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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -48.798657 0.0000000) to (39.843936 48.798657 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6919909 5.6433821 6.5725450 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -48.798657 0.0000000) to (39.843936 48.798657 9.8588175) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6919909 5.6433821 6.5725450 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -48.798657 0.0000000) to (39.843936 48.798657 9.8588175) create_atoms CPU = 0.001 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.996 | 5.996 | 5.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5690.8486 0 -5690.8486 31982.353 91 0 -6200.0429 0 -6200.0429 5873.512 Loop time of 3.04926 on 1 procs for 91 steps with 2352 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 = -5690.84860913883 -6200.0374010535 -6200.04291695311 Force two-norm initial, final = 566.91124 0.19421981 Force max component initial, final = 86.951064 0.020708479 Final line search alpha, max atom move = 1.0000000 0.020708479 Iterations, force evaluations = 91 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9726 | 2.9726 | 2.9726 | 0.0 | 97.49 Neigh | 0.043762 | 0.043762 | 0.043762 | 0.0 | 1.44 Comm | 0.01359 | 0.01359 | 0.01359 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01933 | | | 0.63 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8055.00 ave 8055 max 8055 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: 329728.0 ave 329728 max 329728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329728 Ave neighs/atom = 140.19048 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.996 | 5.996 | 5.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -6200.0429 0 -6200.0429 5873.512 38337.601 103 0 -6201.3947 0 -6201.3947 10.985353 38611.559 Loop time of 0.264224 on 1 procs for 12 steps with 2352 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 = -6200.04291695312 -6201.39352202165 -6201.39465421681 Force two-norm initial, final = 292.25227 0.81144439 Force max component initial, final = 272.23223 0.40621602 Final line search alpha, max atom move = 0.00022627335 9.1915860e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23555 | 0.23555 | 0.23555 | 0.0 | 89.15 Neigh | 0.021584 | 0.021584 | 0.021584 | 0.0 | 8.17 Comm | 0.0011212 | 0.0011212 | 0.0011212 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005965 | | | 2.26 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8056.00 ave 8056 max 8056 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: 328816.0 ave 328816 max 328816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328816 Ave neighs/atom = 139.80272 Neighbor list builds = 1 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.134 | 6.134 | 6.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6201.3947 0 -6201.3947 10.985353 Loop time of 2.122e-06 on 1 procs for 0 steps with 2352 atoms 188.5% 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 | | 2.122e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8062.00 ave 8062 max 8062 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: 328768.0 ave 328768 max 328768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328768 Ave neighs/atom = 139.78231 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.134 | 6.134 | 6.134 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 -6201.3947 -6201.3947 39.775153 98.702908 9.8350264 10.985353 10.985353 8.1888637 7.9520441 16.815151 2.5826522 1698.1778 Loop time of 2.448e-06 on 1 procs for 0 steps with 2352 atoms 245.1% 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 | | 2.448e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8062.00 ave 8062 max 8062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164384.0 ave 164384 max 164384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328768.0 ave 328768 max 328768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328768 Ave neighs/atom = 139.78231 Neighbor list builds = 0 Dangerous builds = 0 2352 -6129.1076673935 eV 2.58265221941134 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03