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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -69.692446 0.0000000) to (42.677733 69.692446 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355201 4.9780318 5.7481360 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.692446 0.0000000) to (42.677733 69.692446 8.6222040) create_atoms CPU = 0.010 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355201 4.9780318 5.7481360 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.692446 0.0000000) to (42.677733 69.692446 8.6222040) create_atoms CPU = 0.009 seconds 2358 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 13 41 3 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 4692 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20581.185 0 -20581.185 9082.503 71 0 -20819.701 0 -20819.701 3202.1011 Loop time of 7.14807 on 1 procs for 71 steps with 4692 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 = -20581.1852100498 -20819.6811245919 -20819.7008314981 Force two-norm initial, final = 158.39035 0.49924811 Force max component initial, final = 24.489184 0.035246622 Final line search alpha, max atom move = 1.0000000 0.035246622 Iterations, force evaluations = 71 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8489 | 6.8489 | 6.8489 | 0.0 | 95.82 Neigh | 0.19033 | 0.19033 | 0.19033 | 0.0 | 2.66 Comm | 0.042353 | 0.042353 | 0.042353 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06645 | | | 0.93 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12858.0 ave 12858 max 12858 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: 623208.0 ave 623208 max 623208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623208 Ave neighs/atom = 132.82353 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -20819.701 0 -20819.701 3202.1011 51290.311 75 0 -20819.969 0 -20819.969 -18.460672 51383.244 Loop time of 0.364674 on 1 procs for 4 steps with 4692 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 = -20819.7008314981 -20819.9629637842 -20819.9689414725 Force two-norm initial, final = 222.89359 5.4635449 Force max component initial, final = 209.66900 4.1704638 Final line search alpha, max atom move = 2.2824494e-05 9.5188727e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35362 | 0.35362 | 0.35362 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020667 | 0.0020667 | 0.0020667 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008989 | | | 2.46 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12948.0 ave 12948 max 12948 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: 623208.0 ave 623208 max 623208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623208 Ave neighs/atom = 132.82353 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 10.92 | 10.92 | 10.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20819.969 0 -20819.969 -18.460672 Loop time of 8.68e-06 on 1 procs for 0 steps with 4692 atoms 195.9% 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 | | 8.68e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12948.0 ave 12948 max 12948 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: 623088.0 ave 623088 max 623088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623088 Ave neighs/atom = 132.79795 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 10.92 | 10.92 | 10.92 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 -20819.969 -20819.969 42.664354 139.77156 8.616632 -18.460672 -18.460672 -129.99811 -29.780919 104.39701 2.2039962 1658.5113 Loop time of 6.876e-06 on 1 procs for 0 steps with 4692 atoms 305.4% 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 | | 6.876e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12948.0 ave 12948 max 12948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 311544.0 ave 311544 max 311544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 623088.0 ave 623088 max 623088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623088 Ave neighs/atom = 132.79795 Neighbor list builds = 0 Dangerous builds = 0 4692 -20819.9689414725 eV 2.203996237201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08