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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -36.625743 0.0000000) to (44.857191 36.625743 8.5539306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7090970 5.3273808 5.7026204 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -36.625743 0.0000000) to (44.857191 36.625743 8.5539306) create_atoms CPU = 0.002 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7090970 5.3273808 5.7026204 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -36.625743 0.0000000) to (44.857191 36.625743 8.5539306) create_atoms CPU = 0.002 seconds 1322 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 12 19 3 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2630 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_270337113239_005#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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 12 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.912 | 6.912 | 6.912 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8014.5836 0 -8014.5836 70192.777 70 0 -8706.5717 0 -8706.5717 852.78843 Loop time of 2.91844 on 1 procs for 70 steps with 2630 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8014.58356505045 -8706.5630790499 -8706.57169725104 Force two-norm initial, final = 930.10025 0.25331877 Force max component initial, final = 137.84567 0.040340443 Final line search alpha, max atom move = 1.0000000 0.040340443 Iterations, force evaluations = 70 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8275 | 2.8275 | 2.8275 | 0.0 | 96.89 Neigh | 0.058995 | 0.058995 | 0.058995 | 0.0 | 2.02 Comm | 0.013337 | 0.013337 | 0.013337 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01857 | | | 0.64 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9912.00 ave 9912 max 9912 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: 522220.0 ave 522220 max 522220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522220 Ave neighs/atom = 198.56274 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 12 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.910 | 6.910 | 6.910 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -8706.5717 0 -8706.5717 852.78843 28106.983 73 0 -8706.6316 0 -8706.6316 -186.63186 28134.486 Loop time of 0.114962 on 1 procs for 3 steps with 2630 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 = -8706.57169725104 -8706.62861610861 -8706.63162066748 Force two-norm initial, final = 46.414685 8.0190491 Force max component initial, final = 44.372008 6.5973791 Final line search alpha, max atom move = 7.0135046e-05 0.00046270748 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11248 | 0.11248 | 0.11248 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038021 | 0.00038021 | 0.00038021 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002098 | | | 1.83 Nlocal: 2630.00 ave 2630 max 2630 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: 523120.0 ave 523120 max 523120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 523120 Ave neighs/atom = 198.90494 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 12 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.048 | 7.048 | 7.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8706.6316 0 -8706.6316 -186.63186 Loop time of 2.068e-06 on 1 procs for 0 steps with 2630 atoms 193.4% 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 | | 2.068e-06 | | |100.00 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9655.00 ave 9655 max 9655 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: 522852.0 ave 522852 max 522852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522852 Ave neighs/atom = 198.80304 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 12 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.048 | 7.048 | 7.048 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 -8706.6316 -8706.6316 44.855966 73.414244 8.5435516 -186.63186 -186.63186 -250.60847 65.958413 -375.24553 2.241368 1393.5922 Loop time of 2.73e-06 on 1 procs for 0 steps with 2630 atoms 293.0% 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 | | 2.73e-06 | | |100.00 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9655.00 ave 9655 max 9655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261426.0 ave 261426 max 261426 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 522852.0 ave 522852 max 522852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522852 Ave neighs/atom = 198.80304 Neighbor list builds = 0 Dangerous builds = 0 2630 -8595.58346821819 eV 2.24136796208924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03