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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -62.142411 0.0000000) to (35.877938 62.142411 6.0935647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5196827 5.5768830 6.0935647 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.142411 0.0000000) to (35.877938 62.142411 6.0935647) create_atoms CPU = 0.008 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5196827 5.5768830 6.0935647 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.142411 0.0000000) to (35.877938 62.142411 6.0935647) create_atoms CPU = 0.008 seconds 1250 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2488 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.22 | 11.22 | 11.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10450.684 0 -10450.684 54536.788 83 0 -10873.734 0 -10873.734 980.93445 Loop time of 12.1316 on 1 procs for 83 steps with 2488 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 = -10450.6838495659 -10873.7233434198 -10873.7336583919 Force two-norm initial, final = 548.13912 0.33247687 Force max component initial, final = 125.86705 0.056968962 Final line search alpha, max atom move = 1.0000000 0.056968962 Iterations, force evaluations = 83 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.787 | 11.787 | 11.787 | 0.0 | 97.16 Neigh | 0.25126 | 0.25126 | 0.25126 | 0.0 | 2.07 Comm | 0.052809 | 0.052809 | 0.052809 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04052 | | | 0.33 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14356.0 ave 14356 max 14356 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: 614252.0 ave 614252 max 614252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614252 Ave neighs/atom = 246.88585 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.22 | 11.22 | 11.22 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -10873.734 0 -10873.734 980.93445 27171.712 84 0 -10873.739 0 -10873.739 -61.826167 27187.993 Loop time of 0.240048 on 1 procs for 1 steps with 2488 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 = -10873.7336583918 -10873.7336583918 -10873.7391700763 Force two-norm initial, final = 30.340492 5.6167658 Force max component initial, final = 24.081354 3.9660192 Final line search alpha, max atom move = 4.1525905e-05 0.00016469254 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23642 | 0.23642 | 0.23642 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010302 | 0.0010302 | 0.0010302 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002597 | | | 1.08 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14308.0 ave 14308 max 14308 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: 614258.0 ave 614258 max 614258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614258 Ave neighs/atom = 246.88826 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 10.74 | 10.74 | 10.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10873.739 0 -10873.739 -61.826167 Loop time of 6.455e-06 on 1 procs for 0 steps with 2488 atoms 201.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14308.0 ave 14308 max 14308 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: 614186.0 ave 614186 max 614186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614186 Ave neighs/atom = 246.85932 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 10.74 | 10.74 | 10.74 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 -10873.739 -10873.739 35.888309 124.30688 6.0943722 -61.826167 -61.826167 187.55702 -139.28878 -233.74674 2.185321 874.05239 Loop time of 7.116e-06 on 1 procs for 0 steps with 2488 atoms 253.0% 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 | | 7.116e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14308.0 ave 14308 max 14308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307093.0 ave 307093 max 307093 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614186.0 ave 614186 max 614186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614186 Ave neighs/atom = 246.85932 Neighbor list builds = 0 Dangerous builds = 0 2488 -10873.7391700763 eV 2.18532103538107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13