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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0877866 6.2179219 5.1068646 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068646) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0877866 6.2179219 5.1068646 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068646) create_atoms CPU = 0.002 seconds 916 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_162036141261_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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.151 | 5.151 | 5.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7441.4949 0 -7441.4949 43099.175 577 0 -7766.7556 0 -7766.7556 8339.5833 Loop time of 64.803 on 1 procs for 577 steps with 1828 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 = -7441.4949305542 -7766.74872583586 -7766.75563785013 Force two-norm initial, final = 368.07528 0.28040996 Force max component initial, final = 73.548253 0.055417008 Final line search alpha, max atom move = 1.0000000 0.055417008 Iterations, force evaluations = 577 1112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 64.464 | 64.464 | 64.464 | 0.0 | 99.48 Neigh | 0.16814 | 0.16814 | 0.16814 | 0.0 | 0.26 Comm | 0.084443 | 0.084443 | 0.084443 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08626 | | | 0.13 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7038.00 ave 7038 max 7038 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: 126162.0 ave 126162 max 126162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126162 Ave neighs/atom = 69.016411 Neighbor list builds = 17 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 577 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes Step Temp E_pair E_mol TotEng Press Volume 577 0 -7766.7556 0 -7766.7556 8339.5833 21472.513 600 0 -7776.1098 0 -7776.1098 -1.3346002 21557.422 Loop time of 1.4109 on 1 procs for 23 steps with 1828 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 = -7766.75563785012 -7776.10935232374 -7776.10979392668 Force two-norm initial, final = 677.92434 1.9148973 Force max component initial, final = 585.00076 0.63451471 Final line search alpha, max atom move = 0.00034709901 0.00022023942 Iterations, force evaluations = 23 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4017 | 1.4017 | 1.4017 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013225 | 0.0013225 | 0.0013225 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007844 | | | 0.56 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7037.00 ave 7037 max 7037 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: 126160.0 ave 126160 max 126160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126160 Ave neighs/atom = 69.015317 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 ghost atom cutoff = 6 binsize = 3, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.292 | 5.292 | 5.292 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7776.1098 0 -7776.1098 -1.3346002 Loop time of 1.825e-06 on 1 procs for 0 steps with 1828 atoms 164.4% 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 | | 1.825e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7149.00 ave 7149 max 7149 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: 125246.0 ave 125246 max 125246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125246 Ave neighs/atom = 68.515317 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 ghost atom cutoff = 6 binsize = 3, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.292 | 5.292 | 5.292 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 -7776.1098 -7776.1098 39.410323 108.99932 5.0183743 -1.3346002 -1.3346002 -48.202931 39.289521 4.9096096 2.3209072 5018.2281 Loop time of 1.992e-06 on 1 procs for 0 steps with 1828 atoms 150.6% 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 | | 1.992e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7149.00 ave 7149 max 7149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62623.0 ave 62623 max 62623 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 125246.0 ave 125246 max 125246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125246 Ave neighs/atom = 68.515317 Neighbor list builds = 0 Dangerous builds = 0 1828 -7776.10979392668 eV 2.32090719409953 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:06