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 = 4.0497635 4.0497635 4.0497635 Created orthogonal box = (0.0000000 -74.673950 0.0000000) to (37.336975 74.673950 4.0497635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7103609 5.7103609 4.0497635 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.673950 0.0000000) to (37.336975 74.673950 4.0497635) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7103609 5.7103609 4.0497635 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.673950 0.0000000) to (37.336975 74.673950 4.0497635) create_atoms CPU = 0.002 seconds 682 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 9 35 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_942551040047_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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.508 | 5.508 | 5.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4395.2366 0 -4395.2366 20099.818 93 0 -4515.0036 0 -4515.0036 2541.7954 Loop time of 4.7417 on 1 procs for 93 steps with 1362 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 = -4395.23657364099 -4514.9993558574 -4515.00358106485 Force two-norm initial, final = 138.01731 0.13716285 Force max component initial, final = 25.444381 0.029461139 Final line search alpha, max atom move = 1.0000000 0.029461139 Iterations, force evaluations = 93 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6093 | 4.6093 | 4.6093 | 0.0 | 97.21 Neigh | 0.06197 | 0.06197 | 0.06197 | 0.0 | 1.31 Comm | 0.041498 | 0.041498 | 0.041498 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02891 | | | 0.61 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10162.0 ave 10162 max 10162 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: 235180.0 ave 235180 max 235180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235180 Ave neighs/atom = 172.67254 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -4515.0036 0 -4515.0036 2541.7954 22582.287 97 0 -4515.1027 0 -4515.1027 -153.11709 22660.718 Loop time of 0.171339 on 1 procs for 4 steps with 1362 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 = -4515.00358106483 -4515.10127811206 -4515.10272462106 Force two-norm initial, final = 67.888817 4.8869820 Force max component initial, final = 53.970834 4.6987777 Final line search alpha, max atom move = 0.00018825292 0.00088455862 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16631 | 0.16631 | 0.16631 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011954 | 0.0011954 | 0.0011954 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003833 | | | 2.24 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9758.00 ave 9758 max 9758 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: 235704.0 ave 235704 max 235704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235704 Ave neighs/atom = 173.05727 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.638 | 5.638 | 5.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4515.1027 0 -4515.1027 -153.11709 Loop time of 6.445e-06 on 1 procs for 0 steps with 1362 atoms 186.2% 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 | | 6.445e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9758.00 ave 9758 max 9758 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: 235244.0 ave 235244 max 235244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235244 Ave neighs/atom = 172.71953 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.638 | 5.638 | 5.638 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 -4515.1027 -4515.1027 37.302218 149.77464 4.056026 -153.11709 -153.11709 -331.90754 -84.30909 -43.134628 2.5942034 194.5589 Loop time of 6.725e-06 on 1 procs for 0 steps with 1362 atoms 297.4% 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 | | 6.725e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9758.00 ave 9758 max 9758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117622.0 ave 117622 max 117622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235244.0 ave 235244 max 235244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235244 Ave neighs/atom = 172.71953 Neighbor list builds = 0 Dangerous builds = 0 1362 -4515.10272462106 eV 2.5942033541511 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05