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 -33.774860 0.0000000) to (6.8936352 33.774860 7.5515990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1361811 4.5029036 5.0343993 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -33.774860 0.0000000) to (6.8936352 33.774860 7.5515990) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1361811 4.5029036 5.0343993 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -33.774860 0.0000000) to (6.8936352 33.774860 7.5515990) create_atoms CPU = 0.000 seconds 122 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 = 3 21 3 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 4 atoms, new total = 240 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 = 3 21 3 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) = 4.811 | 4.811 | 4.811 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1455.5372 0 -1455.5372 113140.1 54 0 -1556.8 0 -1556.8 7579.9123 Loop time of 5.97756 on 1 procs for 54 steps with 240 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 = -1455.53716800761 -1556.79861034686 -1556.80004592878 Force two-norm initial, final = 205.54512 0.16699704 Force max component initial, final = 50.284744 0.033320626 Final line search alpha, max atom move = 1.0000000 0.033320626 Iterations, force evaluations = 54 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9656 | 5.9656 | 5.9656 | 0.0 | 99.80 Neigh | 0.0090206 | 0.0090206 | 0.0090206 | 0.0 | 0.15 Comm | 0.0015802 | 0.0015802 | 0.0015802 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001345 | | | 0.02 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2117.00 ave 2117 max 2117 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: 18268.0 ave 18268 max 18268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18268 Ave neighs/atom = 76.116667 Neighbor list builds = 1 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 = 3 21 3 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.812 | 4.812 | 4.812 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1556.8 0 -1556.8 7579.9123 3516.5012 62 0 -1556.9825 0 -1556.9825 10830.934 3510.2719 Loop time of 0.661719 on 1 procs for 8 steps with 240 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 = -1556.80004592878 -1556.98222566682 -1556.98249412745 Force two-norm initial, final = 43.574470 2.3176948 Force max component initial, final = 37.140677 1.6772820 Final line search alpha, max atom move = 0.013701561 0.022981382 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66081 | 0.66081 | 0.66081 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016353 | 0.00016353 | 0.00016353 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007405 | | | 0.11 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2147.00 ave 2147 max 2147 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: 17980.0 ave 17980 max 17980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17980 Ave neighs/atom = 74.916667 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 = 3 21 3 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) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1556.9825 0 -1556.9825 10830.934 Loop time of 1.458e-06 on 1 procs for 0 steps with 240 atoms 137.2% 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 | | 1.458e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2141.00 ave 2141 max 2141 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: 18508.0 ave 18508 max 18508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18508 Ave neighs/atom = 77.116667 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 = 3 21 3 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) = 4.950 | 4.950 | 4.950 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 -1556.9825 -1556.9825 6.9282082 67.549721 7.5006047 10830.934 10830.934 703.70437 31028.713 760.38411 2.4910713 554.9612 Loop time of 1.447e-06 on 1 procs for 0 steps with 240 atoms 138.2% 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 | | 1.447e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2141.00 ave 2141 max 2141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9254.00 ave 9254 max 9254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 18508.0 ave 18508 max 18508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18508 Ave neighs/atom = 77.116667 Neighbor list builds = 0 Dangerous builds = 0 240 -1556.98249412745 eV 2.49107133331794 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07