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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -70.629391 0.0000000) to (43.251492 70.629391 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0018733 5.0449565 5.8254140 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -70.629391 0.0000000) to (43.251492 70.629391 8.7381210) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0018733 5.0449565 5.8254140 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -70.629391 0.0000000) to (43.251492 70.629391 8.7381210) create_atoms CPU = 0.003 seconds 2357 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 4680 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.784 | 5.784 | 5.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19128.936 0 -19128.936 22053.481 135 0 -19732.412 0 -19732.412 31642.988 Loop time of 29.8006 on 1 procs for 135 steps with 4680 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19128.9357314686 -19732.3920988249 -19732.4117747766 Force two-norm initial, final = 646.21653 0.67280116 Force max component initial, final = 123.88977 0.13630589 Final line search alpha, max atom move = 0.57015193 0.077715066 Iterations, force evaluations = 135 258 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.693 | 29.693 | 29.693 | 0.0 | 99.64 Neigh | 0.023201 | 0.023201 | 0.023201 | 0.0 | 0.08 Comm | 0.029604 | 0.029604 | 0.029604 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05511 | | | 0.18 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9609.00 ave 9609 max 9609 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: 259674.0 ave 259674 max 259674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259674 Ave neighs/atom = 55.485897 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.785 | 5.785 | 5.785 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -19732.412 0 -19732.412 31642.988 53386.889 141 0 -19737.229 0 -19737.229 -41.005448 53854.089 Loop time of 1.19264 on 1 procs for 6 steps with 4680 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19732.4117747766 -19737.2287178401 -19737.2288641742 Force two-norm initial, final = 1841.1711 4.2836400 Force max component initial, final = 1234.3273 3.1979264 Final line search alpha, max atom move = 0.00012682051 0.00040556264 Iterations, force evaluations = 6 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.185 | 1.185 | 1.185 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077212 | 0.00077212 | 0.00077212 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006815 | | | 0.57 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9732.00 ave 9732 max 9732 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: 267552.0 ave 267552 max 267552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267552 Ave neighs/atom = 57.169231 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.923 | 5.923 | 5.923 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19737.229 0 -19737.229 -41.005448 Loop time of 2.34e-06 on 1 procs for 0 steps with 4680 atoms 170.9% 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 | | 2.34e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719.00 ave 9719 max 9719 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: 261452.0 ave 261452 max 261452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261452 Ave neighs/atom = 55.865812 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.923 | 5.923 | 5.923 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 -19737.229 -19737.229 43.320152 141.93448 8.7587233 -41.005448 -41.005448 4.7426501 -32.395339 -95.363655 2.2819919 2004.7843 Loop time of 2.259e-06 on 1 procs for 0 steps with 4680 atoms 221.3% 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 | | 2.259e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719.00 ave 9719 max 9719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130726.0 ave 130726 max 130726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261452.0 ave 261452 max 261452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261452 Ave neighs/atom = 55.865812 Neighbor list builds = 0 Dangerous builds = 0 4680 -19737.2288641742 eV 2.28199191163709 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32