 -19204.0688570521 Force two-norm initial, final = 4251.1791 9.4735240 Force max component initial, final = 3325.3297 4.5490404 Final line search alpha, max atom move = 0.00010158482 0.00046211344 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5561 | 1.5561 | 1.5561 | 0.0 | 85.73 Neigh | 0.21094 | 0.21094 | 0.21094 | 0.0 | 11.62 Comm | 0.0072292 | 0.0072292 | 0.0072292 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04076 | | | 2.25 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13128.0 ave 13128 max 13128 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: 664020.0 ave 664020 max 664020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664020 Ave neighs/atom = 140.98089 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 10.96 | 10.96 | 10.96 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19204.069 0 -19204.069 -9.8689714 Loop time of 2.095e-06 on 1 procs for 0 steps with 4710 atoms 190.9% 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 | | 2.095e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13061.0 ave 13061 max 13061 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: 653774.0 ave 653774 max 653774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 653774 Ave neighs/atom = 138.80552 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 10.96 | 10.96 | 10.96 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 -19204.069 -19204.069 43.055329 139.10391 9.3327116 -9.8689714 -9.8689714 57.610417 48.583139 -135.80047 2.21393 5130.6529 Loop time of 2.549e-06 on 1 procs for 0 steps with 4710 atoms 274.6% 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 | | 2.549e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13061.0 ave 13061 max 13061 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 326887.0 ave 326887 max 326887 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 653774.0 ave 653774 max 653774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 653774 Ave neighs/atom = 138.80552 Neighbor list builds = 0 Dangerous builds = 0 4710 -19204.0688570521 eV 2.21392996842622 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:20