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 -48.936165 0.0000000) to (59.934317 48.936165 9.9203987) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471263 6.0332258 6.6135992 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.936165 0.0000000) to (59.934317 48.936165 9.9203987) create_atoms CPU = 0.003 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471263 6.0332258 6.6135992 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.936165 0.0000000) to (59.934317 48.936165 9.9203987) create_atoms CPU = 0.002 seconds 1755 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 = 20 33 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 0 atoms, new total = 3504 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 = 20 33 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) = 5.180 | 5.180 | 5.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11471.471 0 -11471.471 13750.745 67 0 -11713.088 0 -11713.088 3309.9435 Loop time of 7.28568 on 1 procs for 67 steps with 3504 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11471.4714726439 -11713.0781806183 -11713.0879460198 Force two-norm initial, final = 139.59916 0.63526003 Force max component initial, final = 20.166389 0.34904186 Final line search alpha, max atom move = 1.0000000 0.34904186 Iterations, force evaluations = 67 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2364 | 7.2364 | 7.2364 | 0.0 | 99.32 Neigh | 0.018097 | 0.018097 | 0.018097 | 0.0 | 0.25 Comm | 0.010699 | 0.010699 | 0.010699 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02051 | | | 0.28 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6831.00 ave 6831 max 6831 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: 188314.0 ave 188314 max 188314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188314 Ave neighs/atom = 53.742580 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 20 33 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.183 | 5.183 | 5.183 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -11713.088 0 -11713.088 3309.9435 58192.179 76 0 -11714.094 0 -11714.094 -2.6368687 58482.327 Loop time of 0.593926 on 1 procs for 9 steps with 3504 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11713.0879460199 -11714.0855011825 -11714.0939772755 Force two-norm initial, final = 266.03045 0.92364405 Force max component initial, final = 255.09776 0.56523621 Final line search alpha, max atom move = 6.9940943e-05 3.9533154e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5881 | 0.5881 | 0.5881 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063644 | 0.00063644 | 0.00063644 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005191 | | | 0.87 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7107.00 ave 7107 max 7107 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: 188300.0 ave 188300 max 188300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188300 Ave neighs/atom = 53.738584 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 = 20 33 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) = 5.321 | 5.321 | 5.321 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11714.094 0 -11714.094 -2.6368687 Loop time of 2.503e-06 on 1 procs for 0 steps with 3504 atoms 159.8% 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 | | 2.503e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109.00 ave 7109 max 7109 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: 188210.0 ave 188210 max 188210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188210 Ave neighs/atom = 53.712900 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 = 20 33 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) = 5.321 | 5.321 | 5.321 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 -11714.094 -11714.094 59.820186 98.732337 9.9018756 -2.6368687 -2.6368687 -15.455672 -5.4646141 13.00968 2.4972802 1853.3067 Loop time of 2.012e-06 on 1 procs for 0 steps with 3504 atoms 248.5% 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 | | 2.012e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109.00 ave 7109 max 7109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94105.0 ave 94105 max 94105 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188210.0 ave 188210 max 188210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188210 Ave neighs/atom = 53.712900 Neighbor list builds = 0 Dangerous builds = 0 3504 -11714.0939772755 eV 2.49728018519043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08