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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -63.784718 0.0000000) to (36.826124 63.784718 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6655575 5.7242695 6.2546061 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.784718 0.0000000) to (36.826124 63.784718 6.2546061) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6655575 5.7242695 6.2546061 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.784718 0.0000000) to (36.826124 63.784718 6.2546061) create_atoms CPU = 0.003 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.111 | 6.111 | 6.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9839.7908 0 -9839.7908 54404.056 85 0 -10559.424 0 -10559.424 3973.6338 Loop time of 21.5987 on 1 procs for 85 steps with 2494 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9839.79082675873 -10559.4140995036 -10559.4241766752 Force two-norm initial, final = 792.66589 0.33878371 Force max component initial, final = 127.35092 0.12511219 Final line search alpha, max atom move = 0.91645225 0.11465934 Iterations, force evaluations = 85 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.475 | 21.475 | 21.475 | 0.0 | 99.43 Neigh | 0.081514 | 0.081514 | 0.081514 | 0.0 | 0.38 Comm | 0.020681 | 0.020681 | 0.020681 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02113 | | | 0.10 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9951.00 ave 9951 max 9951 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: 319692.0 ave 319692 max 319692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319692 Ave neighs/atom = 128.18444 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.109 | 6.109 | 6.109 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -10559.424 0 -10559.424 3973.6338 29383.438 88 0 -10559.556 0 -10559.556 29.771192 29450.78 Loop time of 0.827971 on 1 procs for 3 steps with 2494 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10559.4241766752 -10559.5527242278 -10559.5562402555 Force two-norm initial, final = 134.83898 1.9521824 Force max component initial, final = 102.29137 1.8300398 Final line search alpha, max atom move = 4.0004755e-05 7.3210296e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82512 | 0.82512 | 0.82512 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002426 | | | 0.29 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9907.00 ave 9907 max 9907 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: 319306.0 ave 319306 max 319306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319306 Ave neighs/atom = 128.02967 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.247 | 6.247 | 6.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10559.556 0 -10559.556 29.771192 Loop time of 2.459e-06 on 1 procs for 0 steps with 2494 atoms 162.7% 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 | | 2.459e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900.00 ave 9900 max 9900 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: 318148.0 ave 318148 max 318148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318148 Ave neighs/atom = 127.56536 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.247 | 6.247 | 6.247 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 -10559.556 -10559.556 36.79807 127.82833 6.2610133 29.771192 29.771192 16.213094 99.759576 -26.659095 2.3106147 1461.2275 Loop time of 2.795e-06 on 1 procs for 0 steps with 2494 atoms 250.4% 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 | | 2.795e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900.00 ave 9900 max 9900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159074.0 ave 159074 max 159074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318148.0 ave 318148 max 318148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318148 Ave neighs/atom = 127.56536 Neighbor list builds = 0 Dangerous builds = 0 2494 -10559.5562402555 eV 2.31061468846638 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23