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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -45.141687 0.0000000) to (27.643525 45.141687 7.0214623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4586330 4.3685503 4.6809748 Created 743 atoms using lattice units in orthogonal box = (0.0000000 -45.141687 0.0000000) to (27.643525 45.141687 7.0214623) create_atoms CPU = 0.001 seconds 743 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4586330 4.3685503 4.6809748 Created 749 atoms using lattice units in orthogonal box = (0.0000000 -45.141687 0.0000000) to (27.643525 45.141687 7.0214623) create_atoms CPU = 0.001 seconds 749 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 10 32 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1488 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5925.9279 0 -5925.9279 17797.965 68 0 -6390.9181 0 -6390.9181 7607.5448 Loop time of 0.473192 on 1 procs for 68 steps with 1488 atoms 91.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5925.92786129127 -6390.91197102095 -6390.91813284598 Force two-norm initial, final = 267.98869 0.29380551 Force max component initial, final = 49.118260 0.062589744 Final line search alpha, max atom move = 1.0000000 0.062589744 Iterations, force evaluations = 68 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44347 | 0.44347 | 0.44347 | 0.0 | 93.72 Neigh | 0.017179 | 0.017179 | 0.017179 | 0.0 | 3.63 Comm | 0.0051198 | 0.0051198 | 0.0051198 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007421 | | | 1.57 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4829.00 ave 4829 max 4829 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: 90668.0 ave 90668 max 90668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90668 Ave neighs/atom = 60.932796 Neighbor list builds = 2 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -6390.9181 0 -6390.9181 7607.5448 17523.819 77 0 -6391.755 0 -6391.755 -26.337394 17595.411 Loop time of 0.0386623 on 1 procs for 9 steps with 1488 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 = -6390.91813284598 -6391.75461598629 -6391.75503400928 Force two-norm initial, final = 217.09173 0.85522100 Force max component initial, final = 215.65353 0.36288030 Final line search alpha, max atom move = 0.00030689439 0.00011136593 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035523 | 0.035523 | 0.035523 | 0.0 | 91.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041455 | 0.00041455 | 0.00041455 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002725 | | | 7.05 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4826.00 ave 4826 max 4826 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: 90014.0 ave 90014 max 90014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90014 Ave neighs/atom = 60.493280 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.775 | 4.775 | 4.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6391.755 0 -6391.755 -26.337394 Loop time of 1.826e-06 on 1 procs for 0 steps with 1488 atoms 164.3% 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 | | 1.826e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4826.00 ave 4826 max 4826 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: 90408.0 ave 90408 max 90408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90408 Ave neighs/atom = 60.758065 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.775 | 4.775 | 4.775 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 -6391.755 -6391.755 27.578356 91.021597 7.009493 -26.337394 -26.337394 -21.465972 -33.312789 -24.233421 2.2966432 1059.3082 Loop time of 1.688e-06 on 1 procs for 0 steps with 1488 atoms 177.7% 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 | | 1.688e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4826.00 ave 4826 max 4826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45204.0 ave 45204 max 45204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90408.0 ave 90408 max 90408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90408 Ave neighs/atom = 60.758065 Neighbor list builds = 0 Dangerous builds = 0 1488 -6391.75503400928 eV 2.29664321958986 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00