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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4756345 5.6201938 6.0992294 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4756345 5.6201938 6.0992294 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) create_atoms CPU = 0.003 seconds 1610 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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_008996216289_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.861 | 5.861 | 5.861 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13723.309 0 -13723.309 48114.613 147 0 -14269.342 0 -14269.342 9358.8938 Loop time of 42.6988 on 1 procs for 147 steps with 3218 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13723.3086968019 -14269.3291643038 -14269.3421443808 Force two-norm initial, final = 497.81876 0.46940602 Force max component initial, final = 85.021153 0.074344260 Final line search alpha, max atom move = 1.0000000 0.074344260 Iterations, force evaluations = 147 270 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.496 | 42.496 | 42.496 | 0.0 | 99.53 Neigh | 0.11125 | 0.11125 | 0.11125 | 0.0 | 0.26 Comm | 0.042982 | 0.042982 | 0.042982 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0485 | | | 0.11 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11252.0 ave 11252 max 11252 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: 281348.0 ave 281348 max 281348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281348 Ave neighs/atom = 87.429459 Neighbor list builds = 5 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 147 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.872 | 5.872 | 5.872 Mbytes Step Temp E_pair E_mol TotEng Press Volume 147 0 -14269.342 0 -14269.342 9358.8938 35107.433 154 0 -14270.465 0 -14270.465 -23.474555 35282.174 Loop time of 1.46691 on 1 procs for 7 steps with 3218 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 = -14269.3421443808 -14270.4645906188 -14270.4650421708 Force two-norm initial, final = 436.84157 2.2601466 Force max component initial, final = 406.72101 1.8072854 Final line search alpha, max atom move = 0.00012686220 0.00022927620 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4601 | 1.4601 | 1.4601 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096381 | 0.00096381 | 0.00096381 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005859 | | | 0.40 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12207.0 ave 12207 max 12207 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: 280656.0 ave 280656 max 280656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280656 Ave neighs/atom = 87.214419 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.010 | 6.010 | 6.010 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14270.465 0 -14270.465 -23.474555 Loop time of 2.616e-06 on 1 procs for 0 steps with 3218 atoms 191.1% 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 | | 2.616e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12183.0 ave 12183 max 12183 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: 280076.0 ave 280076 max 280076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280076 Ave neighs/atom = 87.034183 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.010 | 6.010 | 6.010 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 -14270.465 -14270.465 40.768853 142.00606 6.0942459 -23.474555 -23.474555 -82.081167 -31.162071 42.819573 2.2336974 958.92476 Loop time of 2.809e-06 on 1 procs for 0 steps with 3218 atoms 249.2% 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 | | 2.809e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12183.0 ave 12183 max 12183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140038.0 ave 140038 max 140038 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280076.0 ave 280076 max 280076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280076 Ave neighs/atom = 87.034183 Neighbor list builds = 0 Dangerous builds = 0 3218 -14270.4650421708 eV 2.23369743141055 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:45