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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -42.986434 0.0000000) to (52.647415 42.986434 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0168474 5.5268272 5.9326915 Created 1674 atoms using lattice units in orthogonal box = (0.0000000 -42.986434 0.0000000) to (52.647415 42.986434 8.8990373) create_atoms CPU = 0.002 seconds 1674 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0168474 5.5268272 5.9326915 Created 1698 atoms using lattice units in orthogonal box = (0.0000000 -42.986434 0.0000000) to (52.647415 42.986434 8.8990373) create_atoms CPU = 0.002 seconds 1698 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 3360 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.970 | 6.970 | 6.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13484.996 0 -13484.996 66230.935 59 0 -14305.31 0 -14305.31 6395.491 Loop time of 2.52676 on 1 procs for 59 steps with 3360 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13484.9961034707 -14305.2960969639 -14305.3101013587 Force two-norm initial, final = 521.45194 0.45929445 Force max component initial, final = 49.491864 0.045869712 Final line search alpha, max atom move = 1.0000000 0.045869712 Iterations, force evaluations = 59 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4632 | 2.4632 | 2.4632 | 0.0 | 97.48 Neigh | 0.03324 | 0.03324 | 0.03324 | 0.0 | 1.32 Comm | 0.012203 | 0.012203 | 0.012203 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01815 | | | 0.72 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10736.0 ave 10736 max 10736 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: 569242.0 ave 569242 max 569242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569242 Ave neighs/atom = 169.41726 Neighbor list builds = 1 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.967 | 6.967 | 6.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -14305.31 0 -14305.31 6395.491 40279.261 66 0 -14306.544 0 -14306.544 19.068003 40439.653 Loop time of 0.215312 on 1 procs for 7 steps with 3360 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 = -14305.3101013587 -14306.5429880293 -14306.5443921333 Force two-norm initial, final = 416.69808 1.3100155 Force max component initial, final = 413.87060 0.55766229 Final line search alpha, max atom move = 0.00011492287 6.4088148e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20866 | 0.20866 | 0.20866 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084798 | 0.00084798 | 0.00084798 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005799 | | | 2.69 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10325.0 ave 10325 max 10325 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: 563886.0 ave 563886 max 563886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 563886 Ave neighs/atom = 167.82321 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.105 | 7.105 | 7.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14306.544 0 -14306.544 19.068003 Loop time of 2.417e-06 on 1 procs for 0 steps with 3360 atoms 206.9% 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 | | 2.417e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10342.0 ave 10342 max 10342 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: 557000.0 ave 557000 max 557000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557000 Ave neighs/atom = 165.77381 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.105 | 7.105 | 7.105 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 -14306.544 -14306.544 52.600799 86.503628 8.8875233 19.068003 19.068003 16.792626 18.345976 22.065407 2.4025078 1538.5068 Loop time of 2.997e-06 on 1 procs for 0 steps with 3360 atoms 233.6% 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 | | 2.997e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10342.0 ave 10342 max 10342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278500.0 ave 278500 max 278500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 557000.0 ave 557000 max 557000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557000 Ave neighs/atom = 165.77381 Neighbor list builds = 0 Dangerous builds = 0 3360 -14306.5443921333 eV 2.40250783972538 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03