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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -66.588978 0.0000000) to (33.292684 66.588978 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0918222 5.0918222 3.6110985 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.588978 0.0000000) to (33.292684 66.588978 3.6110985) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0918222 5.0918222 3.6110985 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.588978 0.0000000) to (33.292684 66.588978 3.6110985) create_atoms CPU = 0.003 seconds 682 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 = 10 40 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1358 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_110119204723_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 = 10 40 2 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) = 5.090 | 5.090 | 5.090 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5688.4645 0 -5688.4645 16756.261 144 0 -5753.0856 0 -5753.0856 -83.521339 Loop time of 56.4075 on 1 procs for 144 steps with 1358 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 = -5688.46447156043 -5753.0808094274 -5753.08563639925 Force two-norm initial, final = 46.003172 0.21010444 Force max component initial, final = 12.021298 0.064442233 Final line search alpha, max atom move = 1.0000000 0.064442233 Iterations, force evaluations = 144 252 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.258 | 56.258 | 56.258 | 0.0 | 99.73 Neigh | 0.047078 | 0.047078 | 0.047078 | 0.0 | 0.08 Comm | 0.056476 | 0.056476 | 0.056476 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04593 | | | 0.08 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9137.00 ave 9137 max 9137 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: 171414.0 ave 171414 max 171414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171414 Ave neighs/atom = 126.22533 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 40 2 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 : 144 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press Volume 144 0 -5753.0856 0 -5753.0856 -83.521339 16011.075 150 0 -5753.2757 0 -5753.2757 -1814.778 16027.133 Loop time of 1.87133 on 1 procs for 6 steps with 1358 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 = -5753.08563639925 -5753.2710244949 -5753.27568943827 Force two-norm initial, final = 48.508268 0.32751665 Force max component initial, final = 36.773551 0.063624464 Final line search alpha, max atom move = 0.00016352095 1.0403933e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8626 | 1.8626 | 1.8626 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018093 | 0.0018093 | 0.0018093 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006886 | | | 0.37 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9142.00 ave 9142 max 9142 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: 171756.0 ave 171756 max 171756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171756 Ave neighs/atom = 126.47717 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 = 10 40 2 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) = 5.228 | 5.228 | 5.228 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5753.2757 0 -5753.2757 -1814.778 Loop time of 7.166e-06 on 1 procs for 0 steps with 1358 atoms 181.4% 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 | | 7.166e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9157.00 ave 9157 max 9157 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: 170500.0 ave 170500 max 170500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170500 Ave neighs/atom = 125.55228 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 = 10 40 2 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) = 5.228 | 5.228 | 5.228 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 -5753.2757 -5753.2757 33.129902 133.17796 3.6324809 -1814.778 -1814.778 -4.6765015 -5435.0748 -4.5827244 2.3172688 159.32617 Loop time of 7.006e-06 on 1 procs for 0 steps with 1358 atoms 314.0% 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 | | 7.006e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9157.00 ave 9157 max 9157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85250.0 ave 85250 max 85250 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170500.0 ave 170500 max 170500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170500 Ave neighs/atom = 125.55228 Neighbor list builds = 0 Dangerous builds = 0 1358 -5753.27568943827 eV 2.3172688240166 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:59