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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -36.752400 0.0000000) to (25.987871 36.752400 5.1463654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5860950 5.7650824 5.1463654 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.752400 0.0000000) to (25.987871 36.752400 5.1463654) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5860950 5.7650824 5.1463654 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.752400 0.0000000) to (25.987871 36.752400 5.1463654) create_atoms CPU = 0.002 seconds 410 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 = 7 19 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 6 atoms, new total = 812 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_748636486270_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 = 7 19 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) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2334.8698 0 -2334.8698 126004.89 54 0 -2764.1848 0 -2764.1848 1402.3513 Loop time of 1.65675 on 1 procs for 54 steps with 812 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 = -2334.86978847449 -2764.18266191917 -2764.18475692352 Force two-norm initial, final = 1024.9374 0.11834174 Force max component initial, final = 280.74704 0.013243458 Final line search alpha, max atom move = 1.0000000 0.013243458 Iterations, force evaluations = 54 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5936 | 1.5936 | 1.5936 | 0.0 | 96.19 Neigh | 0.038457 | 0.038457 | 0.038457 | 0.0 | 2.32 Comm | 0.013256 | 0.013256 | 0.013256 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0114 | | | 0.69 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5624.00 ave 5624 max 5624 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: 142444.0 ave 142444 max 142444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142444 Ave neighs/atom = 175.42365 Neighbor list builds = 2 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 = 7 19 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2764.1848 0 -2764.1848 1402.3513 9830.7586 57 0 -2764.2004 0 -2764.2004 -155.11684 9841.6533 Loop time of 0.103229 on 1 procs for 3 steps with 812 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 = -2764.18475692352 -2764.19986681501 -2764.20040365092 Force two-norm initial, final = 20.391133 2.6111502 Force max component initial, final = 19.862299 2.0400803 Final line search alpha, max atom move = 0.00030858746 0.00062954319 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10028 | 0.10028 | 0.10028 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068972 | 0.00068972 | 0.00068972 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002258 | | | 2.19 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5558.00 ave 5558 max 5558 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: 142408.0 ave 142408 max 142408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142408 Ave neighs/atom = 175.37931 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 = 7 19 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) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2764.2004 0 -2764.2004 -155.11684 Loop time of 6.495e-06 on 1 procs for 0 steps with 812 atoms 184.8% 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 | | 6.495e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5574.00 ave 5574 max 5574 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: 142360.0 ave 142360 max 142360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142360 Ave neighs/atom = 175.32020 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 = 7 19 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) = 5.106 | 5.106 | 5.106 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 -2764.2004 -2764.2004 25.976566 73.636466 5.1450949 -155.11684 -155.11684 -331.97133 -241.55888 108.17969 2.2733343 437.11798 Loop time of 6.786e-06 on 1 procs for 0 steps with 812 atoms 265.3% 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 | | 6.786e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5574.00 ave 5574 max 5574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71180.0 ave 71180 max 71180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142360.0 ave 142360 max 142360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142360 Ave neighs/atom = 175.32020 Neighbor list builds = 0 Dangerous builds = 0 812 -2764.20040365092 eV 2.27333434086831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02