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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -37.531810 0.0000000) to (26.536444 37.531810 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8969875 4.8647665 5.1069410 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -37.531810 0.0000000) to (26.536444 37.531810 5.1069410) create_atoms CPU = 0.001 seconds 439 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8969875 4.8647665 5.1069410 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -37.531810 0.0000000) to (26.536444 37.531810 5.1069410) create_atoms CPU = 0.001 seconds 439 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 15 atoms, new total = 863 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3602.5102 0 -3602.5102 16146.374 34 0 -3649.3748 0 -3649.3748 6022.1722 Loop time of 2.61115 on 1 procs for 34 steps with 863 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 = -3602.51019427501 -3649.3721746971 -3649.37478389448 Force two-norm initial, final = 54.457183 0.16312461 Force max component initial, final = 8.8508809 0.028252357 Final line search alpha, max atom move = 1.0000000 0.028252357 Iterations, force evaluations = 34 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.607 | 2.607 | 2.607 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016919 | 0.0016919 | 0.0016919 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002468 | | | 0.09 Nlocal: 863.000 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3253.00 ave 3253 max 3253 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: 46342.0 ave 46342 max 46342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46342 Ave neighs/atom = 53.698725 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -3649.3748 0 -3649.3748 6022.1722 10172.626 37 0 -3649.4265 0 -3649.4265 1078.7032 10203.247 Loop time of 0.241686 on 1 procs for 3 steps with 863 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 = -3649.37478389449 -3649.4264270176 -3649.42646938854 Force two-norm initial, final = 48.625455 0.99269594 Force max component initial, final = 35.420415 0.69539342 Final line search alpha, max atom move = 0.047139904 0.032780779 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24069 | 0.24069 | 0.24069 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015811 | 0.00015811 | 0.00015811 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008401 | | | 0.35 Nlocal: 863.000 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 46176.0 ave 46176 max 46176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46176 Ave neighs/atom = 53.506373 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.060 | 5.060 | 5.060 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3649.4265 0 -3649.4265 1078.7032 Loop time of 1.716e-06 on 1 procs for 0 steps with 863 atoms 116.6% 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 | | 1.716e-06 | | |100.00 Nlocal: 863.000 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 46166.0 ave 46166 max 46166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46166 Ave neighs/atom = 53.494786 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.060 | 5.060 | 5.060 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 -3649.4265 -3649.4265 26.57912 75.06362 5.1140891 1078.7032 1078.7032 -109.37056 3237.1848 108.29545 2.3532633 262.84835 Loop time of 1.452e-06 on 1 procs for 0 steps with 863 atoms 206.6% 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 | | 1.452e-06 | | |100.00 Nlocal: 863.000 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23083.0 ave 23083 max 23083 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46166.0 ave 46166 max 46166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46166 Ave neighs/atom = 53.494786 Neighbor list builds = 0 Dangerous builds = 0 863 -3649.42646938854 eV 2.3532632834221 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03