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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -44.945918 0.0000000) to (14.981973 44.945918 3.6336621) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4064625 4.4064625 3.6336621 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.945918 0.0000000) to (14.981973 44.945918 3.6336621) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4064625 4.4064625 3.6336621 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.945918 0.0000000) to (14.981973 44.945918 3.6336621) create_atoms CPU = 0.000 seconds 206 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 6 32 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1626.3783 0 -1626.3783 6719.921 78 0 -1667.2991 0 -1667.2991 9657.8977 Loop time of 18.8049 on 1 procs for 78 steps with 408 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 = -1626.3783326651 -1667.29796611281 -1667.29905616995 Force two-norm initial, final = 43.017567 0.090545200 Force max component initial, final = 12.346750 0.026212303 Final line search alpha, max atom move = 1.0000000 0.026212303 Iterations, force evaluations = 78 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.79 | 18.79 | 18.79 | 0.0 | 99.92 Neigh | 0.0022597 | 0.0022597 | 0.0022597 | 0.0 | 0.01 Comm | 0.0067299 | 0.0067299 | 0.0067299 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005615 | | | 0.03 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3244.00 ave 3244 max 3244 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: 23220.0 ave 23220 max 23220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23220 Ave neighs/atom = 56.911765 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -1667.2991 0 -1667.2991 9657.8977 4893.6599 83 0 -1667.4 0 -1667.4 132.38807 4925.7503 Loop time of 1.04742 on 1 procs for 5 steps with 408 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 = -1667.29905616995 -1667.39990319265 -1667.39995964304 Force two-norm initial, final = 51.254555 0.74612941 Force max component initial, final = 31.593762 0.59138857 Final line search alpha, max atom move = 0.0026302911 0.0015555241 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.046 | 1.046 | 1.046 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024397 | 0.00024397 | 0.00024397 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001139 | | | 0.11 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3205.00 ave 3205 max 3205 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: 22688.0 ave 22688 max 22688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22688 Ave neighs/atom = 55.607843 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1667.4 0 -1667.4 132.38807 Loop time of 2.556e-06 on 1 procs for 0 steps with 408 atoms 156.5% 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 | | 2.556e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3196.00 ave 3196 max 3196 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: 22408.0 ave 22408 max 22408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22408 Ave neighs/atom = 54.921569 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.586 | 4.586 | 4.586 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 -1667.4 -1667.4 14.991195 90.156345 3.6445159 132.38807 132.38807 100.07478 104.15658 192.93286 2.3743794 190.33313 Loop time of 2.165e-06 on 1 procs for 0 steps with 408 atoms 184.8% 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 | | 2.165e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3196.00 ave 3196 max 3196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11204.0 ave 11204 max 11204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22408.0 ave 22408 max 22408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22408 Ave neighs/atom = 54.921569 Neighbor list builds = 0 Dangerous builds = 0 408 -1041.02407163474 eV 2.37437937515137 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20