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 = 4.0497635 4.0497635 4.0497635 Created orthogonal box = (0.0000000 -73.344337 0.0000000) to (25.931139 73.344337 5.7272305) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9571349 6.2611020 5.7272305 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -73.344337 0.0000000) to (25.931139 73.344337 5.7272305) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9571349 6.2611020 5.7272305 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.344337 0.0000000) to (25.931139 73.344337 5.7272305) create_atoms CPU = 0.002 seconds 658 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 34 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_942551040047_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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.506 | 5.506 | 5.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4024.397 0 -4024.397 32137.571 165 0 -4349.5206 0 -4349.5206 1439.3941 Loop time of 3.73281 on 1 procs for 165 steps with 1312 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 = -4024.39702637791 -4349.51647001392 -4349.52062623617 Force two-norm initial, final = 519.94604 0.12490914 Force max component initial, final = 127.05582 0.012027144 Final line search alpha, max atom move = 1.0000000 0.012027144 Iterations, force evaluations = 165 286 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5945 | 3.5945 | 3.5945 | 0.0 | 96.29 Neigh | 0.089414 | 0.089414 | 0.089414 | 0.0 | 2.40 Comm | 0.027513 | 0.027513 | 0.027513 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02139 | | | 0.57 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 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: 226620.0 ave 226620 max 226620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226620 Ave neighs/atom = 172.72866 Neighbor list builds = 6 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 165 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.507 | 5.507 | 5.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 165 0 -4349.5206 0 -4349.5206 1439.3941 21785.265 168 0 -4349.5577 0 -4349.5577 52.810879 21824.231 Loop time of 0.0594375 on 1 procs for 3 steps with 1312 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 = -4349.52062623616 -4349.55738988011 -4349.55774300723 Force two-norm initial, final = 38.735656 2.0318955 Force max component initial, final = 33.068216 1.3959438 Final line search alpha, max atom move = 0.00026369265 0.00036810012 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057835 | 0.057835 | 0.057835 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031651 | 0.00031651 | 0.00031651 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001286 | | | 2.16 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 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: 226684.0 ave 226684 max 226684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226684 Ave neighs/atom = 172.77744 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.645 | 5.645 | 5.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4349.5577 0 -4349.5577 52.810879 Loop time of 2.07e-06 on 1 procs for 0 steps with 1312 atoms 193.2% 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 | | 2.07e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 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: 226480.0 ave 226480 max 226480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226480 Ave neighs/atom = 172.62195 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.645 | 5.645 | 5.645 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 -4349.5577 -4349.5577 25.982317 146.77865 5.7226631 52.810879 52.810879 102.68231 99.006598 -43.256269 2.6790466 793.66032 Loop time of 2.677e-06 on 1 procs for 0 steps with 1312 atoms 186.8% 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 | | 2.677e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113240.0 ave 113240 max 113240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226480.0 ave 226480 max 226480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226480 Ave neighs/atom = 172.62195 Neighbor list builds = 0 Dangerous builds = 0 1312 -4349.55774300723 eV 2.67904659164469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04