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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -44.204652 0.0000000) to (54.139421 44.204652 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1914513 5.4498886 5.9741471 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -44.204652 0.0000000) to (54.139421 44.204652 8.9612207) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1914513 5.4498886 5.9741471 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -44.204652 0.0000000) to (54.139421 44.204652 8.9612207) create_atoms CPU = 0.002 seconds 1757 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3508 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.819 | 7.819 | 7.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12385.54 0 -12385.54 107649.79 876 0 -13794.854 0 -13794.854 -51860.012 Loop time of 63.0221 on 1 procs for 876 steps with 3508 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 = -12385.5403320808 -13794.8404507145 -13794.8535101834 Force two-norm initial, final = 998.63464 0.32760261 Force max component initial, final = 142.14098 0.031743236 Final line search alpha, max atom move = 0.66855132 0.021221982 Iterations, force evaluations = 876 1696 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.673 | 61.673 | 61.673 | 0.0 | 97.86 Neigh | 0.87966 | 0.87966 | 0.87966 | 0.0 | 1.40 Comm | 0.20115 | 0.20115 | 0.20115 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2686 | | | 0.43 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12330.0 ave 12330 max 12330 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: 722760.0 ave 722760 max 722760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 722760 Ave neighs/atom = 206.03193 Neighbor list builds = 20 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 876 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.841 | 7.841 | 7.841 Mbytes Step Temp E_pair E_mol TotEng Press Volume 876 0 -13794.854 0 -13794.854 -51860.012 42892.243 915 0 -13849.313 0 -13849.313 -5.9644975 41483.352 Loop time of 1.58228 on 1 procs for 39 steps with 3508 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 = -13794.8535101834 -13849.3038403429 -13849.313210875 Force two-norm initial, final = 2826.0187 7.2114912 Force max component initial, final = 2262.2712 1.5774615 Final line search alpha, max atom move = 4.9268539e-05 7.7719223e-05 Iterations, force evaluations = 39 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4291 | 1.4291 | 1.4291 | 0.0 | 90.32 Neigh | 0.12292 | 0.12292 | 0.12292 | 0.0 | 7.77 Comm | 0.0044793 | 0.0044793 | 0.0044793 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02578 | | | 1.63 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12286.0 ave 12286 max 12286 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: 760440.0 ave 760440 max 760440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 760440 Ave neighs/atom = 216.77309 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.978 | 7.978 | 7.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13849.313 0 -13849.313 -5.9644975 Loop time of 2.06e-06 on 1 procs for 0 steps with 3508 atoms 194.2% 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 | | 2.06e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12282.0 ave 12282 max 12282 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: 760490.0 ave 760490 max 760490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 760490 Ave neighs/atom = 216.78734 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.978 | 7.978 | 7.978 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 -13849.313 -13849.313 53.163496 85.303076 9.1473568 -5.9644975 -5.9644975 -6.8218959 51.118857 -62.190454 2.2121231 7264.6587 Loop time of 2.481e-06 on 1 procs for 0 steps with 3508 atoms 241.8% 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 | | 2.481e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12282.0 ave 12282 max 12282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 380245.0 ave 380245 max 380245 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 760490.0 ave 760490 max 760490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 760490 Ave neighs/atom = 216.78734 Neighbor list builds = 0 Dangerous builds = 0 3508 -13849.313210875 eV 2.21212308172272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:05