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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -43.192895 0.0000000) to (14.397632 43.192895 3.4919386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2345975 4.2345975 3.4919386 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -43.192895 0.0000000) to (14.397632 43.192895 3.4919386) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2345975 4.2345975 3.4919386 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.192895 0.0000000) to (14.397632 43.192895 3.4919386) create_atoms CPU = 0.001 seconds 206 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 5 26 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 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_108408461881_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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1688.4248 0 -1688.4248 71004.54 65 0 -1802.8672 0 -1802.8672 13248.857 Loop time of 1.3761 on 1 procs for 65 steps with 408 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1688.42480024901 -1802.86573952344 -1802.867233209 Force two-norm initial, final = 307.41606 0.15664876 Force max component initial, final = 106.30282 0.039090095 Final line search alpha, max atom move = 1.0000000 0.039090095 Iterations, force evaluations = 65 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3565 | 1.3565 | 1.3565 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010676 | 0.010676 | 0.010676 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008959 | | | 0.65 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3732.00 ave 3732 max 3732 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: 54340.0 ave 54340 max 54340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54340 Ave neighs/atom = 133.18627 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1802.8672 0 -1802.8672 13248.857 4343.1013 73 0 -1803.0511 0 -1803.0511 55.325533 4374.8026 Loop time of 0.112476 on 1 procs for 8 steps with 408 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1802.867233209 -1803.05061981155 -1803.05114691262 Force two-norm initial, final = 65.041129 0.74466285 Force max component initial, final = 51.299973 0.61282644 Final line search alpha, max atom move = 0.00028364983 0.00017382811 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10889 | 0.10889 | 0.10889 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085339 | 0.00085339 | 0.00085339 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00273 | | | 2.43 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3759.00 ave 3759 max 3759 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: 53976.0 ave 53976 max 53976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53976 Ave neighs/atom = 132.29412 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1803.0511 0 -1803.0511 55.325533 Loop time of 6.685e-06 on 1 procs for 0 steps with 408 atoms 179.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3759.00 ave 3759 max 3759 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: 53960.0 ave 53960 max 53960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53960 Ave neighs/atom = 132.25490 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.603 | 4.603 | 4.603 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 -1803.0511 -1803.0511 14.399691 87.000009 3.4920945 55.325533 55.325533 224.46649 31.95175 -90.441636 2.2840544 179.97638 Loop time of 7.467e-06 on 1 procs for 0 steps with 408 atoms 174.1% 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 | | 7.467e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3759.00 ave 3759 max 3759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26980.0 ave 26980 max 26980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53960.0 ave 53960 max 53960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53960 Ave neighs/atom = 132.25490 Neighbor list builds = 0 Dangerous builds = 0 408 -1803.05114691262 eV 2.28405441874272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01