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 -55.834189 0.0000000) to (19.740367 55.834189 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2961960 4.7663332 4.3599177 Created 327 atoms using lattice units in orthogonal box = (0.0000000 -55.834189 0.0000000) to (19.740367 55.834189 4.3599177) create_atoms CPU = 0.001 seconds 327 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2961960 4.7663332 4.3599177 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -55.834189 0.0000000) to (19.740367 55.834189 4.3599177) create_atoms CPU = 0.001 seconds 329 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 = 6 34 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 656 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 = 6 34 2 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) = 5.283 | 5.283 | 5.283 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3460.2474 0 -3460.2474 214451.9 168 0 -4258.1545 0 -4258.1545 3728.0868 Loop time of 63.094 on 1 procs for 168 steps with 656 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 = -3460.24741045031 -4258.15089478359 -4258.15452043456 Force two-norm initial, final = 2418.1086 0.27280943 Force max component initial, final = 914.11673 0.078936667 Final line search alpha, max atom move = 0.95892817 0.075694594 Iterations, force evaluations = 168 320 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.988 | 62.988 | 62.988 | 0.0 | 99.83 Neigh | 0.079945 | 0.079945 | 0.079945 | 0.0 | 0.13 Comm | 0.014112 | 0.014112 | 0.014112 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01198 | | | 0.02 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4264.00 ave 4264 max 4264 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: 48678.0 ave 48678 max 48678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48678 Ave neighs/atom = 74.204268 Neighbor list builds = 3 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 = 6 34 2 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 : 168 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.283 | 5.283 | 5.283 Mbytes Step Temp E_pair E_mol TotEng Press Volume 168 0 -4258.1545 0 -4258.1545 3728.0868 9610.8927 174 0 -4258.5489 0 -4258.5489 8.2526549 9626.6721 Loop time of 1.57173 on 1 procs for 6 steps with 656 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 = -4258.15452043456 -4258.54733197606 -4258.54886752093 Force two-norm initial, final = 124.60662 1.7152406 Force max component initial, final = 110.49821 1.0616383 Final line search alpha, max atom move = 0.00018512070 0.00019653123 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.57 | 1.57 | 1.57 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029133 | 0.00029133 | 0.00029133 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001461 | | | 0.09 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4240.00 ave 4240 max 4240 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: 48120.0 ave 48120 max 48120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48120 Ave neighs/atom = 73.353659 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 = 6 34 2 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) = 5.420 | 5.420 | 5.420 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4258.5489 0 -4258.5489 8.2526549 Loop time of 2.11e-06 on 1 procs for 0 steps with 656 atoms 142.2% 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 | | 2.11e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4240.00 ave 4240 max 4240 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: 48306.0 ave 48306 max 48306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48306 Ave neighs/atom = 73.637195 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 = 6 34 2 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) = 5.420 | 5.420 | 5.420 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 -4258.5489 -4258.5489 19.841372 111.73414 4.3422877 8.2526549 8.2526549 -177.21861 176.79356 25.183013 2.4944805 1274.6741 Loop time of 1.982e-06 on 1 procs for 0 steps with 656 atoms 151.4% 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 | | 1.982e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4240.00 ave 4240 max 4240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24153.0 ave 24153 max 24153 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48306.0 ave 48306 max 48306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48306 Ave neighs/atom = 73.637195 Neighbor list builds = 0 Dangerous builds = 0 656 -4258.54886752093 eV 2.49448050349503 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:05