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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -58.149882 0.0000000) to (29.074941 58.149882 3.6063026) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0257611 4.0257611 3.6063026 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.149882 0.0000000) to (29.074941 58.149882 3.6063026) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0257611 4.0257611 3.6063026 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.149882 0.0000000) to (29.074941 58.149882 3.6063026) create_atoms CPU = 0.001 seconds 522 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 20 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, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 10.97 | 10.97 | 10.97 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3956.6053 0 -3956.6053 47500.146 68 0 -4336.1322 0 -4336.1322 -1097.2116 Loop time of 5.81059 on 1 procs for 68 steps with 1036 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3956.60529107066 -4336.12883428478 -4336.1322201136 Force two-norm initial, final = 651.23099 0.21989128 Force max component initial, final = 215.50392 0.019248020 Final line search alpha, max atom move = 1.0000000 0.019248020 Iterations, force evaluations = 68 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7042 | 5.7042 | 5.7042 | 0.0 | 98.17 Neigh | 0.06162 | 0.06162 | 0.06162 | 0.0 | 1.06 Comm | 0.030077 | 0.030077 | 0.030077 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01467 | | | 0.25 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16049.0 ave 16049 max 16049 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: 638136.0 ave 638136 max 638136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 638136 Ave neighs/atom = 615.96139 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.97 | 10.97 | 10.97 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4336.1322 0 -4336.1322 -1097.2116 12194.383 74 0 -4336.2167 0 -4336.2167 10.728278 12186.346 Loop time of 0.296664 on 1 procs for 6 steps with 1036 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 = -4336.13222011355 -4336.21664913613 -4336.21672545537 Force two-norm initial, final = 32.402159 0.58413649 Force max component initial, final = 26.417788 0.41374946 Final line search alpha, max atom move = 0.00064458258 0.00026669569 Iterations, force evaluations = 6 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29078 | 0.29078 | 0.29078 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012416 | 0.0012416 | 0.0012416 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004644 | | | 1.57 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16033.0 ave 16033 max 16033 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: 639944.0 ave 639944 max 639944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 639944 Ave neighs/atom = 617.70656 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 10.48 | 10.48 | 10.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4336.2167 0 -4336.2167 10.728278 Loop time of 2.367e-06 on 1 procs for 0 steps with 1036 atoms 211.2% 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 | | 2.367e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16049.0 ave 16049 max 16049 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: 636584.0 ave 636584 max 636584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 636584 Ave neighs/atom = 614.46332 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 10.48 | 10.48 | 10.48 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 -4336.2167 -4336.2167 29.039948 115.87732 3.6214229 10.728278 10.728278 -5.7040977 54.199325 -16.310393 2.3017501 217.07021 Loop time of 5.293e-06 on 1 procs for 0 steps with 1036 atoms 226.7% 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 | | 5.293e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16049.0 ave 16049 max 16049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 318292.0 ave 318292 max 318292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 636584.0 ave 636584 max 636584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 636584 Ave neighs/atom = 614.46332 Neighbor list builds = 0 Dangerous builds = 0 1036 -4336.21672545537 eV 2.30175009251543 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06