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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -30.778282 0.0000000) to (21.763532 30.778282 4.0766831) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1999799 4.8597288 4.0766831 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.778282 0.0000000) to (21.763532 30.778282 4.0766831) create_atoms CPU = 0.002 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1999799 4.8597288 4.0766831 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.778282 0.0000000) to (21.763532 30.778282 4.0766831) create_atoms CPU = 0.002 seconds 230 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 6 15 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.892 | 4.892 | 4.892 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1527.5568 0 -1527.5568 66964.419 74 0 -1739.7117 0 -1739.7117 -3353.1597 Loop time of 1.55222 on 1 procs for 74 steps with 452 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 = -1527.55679001848 -1739.71030201241 -1739.71174109455 Force two-norm initial, final = 392.34720 0.17307489 Force max component initial, final = 135.19855 0.040851113 Final line search alpha, max atom move = 1.0000000 0.040851113 Iterations, force evaluations = 74 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5019 | 1.5019 | 1.5019 | 0.0 | 96.76 Neigh | 0.02529 | 0.02529 | 0.02529 | 0.0 | 1.63 Comm | 0.014931 | 0.014931 | 0.014931 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01009 | | | 0.65 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5273.00 ave 5273 max 5273 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: 107612.0 ave 107612 max 107612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107612 Ave neighs/atom = 238.07965 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.892 | 4.892 | 4.892 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -1739.7117 0 -1739.7117 -3353.1597 5461.4845 83 0 -1739.9797 0 -1739.9797 55.170757 5449.7712 Loop time of 0.139805 on 1 procs for 9 steps with 452 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 = -1739.71174109455 -1739.97909738913 -1739.9796945684 Force two-norm initial, final = 55.265815 0.58655223 Force max component initial, final = 46.175164 0.25136287 Final line search alpha, max atom move = 0.00051436470 0.00012929219 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13487 | 0.13487 | 0.13487 | 0.0 | 96.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012242 | 0.0012242 | 0.0012242 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003711 | | | 2.65 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5276.00 ave 5276 max 5276 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: 108840.0 ave 108840 max 108840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108840 Ave neighs/atom = 240.79646 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.030 | 5.030 | 5.030 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1739.9797 0 -1739.9797 55.170757 Loop time of 6.896e-06 on 1 procs for 0 steps with 452 atoms 188.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5291.00 ave 5291 max 5291 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: 108216.0 ave 108216 max 108216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108216 Ave neighs/atom = 239.41593 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.030 | 5.030 | 5.030 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 -1739.9797 -1739.9797 21.580493 61.597546 4.0997134 55.170757 55.170757 73.276579 45.717188 46.518504 2.2778268 493.87863 Loop time of 9.121e-06 on 1 procs for 0 steps with 452 atoms 416.6% 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 | | 9.121e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5291.00 ave 5291 max 5291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54108.0 ave 54108 max 54108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108216.0 ave 108216 max 108216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108216 Ave neighs/atom = 239.41593 Neighbor list builds = 0 Dangerous builds = 0 452 -1739.9796945684 eV 2.27782684106605 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02