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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6574295 6.2228550 5.1067972 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6574295 6.2228550 5.1067972 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (20.743908 58.672632 5.1067972) create_atoms CPU = 0.002 seconds 530 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.313 | 6.313 | 6.313 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4193.7537 0 -4193.7537 32725.761 66 0 -4377.7019 0 -4377.7019 3643.8265 Loop time of 2.12259 on 1 procs for 66 steps with 1056 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 = -4193.75371414653 -4377.69752306699 -4377.70185227861 Force two-norm initial, final = 315.95051 0.28345192 Force max component initial, final = 102.01963 0.038444606 Final line search alpha, max atom move = 1.0000000 0.038444606 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0811 | 2.0811 | 2.0811 | 0.0 | 98.05 Neigh | 0.019668 | 0.019668 | 0.019668 | 0.0 | 0.93 Comm | 0.013504 | 0.013504 | 0.013504 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008285 | | | 0.39 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11264.0 ave 11264 max 11264 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: 401336.0 ave 401336 max 401336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401336 Ave neighs/atom = 380.05303 Neighbor list builds = 1 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.313 | 6.313 | 6.313 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -4377.7019 0 -4377.7019 3643.8265 12430.963 73 0 -4378.189 0 -4378.189 -37.292406 12456.964 Loop time of 0.179715 on 1 procs for 7 steps with 1056 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 = -4377.70185227861 -4378.18842859073 -4378.18896606125 Force two-norm initial, final = 145.38355 0.70095644 Force max component initial, final = 136.15452 0.30788810 Final line search alpha, max atom move = 0.00024946020 7.6805827e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17448 | 0.17448 | 0.17448 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089194 | 0.00089194 | 0.00089194 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004342 | | | 2.42 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11284.0 ave 11284 max 11284 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: 401056.0 ave 401056 max 401056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401056 Ave neighs/atom = 379.78788 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.451 | 6.451 | 6.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4378.189 0 -4378.189 -37.292406 Loop time of 1.798e-06 on 1 procs for 0 steps with 1056 atoms 111.2% 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 | | 1.798e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11284.0 ave 11284 max 11284 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: 400928.0 ave 400928 max 400928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400928 Ave neighs/atom = 379.66667 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.451 | 6.451 | 6.451 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 -4378.189 -4378.189 20.663658 118.01447 5.108222 -37.292406 -37.292406 -35.423634 -36.842914 -39.610671 2.3421492 430.89796 Loop time of 2.594e-06 on 1 procs for 0 steps with 1056 atoms 231.3% 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 | | 2.594e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11284.0 ave 11284 max 11284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200464.0 ave 200464 max 200464 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 400928.0 ave 400928 max 400928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400928 Ave neighs/atom = 379.66667 Neighbor list builds = 0 Dangerous builds = 0 1056 -4378.18896606125 eV 2.34214917888946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02