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 -53.968825 0.0000000) to (26.984412 53.968825 2.8603420) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9415434 3.9415434 2.8603420 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -53.968825 0.0000000) to (26.984412 53.968825 2.8603420) create_atoms CPU = 0.002 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9415434 3.9415434 2.8603420 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -53.968825 0.0000000) to (26.984412 53.968825 2.8603420) create_atoms CPU = 0.001 seconds 357 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 = 7 28 1 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 = 713 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 = 7 28 1 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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2999.0873 0 -2999.0873 20265.836 169 0 -3077.3284 0 -3077.3284 25346.345 Loop time of 4.61411 on 1 procs for 169 steps with 713 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 = -2999.08732630185 -3077.32542144648 -3077.3283512671 Force two-norm initial, final = 69.561209 0.22091523 Force max component initial, final = 19.412053 0.043800409 Final line search alpha, max atom move = 0.67527913 0.029577502 Iterations, force evaluations = 169 327 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.488 | 4.488 | 4.488 | 0.0 | 97.27 Neigh | 0.032472 | 0.032472 | 0.032472 | 0.0 | 0.70 Comm | 0.057178 | 0.057178 | 0.057178 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03641 | | | 0.79 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7553.00 ave 7553 max 7553 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: 118830.0 ave 118830 max 118830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118830 Ave neighs/atom = 166.66199 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 = 7 28 1 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 : 169 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press Volume 169 0 -3077.3284 0 -3077.3284 25346.345 8331.1295 350 0 -3123.3331 0 -3123.3331 -794.96234 8358.4965 Loop time of 3.24929 on 1 procs for 181 steps with 713 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 = -3077.3283512671 -3123.33136367502 -3123.33311895866 Force two-norm initial, final = 690.34135 8.9411671 Force max component initial, final = 509.13260 5.0717872 Final line search alpha, max atom move = 0.00038022116 0.0019284008 Iterations, force evaluations = 181 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9791 | 2.9791 | 2.9791 | 0.0 | 91.68 Neigh | 0.10968 | 0.10968 | 0.10968 | 0.0 | 3.38 Comm | 0.039982 | 0.039982 | 0.039982 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1206 | | | 3.71 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8166.00 ave 8166 max 8166 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: 111928.0 ave 111928 max 111928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111928 Ave neighs/atom = 156.98177 Neighbor list builds = 7 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 = 8 30 1 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) = 5.099 | 5.099 | 5.099 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3123.3331 0 -3123.3331 -794.96234 Loop time of 6.575e-06 on 1 procs for 0 steps with 713 atoms 182.5% 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 | | 6.575e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8160.00 ave 8160 max 8160 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: 112094.0 ave 112094 max 112094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112094 Ave neighs/atom = 157.21459 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 = 8 30 1 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) = 5.099 | 5.099 | 5.099 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 -3123.3331 -3123.3331 27.513053 115.33882 2.6339884 -794.96234 -794.96234 -991.21765 -836.17467 -557.4947 2.3840236 2206.0131 Loop time of 6.916e-06 on 1 procs for 0 steps with 713 atoms 231.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8160.00 ave 8160 max 8160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56047.0 ave 56047 max 56047 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112094.0 ave 112094 max 112094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112094 Ave neighs/atom = 157.21459 Neighbor list builds = 0 Dangerous builds = 0 713 -3123.33311895866 eV 2.38402356828774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08