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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -71.362361 0.0000000) to (43.700343 71.362361 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0537811 5.0973115 5.8858683 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -71.362361 0.0000000) to (43.700343 71.362361 8.8288024) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0537811 5.0973115 5.8858683 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -71.362361 0.0000000) to (43.700343 71.362361 8.8288024) create_atoms CPU = 0.003 seconds 2357 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 4697 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.208 | 6.208 | 6.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18440.324 0 -18440.324 80639.533 89 0 -19902.21 0 -19902.21 904.09551 Loop time of 25.6644 on 1 procs for 89 steps with 4697 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -18440.3238959726 -19902.1914892855 -19902.2100459868 Force two-norm initial, final = 2390.0206 0.57585653 Force max component initial, final = 338.22677 0.13762674 Final line search alpha, max atom move = 1.0000000 0.13762674 Iterations, force evaluations = 89 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.509 | 25.509 | 25.509 | 0.0 | 99.40 Neigh | 0.089173 | 0.089173 | 0.089173 | 0.0 | 0.35 Comm | 0.025836 | 0.025836 | 0.025836 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03998 | | | 0.16 Nlocal: 4697.00 ave 4697 max 4697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10480.0 ave 10480 max 10480 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: 363418.0 ave 363418 max 363418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363418 Ave neighs/atom = 77.372365 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.209 | 6.209 | 6.209 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -19902.21 0 -19902.21 904.09551 55066.293 93 0 -19902.462 0 -19902.462 32.083239 55095.532 Loop time of 1.1265 on 1 procs for 4 steps with 4697 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 = -19902.2100459868 -19902.4570034461 -19902.46208068 Force two-norm initial, final = 152.99762 8.9784095 Force max component initial, final = 139.58069 8.0121540 Final line search alpha, max atom move = 2.3107065e-05 0.00018513737 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1209 | 1.1209 | 1.1209 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068264 | 0.00068264 | 0.00068264 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004931 | | | 0.44 Nlocal: 4697.00 ave 4697 max 4697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460.0 ave 10460 max 10460 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: 363324.0 ave 363324 max 363324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363324 Ave neighs/atom = 77.352353 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.347 | 6.347 | 6.347 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19902.462 0 -19902.462 32.083239 Loop time of 1.99e-06 on 1 procs for 0 steps with 4697 atoms 201.0% 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 | | 1.99e-06 | | |100.00 Nlocal: 4697.00 ave 4697 max 4697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10458.0 ave 10458 max 10458 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: 363206.0 ave 363206 max 363206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363206 Ave neighs/atom = 77.327230 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.347 | 6.347 | 6.347 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 -19902.462 -19902.462 43.709502 142.39547 8.8520602 32.083239 32.083239 233.04205 -22.218135 -114.57419 2.1983483 2291.581 Loop time of 2.229e-06 on 1 procs for 0 steps with 4697 atoms 269.2% 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 | | 2.229e-06 | | |100.00 Nlocal: 4697.00 ave 4697 max 4697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10458.0 ave 10458 max 10458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181603.0 ave 181603 max 181603 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 363206.0 ave 363206 max 363206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363206 Ave neighs/atom = 77.327230 Neighbor list builds = 0 Dangerous builds = 0 4697 -19902.46208068 eV 2.19834832417317 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27