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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -59.440280 0.0000000) to (21.015313 59.440280 5.1736123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7314489 4.5030515 5.1736123 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.440280 0.0000000) to (21.015313 59.440280 5.1736123) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7314489 4.5030515 5.1736123 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.440280 0.0000000) to (21.015313 59.440280 5.1736123) 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1048 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_942420706858_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 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4011.7206 0 -4011.7206 32889.371 421 0 -4263.3828 0 -4263.3828 -85799.686 Loop time of 7.52321 on 1 procs for 421 steps with 1048 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4011.72064102497 -4263.37873273601 -4263.38275244644 Force two-norm initial, final = 324.67373 0.19705127 Force max component initial, final = 107.15353 0.016262562 Final line search alpha, max atom move = 1.0000000 0.016262562 Iterations, force evaluations = 421 785 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.305 | 7.305 | 7.305 | 0.0 | 97.10 Neigh | 0.11995 | 0.11995 | 0.11995 | 0.0 | 1.59 Comm | 0.056659 | 0.056659 | 0.056659 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04161 | | | 0.55 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528.00 ave 7528 max 7528 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: 176352.0 ave 176352 max 176352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176352 Ave neighs/atom = 168.27481 Neighbor list builds = 11 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 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 421 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 421 0 -4263.3828 0 -4263.3828 -85799.686 12925.298 467 0 -4293.2241 0 -4293.2241 211.01076 12206.409 Loop time of 0.47164 on 1 procs for 46 steps with 1048 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4263.38275244644 -4293.22330751943 -4293.22411313854 Force two-norm initial, final = 1291.1631 4.4047733 Force max component initial, final = 1065.5953 3.4135653 Final line search alpha, max atom move = 0.00046651236 0.0015924704 Iterations, force evaluations = 46 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4427 | 0.4427 | 0.4427 | 0.0 | 93.86 Neigh | 0.011773 | 0.011773 | 0.011773 | 0.0 | 2.50 Comm | 0.0034469 | 0.0034469 | 0.0034469 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01372 | | | 2.91 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7601.00 ave 7601 max 7601 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: 178740.0 ave 178740 max 178740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178740 Ave neighs/atom = 170.55344 Neighbor list builds = 1 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 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.202 | 5.202 | 5.202 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4293.2241 0 -4293.2241 211.01076 Loop time of 1.941e-06 on 1 procs for 0 steps with 1048 atoms 412.2% 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 | | 1.941e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7854.00 ave 7854 max 7854 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: 179860.0 ave 179860 max 179860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179860 Ave neighs/atom = 171.62214 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 ghost atom cutoff = 8 binsize = 4, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.202 | 5.202 | 5.202 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 -4293.2241 -4293.2241 21.041982 117.34893 4.9433591 211.01076 211.01076 51.6819 442.28166 139.06873 2.2128537 3688.2971 Loop time of 2.668e-06 on 1 procs for 0 steps with 1048 atoms 224.9% 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 | | 2.668e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7854.00 ave 7854 max 7854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89930.0 ave 89930 max 89930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179860.0 ave 179860 max 179860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179860 Ave neighs/atom = 171.62214 Neighbor list builds = 0 Dangerous builds = 0 1048 -4293.22411313854 eV 2.21285370344781 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08