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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -70.575788 0.0000000) to (40.746950 70.575788 6.0968195) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734709 5.6179732 6.0968195 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.575788 0.0000000) to (40.746950 70.575788 6.0968195) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734709 5.6179732 6.0968195 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.575788 0.0000000) to (40.746950 70.575788 6.0968195) create_atoms CPU = 0.003 seconds 1610 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 37 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, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.055 | 7.055 | 7.055 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14088.292 0 -14088.292 13254.408 140 0 -14283.876 0 -14283.876 10184.144 Loop time of 7.96418 on 1 procs for 140 steps with 3218 atoms 89.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14088.2923392114 -14283.8640012038 -14283.8756014119 Force two-norm initial, final = 90.232787 0.38960705 Force max component initial, final = 11.066273 0.057302776 Final line search alpha, max atom move = 0.62653591 0.035902247 Iterations, force evaluations = 140 247 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6561 | 7.6561 | 7.6561 | 0.0 | 96.13 Neigh | 0.20852 | 0.20852 | 0.20852 | 0.0 | 2.62 Comm | 0.042613 | 0.042613 | 0.042613 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05695 | | | 0.72 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13113.0 ave 13113 max 13113 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: 562808.0 ave 562808 max 562808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562808 Ave neighs/atom = 174.89372 Neighbor list builds = 5 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.80 | 10.80 | 10.80 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -14283.876 0 -14283.876 10184.144 35065.834 147 0 -14285.094 0 -14285.094 -49.903026 35265.992 Loop time of 0.292806 on 1 procs for 7 steps with 3218 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 = -14283.8756014119 -14285.0931177689 -14285.0936921486 Force two-norm initial, final = 454.36381 3.3990657 Force max component initial, final = 411.23185 3.0457951 Final line search alpha, max atom move = 0.00013364112 0.00040704347 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28519 | 0.28519 | 0.28519 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010958 | 0.0010958 | 0.0010958 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006524 | | | 2.23 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13120.0 ave 13120 max 13120 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: 562968.0 ave 562968 max 562968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562968 Ave neighs/atom = 174.94344 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 10.32 | 10.32 | 10.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14285.094 0 -14285.094 -49.903026 Loop time of 2.194e-06 on 1 procs for 0 steps with 3218 atoms 136.7% 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 | | 2.194e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13111.0 ave 13111 max 13111 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: 562624.0 ave 562624 max 562624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562624 Ave neighs/atom = 174.83654 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 10.32 | 10.32 | 10.32 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 -14285.094 -14285.094 40.766986 141.99017 6.0924112 -49.903026 -49.903026 -138.44218 -50.371929 39.105029 2.2261709 1048.1945 Loop time of 2.577e-06 on 1 procs for 0 steps with 3218 atoms 232.8% 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 | | 2.577e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13111.0 ave 13111 max 13111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 281312.0 ave 281312 max 281312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 562624.0 ave 562624 max 562624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562624 Ave neighs/atom = 174.83654 Neighbor list builds = 0 Dangerous builds = 0 3218 -14285.0936921486 eV 2.22617088839766 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08