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 = 3.9946166 3.9946166 3.9946166 Created orthogonal box = (0.0000000 -48.432153 0.0000000) to (39.544687 48.432153 9.7847725) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6492410 5.6009973 6.5231816 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -48.432153 0.0000000) to (39.544687 48.432153 9.7847725) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6492410 5.6009973 6.5231816 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -48.432153 0.0000000) to (39.544687 48.432153 9.7847725) create_atoms CPU = 0.001 seconds 1184 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 11 26 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.955 | 5.955 | 5.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7487.3312 0 -7487.3312 7769.3976 65 0 -7648.7364 0 -7648.7364 -659.4384 Loop time of 2.93455 on 1 procs for 65 steps with 2336 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7487.3311940143 -7648.72974715925 -7648.73642557872 Force two-norm initial, final = 150.23529 0.15190250 Force max component initial, final = 24.747890 0.013145248 Final line search alpha, max atom move = 1.0000000 0.013145248 Iterations, force evaluations = 65 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8735 | 2.8735 | 2.8735 | 0.0 | 97.92 Neigh | 0.038132 | 0.038132 | 0.038132 | 0.0 | 1.30 Comm | 0.0094614 | 0.0094614 | 0.0094614 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0135 | | | 0.46 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7316.00 ave 7316 max 7316 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: 306080.0 ave 306080 max 306080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306080 Ave neighs/atom = 131.02740 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -7648.7364 0 -7648.7364 -659.4384 37480.264 67 0 -7648.7602 0 -7648.7602 28.393133 37414.721 Loop time of 0.107515 on 1 procs for 2 steps with 2336 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 = -7648.73642557872 -7648.75727788905 -7648.76018877549 Force two-norm initial, final = 31.492441 1.1813496 Force max component initial, final = 29.005403 0.84222908 Final line search alpha, max atom move = 0.00012500505 0.00010528288 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1058 | 0.1058 | 0.1058 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025764 | 0.00025764 | 0.00025764 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001454 | | | 1.35 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7331.00 ave 7331 max 7331 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: 306256.0 ave 306256 max 306256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306256 Ave neighs/atom = 131.10274 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 6.093 | 6.093 | 6.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7648.7602 0 -7648.7602 28.393133 Loop time of 2.134e-06 on 1 procs for 0 steps with 2336 atoms 187.4% 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 | | 2.134e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7331.00 ave 7331 max 7331 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: 306320.0 ave 306320 max 306320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306320 Ave neighs/atom = 131.13014 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 6.093 | 6.093 | 6.093 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 -7648.7602 -7648.7602 39.538947 96.861107 9.769402 28.393133 28.393133 26.067349 36.064817 23.047232 2.5256844 1571.5079 Loop time of 2.571e-06 on 1 procs for 0 steps with 2336 atoms 272.3% 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 | | 2.571e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7331.00 ave 7331 max 7331 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153160.0 ave 153160 max 153160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306320.0 ave 306320 max 306320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306320 Ave neighs/atom = 131.13014 Neighbor list builds = 0 Dangerous builds = 0 2336 -7648.76018877549 eV 2.52568435631955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03