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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -55.678100 0.0000000) to (15.153659 55.678100 9.9203987) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4944254 6.1864555 6.6135992 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -55.678100 0.0000000) to (15.153659 55.678100 9.9203987) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4944254 6.1864555 6.6135992 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -55.678100 0.0000000) to (15.153659 55.678100 9.9203987) create_atoms CPU = 0.001 seconds 507 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 ghost atom cutoff = 6 binsize = 3, bins = 6 38 4 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1007 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 6 38 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3326.4768 0 -3326.4768 7777.8308 24 0 -3365.4888 0 -3365.4888 2836.0881 Loop time of 0.783183 on 1 procs for 24 steps with 1007 atoms 93.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3326.47681092184 -3365.48587823758 -3365.4887667068 Force two-norm initial, final = 56.857771 0.16985398 Force max component initial, final = 13.048275 0.026213581 Final line search alpha, max atom move = 1.0000000 0.026213581 Iterations, force evaluations = 24 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77898 | 0.77898 | 0.77898 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017053 | 0.0017053 | 0.0017053 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002497 | | | 0.32 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3475.00 ave 3475 max 3475 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: 54312.0 ave 54312 max 54312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54312 Ave neighs/atom = 53.934459 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 38 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -3365.4888 0 -3365.4888 2836.0881 16740.216 33 0 -3365.7381 0 -3365.7381 28.828585 16811.866 Loop time of 0.173727 on 1 procs for 9 steps with 1007 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3365.4887667068 -3365.73811998859 -3365.73814663955 Force two-norm initial, final = 68.989053 0.61387453 Force max component initial, final = 67.087303 0.35796105 Final line search alpha, max atom move = 0.0027086218 0.00096958109 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17126 | 0.17126 | 0.17126 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036986 | 0.00036986 | 0.00036986 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0021 | | | 1.21 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3502.00 ave 3502 max 3502 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: 54078.0 ave 54078 max 54078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54078 Ave neighs/atom = 53.702085 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 ghost atom cutoff = 6 binsize = 3, bins = 6 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3365.7381 0 -3365.7381 28.828585 Loop time of 1.988e-06 on 1 procs for 0 steps with 1007 atoms 150.9% 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 | | 1.988e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3502.00 ave 3502 max 3502 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: 54070.0 ave 54070 max 54070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54070 Ave neighs/atom = 53.694141 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 ghost atom cutoff = 6 binsize = 3, bins = 6 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.655 | 4.655 | 4.655 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 -3365.7381 -3365.7381 15.133495 112.25066 9.8966401 28.828585 28.828585 26.767657 34.387825 25.330274 2.5140184 484.19938 Loop time of 1.909e-06 on 1 procs for 0 steps with 1007 atoms 157.2% 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 | | 1.909e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27035.0 ave 27035 max 27035 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54070.0 ave 54070 max 54070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54070 Ave neighs/atom = 53.694141 Neighbor list builds = 0 Dangerous builds = 0 1007 -3365.73814663955 eV 2.51401836462869 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01