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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -71.376993 0.0000000) to (41.209526 71.376993 6.9990900) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3399271 6.4056275 6.9990900 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -71.376993 0.0000000) to (41.209526 71.376993 6.9990900) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3399271 6.4056275 6.9990900 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.376993 0.0000000) to (41.209526 71.376993 6.9990900) create_atoms CPU = 0.002 seconds 1249 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 29 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 2493 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.336 | 7.336 | 7.336 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9484.8736 0 -9484.8736 16245.915 77 0 -9715.1706 0 -9715.1706 3512.9777 Loop time of 5.16758 on 1 procs for 77 steps with 2493 atoms 93.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9484.87361566913 -9715.16121058398 -9715.17058285778 Force two-norm initial, final = 316.79841 0.26231847 Force max component initial, final = 83.641427 0.084403375 Final line search alpha, max atom move = 1.0000000 0.084403375 Iterations, force evaluations = 77 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9874 | 4.9874 | 4.9874 | 0.0 | 96.51 Neigh | 0.13637 | 0.13637 | 0.13637 | 0.0 | 2.64 Comm | 0.024151 | 0.024151 | 0.024151 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01962 | | | 0.38 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13006.0 ave 13006 max 13006 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: 615148.0 ave 615148 max 615148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 615148 Ave neighs/atom = 246.75010 Neighbor list builds = 4 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.335 | 7.335 | 7.335 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -9715.1706 0 -9715.1706 3512.9777 41174.415 83 0 -9715.6217 0 -9715.6217 -115.0062 41355.946 Loop time of 0.303847 on 1 procs for 6 steps with 2493 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 = -9715.17058285778 -9715.61745580364 -9715.62170864528 Force two-norm initial, final = 187.07093 5.2916554 Force max component initial, final = 172.19679 3.8647049 Final line search alpha, max atom move = 8.2710949e-05 0.00031965341 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29832 | 0.29832 | 0.29832 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088479 | 0.00088479 | 0.00088479 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004639 | | | 1.53 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12987.0 ave 12987 max 12987 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: 615238.0 ave 615238 max 615238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 615238 Ave neighs/atom = 246.78620 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.473 | 7.473 | 7.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9715.6217 0 -9715.6217 -115.0062 Loop time of 2.354e-06 on 1 procs for 0 steps with 2493 atoms 169.9% 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 | | 2.354e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12987.0 ave 12987 max 12987 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: 614670.0 ave 614670 max 614670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614670 Ave neighs/atom = 246.55836 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.473 | 7.473 | 7.473 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 -9715.6217 -9715.6217 41.20936 143.55215 6.9908884 -115.0062 -115.0062 -149.72248 -83.158575 -112.13756 2.5760034 1250.7464 Loop time of 2.726e-06 on 1 procs for 0 steps with 2493 atoms 256.8% 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 | | 2.726e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12987.0 ave 12987 max 12987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307335.0 ave 307335 max 307335 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614670.0 ave 614670 max 614670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614670 Ave neighs/atom = 246.55836 Neighbor list builds = 0 Dangerous builds = 0 2493 -9715.62170864528 eV 2.57600344699916 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06