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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -43.275631 0.0000000) to (15.300246 43.275631 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1000820 6.0105043 5.1000820 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -43.275631 0.0000000) to (15.300246 43.275631 5.1000820) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1000820 6.0105043 5.1000820 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -43.275631 0.0000000) to (15.300246 43.275631 5.1000820) create_atoms CPU = 0.001 seconds 292 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 572 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.816 | 5.816 | 5.816 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2349.736 0 -2349.736 15673.31 63 0 -2387.2809 0 -2387.2809 -3361.9504 Loop time of 2.12655 on 1 procs for 63 steps with 572 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 = -2349.73601525902 -2387.2788259005 -2387.28087347324 Force two-norm initial, final = 59.670363 0.18553527 Force max component initial, final = 12.902113 0.016777692 Final line search alpha, max atom move = 1.0000000 0.016777692 Iterations, force evaluations = 63 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0894 | 2.0894 | 2.0894 | 0.0 | 98.25 Neigh | 0.018128 | 0.018128 | 0.018128 | 0.0 | 0.85 Comm | 0.012858 | 0.012858 | 0.012858 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006187 | | | 0.29 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10209.0 ave 10209 max 10209 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: 351568.0 ave 351568 max 351568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351568 Ave neighs/atom = 614.62937 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2387.2809 0 -2387.2809 -3361.9504 6753.8122 69 0 -2387.3676 0 -2387.3676 -10.186437 6740.3488 Loop time of 0.156564 on 1 procs for 6 steps with 572 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 = -2387.28087347323 -2387.36752777702 -2387.36759874145 Force two-norm initial, final = 37.644253 0.35144184 Force max component initial, final = 37.378324 0.053166356 Final line search alpha, max atom move = 0.00080350418 4.2719389e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15259 | 0.15259 | 0.15259 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080773 | 0.00080773 | 0.00080773 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00317 | | | 2.02 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10209.0 ave 10209 max 10209 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: 352288.0 ave 352288 max 352288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352288 Ave neighs/atom = 615.88811 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.955 | 5.955 | 5.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2387.3676 0 -2387.3676 -10.186437 Loop time of 2.086e-06 on 1 procs for 0 steps with 572 atoms 191.8% 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 | | 2.086e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10245.0 ave 10245 max 10245 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: 352024.0 ave 352024 max 352024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352024 Ave neighs/atom = 615.42657 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.955 | 5.955 | 5.955 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 -2387.3676 -2387.3676 15.22691 86.645955 5.1088399 -10.186437 -10.186437 -5.5625734 -12.651434 -12.345305 2.3455525 377.82958 Loop time of 2.502e-06 on 1 procs for 0 steps with 572 atoms 279.8% 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 | | 2.502e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10245.0 ave 10245 max 10245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176012.0 ave 176012 max 176012 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 352024.0 ave 352024 max 352024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352024 Ave neighs/atom = 615.42657 Neighbor list builds = 0 Dangerous builds = 0 572 -2387.36759874145 eV 2.34555249530443 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02