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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -55.538047 0.0000000) to (15.115542 55.538047 9.8954449) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4780893 6.1708941 6.5969632 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -55.538047 0.0000000) to (15.115542 55.538047 9.8954449) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4780893 6.1708941 6.5969632 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -55.538047 0.0000000) to (15.115542 55.538047 9.8954449) create_atoms CPU = 0.001 seconds 507 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 19 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.361 | 6.361 | 6.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2545.6597 0 -2545.6597 29935.609 51 0 -2896.6203 0 -2896.6203 2447.7323 Loop time of 1.3921 on 1 procs for 51 steps with 1008 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2545.6597442329 -2896.61746288305 -2896.62029523088 Force two-norm initial, final = 414.23336 0.16494481 Force max component initial, final = 88.938345 0.019497239 Final line search alpha, max atom move = 1.0000000 0.019497239 Iterations, force evaluations = 51 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3305 | 1.3305 | 1.3305 | 0.0 | 95.57 Neigh | 0.047723 | 0.047723 | 0.047723 | 0.0 | 3.43 Comm | 0.0086734 | 0.0086734 | 0.0086734 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00523 | | | 0.38 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9666.00 ave 9666 max 9666 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: 420014.0 ave 420014 max 420014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420014 Ave neighs/atom = 416.68056 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.361 | 6.361 | 6.361 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -2896.6203 0 -2896.6203 2447.7323 16614.208 54 0 -2896.6844 0 -2896.6844 41.014377 16666.683 Loop time of 0.0837694 on 1 procs for 3 steps with 1008 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2896.62029523089 -2896.6816520406 -2896.68441944227 Force two-norm initial, final = 49.901139 0.77257446 Force max component initial, final = 41.877397 0.53160226 Final line search alpha, max atom move = 0.00015916317 8.4611499e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082009 | 0.082009 | 0.082009 | 0.0 | 97.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035641 | 0.00035641 | 0.00035641 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001404 | | | 1.68 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711.00 ave 9711 max 9711 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: 416864.0 ave 416864 max 416864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416864 Ave neighs/atom = 413.55556 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.499 | 6.499 | 6.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2896.6844 0 -2896.6844 41.014377 Loop time of 1.746e-06 on 1 procs for 0 steps with 1008 atoms 171.8% 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 | | 1.746e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711.00 ave 9711 max 9711 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: 404550.0 ave 404550 max 404550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404550 Ave neighs/atom = 401.33929 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.499 | 6.499 | 6.499 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 -2896.6844 -2896.6844 15.152293 111.19823 9.8917461 41.014377 41.014377 39.80818 51.159378 32.075571 2.5926046 477.17179 Loop time of 2.484e-06 on 1 procs for 0 steps with 1008 atoms 241.5% 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 | | 2.484e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9711.00 ave 9711 max 9711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 202275.0 ave 202275 max 202275 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 404550.0 ave 404550 max 404550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404550 Ave neighs/atom = 401.33929 Neighbor list builds = 0 Dangerous builds = 0 1008 -2896.68441944227 eV 2.59260457533885 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01