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 = 4.0497635 4.0497635 4.0497635 Created orthogonal box = (0.0000000 -61.684161 0.0000000) to (30.842080 61.684161 4.0497635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3176001 5.3176001 4.0497635 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -61.684161 0.0000000) to (30.842080 61.684161 4.0497635) create_atoms CPU = 0.002 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3176001 5.3176001 4.0497635 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -61.684161 0.0000000) to (30.842080 61.684161 4.0497635) create_atoms CPU = 0.002 seconds 466 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 8 29 1 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 930 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_942551040047_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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2971.5442 0 -2971.5442 23099.301 25 0 -3078.2646 0 -3078.2646 5688.1415 Loop time of 0.860431 on 1 procs for 25 steps with 930 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 = -2971.54415896064 -3078.2624522135 -3078.26462057599 Force two-norm initial, final = 185.91839 0.10660736 Force max component initial, final = 55.819528 0.019804503 Final line search alpha, max atom move = 1.0000000 0.019804503 Iterations, force evaluations = 25 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84741 | 0.84741 | 0.84741 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071067 | 0.0071067 | 0.0071067 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005913 | | | 0.69 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7340.00 ave 7340 max 7340 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: 163252.0 ave 163252 max 163252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163252 Ave neighs/atom = 175.53978 Neighbor list builds = 0 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3078.2646 0 -3078.2646 5688.1415 15409.09 34 0 -3078.5867 0 -3078.5867 -11.292529 15521.579 Loop time of 0.238164 on 1 procs for 9 steps with 930 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 = -3078.26462057599 -3078.58522089166 -3078.58672195506 Force two-norm initial, final = 100.34254 1.2472920 Force max component initial, final = 80.207806 0.85868422 Final line search alpha, max atom move = 0.00035587712 0.00030558607 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21105 | 0.21105 | 0.21105 | 0.0 | 88.62 Neigh | 0.019205 | 0.019205 | 0.019205 | 0.0 | 8.06 Comm | 0.0021468 | 0.0021468 | 0.0021468 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005762 | | | 2.42 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7325.00 ave 7325 max 7325 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: 161240.0 ave 161240 max 161240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161240 Ave neighs/atom = 173.37634 Neighbor list builds = 1 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.152 | 5.152 | 5.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3078.5867 0 -3078.5867 -11.292529 Loop time of 6.375e-06 on 1 procs for 0 steps with 930 atoms 219.6% 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 | | 6.375e-06 | | |100.00 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7325.00 ave 7325 max 7325 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: 161248.0 ave 161248 max 161248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161248 Ave neighs/atom = 173.38495 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.152 | 5.152 | 5.152 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 -3078.5867 -3078.5867 30.783933 124.46177 4.0511267 -11.292529 -11.292529 85.410868 -30.623071 -88.665382 2.5626545 495.33484 Loop time of 6.836e-06 on 1 procs for 0 steps with 930 atoms 248.7% 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 | | 6.836e-06 | | |100.00 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7325.00 ave 7325 max 7325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80624.0 ave 80624 max 80624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161248.0 ave 161248 max 161248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161248 Ave neighs/atom = 173.38495 Neighbor list builds = 0 Dangerous builds = 0 930 -3078.58672195506 eV 2.56265449445479 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01