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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -42.438660 0.0000000) to (15.004332 42.438660 5.1464435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1782545 6.2409795 5.1464435 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.438660 0.0000000) to (15.004332 42.438660 5.1464435) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1782545 6.2409795 5.1464435 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.438660 0.0000000) to (15.004332 42.438660 5.1464435) create_atoms CPU = 0.002 seconds 274 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 18 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_600021860456_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1292.8532 0 -1292.8532 184058.89 84 0 -1779.3765 0 -1779.3765 5890.2674 Loop time of 3.54557 on 1 procs for 84 steps with 544 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 = -1292.8531782051 -1779.37531599955 -1779.37648604302 Force two-norm initial, final = 1326.7394 0.082817268 Force max component initial, final = 422.30319 0.0080607076 Final line search alpha, max atom move = 1.0000000 0.0080607076 Iterations, force evaluations = 84 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5072 | 3.5072 | 3.5072 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023513 | 0.023513 | 0.023513 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01484 | | | 0.42 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6618.00 ave 6618 max 6618 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: 173432.0 ave 173432 max 173432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173432 Ave neighs/atom = 318.80882 Neighbor list builds = 0 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -1779.3765 0 -1779.3765 5890.2674 6554.1374 89 0 -1779.4648 0 -1779.4648 -81.936639 6580.7497 Loop time of 0.156525 on 1 procs for 5 steps with 544 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 = -1779.37648604303 -1779.46451162756 -1779.46480818716 Force two-norm initial, final = 47.583281 0.61677772 Force max component initial, final = 42.755098 0.44967688 Final line search alpha, max atom move = 0.00065427965 0.00029421443 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15272 | 0.15272 | 0.15272 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092965 | 0.00092965 | 0.00092965 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00288 | | | 1.84 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6716.00 ave 6716 max 6716 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: 172344.0 ave 172344 max 172344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172344 Ave neighs/atom = 316.80882 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1779.4648 0 -1779.4648 -81.936639 Loop time of 6.775e-06 on 1 procs for 0 steps with 544 atoms 177.1% 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 | | 6.775e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6662.00 ave 6662 max 6662 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: 172216.0 ave 172216 max 172216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172216 Ave neighs/atom = 316.57353 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.094 | 5.094 | 5.094 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 -1779.4648 -1779.4648 15.068123 84.883209 5.1451071 -81.936639 -81.936639 -80.60543 -55.752726 -109.45176 2.376003 431.74606 Loop time of 7.127e-06 on 1 procs for 0 steps with 544 atoms 210.5% 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 | | 7.127e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6662.00 ave 6662 max 6662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86108.0 ave 86108 max 86108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172216.0 ave 172216 max 172216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172216 Ave neighs/atom = 316.57353 Neighbor list builds = 0 Dangerous builds = 0 544 -1779.46480818716 eV 2.37600304962113 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04