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 -60.992295 0.0000000) to (24.900000 60.992295 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9760000 5.2859989 5.7504087 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -60.992295 0.0000000) to (24.900000 60.992295 8.6256130) create_atoms CPU = 0.002 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9760000 5.2859989 5.7504087 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.992295 0.0000000) to (24.900000 60.992295 8.6256130) create_atoms CPU = 0.002 seconds 1203 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 38 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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 38 3 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9920.5105 0 -9920.5105 63041.487 104 0 -10636.113 0 -10636.113 4812.5939 Loop time of 20.7916 on 1 procs for 104 steps with 2398 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9920.51049874772 -10636.1042487504 -10636.1132883209 Force two-norm initial, final = 745.59312 0.40856532 Force max component initial, final = 127.07012 0.13627029 Final line search alpha, max atom move = 1.0000000 0.13627029 Iterations, force evaluations = 104 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.687 | 20.687 | 20.687 | 0.0 | 99.49 Neigh | 0.05961 | 0.05961 | 0.05961 | 0.0 | 0.29 Comm | 0.01934 | 0.01934 | 0.01934 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02617 | | | 0.13 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667.00 ave 7667 max 7667 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: 209662.0 ave 209662 max 209662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209662 Ave neighs/atom = 87.432027 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 38 3 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.583 | 5.583 | 5.583 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -10636.113 0 -10636.113 4812.5939 26199.577 109 0 -10636.445 0 -10636.445 -4.4261657 26266.644 Loop time of 0.931248 on 1 procs for 5 steps with 2398 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 = -10636.1132883209 -10636.4449949948 -10636.4454951998 Force two-norm initial, final = 187.10028 0.78446787 Force max component initial, final = 181.83871 0.42463830 Final line search alpha, max atom move = 0.00012673988 5.3818607e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92707 | 0.92707 | 0.92707 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000569 | 0.000569 | 0.000569 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003607 | | | 0.39 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667.00 ave 7667 max 7667 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: 210272.0 ave 210272 max 210272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210272 Ave neighs/atom = 87.686405 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 38 3 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) = 5.721 | 5.721 | 5.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10636.445 0 -10636.445 -4.4261657 Loop time of 2.291e-06 on 1 procs for 0 steps with 2398 atoms 174.6% 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 | | 2.291e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667.00 ave 7667 max 7667 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: 209952.0 ave 209952 max 209952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209952 Ave neighs/atom = 87.552961 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 38 3 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) = 5.721 | 5.721 | 5.721 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 -10636.445 -10636.445 24.89814 122.44503 8.6158178 -4.4261657 -4.4261657 25.899567 -13.970244 -25.207819 2.2194007 652.54516 Loop time of 2.302e-06 on 1 procs for 0 steps with 2398 atoms 217.2% 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 | | 2.302e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667.00 ave 7667 max 7667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104976.0 ave 104976 max 104976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209952.0 ave 209952 max 209952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209952 Ave neighs/atom = 87.552961 Neighbor list builds = 0 Dangerous builds = 0 2398 -10636.4454951998 eV 2.21940072598114 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22