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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -43.305936 0.0000000) to (20.414614 43.305936 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2978134 5.3182728 4.6834336 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -43.305936 0.0000000) to (20.414614 43.305936 4.6834336) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2978134 5.3182728 4.6834336 Created 462 atoms using lattice units in orthogonal box = (0.0000000 -43.305936 0.0000000) to (20.414614 43.305936 4.6834336) create_atoms CPU = 0.001 seconds 462 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 24 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 916 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2789.3459 0 -2789.3459 265611.23 174 0 -3554.2993 0 -3554.2993 226356.94 Loop time of 3.33174 on 1 procs for 174 steps with 916 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 = -2789.34589765446 -3554.29635634746 -3554.29932630149 Force two-norm initial, final = 1039.7533 0.33823179 Force max component initial, final = 212.55713 0.036841569 Final line search alpha, max atom move = 0.62256723 0.022936354 Iterations, force evaluations = 174 338 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2698 | 3.2698 | 3.2698 | 0.0 | 98.14 Neigh | 0.02044 | 0.02044 | 0.02044 | 0.0 | 0.61 Comm | 0.02388 | 0.02388 | 0.02388 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01758 | | | 0.53 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6700.00 ave 6700 max 6700 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: 177344.0 ave 177344 max 177344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177344 Ave neighs/atom = 193.60699 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 174 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press Volume 174 0 -3554.2993 0 -3554.2993 226356.94 8281.0033 1174 0 -3674.433 0 -3674.433 635.32769 10207.047 Loop time of 10.5309 on 1 procs for 1000 steps with 916 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3554.29932630149 -3674.37942432518 -3674.43303275315 Force two-norm initial, final = 2067.8918 15.665847 Force max component initial, final = 1355.0736 11.842935 Final line search alpha, max atom move = 3.8056570e-05 0.00045070149 Iterations, force evaluations = 1000 1140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9618 | 9.9618 | 9.9618 | 0.0 | 94.60 Neigh | 0.18494 | 0.18494 | 0.18494 | 0.0 | 1.76 Comm | 0.065924 | 0.065924 | 0.065924 | 0.0 | 0.63 Output | 7.7718e-05 | 7.7718e-05 | 7.7718e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3181 | | | 3.02 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5879.00 ave 5879 max 5879 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: 143440.0 ave 143440 max 143440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143440 Ave neighs/atom = 156.59389 Neighbor list builds = 19 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.141 | 5.141 | 5.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3674.433 0 -3674.433 635.32769 Loop time of 2.199e-06 on 1 procs for 0 steps with 916 atoms 227.4% 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 | | 2.199e-06 | | |100.00 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5833.00 ave 5833 max 5833 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: 144208.0 ave 144208 max 144208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144208 Ave neighs/atom = 157.43231 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.141 | 5.141 | 5.141 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 -3674.433 -3674.433 18.605184 97.760275 5.6118204 635.32769 635.32769 1694.191 -84.894914 296.68697 2.2700915 1430.2247 Loop time of 2.769e-06 on 1 procs for 0 steps with 916 atoms 216.7% 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 | | 2.769e-06 | | |100.00 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5833.00 ave 5833 max 5833 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72104.0 ave 72104 max 72104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 144208.0 ave 144208 max 144208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144208 Ave neighs/atom = 157.43231 Neighbor list builds = 0 Dangerous builds = 0 916 -3674.43303275316 eV 2.27009148018032 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14