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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4487539 6.6048871 5.7200000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4487539 6.6048871 5.7200000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.001 seconds 434 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 6 atoms, new total = 860 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_793141037706_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 = 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) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2794.9869 0 -2794.9869 15253.14 58 0 -2881.5443 0 -2881.5443 507.90286 Loop time of 6.01019 on 1 procs for 58 steps with 860 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 = -2794.98685476712 -2881.54184525162 -2881.54432156136 Force two-norm initial, final = 169.17776 0.11037741 Force max component initial, final = 46.914660 0.013955099 Final line search alpha, max atom move = 1.0000000 0.013955099 Iterations, force evaluations = 58 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9918 | 5.9918 | 5.9918 | 0.0 | 99.69 Neigh | 0.0065095 | 0.0065095 | 0.0065095 | 0.0 | 0.11 Comm | 0.0064308 | 0.0064308 | 0.0064308 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005422 | | | 0.09 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5631.00 ave 5631 max 5631 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: 114552.0 ave 114552 max 114552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114552 Ave neighs/atom = 133.20000 Neighbor list builds = 1 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2881.5443 0 -2881.5443 507.90286 14292.126 61 0 -2881.564 0 -2881.564 -44.971639 14302.296 Loop time of 0.29589 on 1 procs for 3 steps with 860 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 = -2881.54432156136 -2881.56254245279 -2881.56395312962 Force two-norm initial, final = 16.326350 0.84386040 Force max component initial, final = 14.406763 0.75847515 Final line search alpha, max atom move = 0.00015392758 0.00011675025 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29479 | 0.29479 | 0.29479 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021938 | 0.00021938 | 0.00021938 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008854 | | | 0.30 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5510.00 ave 5510 max 5510 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: 114404.0 ave 114404 max 114404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114404 Ave neighs/atom = 133.02791 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.564 0 -2881.564 -44.971639 Loop time of 1.848e-06 on 1 procs for 0 steps with 860 atoms 162.3% 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 | | 1.848e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496.00 ave 5496 max 5496 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: 114380.0 ave 114380 max 114380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114380 Ave neighs/atom = 133.00000 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) = 5.126 | 5.126 | 5.126 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 -2881.564 -2881.564 21.023686 119.11698 5.7111458 -44.971639 -44.971639 -37.237156 -12.843132 -84.834628 2.584219 583.98676 Loop time of 2.748e-06 on 1 procs for 0 steps with 860 atoms 182.0% 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 | | 2.748e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496.00 ave 5496 max 5496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57190.0 ave 57190 max 57190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114380.0 ave 114380 max 114380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114380 Ave neighs/atom = 133.00000 Neighbor list builds = 0 Dangerous builds = 0 860 -2881.56395312962 eV 2.58421903477189 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06