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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1174 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.002 seconds 1174 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.001 seconds 1182 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2342 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_694335101831_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8014.0872 0 -8014.0872 29097.059 21 0 -8250.9571 0 -8250.9571 3328.4607 Loop time of 2.48295 on 1 procs for 21 steps with 2342 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8014.08717623822 -8250.94895204574 -8250.95713646702 Force two-norm initial, final = 310.14567 0.31753237 Force max component initial, final = 53.795725 0.061162397 Final line search alpha, max atom move = 1.0000000 0.061162397 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4748 | 2.4748 | 2.4748 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032087 | 0.0032087 | 0.0032087 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004982 | | | 0.20 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7233.00 ave 7233 max 7233 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: 308212.0 ave 308212 max 308212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308212 Ave neighs/atom = 131.60205 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -8250.9571 0 -8250.9571 3328.4607 27739.27 26 0 -8251.2147 0 -8251.2147 -234.28427 27809.142 Loop time of 0.477019 on 1 procs for 5 steps with 2342 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 = -8250.95713646703 -8251.21309513468 -8251.21472434245 Force two-norm initial, final = 132.74497 8.1510175 Force max component initial, final = 125.71032 6.9357922 Final line search alpha, max atom move = 0.00011146738 0.00077311459 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47409 | 0.47409 | 0.47409 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040434 | 0.00040434 | 0.00040434 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00252 | | | 0.53 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7261.00 ave 7261 max 7261 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: 301464.0 ave 301464 max 301464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301464 Ave neighs/atom = 128.72075 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.096 | 6.096 | 6.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8251.2147 0 -8251.2147 -234.28427 Loop time of 2.051e-06 on 1 procs for 0 steps with 2342 atoms 146.3% 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 | | 2.051e-06 | | |100.00 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7271.00 ave 7271 max 7271 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: 301208.0 ave 301208 max 301208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301208 Ave neighs/atom = 128.61144 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.096 | 6.096 | 6.096 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 -8251.2147 -8251.2147 35.754841 87.994744 8.8388548 -234.28427 -234.28427 -399.42455 -68.356434 -235.07182 2.2692893 1468.0758 Loop time of 1.99e-06 on 1 procs for 0 steps with 2342 atoms 201.0% 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 | | 1.99e-06 | | |100.00 Nlocal: 2342.00 ave 2342 max 2342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7271.00 ave 7271 max 7271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150604.0 ave 150604 max 150604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 301208.0 ave 301208 max 301208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301208 Ave neighs/atom = 128.61144 Neighbor list builds = 0 Dangerous builds = 0 2342 -8251.21472434245 eV 2.26928931521732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03