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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -69.989405 0.0000000) to (40.408402 69.989405 6.3365430) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618954 5.3543807 6.3365430 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.989405 0.0000000) to (40.408402 69.989405 6.3365430) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618954 5.3543807 6.3365430 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.989405 0.0000000) to (40.408402 69.989405 6.3365430) create_atoms CPU = 0.003 seconds 1465 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2925 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.213 | 6.213 | 6.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10371.879 0 -10371.879 73533.152 855 0 -11549.178 0 -11549.178 -66304.947 Loop time of 34.368 on 1 procs for 855 steps with 2925 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 = -10371.8789855264 -11549.1679924567 -11549.1779348492 Force two-norm initial, final = 1877.5234 0.29715324 Force max component initial, final = 468.86885 0.061210781 Final line search alpha, max atom move = 0.91781915 0.056180427 Iterations, force evaluations = 855 1662 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.503 | 33.503 | 33.503 | 0.0 | 97.48 Neigh | 0.39535 | 0.39535 | 0.39535 | 0.0 | 1.15 Comm | 0.23385 | 0.23385 | 0.23385 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2361 | | | 0.69 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11615.0 ave 11615 max 11615 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: 395758.0 ave 395758 max 395758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395758 Ave neighs/atom = 135.30188 Neighbor list builds = 16 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 855 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.593 | 6.593 | 6.593 Mbytes Step Temp E_pair E_mol TotEng Press Volume 855 0 -11549.178 0 -11549.178 -66304.947 35841.516 883 0 -11591.187 0 -11591.187 -2.3021845 34245.22 Loop time of 0.671167 on 1 procs for 28 steps with 2925 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 = -11549.1779348491 -11591.1838790569 -11591.1874540563 Force two-norm initial, final = 2654.4335 5.1510295 Force max component initial, final = 1785.5195 1.4555133 Final line search alpha, max atom move = 9.0801641e-05 0.00013216300 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57649 | 0.57649 | 0.57649 | 0.0 | 85.89 Neigh | 0.075239 | 0.075239 | 0.075239 | 0.0 | 11.21 Comm | 0.0035474 | 0.0035474 | 0.0035474 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01589 | | | 2.37 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11753.0 ave 11753 max 11753 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: 412232.0 ave 412232 max 412232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412232 Ave neighs/atom = 140.93402 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.730 | 6.730 | 6.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11591.187 0 -11591.187 -2.3021845 Loop time of 2.193e-06 on 1 procs for 0 steps with 2925 atoms 182.4% 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 | | 2.193e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11700.0 ave 11700 max 11700 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: 412314.0 ave 412314 max 412314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412314 Ave neighs/atom = 140.96205 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.730 | 6.730 | 6.730 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 -11591.187 -11591.187 39.470046 136.47484 6.3574028 -2.3021845 -2.3021845 27.2233 34.1911 -68.320954 2.2230465 9915.1309 Loop time of 2.379e-06 on 1 procs for 0 steps with 2925 atoms 252.2% 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 | | 2.379e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11700.0 ave 11700 max 11700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206157.0 ave 206157 max 206157 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412314.0 ave 412314 max 412314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412314 Ave neighs/atom = 140.96205 Neighbor list builds = 0 Dangerous builds = 0 2925 -11591.1874540563 eV 2.22304653205219 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35