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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -37.946725 0.0000000) to (13.416193 37.946725 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8786157 4.3121278 4.0451344 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.946725 0.0000000) to (13.416193 37.946725 4.0451344) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8786157 4.3121278 4.0451344 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.946725 0.0000000) to (13.416193 37.946725 4.0451344) create_atoms CPU = 0.000 seconds 178 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 354 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1428.4137 0 -1428.4137 63502.132 303 0 -1545.1112 0 -1545.1112 22405.483 Loop time of 1.88304 on 1 procs for 303 steps with 354 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1428.41370733644 -1545.10989624695 -1545.11118099811 Force two-norm initial, final = 205.93290 0.18801515 Force max component initial, final = 98.847311 0.048182178 Final line search alpha, max atom move = 1.0000000 0.048182178 Iterations, force evaluations = 303 583 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.83 | 1.83 | 1.83 | 0.0 | 97.18 Neigh | 0.021158 | 0.021158 | 0.021158 | 0.0 | 1.12 Comm | 0.019086 | 0.019086 | 0.019086 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01281 | | | 0.68 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 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: 57460.0 ave 57460 max 57460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57460 Ave neighs/atom = 162.31638 Neighbor list builds = 5 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 303 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 303 0 -1545.1112 0 -1545.1112 22405.483 4118.7607 315 0 -1545.6147 0 -1545.6147 -337.93181 4157.3676 Loop time of 0.0437233 on 1 procs for 12 steps with 354 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 = -1545.11118099813 -1545.61440232862 -1545.61473500135 Force two-norm initial, final = 109.70915 1.9032568 Force max component initial, final = 88.995444 1.3763158 Final line search alpha, max atom move = 0.0017375156 0.0023913702 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041712 | 0.041712 | 0.041712 | 0.0 | 95.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038584 | 0.00038584 | 0.00038584 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001626 | | | 3.72 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3723.00 ave 3723 max 3723 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: 57240.0 ave 57240 max 57240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57240 Ave neighs/atom = 161.69492 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1545.6147 0 -1545.6147 -337.93181 Loop time of 1.756e-06 on 1 procs for 0 steps with 354 atoms 170.8% 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 | | 1.756e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 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: 56374.0 ave 56374 max 56374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56374 Ave neighs/atom = 159.24859 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.599 | 4.599 | 4.599 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 -1545.6147 -1545.6147 13.356688 76.753103 4.0553068 -337.93181 -337.93181 -116.89198 -536.41595 -360.4875 2.3293945 2271.4831 Loop time of 1.482e-06 on 1 procs for 0 steps with 354 atoms 202.4% 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 | | 1.482e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28187.0 ave 28187 max 28187 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56374.0 ave 56374 max 56374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56374 Ave neighs/atom = 159.24859 Neighbor list builds = 0 Dangerous builds = 0 354 -1545.61473500135 eV 2.32939451702498 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02