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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7504087 4.7438451 4.9800000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7504087 4.7438451 4.9800000 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) create_atoms CPU = 0.001 seconds 440 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 864 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_500937681860_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3663.3504 0 -3663.3504 63469.639 51 0 -3825.6949 0 -3825.6949 12576.969 Loop time of 4.28797 on 1 procs for 51 steps with 864 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 = -3663.35041421111 -3825.69152100272 -3825.69492494169 Force two-norm initial, final = 235.51847 0.19442074 Force max component initial, final = 36.584488 0.019856814 Final line search alpha, max atom move = 1.0000000 0.019856814 Iterations, force evaluations = 51 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2687 | 4.2687 | 4.2687 | 0.0 | 99.55 Neigh | 0.0067485 | 0.0067485 | 0.0067485 | 0.0 | 0.16 Comm | 0.0065698 | 0.0065698 | 0.0065698 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005989 | | | 0.14 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4818.00 ave 4818 max 4818 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: 77488.0 ave 77488 max 77488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77488 Ave neighs/atom = 89.685185 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -3825.6949 0 -3825.6949 12576.969 9431.8479 68 0 -3826.8047 0 -3826.8047 -107.05405 9494.3749 Loop time of 1.07946 on 1 procs for 17 steps with 864 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 = -3825.69492494169 -3826.80462231778 -3826.80466303386 Force two-norm initial, final = 182.17722 1.3128560 Force max component initial, final = 169.46636 0.92065707 Final line search alpha, max atom move = 0.010838360 0.0099784130 Iterations, force evaluations = 17 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0661 | 1.0661 | 1.0661 | 0.0 | 98.76 Neigh | 0.006389 | 0.006389 | 0.006389 | 0.0 | 0.59 Comm | 0.001174 | 0.001174 | 0.001174 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00577 | | | 0.53 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4883.00 ave 4883 max 4883 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: 75280.0 ave 75280 max 75280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75280 Ave neighs/atom = 87.129630 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.705 | 4.705 | 4.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3826.8047 0 -3826.8047 -107.05405 Loop time of 2.207e-06 on 1 procs for 0 steps with 864 atoms 181.2% 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 | | 2.207e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4883.00 ave 4883 max 4883 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: 75280.0 ave 75280 max 75280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75280 Ave neighs/atom = 87.129630 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.705 | 4.705 | 4.705 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 -3826.8047 -3826.8047 25.72953 74.158055 4.9759521 -107.05405 -107.05405 -19.038865 -146.88863 -155.23467 2.3717931 689.17293 Loop time of 3.432e-06 on 1 procs for 0 steps with 864 atoms 262.2% 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 | | 3.432e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4883.00 ave 4883 max 4883 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37640.0 ave 37640 max 37640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75280.0 ave 75280 max 75280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75280 Ave neighs/atom = 87.129630 Neighbor list builds = 0 Dangerous builds = 0 864 -3826.80466303386 eV 2.37179308574994 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05