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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -49.805980 0.0000000) to (17.609073 49.805980 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4875533 5.2427348 5.7131378 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -49.805980 0.0000000) to (17.609073 49.805980 5.7131378) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4875533 5.2427348 5.7131378 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -49.805980 0.0000000) to (17.609073 49.805980 5.7131378) create_atoms CPU = 0.001 seconds 306 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 606 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.408 | 5.408 | 5.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1571.4466 0 -1571.4466 25162.76 138 0 -1741.6106 0 -1741.6106 -24.350993 Loop time of 2.99825 on 1 procs for 138 steps with 606 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1571.4466469267 -1741.60895099095 -1741.61061334199 Force two-norm initial, final = 263.72550 0.12778482 Force max component initial, final = 84.065862 0.019020180 Final line search alpha, max atom move = 1.0000000 0.019020180 Iterations, force evaluations = 138 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.92 | 2.92 | 2.92 | 0.0 | 97.39 Neigh | 0.045333 | 0.045333 | 0.045333 | 0.0 | 1.51 Comm | 0.020894 | 0.020894 | 0.020894 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01201 | | | 0.40 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8608.00 ave 8608 max 8608 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: 245804.0 ave 245804 max 245804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245804 Ave neighs/atom = 405.61716 Neighbor list builds = 3 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 138 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.410 | 5.410 | 5.410 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -1741.6106 0 -1741.6106 -24.350993 10021.268 140 0 -1741.6179 0 -1741.6179 -25.585851 10021.207 Loop time of 0.0422489 on 1 procs for 2 steps with 606 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 = -1741.61061334199 -1741.61790709363 -1741.61791677986 Force two-norm initial, final = 10.792060 0.32214161 Force max component initial, final = 7.9982979 0.20309226 Final line search alpha, max atom move = 0.0035402847 0.00071900444 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041148 | 0.041148 | 0.041148 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002499 | 0.0002499 | 0.0002499 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008507 | | | 2.01 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 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: 245384.0 ave 245384 max 245384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245384 Ave neighs/atom = 404.92409 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.548 | 5.548 | 5.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1741.6179 0 -1741.6179 -25.585851 Loop time of 2.111e-06 on 1 procs for 0 steps with 606 atoms 142.1% 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 | | 2.111e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 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: 244212.0 ave 244212 max 244212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244212 Ave neighs/atom = 402.99010 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.548 | 5.548 | 5.548 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 -1741.6179 -1741.6179 17.591428 99.62136 5.7182941 -25.585851 -25.585851 -31.065077 -13.193065 -32.49941 2.6802999 608.55544 Loop time of 2.349e-06 on 1 procs for 0 steps with 606 atoms 170.3% 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 | | 2.349e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122106.0 ave 122106 max 122106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 244212.0 ave 244212 max 244212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244212 Ave neighs/atom = 402.99010 Neighbor list builds = 0 Dangerous builds = 0 606 -1741.61791677986 eV 2.680299861733 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03