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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -44.355780 0.0000000) to (36.216342 44.355780 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1737632 5.1295799 5.9741471 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.355780 0.0000000) to (36.216342 44.355780 8.9612207) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1737632 5.1295799 5.9741471 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.355780 0.0000000) to (36.216342 44.355780 8.9612207) create_atoms CPU = 0.001 seconds 1184 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 = 9 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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 = 9 21 3 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) = 6.469 | 6.469 | 6.469 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8448.7379 0 -8448.7379 74696.992 774 0 -9245.4305 0 -9245.4305 -59738.717 Loop time of 35.2151 on 1 procs for 774 steps with 2352 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 = -8448.73786851477 -9245.42208415015 -9245.43049385898 Force two-norm initial, final = 1050.7119 0.29229577 Force max component initial, final = 182.34502 0.042720105 Final line search alpha, max atom move = 1.0000000 0.042720105 Iterations, force evaluations = 774 1499 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.421 | 34.421 | 34.421 | 0.0 | 97.74 Neigh | 0.53776 | 0.53776 | 0.53776 | 0.0 | 1.53 Comm | 0.11948 | 0.11948 | 0.11948 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1369 | | | 0.39 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9542.00 ave 9542 max 9542 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: 479576.0 ave 479576 max 479576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479576 Ave neighs/atom = 203.90136 Neighbor list builds = 18 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 = 9 21 3 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 : 774 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.471 | 6.471 | 6.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 774 0 -9245.4305 0 -9245.4305 -59738.717 28790.683 827 0 -9308.145 0 -9308.145 -17.298188 27748.019 Loop time of 1.36249 on 1 procs for 53 steps with 2352 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 = -9245.43049385894 -9308.1392897138 -9308.14501891023 Force two-norm initial, final = 2347.7075 7.4574564 Force max component initial, final = 1976.8988 2.8234328 Final line search alpha, max atom move = 9.1352170e-05 0.00025792672 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2794 | 1.2794 | 1.2794 | 0.0 | 93.90 Neigh | 0.05638 | 0.05638 | 0.05638 | 0.0 | 4.14 Comm | 0.0040641 | 0.0040641 | 0.0040641 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02269 | | | 1.67 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9585.00 ave 9585 max 9585 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: 506068.0 ave 506068 max 506068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506068 Ave neighs/atom = 215.16497 Neighbor list builds = 2 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 = 9 21 3 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) = 6.990 | 6.990 | 6.990 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9308.145 0 -9308.145 -17.298188 Loop time of 1.924e-06 on 1 procs for 0 steps with 2352 atoms 155.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9487.00 ave 9487 max 9487 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: 509440.0 ave 509440 max 509440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509440 Ave neighs/atom = 216.59864 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 = 9 21 3 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) = 6.990 | 6.990 | 6.990 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 -9308.145 -9308.145 34.502574 86.886485 9.2561045 -17.298188 -17.298188 97.527946 18.967733 -168.39024 2.2246275 5686.8888 Loop time of 2.256e-06 on 1 procs for 0 steps with 2352 atoms 221.6% 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 | | 2.256e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9487.00 ave 9487 max 9487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 254720.0 ave 254720 max 254720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 509440.0 ave 509440 max 509440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509440 Ave neighs/atom = 216.59864 Neighbor list builds = 0 Dangerous builds = 0 2352 -9308.14501891023 eV 2.22462752861301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37