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 = 2.8553247 2.8553247 2.8553247 Created orthogonal box = (0.0000000 -35.318415 0.0000000) to (16.649261 35.318415 4.0380389) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8968414 4.8476257 4.0380389 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.318415 0.0000000) to (16.649261 35.318415 4.0380389) create_atoms CPU = 0.003 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8968414 4.8476257 4.0380389 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.318415 0.0000000) to (16.649261 35.318415 4.0380389) create_atoms CPU = 0.002 seconds 206 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 = 5 20 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 2 atoms, new total = 408 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_769582363439_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 = 5 20 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -137.16101 0 -137.16101 630565.56 122 0 -1672.6121 0 -1672.6121 4137.1194 Loop time of 1.59309 on 1 procs for 122 steps with 408 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 = -137.161007475045 -1672.61090358168 -1672.61209135561 Force two-norm initial, final = 5015.0268 0.13990120 Force max component initial, final = 1680.1218 0.034280944 Final line search alpha, max atom move = 1.0000000 0.034280944 Iterations, force evaluations = 122 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5405 | 1.5405 | 1.5405 | 0.0 | 96.70 Neigh | 0.016754 | 0.016754 | 0.016754 | 0.0 | 1.05 Comm | 0.019712 | 0.019712 | 0.019712 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01609 | | | 1.01 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3741.00 ave 3741 max 3741 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: 55944.0 ave 55944 max 55944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55944 Ave neighs/atom = 137.11765 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 20 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 : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -1672.6121 0 -1672.6121 4137.1194 4748.9397 125 0 -1672.6377 0 -1672.6377 2.541458 4760.3644 Loop time of 0.0438782 on 1 procs for 3 steps with 408 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 = -1672.61209135562 -1672.63701397269 -1672.63771381646 Force two-norm initial, final = 24.023959 0.26022837 Force max component initial, final = 18.308572 0.15621282 Final line search alpha, max atom move = 0.00022200086 3.4679379e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04187 | 0.04187 | 0.04187 | 0.0 | 95.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049318 | 0.00049318 | 0.00049318 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001515 | | | 3.45 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3725.00 ave 3725 max 3725 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: 56264.0 ave 56264 max 56264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56264 Ave neighs/atom = 137.90196 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 = 5 20 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1672.6377 0 -1672.6377 2.541458 Loop time of 6.815e-06 on 1 procs for 0 steps with 408 atoms 176.1% 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 | | 6.815e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3725.00 ave 3725 max 3725 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: 56216.0 ave 56216 max 56216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56216 Ave neighs/atom = 137.78431 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 = 5 20 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) = 4.603 | 4.603 | 4.603 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 -1672.6377 -1672.6377 16.679328 70.7331 4.0349576 2.541458 2.541458 -42.256439 52.647566 -2.7667537 2.2394337 321.17301 Loop time of 6.987e-06 on 1 procs for 0 steps with 408 atoms 229.0% 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 | | 6.987e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3725.00 ave 3725 max 3725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28108.0 ave 28108 max 28108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56216.0 ave 56216 max 56216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56216 Ave neighs/atom = 137.78431 Neighbor list builds = 0 Dangerous builds = 0 408 -1672.63771381646 eV 2.23943366145471 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02