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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -30.486398 0.0000000) to (21.557139 30.486398 4.0380221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9165404 4.8136418 4.0380221 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.486398 0.0000000) to (21.557139 30.486398 4.0380221) create_atoms CPU = 0.002 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9165404 4.8136418 4.0380221 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.486398 0.0000000) to (21.557139 30.486398 4.0380221) create_atoms CPU = 0.002 seconds 230 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 458 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1728.7792 0 -1728.7792 83273.501 46 0 -1826.5147 0 -1826.5147 13235.393 Loop time of 0.681793 on 1 procs for 46 steps with 458 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 = -1728.77924657157 -1826.51296984635 -1826.51465388332 Force two-norm initial, final = 206.87585 0.18021076 Force max component initial, final = 54.252998 0.055166239 Final line search alpha, max atom move = 1.0000000 0.055166239 Iterations, force evaluations = 46 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6661 | 0.6661 | 0.6661 | 0.0 | 97.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0087306 | 0.0087306 | 0.0087306 | 0.0 | 1.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006963 | | | 1.02 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4297.00 ave 4297 max 4297 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: 62716.0 ave 62716 max 62716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62716 Ave neighs/atom = 136.93450 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1826.5147 0 -1826.5147 13235.393 5307.5722 54 0 -1826.8019 0 -1826.8019 97.125925 5348.0994 Loop time of 0.0825266 on 1 procs for 8 steps with 458 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 = -1826.51465388332 -1826.80083901695 -1826.80192280399 Force two-norm initial, final = 86.083674 0.69379672 Force max component initial, final = 76.942542 0.50607093 Final line search alpha, max atom move = 0.00035969243 0.00018202988 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07852 | 0.07852 | 0.07852 | 0.0 | 95.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094406 | 0.00094406 | 0.00094406 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003063 | | | 3.71 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4302.00 ave 4302 max 4302 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: 63460.0 ave 63460 max 63460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63460 Ave neighs/atom = 138.55895 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.609 | 4.609 | 4.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1826.8019 0 -1826.8019 97.125925 Loop time of 6.405e-06 on 1 procs for 0 steps with 458 atoms 156.1% 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 | | 6.405e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4272.00 ave 4272 max 4272 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: 63160.0 ave 63160 max 63160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63160 Ave neighs/atom = 137.90393 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.609 | 4.609 | 4.609 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 -1826.8019 -1826.8019 21.566526 61.425616 4.0371023 97.125925 97.125925 151.67407 83.496706 56.206995 2.2454581 349.22365 Loop time of 6.585e-06 on 1 procs for 0 steps with 458 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4272.00 ave 4272 max 4272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31580.0 ave 31580 max 31580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63160.0 ave 63160 max 63160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63160 Ave neighs/atom = 137.90393 Neighbor list builds = 0 Dangerous builds = 0 458 -1826.80192280399 eV 2.24545814175962 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01