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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -31.439814 0.0000000) to (27.227677 31.439814 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8870190 4.8368944 5.3397869 Created 309 atoms using lattice units in orthogonal box = (0.0000000 -31.439814 0.0000000) to (27.227677 31.439814 5.3397869) create_atoms CPU = 0.001 seconds 309 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8870190 4.8368944 5.3397869 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -31.439814 0.0000000) to (27.227677 31.439814 5.3397869) create_atoms CPU = 0.000 seconds 316 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 19 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 1 atoms, new total = 624 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.260 | 5.260 | 5.260 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3236.4395 0 -3236.4395 274899.81 198 0 -4047.1978 0 -4047.1978 5110.0128 Loop time of 69.3007 on 1 procs for 198 steps with 624 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 = -3236.43946826992 -4047.19395901015 -4047.19779209275 Force two-norm initial, final = 1510.7965 0.27944452 Force max component initial, final = 432.47283 0.035214040 Final line search alpha, max atom move = 0.65019509 0.022895996 Iterations, force evaluations = 198 375 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 69.158 | 69.158 | 69.158 | 0.0 | 99.79 Neigh | 0.11168 | 0.11168 | 0.11168 | 0.0 | 0.16 Comm | 0.01585 | 0.01585 | 0.01585 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01526 | | | 0.02 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3341.00 ave 3341 max 3341 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: 45804.0 ave 45804 max 45804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45804 Ave neighs/atom = 73.403846 Neighbor list builds = 5 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 198 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.260 | 5.260 | 5.260 Mbytes Step Temp E_pair E_mol TotEng Press Volume 198 0 -4047.1978 0 -4047.1978 5110.0128 9142.0686 205 0 -4047.6823 0 -4047.6823 52.828379 9161.9259 Loop time of 1.65295 on 1 procs for 7 steps with 624 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 = -4047.19779209275 -4047.67940131018 -4047.68230259011 Force two-norm initial, final = 140.51986 1.4508136 Force max component initial, final = 136.12934 0.98192063 Final line search alpha, max atom move = 0.00013190785 0.00012952304 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6511 | 1.6511 | 1.6511 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028993 | 0.00028993 | 0.00028993 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001561 | | | 0.09 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3338.00 ave 3338 max 3338 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: 45642.0 ave 45642 max 45642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45642 Ave neighs/atom = 73.144231 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4047.6823 0 -4047.6823 52.828379 Loop time of 2.38e-06 on 1 procs for 0 steps with 624 atoms 168.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3335.00 ave 3335 max 3335 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: 45730.0 ave 45730 max 45730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45730 Ave neighs/atom = 73.285256 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.398 | 5.398 | 5.398 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 -4047.6823 -4047.6823 27.156553 62.777162 5.3741584 52.828379 52.828379 -17.765141 171.43192 4.8183603 2.5149761 1395.826 Loop time of 2.318e-06 on 1 procs for 0 steps with 624 atoms 215.7% 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 | | 2.318e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3335.00 ave 3335 max 3335 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22865.0 ave 22865 max 22865 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45730.0 ave 45730 max 45730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45730 Ave neighs/atom = 73.285256 Neighbor list builds = 0 Dangerous builds = 0 624 -4047.68230259011 eV 2.51497612460162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:11