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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -35.613616 0.0000000) to (12.591315 35.613616 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6389054 3.7488017 4.0851619 Created 152 atoms using lattice units in orthogonal box = (0.0000000 -35.613616 0.0000000) to (12.591315 35.613616 4.0851619) create_atoms CPU = 0.001 seconds 152 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6389054 3.7488017 4.0851619 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -35.613616 0.0000000) to (12.591315 35.613616 4.0851619) create_atoms CPU = 0.001 seconds 154 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 = 5 27 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 0 atoms, new total = 306 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 = 5 27 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) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1183.3336 0 -1183.3336 80926.612 39 0 -1268.813 0 -1268.813 20958.338 Loop time of 3.19763 on 1 procs for 39 steps with 306 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 = -1183.33359389141 -1268.81178143864 -1268.81295335625 Force two-norm initial, final = 171.44517 0.16266130 Force max component initial, final = 53.694272 0.027438751 Final line search alpha, max atom move = 1.0000000 0.027438751 Iterations, force evaluations = 39 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1906 | 3.1906 | 3.1906 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035294 | 0.0035294 | 0.0035294 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003482 | | | 0.11 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2286.00 ave 2286 max 2286 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: 17764.0 ave 17764 max 17764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17764 Ave neighs/atom = 58.052288 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 = 5 27 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1268.813 0 -1268.813 20958.338 3663.7549 57 0 -1269.4721 0 -1269.4721 -26.466344 3706.7751 Loop time of 0.912604 on 1 procs for 18 steps with 306 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1268.81295335625 -1269.47125396628 -1269.47205607274 Force two-norm initial, final = 94.871448 1.1701505 Force max component initial, final = 85.420176 0.57791201 Final line search alpha, max atom move = 0.00083263448 0.00048118946 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88663 | 0.88663 | 0.88663 | 0.0 | 97.15 Neigh | 0.02085 | 0.02085 | 0.02085 | 0.0 | 2.28 Comm | 0.00091717 | 0.00091717 | 0.00091717 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004202 | | | 0.46 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2282.00 ave 2282 max 2282 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: 17508.0 ave 17508 max 17508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17508 Ave neighs/atom = 57.215686 Neighbor list builds = 1 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 = 5 28 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) = 4.935 | 4.935 | 4.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1269.4721 0 -1269.4721 -26.466344 Loop time of 3.597e-06 on 1 procs for 0 steps with 306 atoms 166.8% 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 | | 3.597e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2282.00 ave 2282 max 2282 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: 17500.0 ave 17500 max 17500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17500 Ave neighs/atom = 57.189542 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 = 5 28 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) = 4.935 | 4.935 | 4.935 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 -1269.4721 -1269.4721 12.560242 72.48439 4.0714935 -26.466344 -26.466344 71.464518 -254.19925 103.33569 2.285244 229.35017 Loop time of 3.785e-06 on 1 procs for 0 steps with 306 atoms 184.9% 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 | | 3.785e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2282.00 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8750.00 ave 8750 max 8750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17500.0 ave 17500 max 17500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17500 Ave neighs/atom = 57.189542 Neighbor list builds = 0 Dangerous builds = 0 306 -1269.47205607273 eV 2.28524396326857 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04