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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -35.656414 0.0000000) to (16.808595 35.656414 4.0766831) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9437044 4.8940177 4.0766831 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.656414 0.0000000) to (16.808595 35.656414 4.0766831) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9437044 4.8940177 4.0766831 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.656414 0.0000000) to (16.808595 35.656414 4.0766831) create_atoms CPU = 0.002 seconds 206 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 17 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 406 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.888 | 4.888 | 4.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1425.1189 0 -1425.1189 57762.665 119 0 -1565.6557 0 -1565.6557 240.01644 Loop time of 2.50163 on 1 procs for 119 steps with 406 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 = -1425.11885291712 -1565.65417122484 -1565.65565547079 Force two-norm initial, final = 264.12844 0.17374791 Force max component initial, final = 79.358905 0.029144373 Final line search alpha, max atom move = 1.0000000 0.029144373 Iterations, force evaluations = 119 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4193 | 2.4193 | 2.4193 | 0.0 | 96.71 Neigh | 0.039412 | 0.039412 | 0.039412 | 0.0 | 1.58 Comm | 0.026187 | 0.026187 | 0.026187 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01678 | | | 0.67 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5244.00 ave 5244 max 5244 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: 97916.0 ave 97916 max 97916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97916 Ave neighs/atom = 241.17241 Neighbor list builds = 3 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -1565.6557 0 -1565.6557 240.01644 4886.5914 125 0 -1565.8013 0 -1565.8013 -11.303157 4887.1837 Loop time of 0.105117 on 1 procs for 6 steps with 406 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 = -1565.65565547078 -1565.80122598663 -1565.80125270257 Force two-norm initial, final = 47.565771 0.52394364 Force max component initial, final = 34.403969 0.32397770 Final line search alpha, max atom move = 0.0035353393 0.0011453711 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10129 | 0.10129 | 0.10129 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093164 | 0.00093164 | 0.00093164 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002892 | | | 2.75 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 98048.0 ave 98048 max 98048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98048 Ave neighs/atom = 241.49754 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.644 | 4.644 | 4.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1565.8013 0 -1565.8013 -11.303157 Loop time of 3.1513e-05 on 1 procs for 0 steps with 406 atoms 34.9% 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 | | 3.151e-05 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 96488.0 ave 96488 max 96488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96488 Ave neighs/atom = 237.65517 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.644 | 4.644 | 4.644 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 -1565.8013 -1565.8013 16.872607 71.3895 4.0573467 -11.303157 -11.303157 65.189816 -106.32453 7.2252464 2.3269077 313.90814 Loop time of 6.745e-06 on 1 procs for 0 steps with 406 atoms 266.9% 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 | | 6.745e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48244.0 ave 48244 max 48244 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96488.0 ave 96488 max 96488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96488 Ave neighs/atom = 237.65517 Neighbor list builds = 0 Dangerous builds = 0 406 -1565.80125270257 eV 2.32690765593322 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02