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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -63.365399 0.0000000) to (25.868816 63.365399 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2085158 5.4916679 5.9741471 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -63.365399 0.0000000) to (25.868816 63.365399 8.9612207) create_atoms CPU = 0.002 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2085158 5.4916679 5.9741471 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -63.365399 0.0000000) to (25.868816 63.365399 8.9612207) create_atoms CPU = 0.002 seconds 1205 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 30 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2400 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.530 | 6.530 | 6.530 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8501.7473 0 -8501.7473 82571.167 938 0 -9463.1562 0 -9463.1562 -70599.894 Loop time of 54.0829 on 1 procs for 938 steps with 2400 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 = -8501.74732888818 -9463.1472229297 -9463.15619203382 Force two-norm initial, final = 1259.5517 0.29722428 Force max component initial, final = 158.98570 0.044351707 Final line search alpha, max atom move = 0.72939831 0.032350060 Iterations, force evaluations = 938 1856 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.2 | 53.2 | 53.2 | 0.0 | 98.37 Neigh | 0.41059 | 0.41059 | 0.41059 | 0.0 | 0.76 Comm | 0.22568 | 0.22568 | 0.22568 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2467 | | | 0.46 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10724.0 ave 10724 max 10724 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: 485082.0 ave 485082 max 485082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 485082 Ave neighs/atom = 202.11750 Neighbor list builds = 13 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 938 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.532 | 6.532 | 6.532 Mbytes Step Temp E_pair E_mol TotEng Press Volume 938 0 -9463.1562 0 -9463.1562 -70599.894 29378.248 1004 0 -9545.3169 0 -9545.3169 38.133023 28162.515 Loop time of 2.24434 on 1 procs for 66 steps with 2400 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 = -9463.15619203373 -9545.31283615701 -9545.31694779234 Force two-norm initial, final = 2803.7861 7.7329452 Force max component initial, final = 2284.8347 2.8204750 Final line search alpha, max atom move = 4.8515776e-05 0.00013683753 Iterations, force evaluations = 66 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0986 | 2.0986 | 2.0986 | 0.0 | 93.51 Neigh | 0.094465 | 0.094465 | 0.094465 | 0.0 | 4.21 Comm | 0.0075974 | 0.0075974 | 0.0075974 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04365 | | | 1.95 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10736.0 ave 10736 max 10736 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: 517704.0 ave 517704 max 517704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517704 Ave neighs/atom = 215.71000 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.049 | 7.049 | 7.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9545.3169 0 -9545.3169 38.133023 Loop time of 2.561e-06 on 1 procs for 0 steps with 2400 atoms 195.2% 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 | | 2.561e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10613.0 ave 10613 max 10613 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: 520086.0 ave 520086 max 520086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 520086 Ave neighs/atom = 216.70250 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.049 | 7.049 | 7.049 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 -9545.3169 -9545.3169 24.607238 123.07487 9.2990623 38.133023 38.133023 -152.63267 140.20286 126.82887 2.2793322 4236.0739 Loop time of 3.074e-06 on 1 procs for 0 steps with 2400 atoms 260.2% 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 | | 3.074e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10613.0 ave 10613 max 10613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 260043.0 ave 260043 max 260043 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 520086.0 ave 520086 max 520086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 520086 Ave neighs/atom = 216.70250 Neighbor list builds = 0 Dangerous builds = 0 2400 -9545.31694779234 eV 2.27933220566705 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:57