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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -44.336706 0.0000000) to (9.0493661 44.336706 9.9130839) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4296197 5.9110212 6.6087226 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.336706 0.0000000) to (9.0493661 44.336706 9.9130839) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4296197 5.9110212 6.6087226 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.336706 0.0000000) to (9.0493661 44.336706 9.9130839) create_atoms CPU = 0.000 seconds 242 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 3 25 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, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 474 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1573.7296 0 -1573.7296 3639.3292 70 0 -1587.2993 0 -1587.2993 -5334.1259 Loop time of 2.628 on 1 procs for 70 steps with 474 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 = -1573.72960481339 -1587.2979620207 -1587.29930419535 Force two-norm initial, final = 20.027087 0.11110994 Force max component initial, final = 6.7049808 0.027585272 Final line search alpha, max atom move = 1.0000000 0.027585272 Iterations, force evaluations = 70 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6187 | 2.6187 | 2.6187 | 0.0 | 99.65 Neigh | 0.0031987 | 0.0031987 | 0.0031987 | 0.0 | 0.12 Comm | 0.0031618 | 0.0031618 | 0.0031618 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002911 | | | 0.11 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2977.00 ave 2977 max 2977 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: 40324.0 ave 40324 max 40324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40324 Ave neighs/atom = 85.071730 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -1587.2993 0 -1587.2993 -5334.1259 7954.6369 75 0 -1587.3755 0 -1587.3755 -901.52883 7908.8381 Loop time of 0.15962 on 1 procs for 5 steps with 474 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 = -1587.29930419535 -1587.37479845355 -1587.37546110928 Force two-norm initial, final = 35.412312 0.15011305 Force max component initial, final = 28.206550 0.037829345 Final line search alpha, max atom move = 0.00051337718 1.9420722e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15866 | 0.15866 | 0.15866 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018166 | 0.00018166 | 0.00018166 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007784 | | | 0.49 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2980.00 ave 2980 max 2980 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: 40408.0 ave 40408 max 40408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40408 Ave neighs/atom = 85.248945 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1587.3755 0 -1587.3755 -901.52883 Loop time of 3.032e-06 on 1 procs for 0 steps with 474 atoms 164.9% 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 | | 3.032e-06 | | |100.00 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3009.00 ave 3009 max 3009 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: 40448.0 ave 40448 max 40448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40448 Ave neighs/atom = 85.333333 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.615 | 4.615 | 4.615 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 -1587.3755 -1587.3755 9.0346065 88.673412 9.8721109 -901.52883 -901.52883 -2.8550878 -2703.2902 1.5587659 2.4602648 418.17574 Loop time of 1.541e-06 on 1 procs for 0 steps with 474 atoms 194.7% 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 | | 1.541e-06 | | |100.00 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3009.00 ave 3009 max 3009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20224.0 ave 20224 max 20224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40448.0 ave 40448 max 40448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40448 Ave neighs/atom = 85.333333 Neighbor list builds = 0 Dangerous builds = 0 474 -1587.37546110928 eV 2.46026476592974 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03