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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -63.665400 0.0000000) to (36.757236 63.665400 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6549593 5.7135615 6.2429061 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -63.665400 0.0000000) to (36.757236 63.665400 6.2429061) create_atoms CPU = 0.006 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6549593 5.7135615 6.2429061 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -63.665400 0.0000000) to (36.757236 63.665400 6.2429061) create_atoms CPU = 0.006 seconds 1252 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2500 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_304347095149_000#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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.315 | 5.315 | 5.315 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9166.9183 0 -9166.9183 128299.48 77 0 -10595.802 0 -10595.802 5451.1733 Loop time of 14.4894 on 1 procs for 77 steps with 2500 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9166.91833701054 -10595.7919681276 -10595.8015160365 Force two-norm initial, final = 2198.1140 0.33313871 Force max component initial, final = 361.68541 0.039964865 Final line search alpha, max atom move = 1.0000000 0.039964865 Iterations, force evaluations = 77 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.386 | 14.386 | 14.386 | 0.0 | 99.29 Neigh | 0.059787 | 0.059787 | 0.059787 | 0.0 | 0.41 Comm | 0.018461 | 0.018461 | 0.018461 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02475 | | | 0.17 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8404.00 ave 8404 max 8404 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: 194136.0 ave 194136 max 194136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194136 Ave neighs/atom = 77.654400 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.315 | 5.315 | 5.315 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -10595.802 0 -10595.802 5451.1733 29218.849 79 0 -10595.969 0 -10595.969 -48.814023 29317.841 Loop time of 0.380561 on 1 procs for 2 steps with 2500 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 = -10595.8015160365 -10595.9636830541 -10595.9694476271 Force two-norm initial, final = 172.51274 5.7454382 Force max component initial, final = 107.92243 3.6010494 Final line search alpha, max atom move = 4.1927058e-05 0.00015098140 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37859 | 0.37859 | 0.37859 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027797 | 0.00027797 | 0.00027797 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001697 | | | 0.45 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8457.00 ave 8457 max 8457 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: 194088.0 ave 194088 max 194088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194088 Ave neighs/atom = 77.635200 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10595.969 0 -10595.969 -48.814023 Loop time of 3.8e-06 on 1 procs for 0 steps with 2500 atoms 184.2% 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 | | 3.8e-06 | | |100.00 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8449.00 ave 8449 max 8449 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: 193984.0 ave 193984 max 193984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193984 Ave neighs/atom = 77.593600 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.453 | 5.453 | 5.453 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 -10595.969 -10595.969 36.796617 127.4942 6.2493331 -48.814023 -48.814023 -153.8287 197.04454 -189.65791 2.2615663 1543.6627 Loop time of 3.95e-06 on 1 procs for 0 steps with 2500 atoms 227.8% 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 | | 3.95e-06 | | |100.00 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8449.00 ave 8449 max 8449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96992.0 ave 96992 max 96992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193984.0 ave 193984 max 193984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193984 Ave neighs/atom = 77.593600 Neighbor list builds = 0 Dangerous builds = 0 2500 -10595.9694476271 eV 2.26156625162554 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16