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 = 3.5927866 3.5927866 3.5927866 Created orthogonal box = (0.0000000 -68.734054 0.0000000) to (39.683625 68.734054 6.2228888) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8549610 5.2583429 6.2228888 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -68.734054 0.0000000) to (39.683625 68.734054 6.2228888) create_atoms CPU = 0.008 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8549610 5.2583429 6.2228888 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -68.734054 0.0000000) to (39.683625 68.734054 6.2228888) create_atoms CPU = 0.007 seconds 1465 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 12 40 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 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_396616545191_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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.207 | 6.207 | 6.207 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9789.2001 0 -9789.2001 34161.518 170 0 -10238.157 0 -10238.157 3405.1591 Loop time of 23.7495 on 1 procs for 170 steps with 2924 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 = -9789.20009740926 -10238.1471238518 -10238.1572069883 Force two-norm initial, final = 624.72447 0.34877691 Force max component initial, final = 275.31169 0.091344534 Final line search alpha, max atom move = 0.74631994 0.068172247 Iterations, force evaluations = 170 313 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.195 | 23.195 | 23.195 | 0.0 | 97.66 Neigh | 0.36605 | 0.36605 | 0.36605 | 0.0 | 1.54 Comm | 0.093762 | 0.093762 | 0.093762 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09512 | | | 0.40 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11563.0 ave 11563 max 11563 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: 388602.0 ave 388602 max 388602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388602 Ave neighs/atom = 132.90082 Neighbor list builds = 7 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 170 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.207 | 6.207 | 6.207 Mbytes Step Temp E_pair E_mol TotEng Press Volume 170 0 -10238.157 0 -10238.157 3405.1591 33947.307 172 0 -10238.261 0 -10238.261 -288.01405 34040.684 Loop time of 0.292961 on 1 procs for 2 steps with 2924 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 = -10238.1572069883 -10238.2547462429 -10238.2607785666 Force two-norm initial, final = 128.39903 12.929170 Force max component initial, final = 96.144832 10.573566 Final line search alpha, max atom move = 4.1585314e-05 0.00043970505 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28838 | 0.28838 | 0.28838 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010488 | 0.0010488 | 0.0010488 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003532 | | | 1.21 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11566.0 ave 11566 max 11566 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: 388606.0 ave 388606 max 388606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388606 Ave neighs/atom = 132.90219 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.345 | 6.345 | 6.345 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10238.261 0 -10238.261 -288.01405 Loop time of 6.565e-06 on 1 procs for 0 steps with 2924 atoms 198.0% 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 | | 6.565e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11563.0 ave 11563 max 11563 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: 388452.0 ave 388452 max 388452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388452 Ave neighs/atom = 132.84952 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.345 | 6.345 | 6.345 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 -10238.261 -10238.261 39.706181 137.67414 6.2271277 -288.01405 -288.01405 -497.94381 -16.431584 -349.66675 2.318956 980.70159 Loop time of 7.066e-06 on 1 procs for 0 steps with 2924 atoms 297.2% 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 | | 7.066e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11563.0 ave 11563 max 11563 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194226.0 ave 194226 max 194226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 388452.0 ave 388452 max 388452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388452 Ave neighs/atom = 132.84952 Neighbor list builds = 0 Dangerous builds = 0 2924 -10238.2607785666 eV 2.31895596905662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:25