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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -70.575796 0.0000000) to (40.746955 70.575796 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734715 5.6179738 6.0968202 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.575796 0.0000000) to (40.746955 70.575796 6.0968202) create_atoms CPU = 0.011 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734715 5.6179738 6.0968202 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.575796 0.0000000) to (40.746955 70.575796 6.0968202) create_atoms CPU = 0.011 seconds 1610 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 = 11 37 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 2 atoms, new total = 3216 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 = 11 37 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) = 10.94 | 10.94 | 10.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13606.17 0 -13606.17 45937.872 126 0 -14263.07 0 -14263.07 7074.786 Loop time of 14.5771 on 1 procs for 126 steps with 3216 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 = -13606.1702874189 -14263.056938905 -14263.0701422227 Force two-norm initial, final = 873.42569 0.56618717 Force max component initial, final = 182.18656 0.10004282 Final line search alpha, max atom move = 1.0000000 0.10004282 Iterations, force evaluations = 126 230 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.267 | 14.267 | 14.267 | 0.0 | 97.87 Neigh | 0.15583 | 0.15583 | 0.15583 | 0.0 | 1.07 Comm | 0.079231 | 0.079231 | 0.079231 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07534 | | | 0.52 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13239.0 ave 13239 max 13239 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: 568140.0 ave 568140 max 568140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568140 Ave neighs/atom = 176.66045 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 37 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 : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.94 | 10.94 | 10.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -14263.07 0 -14263.07 7074.786 35065.846 131 0 -14263.766 0 -14263.766 245.97523 35194.004 Loop time of 0.425857 on 1 procs for 5 steps with 3216 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14263.0701422228 -14263.7591880087 -14263.7655921201 Force two-norm initial, final = 339.50850 9.9834843 Force max component initial, final = 312.92533 7.3425821 Final line search alpha, max atom move = 6.0060810e-05 0.00044100143 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41609 | 0.41609 | 0.41609 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020756 | 0.0020756 | 0.0020756 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007686 | | | 1.80 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13224.0 ave 13224 max 13224 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: 566712.0 ave 566712 max 566712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 566712 Ave neighs/atom = 176.21642 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 = 11 37 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) = 10.45 | 10.45 | 10.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14263.766 0 -14263.766 245.97523 Loop time of 6.245e-06 on 1 procs for 0 steps with 3216 atoms 208.2% 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 | | 6.245e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13224.0 ave 13224 max 13224 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: 566060.0 ave 566060 max 566060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 566060 Ave neighs/atom = 176.01368 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 = 11 37 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) = 10.45 | 10.45 | 10.45 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 -14263.766 -14263.766 40.763471 141.76056 6.090348 245.97523 245.97523 121.37774 335.70679 280.84116 2.2513728 1029.1784 Loop time of 6.535e-06 on 1 procs for 0 steps with 3216 atoms 275.4% 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 | | 6.535e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13224.0 ave 13224 max 13224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 283030.0 ave 283030 max 283030 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 566060.0 ave 566060 max 566060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 566060 Ave neighs/atom = 176.01368 Neighbor list builds = 0 Dangerous builds = 0 3216 -14263.7655921201 eV 2.25137276658159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16