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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -42.141753 0.0000000) to (21.069070 42.141753 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9574282 4.9574282 3.6133157 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.141753 0.0000000) to (21.069070 42.141753 3.6133157) create_atoms CPU = 0.002 seconds 273 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9574282 4.9574282 3.6133157 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.141753 0.0000000) to (21.069070 42.141753 3.6133157) create_atoms CPU = 0.001 seconds 273 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 536 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_380272712420_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1868.5865 0 -1868.5865 6680.6843 72 0 -1889.082 0 -1889.082 -11618.386 Loop time of 11.1189 on 1 procs for 72 steps with 536 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 = -1868.58654906968 -1889.08067845659 -1889.08204183555 Force two-norm initial, final = 41.694997 0.098714371 Force max component initial, final = 12.563052 0.024590381 Final line search alpha, max atom move = 1.0000000 0.024590381 Iterations, force evaluations = 72 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.061 | 11.061 | 11.061 | 0.0 | 99.48 Neigh | 0.025901 | 0.025901 | 0.025901 | 0.0 | 0.23 Comm | 0.019283 | 0.019283 | 0.019283 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01276 | | | 0.11 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5581.00 ave 5581 max 5581 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: 94022.0 ave 94022 max 94022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94022 Ave neighs/atom = 175.41418 Neighbor list builds = 2 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -1889.082 0 -1889.082 -11618.386 6416.4359 78 0 -1889.2472 0 -1889.2472 -1954.0495 6371.3038 Loop time of 0.630574 on 1 procs for 6 steps with 536 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 = -1889.08204183555 -1889.24663798503 -1889.24724767269 Force two-norm initial, final = 62.511754 2.0631026 Force max component initial, final = 46.360114 2.0229110 Final line search alpha, max atom move = 0.00034395020 0.00069578064 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62692 | 0.62692 | 0.62692 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085222 | 0.00085222 | 0.00085222 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002806 | | | 0.44 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5044.00 ave 5044 max 5044 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: 93784.0 ave 93784 max 93784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93784 Ave neighs/atom = 174.97015 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1889.2472 0 -1889.2472 -1954.0495 Loop time of 6.455e-06 on 1 procs for 0 steps with 536 atoms 185.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5059.00 ave 5059 max 5059 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: 93984.0 ave 93984 max 93984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93984 Ave neighs/atom = 175.34328 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.662 | 4.662 | 4.662 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 -1889.2472 -1889.2472 21.027385 84.283506 3.5950129 -1954.0495 -1954.0495 -87.550607 -5268.4781 -506.11985 2.3336577 316.27347 Loop time of 7.176e-06 on 1 procs for 0 steps with 536 atoms 250.8% 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 | | 7.176e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5059.00 ave 5059 max 5059 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46992.0 ave 46992 max 46992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93984.0 ave 93984 max 93984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93984 Ave neighs/atom = 175.34328 Neighbor list builds = 0 Dangerous builds = 0 536 -1889.24724767269 eV 2.33365767589581 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12