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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1174 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.002 seconds 1174 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.001 seconds 1182 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 31 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2342 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8014.0872 0 -8014.0872 29097.068 21 0 -8250.9571 0 -8250.9571 3328.4639 Loop time of 1.37896 on 1 procs for 21 steps with 2342 atoms 95.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8014.08717625931 -8250.94895175396 -8250.95713617974 Force two-norm initial, final = 310.14568 0.31753323 Force max component initial, final = 53.795726 0.061163766 Final line search alpha, max atom move = 1.0000000 0.061163766 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3711 | 1.3711 | 1.3711 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027256 | 0.0027256 | 0.0027256 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005093 | | | 0.37 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 127300.0 ave 127300 max 127300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127300 Ave neighs/atom = 54.355252 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -8250.9571 0 -8250.9571 3328.4639 27739.27 26 0 -8251.2147 0 -8251.2147 -234.28223 27809.142 Loop time of 0.358636 on 1 procs for 5 steps with 2342 atoms 95.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8250.95713617978 -8251.21309477904 -8251.21472397209 Force two-norm initial, final = 132.74501 8.1509688 Force max component initial, final = 125.71034 6.9357650 Final line search alpha, max atom move = 0.00011146729 0.00077311095 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35508 | 0.35508 | 0.35508 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044076 | 0.00044076 | 0.00044076 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00312 | | | 0.87 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5508.00 ave 5508 max 5508 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: 140104.0 ave 140104 max 140104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140104 Ave neighs/atom = 59.822374 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.212 | 5.212 | 5.212 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8251.2147 0 -8251.2147 -234.28223 Loop time of 3.865e-06 on 1 procs for 0 steps with 2342 atoms 155.2% 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 | | 3.865e-06 | | |100.00 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5454.00 ave 5454 max 5454 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: 133488.0 ave 133488 max 133488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133488 Ave neighs/atom = 56.997438 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 13 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.212 | 5.212 | 5.212 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 -8251.2147 -8251.2147 35.754841 87.994744 8.8388548 -234.28223 -234.28223 -399.42299 -68.354195 -235.06952 2.2692893 1468.0758 Loop time of 4.422e-06 on 1 procs for 0 steps with 2342 atoms 180.9% 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 | | 4.422e-06 | | |100.00 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5454.00 ave 5454 max 5454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66744.0 ave 66744 max 66744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133488.0 ave 133488 max 133488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133488 Ave neighs/atom = 56.997438 Neighbor list builds = 0 Dangerous builds = 0 2342 -8251.21472397209 eV 2.26928934264763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02