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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1045080 6.2786022 5.1464435 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1045080 6.2786022 5.1464435 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) create_atoms CPU = 0.002 seconds 690 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1372 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_120596890176_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.360 | 6.360 | 6.360 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4203.5662 0 -4203.5662 51358.864 56 0 -4496.0571 0 -4496.0571 -617.06177 Loop time of 1.91417 on 1 procs for 56 steps with 1372 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 = -4203.56618032078 -4496.05325751172 -4496.05707089464 Force two-norm initial, final = 768.46514 0.15352746 Force max component initial, final = 265.13374 0.010555029 Final line search alpha, max atom move = 1.0000000 0.010555029 Iterations, force evaluations = 56 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8217 | 1.8217 | 1.8217 | 0.0 | 95.17 Neigh | 0.074147 | 0.074147 | 0.074147 | 0.0 | 3.87 Comm | 0.010621 | 0.010621 | 0.010621 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007695 | | | 0.40 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436800.0 ave 436800 max 436800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436800 Ave neighs/atom = 318.36735 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.365 | 6.365 | 6.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -4496.0571 0 -4496.0571 -617.06177 16578.112 57 0 -4496.0607 0 -4496.0607 273.23923 16567.85 Loop time of 0.0685812 on 1 procs for 1 steps with 1372 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 = -4496.05707089464 -4496.05707089464 -4496.06065314279 Force two-norm initial, final = 14.899605 7.2822230 Force max component initial, final = 13.347408 6.5997805 Final line search alpha, max atom move = 7.4920914e-05 0.00049446159 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0673 | 0.0673 | 0.0673 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028051 | 0.00028051 | 0.00028051 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001 | | | 1.46 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436700.0 ave 436700 max 436700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436700 Ave neighs/atom = 318.29446 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4496.0607 0 -4496.0607 273.23923 Loop time of 2.311e-06 on 1 procs for 0 steps with 1372 atoms 216.4% 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 | | 2.311e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436740.0 ave 436740 max 436740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436740 Ave neighs/atom = 318.32362 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 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 -4496.0607 -4496.0607 23.863669 134.96126 5.1442234 273.23923 273.23923 638.24065 280.29825 -98.821204 2.3541897 370.4825 Loop time of 2.895e-06 on 1 procs for 0 steps with 1372 atoms 241.8% 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 | | 2.895e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218370.0 ave 218370 max 218370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436740.0 ave 436740 max 436740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436740 Ave neighs/atom = 318.32362 Neighbor list builds = 0 Dangerous builds = 0 1372 -4496.06065314279 eV 2.35418972891064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02