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 = 3.5204258 3.5204258 3.5204258 Created orthogonal box = (0.0000000 -67.349712 0.0000000) to (38.884374 67.349712 6.0975564) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7370388 5.1524370 6.0975564 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -67.349712 0.0000000) to (38.884374 67.349712 6.0975564) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7370388 5.1524370 6.0975564 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.349712 0.0000000) to (38.884374 67.349712 6.0975564) create_atoms CPU = 0.003 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 46 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2928 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_913991514986_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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.780 | 5.780 | 5.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16712.823 0 -16712.823 10146.771 162 0 -16888.508 0 -16888.508 7259.7741 Loop time of 273.313 on 1 procs for 162 steps with 2928 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 = -16712.8226682175 -16888.4935840635 -16888.5078211952 Force two-norm initial, final = 138.32161 0.44485648 Force max component initial, final = 37.723126 0.10751715 Final line search alpha, max atom move = 0.29799278 0.032039336 Iterations, force evaluations = 162 300 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 273.09 | 273.09 | 273.09 | 0.0 | 99.92 Neigh | 0.13211 | 0.13211 | 0.13211 | 0.0 | 0.05 Comm | 0.038719 | 0.038719 | 0.038719 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04902 | | | 0.02 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9480.00 ave 9480 max 9480 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: 226942.0 ave 226942 max 226942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226942 Ave neighs/atom = 77.507514 Neighbor list builds = 7 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 162 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.780 | 5.780 | 5.780 Mbytes Step Temp E_pair E_mol TotEng Press Volume 162 0 -16888.508 0 -16888.508 7259.7741 31937.188 166 0 -16888.893 0 -16888.893 117.70908 32050.9 Loop time of 5.72764 on 1 procs for 4 steps with 2928 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 = -16888.5078211952 -16888.8906038702 -16888.8932027077 Force two-norm initial, final = 272.66618 6.7423200 Force max component initial, final = 230.94013 6.2302254 Final line search alpha, max atom move = 5.5443024e-05 0.00034542254 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7238 | 5.7238 | 5.7238 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050448 | 0.00050448 | 0.00050448 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00331 | | | 0.06 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9481.00 ave 9481 max 9481 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: 226948.0 ave 226948 max 226948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226948 Ave neighs/atom = 77.509563 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.917 | 5.917 | 5.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16888.893 0 -16888.893 117.70908 Loop time of 2.495e-06 on 1 procs for 0 steps with 2928 atoms 200.4% 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 | | 2.495e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9472.00 ave 9472 max 9472 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: 226880.0 ave 226880 max 226880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226880 Ave neighs/atom = 77.486339 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.917 | 5.917 | 5.917 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 -16888.893 -16888.893 38.901975 135.10494 6.0981394 117.70908 117.70908 -66.659553 312.37724 107.40957 2.2182858 1249.3281 Loop time of 2.548e-06 on 1 procs for 0 steps with 2928 atoms 235.5% 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 | | 2.548e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9472.00 ave 9472 max 9472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113440.0 ave 113440 max 113440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226880.0 ave 226880 max 226880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226880 Ave neighs/atom = 77.486339 Neighbor list builds = 0 Dangerous builds = 0 2928 -7124.59457589975 eV 2.21828582228118 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:04:43