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 = 3.5927866 3.5927866 3.5927866 Created orthogonal box = (0.0000000 -36.639377 0.0000000) to (31.730632 36.639377 6.2228888) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6952416 5.6368273 6.2228888 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -36.639377 0.0000000) to (31.730632 36.639377 6.2228888) create_atoms CPU = 0.004 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6952416 5.6368273 6.2228888 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.639377 0.0000000) to (31.730632 36.639377 6.2228888) create_atoms CPU = 0.003 seconds 629 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 10 21 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 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1250 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_396616545191_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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3964.2688 0 -3964.2688 78809.488 192 0 -4364.2429 0 -4364.2429 12462.442 Loop time of 11.7409 on 1 procs for 192 steps with 1250 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 = -3964.26883825885 -4364.23875059259 -4364.24287203718 Force two-norm initial, final = 534.54933 0.21644651 Force max component initial, final = 129.89376 0.058483495 Final line search alpha, max atom move = 1.0000000 0.058483495 Iterations, force evaluations = 192 357 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.452 | 11.452 | 11.452 | 0.0 | 97.54 Neigh | 0.18079 | 0.18079 | 0.18079 | 0.0 | 1.54 Comm | 0.052163 | 0.052163 | 0.052163 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05563 | | | 0.47 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 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: 165040.0 ave 165040 max 165040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165040 Ave neighs/atom = 132.03200 Neighbor list builds = 8 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 192 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 192 0 -4364.2429 0 -4364.2429 12462.442 14469.344 201 0 -4365.0718 0 -4365.0718 46.449449 14601.547 Loop time of 0.356532 on 1 procs for 9 steps with 1250 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 = -4364.24287203718 -4365.06847136354 -4365.07183776493 Force two-norm initial, final = 217.29765 1.1846675 Force max component initial, final = 188.75133 1.0071203 Final line search alpha, max atom move = 0.00013758846 0.00013856813 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3489 | 0.3489 | 0.3489 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015539 | 0.0015539 | 0.0015539 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006082 | | | 1.71 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 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: 165066.0 ave 165066 max 165066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165066 Ave neighs/atom = 132.05280 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4365.0718 0 -4365.0718 46.449449 Loop time of 7.908e-06 on 1 procs for 0 steps with 1250 atoms 215.0% 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 | | 7.908e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 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: 164726.0 ave 164726 max 164726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164726 Ave neighs/atom = 131.78080 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.187 | 5.187 | 5.187 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 -4365.0718 -4365.0718 31.759423 73.907213 6.2207028 46.449449 46.449449 -7.4695647 36.34896 110.46895 2.3259095 904.23066 Loop time of 6.976e-06 on 1 procs for 0 steps with 1250 atoms 286.7% 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 | | 6.976e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82363.0 ave 82363 max 82363 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164726.0 ave 164726 max 164726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164726 Ave neighs/atom = 131.78080 Neighbor list builds = 0 Dangerous builds = 0 1250 -4365.07183776493 eV 2.32590947655642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12