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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -45.888473 0.0000000) to (32.445577 45.888473 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0363864 5.8690084 4.9479041 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -45.888473 0.0000000) to (32.445577 45.888473 4.9479041) create_atoms CPU = 0.002 seconds 693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0363864 5.8690084 4.9479041 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -45.888473 0.0000000) to (32.445577 45.888473 4.9479041) create_atoms CPU = 0.002 seconds 693 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1368 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_677715648236_000#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5534.3132 0 -5534.3132 33998.8 88 0 -5615.4661 0 -5615.4661 -6120.835 Loop time of 1.96792 on 1 procs for 88 steps with 1368 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 = -5534.31320630717 -5615.46097107542 -5615.46607791563 Force two-norm initial, final = 120.31505 0.32011110 Force max component initial, final = 24.239324 0.10128890 Final line search alpha, max atom move = 1.0000000 0.10128890 Iterations, force evaluations = 88 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9325 | 1.9325 | 1.9325 | 0.0 | 98.20 Neigh | 0.013614 | 0.013614 | 0.013614 | 0.0 | 0.69 Comm | 0.011751 | 0.011751 | 0.011751 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01002 | | | 0.51 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8630.00 ave 8630 max 8630 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: 238374.0 ave 238374 max 238374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238374 Ave neighs/atom = 174.25000 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -5615.4661 0 -5615.4661 -6120.835 14733.651 90 0 -5615.5059 0 -5615.5059 -3299.356 14698.733 Loop time of 0.0476086 on 1 procs for 2 steps with 1368 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 = -5615.46607791563 -5615.50377465742 -5615.50590679155 Force two-norm initial, final = 47.122564 0.47301549 Force max component initial, final = 36.346169 0.27010854 Final line search alpha, max atom move = 0.00012289273 3.3194374e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046352 | 0.046352 | 0.046352 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025034 | 0.00025034 | 0.00025034 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001007 | | | 2.11 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8629.00 ave 8629 max 8629 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: 238612.0 ave 238612 max 238612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238612 Ave neighs/atom = 174.42398 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5615.5059 0 -5615.5059 -3299.356 Loop time of 2.058e-06 on 1 procs for 0 steps with 1368 atoms 194.4% 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 | | 2.058e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8629.00 ave 8629 max 8629 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: 238692.0 ave 238692 max 238692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238692 Ave neighs/atom = 174.48246 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.641 | 5.641 | 5.641 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 -5615.5059 -5615.5059 32.403799 91.776947 4.9425421 -3299.356 -3299.356 18.564931 -9887.2228 -29.410192 2.3294797 939.45322 Loop time of 2.547e-06 on 1 procs for 0 steps with 1368 atoms 196.3% 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 | | 2.547e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8629.00 ave 8629 max 8629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119346.0 ave 119346 max 119346 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238692.0 ave 238692 max 238692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238692 Ave neighs/atom = 174.48246 Neighbor list builds = 0 Dangerous builds = 0 1368 -5615.50590679155 eV 2.3294796925271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02