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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -45.900738 0.0000000) to (32.456723 45.900738 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0105043 6.2334336 5.1000820 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -45.900738 0.0000000) to (32.456723 45.900738 5.1000820) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0105043 6.2334336 5.1000820 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.900738 0.0000000) to (32.456723 45.900738 5.1000820) create_atoms CPU = 0.002 seconds 650 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.924 | 7.924 | 7.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5167.6933 0 -5167.6933 43982.522 88 0 -5443.5814 0 -5443.5814 5599.5655 Loop time of 5.79496 on 1 procs for 88 steps with 1298 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5167.69326041288 -5443.57686520852 -5443.58138966537 Force two-norm initial, final = 365.34140 0.29257033 Force max component initial, final = 113.47397 0.024595712 Final line search alpha, max atom move = 1.0000000 0.024595712 Iterations, force evaluations = 88 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7224 | 5.7224 | 5.7224 | 0.0 | 98.75 Neigh | 0.034718 | 0.034718 | 0.034718 | 0.0 | 0.60 Comm | 0.025226 | 0.025226 | 0.025226 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01261 | | | 0.22 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15012.0 ave 15012 max 15012 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: 799964.0 ave 799964 max 799964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 799964 Ave neighs/atom = 616.30508 Neighbor list builds = 1 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.923 | 7.923 | 7.923 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -5443.5814 0 -5443.5814 5599.5655 15196.078 93 0 -5443.977 0 -5443.977 5.9965127 15244.699 Loop time of 0.274817 on 1 procs for 5 steps with 1298 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 = -5443.58138966537 -5443.97699638366 -5443.9770455844 Force two-norm initial, final = 162.24869 0.45584121 Force max component initial, final = 129.31515 0.14764983 Final line search alpha, max atom move = 0.00071926491 0.00010619934 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27067 | 0.27067 | 0.27067 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084818 | 0.00084818 | 0.00084818 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0033 | | | 1.20 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14953.0 ave 14953 max 14953 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: 799312.0 ave 799312 max 799312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 799312 Ave neighs/atom = 615.80277 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 8.061 | 8.061 | 8.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5443.977 0 -5443.977 5.9965127 Loop time of 1.734e-06 on 1 procs for 0 steps with 1298 atoms 173.0% 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 | | 1.734e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14936.0 ave 14936 max 14936 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: 796604.0 ave 796604 max 796604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 796604 Ave neighs/atom = 613.71649 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 8.061 | 8.061 | 8.061 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 -5443.977 -5443.977 32.578649 91.560418 5.1106721 5.9965127 5.9965127 15.575889 12.169866 -9.7562172 2.4051753 958.61036 Loop time of 2.409e-06 on 1 procs for 0 steps with 1298 atoms 207.6% 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 | | 2.409e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14936.0 ave 14936 max 14936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 398302.0 ave 398302 max 398302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 796604.0 ave 796604 max 796604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 796604 Ave neighs/atom = 613.71649 Neighbor list builds = 0 Dangerous builds = 0 1298 -5443.9770455844 eV 2.40517533774956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06