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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -79.687873 0.0000000) to (48.798657 79.687873 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6433821 5.6919909 6.5725450 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -79.687873 0.0000000) to (48.798657 79.687873 9.8588175) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6433821 5.6919909 6.5725450 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -79.687873 0.0000000) to (48.798657 79.687873 9.8588175) create_atoms CPU = 0.003 seconds 2358 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 3 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 11.47 | 11.47 | 11.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11515.738 0 -11515.738 25502.53 103 0 -12419.2 0 -12419.2 3626.8287 Loop time of 6.38221 on 1 procs for 103 steps with 4704 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 = -11515.7382218918 -12419.1884334333 -12419.1999800172 Force two-norm initial, final = 863.73265 0.28320790 Force max component initial, final = 107.50007 0.026192625 Final line search alpha, max atom move = 1.0000000 0.026192625 Iterations, force evaluations = 103 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1315 | 6.1315 | 6.1315 | 0.0 | 96.07 Neigh | 0.17855 | 0.17855 | 0.17855 | 0.0 | 2.80 Comm | 0.029381 | 0.029381 | 0.029381 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04279 | | | 0.67 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13903.0 ave 13903 max 13903 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: 658260.0 ave 658260 max 658260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658260 Ave neighs/atom = 139.93622 Neighbor list builds = 4 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.48 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -12419.2 0 -12419.2 3626.8287 76675.201 111 0 -12420.206 0 -12420.206 1.5193602 77017.527 Loop time of 0.406806 on 1 procs for 8 steps with 4704 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 = -12419.1999800172 -12420.2055300568 -12420.2056632218 Force two-norm initial, final = 355.56163 0.82611048 Force max component initial, final = 328.56974 0.57866762 Final line search alpha, max atom move = 0.00023785208 0.00013763730 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35382 | 0.35382 | 0.35382 | 0.0 | 86.98 Neigh | 0.043368 | 0.043368 | 0.043368 | 0.0 | 10.66 Comm | 0.001559 | 0.001559 | 0.001559 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008057 | | | 1.98 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14191.0 ave 14191 max 14191 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: 657456.0 ave 657456 max 657456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657456 Ave neighs/atom = 139.76531 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 10.99 | 10.99 | 10.99 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12420.206 0 -12420.206 1.5193602 Loop time of 1.859e-06 on 1 procs for 0 steps with 4704 atoms 161.4% 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 | | 1.859e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14195.0 ave 14195 max 14195 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: 657468.0 ave 657468 max 657468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657468 Ave neighs/atom = 139.76786 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 10.99 | 10.99 | 10.99 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 -12420.206 -12420.206 48.735266 160.483 9.8473009 1.5193602 1.5193602 -7.869822 0.40408566 12.023817 2.6356065 2427.2115 Loop time of 2.797e-06 on 1 procs for 0 steps with 4704 atoms 250.3% 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 | | 2.797e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14195.0 ave 14195 max 14195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328734.0 ave 328734 max 328734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 657468.0 ave 657468 max 657468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657468 Ave neighs/atom = 139.76786 Neighbor list builds = 0 Dangerous builds = 0 4704 -12275.6316895752 eV 2.63560654811844 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07