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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0636522 4.2659462 4.6763140 Created 873 atoms using lattice units in orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) create_atoms CPU = 0.001 seconds 873 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0636522 4.2659462 4.6763140 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.601564 0.0000000) to (42.378088 34.601564 7.0144710) create_atoms CPU = 0.001 seconds 879 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 14 22 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1738 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_343168101490_001#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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6737.0029 0 -6737.0029 66439.05 84 0 -7414.7588 0 -7414.7588 -4293.7124 Loop time of 18.2434 on 1 procs for 84 steps with 1738 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 = -6737.002868904 -7414.75142909171 -7414.75883916555 Force two-norm initial, final = 771.68118 0.26390602 Force max component initial, final = 139.85625 0.044693229 Final line search alpha, max atom move = 1.0000000 0.044693229 Iterations, force evaluations = 84 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.19 | 18.19 | 18.19 | 0.0 | 99.71 Neigh | 0.025696 | 0.025696 | 0.025696 | 0.0 | 0.14 Comm | 0.011378 | 0.011378 | 0.011378 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01625 | | | 0.09 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5855.00 ave 5855 max 5855 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: 164882.0 ave 164882 max 164882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164882 Ave neighs/atom = 94.868815 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -7414.7588 0 -7414.7588 -4293.7124 20571.312 87 0 -7414.8624 0 -7414.8624 -6.568629 20519.424 Loop time of 0.78554 on 1 procs for 3 steps with 1738 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 = -7414.7588391656 -7414.85782579299 -7414.86236641802 Force two-norm initial, final = 103.61449 1.9059705 Force max component initial, final = 86.571693 1.6039655 Final line search alpha, max atom move = 5.6955487e-05 9.1354638e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78327 | 0.78327 | 0.78327 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031953 | 0.00031953 | 0.00031953 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001952 | | | 0.25 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5861.00 ave 5861 max 5861 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: 160758.0 ave 160758 max 160758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160758 Ave neighs/atom = 92.495972 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7414.8624 0 -7414.8624 -6.568629 Loop time of 2.598e-06 on 1 procs for 0 steps with 1738 atoms 154.0% 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 | | 2.598e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5861.00 ave 5861 max 5861 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: 171924.0 ave 171924 max 171924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171924 Ave neighs/atom = 98.920598 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.265 | 5.265 | 5.265 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 -7414.8624 -7414.8624 42.352906 69.217005 6.9995343 -6.568629 -6.568629 -125.16476 66.192522 39.266356 2.2706096 1726.4392 Loop time of 2.635e-06 on 1 procs for 0 steps with 1738 atoms 227.7% 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 | | 2.635e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5861.00 ave 5861 max 5861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85962.0 ave 85962 max 85962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171924.0 ave 171924 max 171924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171924 Ave neighs/atom = 98.920598 Neighbor list builds = 0 Dangerous builds = 0 1738 -7414.86236641802 eV 2.27060964153664 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19