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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -66.225287 0.0000000) to (46.828349 66.225287 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9893059 6.4248412 5.7209934 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -66.225287 0.0000000) to (46.828349 66.225287 5.7209934) create_atoms CPU = 0.003 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9893059 6.4248412 5.7209934 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -66.225287 0.0000000) to (46.828349 66.225287 5.7209934) create_atoms CPU = 0.003 seconds 1079 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2144 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6879.5931 0 -6879.5931 18142.63 68 0 -7189.2126 0 -7189.2126 2326.1161 Loop time of 8.33944 on 1 procs for 68 steps with 2144 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6879.59306111342 -7189.20725883002 -7189.21259550212 Force two-norm initial, final = 327.56606 0.16957295 Force max component initial, final = 46.546832 0.011651102 Final line search alpha, max atom move = 1.0000000 0.011651102 Iterations, force evaluations = 68 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3015 | 8.3015 | 8.3015 | 0.0 | 99.54 Neigh | 0.0098244 | 0.0098244 | 0.0098244 | 0.0 | 0.12 Comm | 0.013037 | 0.013037 | 0.013037 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01513 | | | 0.18 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7514.00 ave 7514 max 7514 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: 116724.0 ave 116724 max 116724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116724 Ave neighs/atom = 54.442164 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -7189.2126 0 -7189.2126 2326.1161 35484.128 73 0 -7189.4101 0 -7189.4101 -154.54095 35602.939 Loop time of 0.483011 on 1 procs for 5 steps with 2144 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 = -7189.21259550211 -7189.40798950995 -7189.41011215096 Force two-norm initial, final = 104.28855 7.2717983 Force max component initial, final = 95.371195 5.5927296 Final line search alpha, max atom move = 9.9544211e-05 0.00055672385 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47967 | 0.47967 | 0.47967 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045569 | 0.00045569 | 0.00045569 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002881 | | | 0.60 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7485.00 ave 7485 max 7485 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: 116146.0 ave 116146 max 116146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116146 Ave neighs/atom = 54.172575 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7189.4101 0 -7189.4101 -154.54095 Loop time of 2.428e-06 on 1 procs for 0 steps with 2144 atoms 205.9% 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 | | 2.428e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7491.00 ave 7491 max 7491 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: 116064.0 ave 116064 max 116064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116064 Ave neighs/atom = 54.134328 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.346 | 5.346 | 5.346 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 -7189.4101 -7189.4101 46.818691 133.03563 5.7160841 -154.54095 -154.54095 -208.8872 -3.2718282 -251.46381 2.6391169 935.20199 Loop time of 2.996e-06 on 1 procs for 0 steps with 2144 atoms 267.0% 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 | | 2.996e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7491.00 ave 7491 max 7491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58032.0 ave 58032 max 58032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116064.0 ave 116064 max 116064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116064 Ave neighs/atom = 54.134328 Neighbor list builds = 0 Dangerous builds = 0 2144 -7189.41011215096 eV 2.63911689955924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09