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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -58.972946 0.0000000) to (29.484448 58.972946 4.0500004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0067931 5.0067931 4.0500004 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.972946 0.0000000) to (29.484448 58.972946 4.0500004) create_atoms CPU = 0.001 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0067931 5.0067931 4.0500004 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.972946 0.0000000) to (29.484448 58.972946 4.0500004) create_atoms CPU = 0.000 seconds 426 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 = 8 31 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 14 atoms, new total = 838 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_820335782779_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 = 8 31 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2790.4055 0 -2790.4055 3848.0812 85 0 -2807.5513 0 -2807.5513 -3142.923 Loop time of 0.861368 on 1 procs for 85 steps with 838 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 = -2790.40553109291 -2807.54851351995 -2807.55127579773 Force two-norm initial, final = 17.866915 0.16856032 Force max component initial, final = 5.6535323 0.043381047 Final line search alpha, max atom move = 1.0000000 0.043381047 Iterations, force evaluations = 85 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83665 | 0.83665 | 0.83665 | 0.0 | 97.13 Neigh | 0.011466 | 0.011466 | 0.011466 | 0.0 | 1.33 Comm | 0.007657 | 0.007657 | 0.007657 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005594 | | | 0.65 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6417.00 ave 6417 max 6417 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: 110356.0 ave 110356 max 110356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110356 Ave neighs/atom = 131.68974 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 31 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -2807.5513 0 -2807.5513 -3142.923 14084.158 88 0 -2807.5979 0 -2807.5979 -425.46243 14036.762 Loop time of 0.0335678 on 1 procs for 3 steps with 838 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 = -2807.55127579772 -2807.59715256526 -2807.59789038108 Force two-norm initial, final = 37.903198 0.17388595 Force max component initial, final = 29.238620 0.034609825 Final line search alpha, max atom move = 0.00049363575 1.7084647e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0322 | 0.0322 | 0.0322 | 0.0 | 95.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027815 | 0.00027815 | 0.00027815 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00109 | | | 3.25 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6417.00 ave 6417 max 6417 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: 110316.0 ave 110316 max 110316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110316 Ave neighs/atom = 131.64200 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 = 8 31 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2807.5979 0 -2807.5979 -425.46243 Loop time of 1.744e-06 on 1 procs for 0 steps with 838 atoms 114.7% 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 | | 1.744e-06 | | |100.00 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6422.00 ave 6422 max 6422 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: 110340.0 ave 110340 max 110340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110340 Ave neighs/atom = 131.67064 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 = 8 31 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) = 5.097 | 5.097 | 5.097 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 -2807.5979 -2807.5979 29.453354 117.94589 4.0406325 -425.46243 -425.46243 -1.0062661 -1276.3369 0.95590482 2.6208283 574.4518 Loop time of 1.799e-06 on 1 procs for 0 steps with 838 atoms 166.8% 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 | | 1.799e-06 | | |100.00 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6422.00 ave 6422 max 6422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55170.0 ave 55170 max 55170 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110340.0 ave 110340 max 110340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110340 Ave neighs/atom = 131.67064 Neighbor list builds = 0 Dangerous builds = 0 838 -2807.59789038108 eV 2.62082831722688 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01