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 -38.107034 0.0000000) to (46.666945 38.107034 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9394294 5.5423129 5.9326915 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -38.107034 0.0000000) to (46.666945 38.107034 8.8990373) create_atoms CPU = 0.006 seconds 1322 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9394294 5.5423129 5.9326915 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -38.107034 0.0000000) to (46.666945 38.107034 8.8990373) create_atoms CPU = 0.005 seconds 1322 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 = 13 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 2604 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 = 13 20 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) = 6.476 | 6.476 | 6.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10940.952 0 -10940.952 10510.395 89 0 -11068.507 0 -11068.507 -14658.88 Loop time of 6.80517 on 1 procs for 89 steps with 2604 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 = -10940.9519958874 -11068.4974738959 -11068.5074932005 Force two-norm initial, final = 98.211444 0.42057002 Force max component initial, final = 15.074413 0.056322413 Final line search alpha, max atom move = 1.0000000 0.056322413 Iterations, force evaluations = 89 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6042 | 6.6042 | 6.6042 | 0.0 | 97.05 Neigh | 0.11945 | 0.11945 | 0.11945 | 0.0 | 1.76 Comm | 0.035607 | 0.035607 | 0.035607 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04587 | | | 0.67 Nlocal: 2604.00 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8843.00 ave 8843 max 8843 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: 394092.0 ave 394092 max 394092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394092 Ave neighs/atom = 151.34101 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 13 20 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.476 | 6.476 | 6.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -11068.507 0 -11068.507 -14658.88 31651.008 95 0 -11069.509 0 -11069.509 -5117.9031 31444.967 Loop time of 0.307666 on 1 procs for 6 steps with 2604 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 = -11068.5074932006 -11069.5000490289 -11069.5087757205 Force two-norm initial, final = 361.19987 6.2298644 Force max component initial, final = 341.64077 5.7996123 Final line search alpha, max atom move = 3.5265663e-05 0.00020452718 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29939 | 0.29939 | 0.29939 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014375 | 0.0014375 | 0.0014375 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006835 | | | 2.22 Nlocal: 2604.00 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8790.00 ave 8790 max 8790 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: 396024.0 ave 396024 max 396024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396024 Ave neighs/atom = 152.08295 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 = 13 20 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) = 6.614 | 6.614 | 6.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11069.509 0 -11069.509 -5117.9031 Loop time of 6.565e-06 on 1 procs for 0 steps with 2604 atoms 198.0% 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 | | 6.565e-06 | | |100.00 Nlocal: 2604.00 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8790.00 ave 8790 max 8790 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: 411650.0 ave 411650 max 411650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411650 Ave neighs/atom = 158.08372 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 = 13 20 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) = 6.614 | 6.614 | 6.614 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 -11069.509 -11069.509 46.408324 76.214069 8.8903756 -5117.9031 -5117.9031 107.40126 -15756.324 295.21285 2.3482819 1968.5665 Loop time of 7.768e-06 on 1 procs for 0 steps with 2604 atoms 296.1% 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 | | 7.768e-06 | | |100.00 Nlocal: 2604.00 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8790.00 ave 8790 max 8790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205825.0 ave 205825 max 205825 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411650.0 ave 411650 max 411650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411650 Ave neighs/atom = 158.08372 Neighbor list builds = 0 Dangerous builds = 0 2604 -11069.5087757205 eV 2.34828194508903 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08