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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -49.103642 0.0000000) to (40.092956 49.103642 9.9204338) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7275651 5.6786525 6.6136225 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -49.103642 0.0000000) to (40.092956 49.103642 9.9204338) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7275651 5.6786525 6.6136225 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.103642 0.0000000) to (40.092956 49.103642 9.9204338) create_atoms CPU = 0.002 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 24 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 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_678952612413_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 = 10 24 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) = 6.023 | 6.023 | 6.023 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7761.7636 0 -7761.7636 125.72895 81 0 -7824.5489 0 -7824.5489 -1303.7229 Loop time of 3.03515 on 1 procs for 81 steps with 2336 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7761.76360642583 -7824.54194712738 -7824.54891233056 Force two-norm initial, final = 27.045478 0.20654859 Force max component initial, final = 3.3643873 0.022040165 Final line search alpha, max atom move = 1.0000000 0.022040165 Iterations, force evaluations = 81 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9544 | 2.9544 | 2.9544 | 0.0 | 97.34 Neigh | 0.048423 | 0.048423 | 0.048423 | 0.0 | 1.60 Comm | 0.013565 | 0.013565 | 0.013565 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01874 | | | 0.62 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8355.00 ave 8355 max 8355 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: 330816.0 ave 330816 max 330816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330816 Ave neighs/atom = 141.61644 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 24 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.021 | 6.021 | 6.021 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -7824.5489 0 -7824.5489 -1303.7229 39060.918 84 0 -7824.6011 0 -7824.6011 1.7392149 38996.025 Loop time of 0.118981 on 1 procs for 3 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 = -7824.54891233051 -7824.60089429236 -7824.60106511908 Force two-norm initial, final = 61.564917 0.55018235 Force max component initial, final = 52.004343 0.35986137 Final line search alpha, max atom move = 0.00027369065 9.8490693e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1161 | 0.1161 | 0.1161 | 0.0 | 97.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040739 | 0.00040739 | 0.00040739 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002468 | | | 2.07 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 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: 330160.0 ave 330160 max 330160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330160 Ave neighs/atom = 141.33562 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 = 10 24 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) = 6.158 | 6.158 | 6.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7824.6011 0 -7824.6011 1.7392149 Loop time of 2.386e-06 on 1 procs for 0 steps with 2336 atoms 167.6% 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 | | 2.386e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 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: 330336.0 ave 330336 max 330336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330336 Ave neighs/atom = 141.41096 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 = 10 24 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) = 6.158 | 6.158 | 6.158 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 -7824.6011 -7824.6011 40.073794 98.278782 9.90148 1.7392149 1.7392149 -14.778067 9.8570607 10.138651 2.5819254 1814.2397 Loop time of 2.513e-06 on 1 procs for 0 steps with 2336 atoms 238.8% 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 | | 2.513e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165168.0 ave 165168 max 165168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330336.0 ave 330336 max 330336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330336 Ave neighs/atom = 141.41096 Neighbor list builds = 0 Dangerous builds = 0 2336 -7824.60106511908 eV 2.58192541861947 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03