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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -51.335552 0.0000000) to (12.099906 51.335552 5.7039502) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7221697 5.7039502 5.7039502 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -51.335552 0.0000000) to (12.099906 51.335552 5.7039502) create_atoms CPU = 0.002 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7221697 5.7039502 5.7039502 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.335552 0.0000000) to (12.099906 51.335552 5.7039502) create_atoms CPU = 0.002 seconds 218 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 432 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1411.6912 0 -1411.6912 17732.935 60 0 -1452.3304 0 -1452.3304 4310.5304 Loop time of 1.02462 on 1 procs for 60 steps with 432 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 = -1411.69117136916 -1452.3292925113 -1452.33035679437 Force two-norm initial, final = 82.762299 0.074559541 Force max component initial, final = 27.250212 0.012326084 Final line search alpha, max atom move = 1.0000000 0.012326084 Iterations, force evaluations = 60 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99338 | 0.99338 | 0.99338 | 0.0 | 96.95 Neigh | 0.010409 | 0.010409 | 0.010409 | 0.0 | 1.02 Comm | 0.012048 | 0.012048 | 0.012048 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00878 | | | 0.86 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4263.00 ave 4263 max 4263 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: 62276.0 ave 62276 max 62276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62276 Ave neighs/atom = 144.15741 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1452.3304 0 -1452.3304 4310.5304 7086.078 69 0 -1452.457 0 -1452.457 9.7127873 7123.3655 Loop time of 0.111048 on 1 procs for 9 steps with 432 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 = -1452.33035679437 -1452.45697515483 -1452.45697923615 Force two-norm initial, final = 38.992415 0.14915446 Force max component initial, final = 35.947223 0.059015899 Final line search alpha, max atom move = 0.0065359057 0.00038572235 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10634 | 0.10634 | 0.10634 | 0.0 | 95.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010893 | 0.0010893 | 0.0010893 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003614 | | | 3.25 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4053.00 ave 4053 max 4053 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: 62180.0 ave 62180 max 62180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62180 Ave neighs/atom = 143.93519 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1452.457 0 -1452.457 9.7127873 Loop time of 6.505e-06 on 1 procs for 0 steps with 432 atoms 199.8% 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 | | 6.505e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 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: 61452.0 ave 61452 max 61452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61452 Ave neighs/atom = 142.25000 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.646 | 4.646 | 4.646 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 -1452.457 -1452.457 12.079853 103.48977 5.6980487 9.7127873 9.7127873 13.251768 8.3742306 7.5123637 2.6591254 298.505 Loop time of 6.916e-06 on 1 procs for 0 steps with 432 atoms 260.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30726.0 ave 30726 max 30726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61452.0 ave 61452 max 61452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61452 Ave neighs/atom = 142.25000 Neighbor list builds = 0 Dangerous builds = 0 432 -1452.45697923615 eV 2.65912538987038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01