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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7031517 5.7031517 4.0446508 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7031517 5.7031517 4.0446508 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) create_atoms CPU = 0.002 seconds 682 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 45 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1356 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4521.8851 0 -4521.8851 5229.7689 83 0 -4550.1394 0 -4550.1394 -943.48154 Loop time of 15.3367 on 1 procs for 83 steps with 1356 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 = -4521.88507747444 -4550.13538209476 -4550.13943504306 Force two-norm initial, final = 20.375135 0.16130143 Force max component initial, final = 5.2642362 0.023281221 Final line search alpha, max atom move = 1.0000000 0.023281221 Iterations, force evaluations = 83 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.26 | 15.26 | 15.26 | 0.0 | 99.50 Neigh | 0.030805 | 0.030805 | 0.030805 | 0.0 | 0.20 Comm | 0.022748 | 0.022748 | 0.022748 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02344 | | | 0.15 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6708.00 ave 6708 max 6708 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: 105244.0 ave 105244 max 105244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105244 Ave neighs/atom = 77.613569 Neighbor list builds = 2 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4550.1394 0 -4550.1394 -943.48154 22498.086 85 0 -4550.1496 0 -4550.1496 -51.278794 22472.624 Loop time of 0.537058 on 1 procs for 2 steps with 1356 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4550.13943504306 -4550.14843942604 -4550.14959367733 Force two-norm initial, final = 20.527516 0.16134084 Force max component initial, final = 17.994725 0.021310319 Final line search alpha, max atom move = 0.00029699368 6.3290301e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53394 | 0.53394 | 0.53394 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069648 | 0.00069648 | 0.00069648 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00242 | | | 0.45 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6680.00 ave 6680 max 6680 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: 105272.0 ave 105272 max 105272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105272 Ave neighs/atom = 77.634218 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4550.1496 0 -4550.1496 -51.278794 Loop time of 6.686e-06 on 1 procs for 0 steps with 1356 atoms 164.5% 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 | | 6.686e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6680.00 ave 6680 max 6680 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: 105272.0 ave 105272 max 105272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105272 Ave neighs/atom = 77.634218 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.190 | 5.190 | 5.190 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 -4550.1496 -4550.1496 37.289477 149.16744 4.0401125 -51.278794 -51.278794 -1.2522624 -152.72738 0.14326575 2.5564532 174.09156 Loop time of 7.047e-06 on 1 procs for 0 steps with 1356 atoms 269.6% 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 | | 7.047e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6680.00 ave 6680 max 6680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52636.0 ave 52636 max 52636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105272.0 ave 105272 max 105272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105272 Ave neighs/atom = 77.634218 Neighbor list builds = 0 Dangerous builds = 0 1356 -4550.14959367733 eV 2.55645315051083 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16