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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -37.404769 0.0000000) to (17.631429 37.404769 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7118798 4.5932169 4.0449272 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.404769 0.0000000) to (17.631429 37.404769 4.0449272) create_atoms CPU = 0.001 seconds 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7118798 4.5932169 4.0449272 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.404769 0.0000000) to (17.631429 37.404769 4.0449272) create_atoms CPU = 0.001 seconds 229 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 3 atoms, new total = 455 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.828 | 4.828 | 4.828 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1896.3036 0 -1896.3036 21804.563 38 0 -1934.3614 0 -1934.3614 2213.8626 Loop time of 1.99704 on 1 procs for 38 steps with 455 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 = -1896.30364616635 -1934.36001759172 -1934.3614010933 Force two-norm initial, final = 72.834408 0.14254433 Force max component initial, final = 19.757030 0.034009080 Final line search alpha, max atom move = 1.0000000 0.034009080 Iterations, force evaluations = 38 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.994 | 1.994 | 1.994 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015401 | 0.0015401 | 0.0015401 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001551 | | | 0.08 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2473.00 ave 2473 max 2473 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: 26288.0 ave 26288 max 26288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26288 Ave neighs/atom = 57.775824 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.828 | 4.828 | 4.828 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -1934.3614 0 -1934.3614 2213.8626 5335.2551 39 0 -1934.363 0 -1934.363 2772.8285 5333.5733 Loop time of 0.0825434 on 1 procs for 1 steps with 455 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 = -1934.3614010933 -1934.3614010933 -1934.36303345329 Force two-norm initial, final = 4.6737059 2.5006918 Force max component initial, final = 4.1851318 2.2358206 Final line search alpha, max atom move = 0.00023894110 0.00053422944 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082279 | 0.082279 | 0.082279 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.5861e-05 | 5.5861e-05 | 5.5861e-05 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002082 | | | 0.25 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2473.00 ave 2473 max 2473 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: 26230.0 ave 26230 max 26230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26230 Ave neighs/atom = 57.648352 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1934.363 0 -1934.363 2772.8285 Loop time of 1.846e-06 on 1 procs for 0 steps with 455 atoms 162.5% 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 | | 1.846e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2473.00 ave 2473 max 2473 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: 26230.0 ave 26230 max 26230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26230 Ave neighs/atom = 57.648352 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.966 | 4.966 | 4.966 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 -1934.363 -1934.363 17.636894 74.809538 4.0423992 2772.8285 2772.8285 671.83655 7313.1983 333.45054 2.2100794 306.32728 Loop time of 1.527e-06 on 1 procs for 0 steps with 455 atoms 196.5% 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 | | 1.527e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2473.00 ave 2473 max 2473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13115.0 ave 13115 max 13115 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26230.0 ave 26230 max 26230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26230 Ave neighs/atom = 57.648352 Neighbor list builds = 0 Dangerous builds = 0 455 -1934.36303345329 eV 2.21007942890224 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02