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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -62.754296 0.0000000) to (31.375325 62.754296 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0878905 5.0878905 3.6473074 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.754296 0.0000000) to (31.375325 62.754296 3.6473074) create_atoms CPU = 0.003 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0878905 5.0878905 3.6473074 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.754296 0.0000000) to (31.375325 62.754296 3.6473074) create_atoms CPU = 0.002 seconds 594 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 1180 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4835.7775 0 -4835.7775 11438.998 104 0 -4883.1809 0 -4883.1809 -1012.0574 Loop time of 33.4789 on 1 procs for 104 steps with 1180 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 = -4835.7775161182 -4883.17659852667 -4883.18089143154 Force two-norm initial, final = 43.022434 0.24598868 Force max component initial, final = 12.623741 0.039267137 Final line search alpha, max atom move = 1.0000000 0.039267137 Iterations, force evaluations = 104 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.428 | 33.428 | 33.428 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023448 | 0.023448 | 0.023448 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02786 | | | 0.08 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4842.00 ave 4842 max 4842 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: 63344.0 ave 63344 max 63344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63344 Ave neighs/atom = 53.681356 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -4883.1809 0 -4883.1809 -1012.0574 14362.633 107 0 -4883.2148 0 -4883.2148 98.556649 14352.832 Loop time of 0.787245 on 1 procs for 3 steps with 1180 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4883.18089143154 -4883.21292837629 -4883.21477051575 Force two-norm initial, final = 29.740372 5.6248510 Force max component initial, final = 29.394620 5.3810512 Final line search alpha, max atom move = 0.00013355922 0.00071868899 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78467 | 0.78467 | 0.78467 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052982 | 0.00052982 | 0.00052982 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002049 | | | 0.26 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 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: 63416.0 ave 63416 max 63416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63416 Ave neighs/atom = 53.742373 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.517 | 5.517 | 5.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4883.2148 0 -4883.2148 98.556649 Loop time of 6.395e-06 on 1 procs for 0 steps with 1180 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 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: 63420.0 ave 63420 max 63420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63420 Ave neighs/atom = 53.745763 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.517 | 5.517 | 5.517 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 -4883.2148 -4883.2148 31.31353 125.50859 3.6520114 98.556649 98.556649 180.22183 -486.00201 601.45013 2.3263876 136.5085 Loop time of 6.766e-06 on 1 procs for 0 steps with 1180 atoms 280.8% 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 | | 6.766e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31710.0 ave 31710 max 31710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63420.0 ave 63420 max 63420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63420 Ave neighs/atom = 53.745763 Neighbor list builds = 0 Dangerous builds = 0 1180 -4883.21477051575 eV 2.3263875832999 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35