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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) create_atoms CPU = 0.008 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) create_atoms CPU = 0.008 seconds 1250 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 13 43 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2490 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.242 | 5.242 | 5.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7925.4493 0 -7925.4493 21927.518 91 0 -8344.315 0 -8344.315 1634.8449 Loop time of 35.1429 on 1 procs for 91 steps with 2490 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 = -7925.4493125559 -8344.30671036974 -8344.31496292146 Force two-norm initial, final = 432.67750 0.24504453 Force max component initial, final = 75.642823 0.047349700 Final line search alpha, max atom move = 1.0000000 0.047349700 Iterations, force evaluations = 91 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.953 | 34.953 | 34.953 | 0.0 | 99.46 Neigh | 0.11755 | 0.11755 | 0.11755 | 0.0 | 0.33 Comm | 0.02949 | 0.02949 | 0.02949 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04302 | | | 0.12 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7142.00 ave 7142 max 7142 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: 192824.0 ave 192824 max 192824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192824 Ave neighs/atom = 77.439357 Neighbor list builds = 4 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.241 | 5.241 | 5.241 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -8344.315 0 -8344.315 1634.8449 41288.365 95 0 -8344.4734 0 -8344.4734 -203.20765 41384.45 Loop time of 1.43636 on 1 procs for 4 steps with 2490 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8344.31496292141 -8344.46727829471 -8344.47341851908 Force two-norm initial, final = 94.854769 9.4475858 Force max component initial, final = 90.965163 6.3418767 Final line search alpha, max atom move = 7.0221220e-05 0.00044533432 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4299 | 1.4299 | 1.4299 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010492 | 0.0010492 | 0.0010492 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005373 | | | 0.37 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7129.00 ave 7129 max 7129 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: 192784.0 ave 192784 max 192784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192784 Ave neighs/atom = 77.423293 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8344.4734 0 -8344.4734 -203.20765 Loop time of 6.545e-06 on 1 procs for 0 steps with 2490 atoms 183.3% 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 | | 6.545e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7114.00 ave 7114 max 7114 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: 192742.0 ave 192742 max 192742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192742 Ave neighs/atom = 77.406426 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.379 | 5.379 | 5.379 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 -8344.4734 -8344.4734 41.233137 143.42298 6.9979699 -203.20765 -203.20765 -245.43677 -122.72084 -241.46535 2.5141966 1122.2827 Loop time of 7.067e-06 on 1 procs for 0 steps with 2490 atoms 325.5% 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 | | 7.067e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7114.00 ave 7114 max 7114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96371.0 ave 96371 max 96371 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192742.0 ave 192742 max 192742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192742 Ave neighs/atom = 77.406426 Neighbor list builds = 0 Dangerous builds = 0 2490 -8344.47341851908 eV 2.51419660057278 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38