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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -51.075834 0.0000000) to (18.058034 51.075834 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9249184 5.4171339 4.4455807 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -51.075834 0.0000000) to (18.058034 51.075834 4.4455807) create_atoms CPU = 0.001 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9249184 5.4171339 4.4455807 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.075834 0.0000000) to (18.058034 51.075834 4.4455807) create_atoms CPU = 0.001 seconds 265 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 21 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 527 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2980.2059 0 -2980.2059 147459.24 372 0 -3522.8127 0 -3522.8127 5479.7115 Loop time of 4.45302 on 1 procs for 372 steps with 527 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 = -2980.20594202869 -3522.80969975928 -3522.8127387036 Force two-norm initial, final = 1124.8173 0.30470117 Force max component initial, final = 366.69753 0.072296206 Final line search alpha, max atom move = 0.71827090 0.051928261 Iterations, force evaluations = 372 689 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2792 | 4.2792 | 4.2792 | 0.0 | 96.10 Neigh | 0.10954 | 0.10954 | 0.10954 | 0.0 | 2.46 Comm | 0.041581 | 0.041581 | 0.041581 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0227 | | | 0.51 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6780.00 ave 6780 max 6780 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: 142616.0 ave 142616 max 142616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142616 Ave neighs/atom = 270.61860 Neighbor list builds = 13 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 372 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press Volume 372 0 -3522.8127 0 -3522.8127 5479.7115 8200.5775 412 0 -3539.264 0 -3539.264 -905.97133 8199.4355 Loop time of 0.276053 on 1 procs for 40 steps with 527 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 = -3522.81273870358 -3539.26126341268 -3539.26398120448 Force two-norm initial, final = 730.39496 10.922523 Force max component initial, final = 557.97226 5.9712552 Final line search alpha, max atom move = 0.00018279404 0.0010915099 Iterations, force evaluations = 40 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25672 | 0.25672 | 0.25672 | 0.0 | 93.00 Neigh | 0.007777 | 0.007777 | 0.007777 | 0.0 | 2.82 Comm | 0.0023587 | 0.0023587 | 0.0023587 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009196 | | | 3.33 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6843.00 ave 6843 max 6843 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: 143564.0 ave 143564 max 143564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143564 Ave neighs/atom = 272.41746 Neighbor list builds = 1 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3539.264 0 -3539.264 -905.97133 Loop time of 1.555e-06 on 1 procs for 0 steps with 527 atoms 192.9% 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 | | 1.555e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 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: 143876.0 ave 143876 max 143876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143876 Ave neighs/atom = 273.00949 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.081 | 5.081 | 5.081 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 -3539.264 -3539.264 17.436186 103.4908 4.5439202 -905.97133 -905.97133 -488.508 -1182.084 -1047.322 2.602635 2379.3105 Loop time of 2.002e-06 on 1 procs for 0 steps with 527 atoms 199.8% 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 | | 2.002e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71938.0 ave 71938 max 71938 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143876.0 ave 143876 max 143876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143876 Ave neighs/atom = 273.00949 Neighbor list builds = 0 Dangerous builds = 0 527 -3539.2639812045 eV 2.60263496999533 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04