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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -29.521648 0.0000000) to (36.156487 29.521648 6.8947716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6017348 4.2940579 4.5965144 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -29.521648 0.0000000) to (36.156487 29.521648 6.8947716) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6017348 4.2940579 4.5965144 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -29.521648 0.0000000) to (36.156487 29.521648 6.8947716) create_atoms CPU = 0.001 seconds 662 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 16 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1318 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_255315407910_000#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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4928.7909 0 -4928.7909 111371.13 102 0 -5395.4056 0 -5395.4056 9029.7145 Loop time of 2.24251 on 1 procs for 102 steps with 1318 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4928.79092776212 -5395.40022516279 -5395.4055761514 Force two-norm initial, final = 548.70655 0.34905467 Force max component initial, final = 141.88863 0.083763288 Final line search alpha, max atom move = 0.40029843 0.033530313 Iterations, force evaluations = 102 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1867 | 2.1867 | 2.1867 | 0.0 | 97.51 Neigh | 0.027534 | 0.027534 | 0.027534 | 0.0 | 1.23 Comm | 0.014042 | 0.014042 | 0.014042 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01418 | | | 0.63 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6074.00 ave 6074 max 6074 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: 217448.0 ave 217448 max 217448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217448 Ave neighs/atom = 164.98331 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -5395.4056 0 -5395.4056 9029.7145 14718.946 107 0 -5395.6756 0 -5395.6756 -5.264103 14788.089 Loop time of 0.0903657 on 1 procs for 5 steps with 1318 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5395.40557615139 -5395.67508148712 -5395.67557752228 Force two-norm initial, final = 153.19492 0.77990538 Force max component initial, final = 126.24080 0.13380083 Final line search alpha, max atom move = 0.00015353046 2.0542503e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087686 | 0.087686 | 0.087686 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040548 | 0.00040548 | 0.00040548 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002274 | | | 2.52 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6073.00 ave 6073 max 6073 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: 217778.0 ave 217778 max 217778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217778 Ave neighs/atom = 165.23369 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.603 | 5.603 | 5.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5395.6756 0 -5395.6756 -5.264103 Loop time of 1.956e-06 on 1 procs for 0 steps with 1318 atoms 153.4% 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 | | 1.956e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6073.00 ave 6073 max 6073 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: 217490.0 ave 217490 max 217490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217490 Ave neighs/atom = 165.01517 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.603 | 5.603 | 5.603 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 -5395.6756 -5395.6756 36.176286 59.272558 6.89659 -5.264103 -5.264103 8.1268113 -9.7655205 -14.1536 2.2346638 1528.448 Loop time of 2.371e-06 on 1 procs for 0 steps with 1318 atoms 210.9% 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 | | 2.371e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6073.00 ave 6073 max 6073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108745.0 ave 108745 max 108745 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217490.0 ave 217490 max 217490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217490 Ave neighs/atom = 165.01517 Neighbor list builds = 0 Dangerous builds = 0 1318 -5395.67557752228 eV 2.23466377422909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03