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 -51.800848 0.0000000) to (25.898402 51.800848 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6850150 5.6850150 4.0446508 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -51.800848 0.0000000) to (25.898402 51.800848 4.0446508) create_atoms CPU = 0.002 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6850150 5.6850150 4.0446508 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -51.800848 0.0000000) to (25.898402 51.800848 4.0446508) create_atoms CPU = 0.001 seconds 329 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 8 31 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 652 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2168.5449 0 -2168.5449 6113.1323 71 0 -2185.6539 0 -2185.6539 -2268.9777 Loop time of 6.22294 on 1 procs for 71 steps with 652 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 = -2168.54488415818 -2185.65201788963 -2185.65389386979 Force two-norm initial, final = 15.614127 0.11256246 Force max component initial, final = 4.5634782 0.036406092 Final line search alpha, max atom move = 1.0000000 0.036406092 Iterations, force evaluations = 71 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.174 | 6.174 | 6.174 | 0.0 | 99.21 Neigh | 0.025431 | 0.025431 | 0.025431 | 0.0 | 0.41 Comm | 0.01209 | 0.01209 | 0.01209 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01145 | | | 0.18 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4375.00 ave 4375 max 4375 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: 50430.0 ave 50430 max 50430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50430 Ave neighs/atom = 77.346626 Neighbor list builds = 3 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -2185.6539 0 -2185.6539 -2268.9777 10852.277 74 0 -2185.6764 0 -2185.6764 -252.0986 10824.325 Loop time of 0.334666 on 1 procs for 3 steps with 652 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 = -2185.65389386979 -2185.67549039453 -2185.67639176117 Force two-norm initial, final = 22.022320 0.11697878 Force max component initial, final = 18.352253 0.040772904 Final line search alpha, max atom move = 0.00042693037 1.7407191e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3322 | 0.3322 | 0.3322 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061147 | 0.00061147 | 0.00061147 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001853 | | | 0.55 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4397.00 ave 4397 max 4397 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: 50482.0 ave 50482 max 50482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50482 Ave neighs/atom = 77.426380 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2185.6764 0 -2185.6764 -252.0986 Loop time of 6.716e-06 on 1 procs for 0 steps with 652 atoms 193.6% 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 | | 6.716e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4397.00 ave 4397 max 4397 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: 50484.0 ave 50484 max 50484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50484 Ave neighs/atom = 77.429448 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.648 | 4.648 | 4.648 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 -2185.6764 -2185.6764 25.888364 103.6017 4.0357974 -252.0986 -252.0986 -1.3147787 -755.71098 0.72996311 2.5569072 180.04361 Loop time of 6.676e-06 on 1 procs for 0 steps with 652 atoms 254.6% 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 | | 6.676e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4397.00 ave 4397 max 4397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25242.0 ave 25242 max 25242 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50484.0 ave 50484 max 50484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50484 Ave neighs/atom = 77.429448 Neighbor list builds = 0 Dangerous builds = 0 652 -2185.67639176117 eV 2.55690718360787 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07