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 = 3.6056636 3.6056636 3.6056636 Created orthogonal box = (0.0000000 -37.816519 0.0000000) to (46.315587 37.816519 8.8320359) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8947111 5.5005845 5.8880240 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.816519 0.0000000) to (46.315587 37.816519 8.8320359) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8947111 5.5005845 5.8880240 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.816519 0.0000000) to (46.315587 37.816519 8.8320359) create_atoms CPU = 0.002 seconds 1323 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 13 20 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2640 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.459 | 6.459 | 6.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 39176.937 0 39176.937 11138095 448 0 -11187.449 0 -11187.449 -14738.702 Loop time of 15.6219 on 1 procs for 448 steps with 2640 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 = 39176.9372358813 -11187.4381360618 -11187.4491834461 Force two-norm initial, final = 198658.52 0.37552833 Force max component initial, final = 63487.433 0.040167890 Final line search alpha, max atom move = 1.0000000 0.040167890 Iterations, force evaluations = 448 793 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.802 | 14.802 | 14.802 | 0.0 | 94.75 Neigh | 0.65835 | 0.65835 | 0.65835 | 0.0 | 4.21 Comm | 0.067208 | 0.067208 | 0.067208 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09485 | | | 0.61 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8939.00 ave 8939 max 8939 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: 418792.0 ave 418792 max 418792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418792 Ave neighs/atom = 158.63333 Neighbor list builds = 24 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 448 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.459 | 6.459 | 6.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 448 0 -11187.449 0 -11187.449 -14738.702 30938.521 511 0 -11240.505 0 -11240.505 -130.79926 31021.984 Loop time of 1.233 on 1 procs for 63 steps with 2640 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11187.4491834461 -11240.5026464934 -11240.5048398355 Force two-norm initial, final = 1739.5607 10.838740 Force max component initial, final = 1120.2158 9.6090036 Final line search alpha, max atom move = 0.00013127877 0.0012614582 Iterations, force evaluations = 63 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1446 | 1.1446 | 1.1446 | 0.0 | 92.83 Neigh | 0.054187 | 0.054187 | 0.054187 | 0.0 | 4.39 Comm | 0.004864 | 0.004864 | 0.004864 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02934 | | | 2.38 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8689.00 ave 8689 max 8689 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: 436300.0 ave 436300 max 436300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436300 Ave neighs/atom = 165.26515 Neighbor list builds = 2 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.594 | 6.594 | 6.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11240.505 0 -11240.505 -130.79926 Loop time of 1.722e-06 on 1 procs for 0 steps with 2640 atoms 232.3% 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 | | 1.722e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8667.00 ave 8667 max 8667 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: 437316.0 ave 437316 max 437316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437316 Ave neighs/atom = 165.65000 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.594 | 6.594 | 6.594 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 -11240.505 -11240.505 44.975493 74.00163 9.3207819 -130.79926 -130.79926 -481.91218 194.28614 -104.77174 2.4166621 2514.3404 Loop time of 2.265e-06 on 1 procs for 0 steps with 2640 atoms 264.9% 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 | | 2.265e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8667.00 ave 8667 max 8667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218658.0 ave 218658 max 218658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 437316.0 ave 437316 max 437316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437316 Ave neighs/atom = 165.65000 Neighbor list builds = 0 Dangerous builds = 0 2640 -11240.5048398355 eV 2.4166620955519 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17