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 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1421550 5.9718442 5.0346005 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) create_atoms CPU = 0.002 seconds 695 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1421550 5.9718442 5.0346005 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) create_atoms CPU = 0.002 seconds 695 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 = 9 24 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 22 atoms, new total = 1368 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 = 9 24 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) = 5.496 | 5.496 | 5.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5926.0727 0 -5926.0727 9381.2058 59 0 -6000.4068 0 -6000.4068 2835.9172 Loop time of 1.2801 on 1 procs for 59 steps with 1368 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 = -5926.07273809627 -6000.4009957346 -6000.40676438495 Force two-norm initial, final = 59.908805 0.34979382 Force max component initial, final = 11.832706 0.040884477 Final line search alpha, max atom move = 1.0000000 0.040884477 Iterations, force evaluations = 59 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2527 | 1.2527 | 1.2527 | 0.0 | 97.86 Neigh | 0.012765 | 0.012765 | 0.012765 | 0.0 | 1.00 Comm | 0.007701 | 0.007701 | 0.007701 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006905 | | | 0.54 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8048.00 ave 8048 max 8048 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: 238948.0 ave 238948 max 238948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238948 Ave neighs/atom = 174.66959 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 = 9 24 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.496 | 5.496 | 5.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -6000.4068 0 -6000.4068 2835.9172 15521.783 64 0 -6000.5709 0 -6000.5709 99.651175 15543.518 Loop time of 0.093896 on 1 procs for 5 steps with 1368 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 = -6000.40676438493 -6000.57075919166 -6000.57092890734 Force two-norm initial, final = 79.670870 0.52105772 Force max component initial, final = 78.315178 0.093558794 Final line search alpha, max atom move = 0.00030369020 2.8412889e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091344 | 0.091344 | 0.091344 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047315 | 0.00047315 | 0.00047315 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002079 | | | 2.21 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8056.00 ave 8056 max 8056 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: 238784.0 ave 238784 max 238784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238784 Ave neighs/atom = 174.54971 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 = 9 24 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) = 5.634 | 5.634 | 5.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6000.5709 0 -6000.5709 99.651175 Loop time of 1.72e-06 on 1 procs for 0 steps with 1368 atoms 116.3% 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 | | 1.72e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8056.00 ave 8056 max 8056 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: 238556.0 ave 238556 max 238556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238556 Ave neighs/atom = 174.38304 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 = 9 24 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) = 5.634 | 5.634 | 5.634 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 -6000.5709 -6000.5709 33.138313 93.385048 5.0227503 99.651175 99.651175 -9.0152593 317.58983 -9.6210445 2.3986708 976.12061 Loop time of 1.922e-06 on 1 procs for 0 steps with 1368 atoms 208.1% 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 | | 1.922e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8056.00 ave 8056 max 8056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119278.0 ave 119278 max 119278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238556.0 ave 238556 max 238556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238556 Ave neighs/atom = 174.38304 Neighbor list builds = 0 Dangerous builds = 0 1368 -6000.57092890734 eV 2.39867079221092 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01