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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -60.602700 0.0000000) to (24.739520 60.602700 8.5700212) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9374849 5.2519308 5.7133475 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.602700 0.0000000) to (24.739520 60.602700 8.5700212) create_atoms CPU = 0.006 seconds 1205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9374849 5.2519308 5.7133475 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.602700 0.0000000) to (24.739520 60.602700 8.5700212) create_atoms CPU = 0.005 seconds 1205 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 32 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2384 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.490 | 6.490 | 6.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9739.6228 0 -9739.6228 9218.5258 29 0 -9790.3589 0 -9790.3589 -6123.9559 Loop time of 2.54501 on 1 procs for 29 steps with 2384 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9739.62280451505 -9790.35135837789 -9790.35890326617 Force two-norm initial, final = 63.284862 0.31818422 Force max component initial, final = 10.973555 0.071428041 Final line search alpha, max atom move = 1.0000000 0.071428041 Iterations, force evaluations = 29 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4565 | 2.4565 | 2.4565 | 0.0 | 96.52 Neigh | 0.062389 | 0.062389 | 0.062389 | 0.0 | 2.45 Comm | 0.01237 | 0.01237 | 0.01237 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01376 | | | 0.54 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 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: 416474.0 ave 416474 max 416474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416474 Ave neighs/atom = 174.69547 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.490 | 6.490 | 6.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -9790.3589 0 -9790.3589 -6123.9559 25697.753 32 0 -9790.5229 0 -9790.5229 -1955.2722 25604.948 Loop time of 0.221105 on 1 procs for 3 steps with 2384 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 = -9790.35890326614 -9790.51402295305 -9790.52285145082 Force two-norm initial, final = 117.34053 5.1012158 Force max component initial, final = 104.83002 5.0703633 Final line search alpha, max atom move = 3.8780696e-05 0.00019663222 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2163 | 0.2163 | 0.2163 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096627 | 0.00096627 | 0.00096627 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003835 | | | 1.73 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 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: 416590.0 ave 416590 max 416590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416590 Ave neighs/atom = 174.74413 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.628 | 6.628 | 6.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9790.5229 0 -9790.5229 -1955.2722 Loop time of 7.156e-06 on 1 procs for 0 steps with 2384 atoms 181.7% 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 | | 7.156e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 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: 416820.0 ave 416820 max 416820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416820 Ave neighs/atom = 174.84060 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.628 | 6.628 | 6.628 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 -9790.5229 -9790.5229 24.716401 121.2054 8.5470588 -1955.2722 -1955.2722 316.97098 -6158.0668 -24.720879 2.311844 543.82636 Loop time of 7.076e-06 on 1 procs for 0 steps with 2384 atoms 254.4% 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 | | 7.076e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 208410.0 ave 208410 max 208410 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 416820.0 ave 416820 max 416820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416820 Ave neighs/atom = 174.84060 Neighbor list builds = 0 Dangerous builds = 0 2384 -9790.52285145082 eV 2.31184397005763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03