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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -31.439814 0.0000000) to (15.719907 31.439814 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6276708 3.6276708 3.0829274 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -31.439814 0.0000000) to (15.719907 31.439814 3.0829274) create_atoms CPU = 0.001 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6276708 3.6276708 3.0829274 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -31.439814 0.0000000) to (15.719907 31.439814 3.0829274) create_atoms CPU = 0.000 seconds 106 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 19 1 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 208 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.782 | 4.782 | 4.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1294.9917 0 -1294.9917 73043.796 47 0 -1349.1389 0 -1349.1389 9197.0755 Loop time of 4.64559 on 1 procs for 47 steps with 208 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 = -1294.99171571508 -1349.13798193477 -1349.13893878797 Force two-norm initial, final = 121.78168 0.14318063 Force max component initial, final = 43.373830 0.029709321 Final line search alpha, max atom move = 1.0000000 0.029709321 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6423 | 4.6423 | 4.6423 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001369 | | | 0.03 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2366.00 ave 2366 max 2366 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: 13752.0 ave 13752 max 13752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13752 Ave neighs/atom = 66.115385 Neighbor list builds = 0 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1349.1389 0 -1349.1389 9197.0755 3047.3562 75 0 -1349.5063 0 -1349.5063 -208.88512 3055.2159 Loop time of 1.6496 on 1 procs for 28 steps with 208 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 = -1349.13893878797 -1349.50598278637 -1349.50634030531 Force two-norm initial, final = 40.902478 1.3945001 Force max component initial, final = 36.136584 0.77981216 Final line search alpha, max atom move = 0.00049748559 0.00038794532 Iterations, force evaluations = 28 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6468 | 1.6468 | 1.6468 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052241 | 0.00052241 | 0.00052241 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00225 | | | 0.14 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2344.00 ave 2344 max 2344 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: 15612.0 ave 15612 max 15612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15612 Ave neighs/atom = 75.057692 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1349.5063 0 -1349.5063 -208.88512 Loop time of 1.733e-06 on 1 procs for 0 steps with 208 atoms 115.4% 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 | | 1.733e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2328.00 ave 2328 max 2328 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: 16660.0 ave 16660 max 16660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16660 Ave neighs/atom = 80.096154 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.920 | 4.920 | 4.920 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 -1349.5063 -1349.5063 15.888013 63.739053 3.0169404 -208.88512 -208.88512 -413.31204 -348.49333 135.15003 2.5926479 416.67878 Loop time of 2.872e-06 on 1 procs for 0 steps with 208 atoms 174.1% 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 | | 2.872e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2328.00 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8330.00 ave 8330 max 8330 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16660.0 ave 16660 max 16660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16660 Ave neighs/atom = 80.096154 Neighbor list builds = 0 Dangerous builds = 0 208 -1349.50634030531 eV 2.59264792413354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06