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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -37.337596 0.0000000) to (45.729030 37.337596 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8200583 5.4309231 5.8134559 Created 1315 atoms using lattice units in orthogonal box = (0.0000000 -37.337596 0.0000000) to (45.729030 37.337596 8.7201838) create_atoms CPU = 0.002 seconds 1315 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8200583 5.4309231 5.8134559 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -37.337596 0.0000000) to (45.729030 37.337596 8.7201838) create_atoms CPU = 0.002 seconds 1321 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 2629 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.490 | 6.490 | 6.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9923.6204 0 -9923.6204 111512.53 103 0 -11506.5 0 -11506.5 11236.957 Loop time of 4.37776 on 1 procs for 103 steps with 2629 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9923.62040042313 -11506.4895410601 -11506.4999785171 Force two-norm initial, final = 1631.3401 0.50233157 Force max component initial, final = 243.09557 0.11537105 Final line search alpha, max atom move = 0.42330058 0.048836633 Iterations, force evaluations = 103 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1701 | 4.1701 | 4.1701 | 0.0 | 95.26 Neigh | 0.15775 | 0.15775 | 0.15775 | 0.0 | 3.60 Comm | 0.02127 | 0.02127 | 0.02127 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02864 | | | 0.65 Nlocal: 2629.00 ave 2629 max 2629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9400.00 ave 9400 max 9400 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: 459166.0 ave 459166 max 459166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459166 Ave neighs/atom = 174.65424 Neighbor list builds = 5 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.490 | 6.490 | 6.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -11506.5 0 -11506.5 11236.957 29777.894 112 0 -11507.964 0 -11507.964 -22.106941 29917.783 Loop time of 0.277807 on 1 procs for 9 steps with 2629 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 = -11506.4999785172 -11507.96376589 -11507.9638197405 Force two-norm initial, final = 440.55634 1.5201497 Force max component initial, final = 398.21299 0.66494645 Final line search alpha, max atom move = 0.00047365880 0.00031495774 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27014 | 0.27014 | 0.27014 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010028 | 0.0010028 | 0.0010028 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006667 | | | 2.40 Nlocal: 2629.00 ave 2629 max 2629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9404.00 ave 9404 max 9404 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: 459246.0 ave 459246 max 459246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459246 Ave neighs/atom = 174.68467 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.628 | 6.628 | 6.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11507.964 0 -11507.964 -22.106941 Loop time of 2.444e-06 on 1 procs for 0 steps with 2629 atoms 204.6% 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 | | 2.444e-06 | | |100.00 Nlocal: 2629.00 ave 2629 max 2629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9398.00 ave 9398 max 9398 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: 458388.0 ave 458388 max 458388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458388 Ave neighs/atom = 174.35831 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.628 | 6.628 | 6.628 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 -11507.964 -11507.964 45.770481 75.252921 8.6860149 -22.106941 -22.106941 -35.641922 -20.330276 -10.348626 2.3126337 1479.0076 Loop time of 2.735e-06 on 1 procs for 0 steps with 2629 atoms 255.9% 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 | | 2.735e-06 | | |100.00 Nlocal: 2629.00 ave 2629 max 2629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9398.00 ave 9398 max 9398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229194.0 ave 229194 max 229194 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 458388.0 ave 458388 max 458388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458388 Ave neighs/atom = 174.35831 Neighbor list builds = 0 Dangerous builds = 0 2629 -11507.9638197405 eV 2.31263366991073 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05