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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481360 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222040) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481360 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222040) create_atoms CPU = 0.002 seconds 1756 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 3492 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15285.047 0 -15285.047 4486.1692 79 0 -15484.011 0 -15484.011 1287.8532 Loop time of 5.80634 on 1 procs for 79 steps with 3492 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15285.0465225753 -15483.9961352344 -15484.0113383942 Force two-norm initial, final = 48.514952 0.40564302 Force max component initial, final = 3.8185252 0.022504277 Final line search alpha, max atom move = 1.0000000 0.022504277 Iterations, force evaluations = 79 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7041 | 5.7041 | 5.7041 | 0.0 | 98.24 Neigh | 0.048715 | 0.048715 | 0.048715 | 0.0 | 0.84 Comm | 0.023348 | 0.023348 | 0.023348 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03016 | | | 0.52 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13105.0 ave 13105 max 13105 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: 785556.0 ave 785556 max 785556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785556 Ave neighs/atom = 224.95876 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.18 | 12.18 | 12.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -15484.011 0 -15484.011 1287.8532 38206.047 80 0 -15484.026 0 -15484.026 -153.93924 38236.956 Loop time of 0.117405 on 1 procs for 1 steps with 3492 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 = -15484.0113383942 -15484.0113383942 -15484.0259108906 Force two-norm initial, final = 57.707516 16.076358 Force max component initial, final = 41.688029 15.543125 Final line search alpha, max atom move = 2.3987701e-05 0.00037284383 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11533 | 0.11533 | 0.11533 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034478 | 0.00034478 | 0.00034478 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001729 | | | 1.47 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13132.0 ave 13132 max 13132 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: 785676.0 ave 785676 max 785676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785676 Ave neighs/atom = 224.99313 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.69 | 11.69 | 11.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15484.026 0 -15484.026 -153.93924 Loop time of 2.51e-06 on 1 procs for 0 steps with 3492 atoms 199.2% 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 | | 2.51e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13131.0 ave 13131 max 13131 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: 785566.0 ave 785566 max 785566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785566 Ave neighs/atom = 224.96163 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.69 | 11.69 | 11.69 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 -15484.026 -15484.026 52.110307 85.074036 8.6250702 -153.93924 -153.93924 170.17233 -651.34835 19.358308 2.2882918 1450.5864 Loop time of 2.638e-06 on 1 procs for 0 steps with 3492 atoms 303.3% 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 | | 2.638e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13131.0 ave 13131 max 13131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 392783.0 ave 392783 max 392783 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 785566.0 ave 785566 max 785566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785566 Ave neighs/atom = 224.96163 Neighbor list builds = 0 Dangerous builds = 0 3492 -15484.0259108906 eV 2.2882917864164 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06