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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -40.498230 0.0000000) to (20.249115 40.498230 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2398584 3.2398584 2.8636573 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -40.498230 0.0000000) to (20.249115 40.498230 2.8636573) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2398584 3.2398584 2.8636573 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.498230 0.0000000) to (20.249115 40.498230 2.8636573) create_atoms CPU = 0.001 seconds 202 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 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, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 402 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1637.1335 0 -1637.1335 60175.644 32 0 -1717.3606 0 -1717.3606 15013.46 Loop time of 1.41846 on 1 procs for 32 steps with 402 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 = -1637.13353788054 -1717.35933191502 -1717.36059185861 Force two-norm initial, final = 176.66354 0.10231409 Force max component initial, final = 81.916240 0.011680141 Final line search alpha, max atom move = 1.0000000 0.011680141 Iterations, force evaluations = 32 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4097 | 1.4097 | 1.4097 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044199 | 0.0044199 | 0.0044199 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004317 | | | 0.30 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3153.00 ave 3153 max 3153 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: 23524.0 ave 23524 max 23524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23524 Ave neighs/atom = 58.517413 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1717.3606 0 -1717.3606 15013.46 4696.7035 46 0 -1717.8428 0 -1717.8428 -5.0737058 4736.7362 Loop time of 0.388266 on 1 procs for 14 steps with 402 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 = -1717.36059185861 -1717.8416525749 -1717.84283044977 Force two-norm initial, final = 87.866884 0.34070086 Force max component initial, final = 78.556530 0.077844353 Final line search alpha, max atom move = 0.00048106721 3.7448365e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37925 | 0.37925 | 0.37925 | 0.0 | 97.68 Neigh | 0.003767 | 0.003767 | 0.003767 | 0.0 | 0.97 Comm | 0.0012188 | 0.0012188 | 0.0012188 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004034 | | | 1.04 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3138.00 ave 3138 max 3138 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: 23324.0 ave 23324 max 23324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23324 Ave neighs/atom = 58.019900 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1717.8428 0 -1717.8428 -5.0737058 Loop time of 6.526e-06 on 1 procs for 0 steps with 402 atoms 168.6% 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 | | 6.526e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3138.00 ave 3138 max 3138 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: 23316.0 ave 23316 max 23316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23316 Ave neighs/atom = 58.000000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.573 | 4.573 | 4.573 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 -1717.8428 -1717.8428 20.251686 82.105525 2.8486928 -5.0737058 -5.0737058 -5.4518338 -15.563044 5.7937602 2.3614345 147.36929 Loop time of 7.137e-06 on 1 procs for 0 steps with 402 atoms 210.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3138.00 ave 3138 max 3138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11658.0 ave 11658 max 11658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23316.0 ave 23316 max 23316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23316 Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 402 -1717.84283044977 eV 2.36143448102187 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02