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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -40.276804 0.0000000) to (17.440368 40.276804 6.1661011) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8134559 5.0346005 6.1661011 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -40.276804 0.0000000) to (17.440368 40.276804 6.1661011) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8134559 5.0346005 6.1661011 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.276804 0.0000000) to (17.440368 40.276804 6.1661011) create_atoms CPU = 0.001 seconds 396 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 776 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3168.7901 0 -3168.7901 84346.869 103 0 -3391.5587 0 -3391.5587 56286.856 Loop time of 1.35625 on 1 procs for 103 steps with 776 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3168.79009140055 -3391.55631621467 -3391.55872569617 Force two-norm initial, final = 215.48472 0.22289589 Force max component initial, final = 27.219112 0.029935508 Final line search alpha, max atom move = 1.0000000 0.029935508 Iterations, force evaluations = 103 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3317 | 1.3317 | 1.3317 | 0.0 | 98.19 Neigh | 0.0081973 | 0.0081973 | 0.0081973 | 0.0 | 0.60 Comm | 0.0093071 | 0.0093071 | 0.0093071 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007035 | | | 0.52 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5654.00 ave 5654 max 5654 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: 136496.0 ave 136496 max 136496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136496 Ave neighs/atom = 175.89691 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -3391.5587 0 -3391.5587 56286.856 8662.66 120 0 -3395.472 0 -3395.472 47.540082 8864.2493 Loop time of 0.138047 on 1 procs for 17 steps with 776 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 = -3391.55872569618 -3395.4715073486 -3395.47197230451 Force two-norm initial, final = 548.07557 1.4137043 Force max component initial, final = 426.74037 0.64468195 Final line search alpha, max atom move = 0.00021795766 0.00014051337 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12572 | 0.12572 | 0.12572 | 0.0 | 91.07 Neigh | 0.0078054 | 0.0078054 | 0.0078054 | 0.0 | 5.65 Comm | 0.00091248 | 0.00091248 | 0.00091248 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003606 | | | 2.61 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5443.00 ave 5443 max 5443 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: 135184.0 ave 135184 max 135184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135184 Ave neighs/atom = 174.20619 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3395.472 0 -3395.472 47.540082 Loop time of 2.084e-06 on 1 procs for 0 steps with 776 atoms 144.0% 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 | | 2.084e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5473.00 ave 5473 max 5473 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: 135168.0 ave 135168 max 135168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135168 Ave neighs/atom = 174.18557 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.123 | 5.123 | 5.123 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 -3395.472 -3395.472 17.490895 81.841325 6.1923755 47.540082 47.540082 -0.91940823 26.519532 117.02012 2.3674877 479.78067 Loop time of 2.036e-06 on 1 procs for 0 steps with 776 atoms 196.5% 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 | | 2.036e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5473.00 ave 5473 max 5473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67584.0 ave 67584 max 67584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135168.0 ave 135168 max 135168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135168 Ave neighs/atom = 174.18557 Neighbor list builds = 0 Dangerous builds = 0 776 -3395.47197230451 eV 2.36748765876866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01