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 = 3.5196184 3.5196184 3.5196184 Created orthogonal box = (0.0000000 -37.579241 0.0000000) to (26.572536 37.579241 4.9774920) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1280333 5.9335643 4.9774920 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.579241 0.0000000) to (26.572536 37.579241 4.9774920) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1280333 5.9335643 4.9774920 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.579241 0.0000000) to (26.572536 37.579241 4.9774920) create_atoms CPU = 0.001 seconds 458 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 8 20 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 7.565005302429199 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_110256178378_005#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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3794.9342 0 -3794.9342 56734.474 81 0 -4021.396 0 -4021.396 5337.8222 Loop time of 1.21743 on 1 procs for 81 steps with 908 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3794.93424530081 -4021.39228830834 -4021.39604733245 Force two-norm initial, final = 446.42942 0.23879800 Force max component initial, final = 136.10806 0.057255076 Final line search alpha, max atom move = 1.0000000 0.057255076 Iterations, force evaluations = 81 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1819 | 1.1819 | 1.1819 | 0.0 | 97.08 Neigh | 0.018561 | 0.018561 | 0.018561 | 0.0 | 1.52 Comm | 0.0094073 | 0.0094073 | 0.0094073 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00754 | | | 0.62 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5992.00 ave 5992 max 5992 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: 156856.0 ave 156856 max 156856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156856 Ave neighs/atom = 172.74890 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4021.396 0 -4021.396 5337.8222 9940.8055 85 0 -4021.4737 0 -4021.4737 31.704954 9971.3488 Loop time of 0.0508762 on 1 procs for 4 steps with 908 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 = -4021.39604733244 -4021.47349005449 -4021.47365095919 Force two-norm initial, final = 64.843619 0.45353199 Force max component initial, final = 57.332243 0.22373472 Final line search alpha, max atom move = 0.00082859420 0.00018538529 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049103 | 0.049103 | 0.049103 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034909 | 0.00034909 | 0.00034909 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001424 | | | 2.80 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 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: 157008.0 ave 157008 max 157008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157008 Ave neighs/atom = 172.91630 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4021.4737 0 -4021.4737 31.704954 Loop time of 1.961e-06 on 1 procs for 0 steps with 908 atoms 204.0% 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 | | 1.961e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 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: 156888.0 ave 156888 max 156888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156888 Ave neighs/atom = 172.78414 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 5.132 | 5.132 | 5.132 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 -4021.4737 -4021.4737 26.579765 75.366682 4.9776387 31.704954 31.704954 35.95903 29.190087 29.965746 2.2783826 624.99524 Loop time of 2.273e-06 on 1 procs for 0 steps with 908 atoms 220.0% 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 | | 2.273e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78444.0 ave 78444 max 78444 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156888.0 ave 156888 max 156888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156888 Ave neighs/atom = 172.78414 Neighbor list builds = 0 Dangerous builds = 0 908 -4021.47386744326 eV 2.27838261316985 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01