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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -41.294749 0.0000000) to (29.199797 41.294749 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6656323 6.1633954 5.0449566 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.294749 0.0000000) to (29.199797 41.294749 5.0449566) create_atoms CPU = 0.001 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6656323 6.1633954 5.0449566 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.294749 0.0000000) to (29.199797 41.294749 5.0449566) create_atoms CPU = 0.001 seconds 538 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1074 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4226.7993 0 -4226.7993 66499.02 153 0 -4534.8301 0 -4534.8301 62536.844 Loop time of 9.08987 on 1 procs for 153 steps with 1074 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 = -4226.79931144617 -4534.82763150046 -4534.83010133601 Force two-norm initial, final = 454.94809 0.21285034 Force max component initial, final = 106.85808 0.044013087 Final line search alpha, max atom move = 1.0000000 0.044013087 Iterations, force evaluations = 153 296 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0502 | 9.0502 | 9.0502 | 0.0 | 99.56 Neigh | 0.0056181 | 0.0056181 | 0.0056181 | 0.0 | 0.06 Comm | 0.015727 | 0.015727 | 0.015727 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01833 | | | 0.20 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 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: 66112.0 ave 66112 max 66112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66112 Ave neighs/atom = 61.556797 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 153 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press Volume 153 0 -4534.8301 0 -4534.8301 62536.844 12166.4 175 0 -4541.77 0 -4541.77 628.56508 12424.469 Loop time of 0.675506 on 1 procs for 22 steps with 1074 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 = -4534.830101336 -4541.76725991729 -4541.7699643424 Force two-norm initial, final = 860.00593 9.5524988 Force max component initial, final = 679.92883 6.4106922 Final line search alpha, max atom move = 0.00031686900 0.0020313497 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66482 | 0.66482 | 0.66482 | 0.0 | 98.42 Neigh | 0.0048616 | 0.0048616 | 0.0048616 | 0.0 | 0.72 Comm | 0.00094605 | 0.00094605 | 0.00094605 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004881 | | | 0.72 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4412.00 ave 4412 max 4412 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: 61888.0 ave 61888 max 61888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61888 Ave neighs/atom = 57.623836 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.736 | 4.736 | 4.736 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4541.77 0 -4541.77 628.56508 Loop time of 3.059e-06 on 1 procs for 0 steps with 1074 atoms 228.8% 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 | | 3.059e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4436.00 ave 4436 max 4436 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: 61128.0 ave 61128 max 61128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61128 Ave neighs/atom = 56.916201 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.736 | 4.736 | 4.736 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 -4541.77 -4541.77 29.344788 84.305827 5.0221451 628.56508 628.56508 271.39975 791.35338 822.9421 2.376882 1010.8199 Loop time of 1.859e-06 on 1 procs for 0 steps with 1074 atoms 215.2% 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 | | 1.859e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4436.00 ave 4436 max 4436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30564.0 ave 30564 max 30564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61128.0 ave 61128 max 61128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61128 Ave neighs/atom = 56.916201 Neighbor list builds = 0 Dangerous builds = 0 1074 -4541.7699643424 eV 2.3768819609716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10