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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6574295 4.4448964 5.1067972 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6574295 4.4448964 5.1067972 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) create_atoms CPU = 0.001 seconds 530 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.318 | 6.318 | 6.318 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4149.689 0 -4149.689 40352.438 168 0 -4374.8676 0 -4374.8676 4235.523 Loop time of 5.27278 on 1 procs for 168 steps with 1056 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4149.68900848886 -4374.8638042189 -4374.86762671358 Force two-norm initial, final = 337.36235 0.27770330 Force max component initial, final = 90.686343 0.035524953 Final line search alpha, max atom move = 0.77993006 0.027706978 Iterations, force evaluations = 168 294 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1047 | 5.1047 | 5.1047 | 0.0 | 96.81 Neigh | 0.1085 | 0.1085 | 0.1085 | 0.0 | 2.06 Comm | 0.038319 | 0.038319 | 0.038319 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02121 | | | 0.40 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11912.0 ave 11912 max 11912 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: 401992.0 ave 401992 max 401992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401992 Ave neighs/atom = 380.67424 Neighbor list builds = 5 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 168 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.318 | 6.318 | 6.318 Mbytes Step Temp E_pair E_mol TotEng Press Volume 168 0 -4374.8676 0 -4374.8676 4235.523 12430.963 170 0 -4374.9087 0 -4374.9087 1.1878541 12461.518 Loop time of 0.0861203 on 1 procs for 2 steps with 1056 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 = -4374.86762671359 -4374.9084084362 -4374.90871115621 Force two-norm initial, final = 57.139384 1.6388162 Force max component initial, final = 36.938759 1.3130202 Final line search alpha, max atom move = 0.00046689282 0.00061303968 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083841 | 0.083841 | 0.083841 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047056 | 0.00047056 | 0.00047056 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001808 | | | 2.10 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11942.0 ave 11942 max 11942 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: 402108.0 ave 402108 max 402108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402108 Ave neighs/atom = 380.78409 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.456 | 6.456 | 6.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4374.9087 0 -4374.9087 1.1878541 Loop time of 2.024e-06 on 1 procs for 0 steps with 1056 atoms 197.6% 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 | | 2.024e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11932.0 ave 11932 max 11932 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: 401828.0 ave 401828 max 401828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401828 Ave neighs/atom = 380.51894 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.456 | 6.456 | 6.456 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 -4374.9087 -4374.9087 20.766349 117.4194 5.1105889 1.1878541 1.1878541 -60.445463 -104.93122 168.94025 2.3687488 609.98567 Loop time of 2.416e-06 on 1 procs for 0 steps with 1056 atoms 248.3% 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 | | 2.416e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11932.0 ave 11932 max 11932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200914.0 ave 200914 max 200914 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 401828.0 ave 401828 max 401828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401828 Ave neighs/atom = 380.51894 Neighbor list builds = 0 Dangerous builds = 0 1056 -4374.90871115621 eV 2.3687488212702 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05