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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4420657 6.0470482 4.9780318 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4420657 6.0470482 4.9780318 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) create_atoms CPU = 0.004 seconds 660 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 8 22 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_751354403791_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.504 | 5.504 | 5.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5749.301 0 -5749.301 1469.7597 63 0 -5784.8442 0 -5784.8442 -3814.9836 Loop time of 3.66268 on 1 procs for 63 steps with 1304 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 = -5749.30099839182 -5784.84000875645 -5784.84423121735 Force two-norm initial, final = 21.609599 0.19967299 Force max component initial, final = 4.3420240 0.013784788 Final line search alpha, max atom move = 1.0000000 0.013784788 Iterations, force evaluations = 63 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5408 | 3.5408 | 3.5408 | 0.0 | 96.67 Neigh | 0.077898 | 0.077898 | 0.077898 | 0.0 | 2.13 Comm | 0.025246 | 0.025246 | 0.025246 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01878 | | | 0.51 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9262.00 ave 9262 max 9262 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: 286648.0 ave 286648 max 286648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286648 Ave neighs/atom = 219.82209 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.505 | 5.505 | 5.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -5784.8442 0 -5784.8442 -3814.9836 14305.461 66 0 -5784.9195 0 -5784.9195 -448.26389 14278.201 Loop time of 0.155467 on 1 procs for 3 steps with 1304 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 = -5784.84423121735 -5784.91484652484 -5784.91954882164 Force two-norm initial, final = 68.638821 8.1498994 Force max component initial, final = 62.476835 7.4023574 Final line search alpha, max atom move = 8.2699559e-05 0.00061217169 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15154 | 0.15154 | 0.15154 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001016 | 0.001016 | 0.001016 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002913 | | | 1.87 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9280.00 ave 9280 max 9280 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: 287128.0 ave 287128 max 287128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287128 Ave neighs/atom = 220.19018 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.643 | 5.643 | 5.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5784.9195 0 -5784.9195 -448.26389 Loop time of 6.655e-06 on 1 procs for 0 steps with 1304 atoms 195.3% 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 | | 6.655e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9280.00 ave 9280 max 9280 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: 287376.0 ave 287376 max 287376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287376 Ave neighs/atom = 220.38037 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.643 | 5.643 | 5.643 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 -5784.9195 -5784.9195 31.803873 90.149983 4.9799829 -448.26389 -448.26389 -828.77628 -337.5742 -178.44119 2.3013801 582.83311 Loop time of 6.826e-06 on 1 procs for 0 steps with 1304 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9280.00 ave 9280 max 9280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143688.0 ave 143688 max 143688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287376.0 ave 287376 max 287376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287376 Ave neighs/atom = 220.38037 Neighbor list builds = 0 Dangerous builds = 0 1304 -5755.51899540787 eV 2.30138007617828 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04