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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -76.999826 0.0000000) to (44.455870 76.999826 6.9712367) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5590628 5.8906971 6.9712367 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -76.999826 0.0000000) to (44.455870 76.999826 6.9712367) create_atoms CPU = 0.008 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5590628 5.8906971 6.9712367 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -76.999826 0.0000000) to (44.455870 76.999826 6.9712367) create_atoms CPU = 0.008 seconds 1465 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 11 37 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2923 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.603 | 6.603 | 6.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7571.413 0 -7571.413 8157.5273 133 0 -7717.0653 0 -7717.0653 2461.7708 Loop time of 12.5113 on 1 procs for 133 steps with 2923 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 = -7571.41299667294 -7717.05804165704 -7717.06530596631 Force two-norm initial, final = 162.27334 0.24355620 Force max component initial, final = 34.883970 0.088808946 Final line search alpha, max atom move = 1.0000000 0.088808946 Iterations, force evaluations = 133 243 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.989 | 11.989 | 11.989 | 0.0 | 95.83 Neigh | 0.37052 | 0.37052 | 0.37052 | 0.0 | 2.96 Comm | 0.076925 | 0.076925 | 0.076925 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07481 | | | 0.60 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11899.0 ave 11899 max 11899 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: 409368.0 ave 409368 max 409368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409368 Ave neighs/atom = 140.05063 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.603 | 6.603 | 6.603 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -7717.0653 0 -7717.0653 2461.7708 47726.401 139 0 -7717.3935 0 -7717.3935 2.3877007 47872.001 Loop time of 0.387749 on 1 procs for 6 steps with 2923 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7717.0653059663 -7717.39305833478 -7717.39353387544 Force two-norm initial, final = 155.84217 0.59122547 Force max component initial, final = 146.80250 0.33212409 Final line search alpha, max atom move = 0.00016089828 5.3438194e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37744 | 0.37744 | 0.37744 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021398 | 0.0021398 | 0.0021398 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008173 | | | 2.11 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11905.0 ave 11905 max 11905 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: 409382.0 ave 409382 max 409382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409382 Ave neighs/atom = 140.05542 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.741 | 6.741 | 6.741 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7717.3935 0 -7717.3935 2.3877007 Loop time of 6.424e-06 on 1 procs for 0 steps with 2923 atoms 186.8% 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 | | 6.424e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11900.0 ave 11900 max 11900 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: 409068.0 ave 409068 max 409068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409068 Ave neighs/atom = 139.94800 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.741 | 6.741 | 6.741 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 -7717.3935 -7717.3935 44.422535 154.76727 6.9630436 2.3877007 2.3877007 -11.107169 8.5850655 9.6852054 2.5699868 1266.8611 Loop time of 6.775e-06 on 1 procs for 0 steps with 2923 atoms 280.4% 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 | | 6.775e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11900.0 ave 11900 max 11900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204534.0 ave 204534 max 204534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 409068.0 ave 409068 max 409068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409068 Ave neighs/atom = 139.94800 Neighbor list builds = 0 Dangerous builds = 0 2923 -7627.55728281909 eV 2.56998683293449 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13