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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -64.620291 0.0000000) to (37.308543 64.620291 6.3365409) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7397758 5.7992569 6.3365409 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -64.620291 0.0000000) to (37.308543 64.620291 6.3365409) create_atoms CPU = 0.002 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7397758 5.7992569 6.3365409 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -64.620291 0.0000000) to (37.308543 64.620291 6.3365409) create_atoms CPU = 0.002 seconds 1251 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2498 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_143977152728_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.119 | 6.119 | 6.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9164.9078 0 -9164.9078 53117.05 754 0 -9832.1486 0 -9832.1486 -54813.726 Loop time of 24.1439 on 1 procs for 754 steps with 2498 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 = -9164.90778438448 -9832.13901457744 -9832.14855481258 Force two-norm initial, final = 1394.9042 0.56513422 Force max component initial, final = 622.10733 0.16452607 Final line search alpha, max atom move = 0.76134668 0.12526138 Iterations, force evaluations = 754 1482 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.599 | 23.599 | 23.599 | 0.0 | 97.74 Neigh | 0.2364 | 0.2364 | 0.2364 | 0.0 | 0.98 Comm | 0.15449 | 0.15449 | 0.15449 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.154 | | | 0.64 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10287.0 ave 10287 max 10287 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: 339472.0 ave 339472 max 339472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339472 Ave neighs/atom = 135.89752 Neighbor list builds = 12 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 754 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.119 | 6.119 | 6.119 Mbytes Step Temp E_pair E_mol TotEng Press Volume 754 0 -9832.1486 0 -9832.1486 -54813.726 30553.392 782 0 -9858.271 0 -9858.271 -27.630596 29392.277 Loop time of 0.540887 on 1 procs for 28 steps with 2498 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 = -9832.14855481254 -9858.26922348769 -9858.2710486023 Force two-norm initial, final = 1882.4644 6.9634066 Force max component initial, final = 1387.9556 4.2914252 Final line search alpha, max atom move = 0.00025051644 0.0010750726 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48235 | 0.48235 | 0.48235 | 0.0 | 89.18 Neigh | 0.042259 | 0.042259 | 0.042259 | 0.0 | 7.81 Comm | 0.0028544 | 0.0028544 | 0.0028544 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01343 | | | 2.48 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10399.0 ave 10399 max 10399 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: 353924.0 ave 353924 max 353924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353924 Ave neighs/atom = 141.68295 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.256 | 6.256 | 6.256 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9858.271 0 -9858.271 -27.630596 Loop time of 1.853e-06 on 1 procs for 0 steps with 2498 atoms 161.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10386.0 ave 10386 max 10386 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: 353536.0 ave 353536 max 353536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353536 Ave neighs/atom = 141.52762 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.256 | 6.256 | 6.256 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 -9858.271 -9858.271 36.308715 127.35984 6.3560871 -27.630596 -27.630596 126.33856 25.417333 -234.64768 2.1953568 6704.9536 Loop time of 2.204e-06 on 1 procs for 0 steps with 2498 atoms 181.5% 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 | | 2.204e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10386.0 ave 10386 max 10386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176768.0 ave 176768 max 176768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 353536.0 ave 353536 max 353536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353536 Ave neighs/atom = 141.52762 Neighbor list builds = 0 Dangerous builds = 0 2498 -9858.2710486023 eV 2.19535684995812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:25