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 = 2.8659524 2.8659524 2.8659524 Created orthogonal box = (0.0000000 -36.477619 0.0000000) to (25.793572 36.477619 4.0530688) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7765874 4.9537507 4.0530688 Created 324 atoms using lattice units in orthogonal box = (0.0000000 -36.477619 0.0000000) to (25.793572 36.477619 4.0530688) create_atoms CPU = 0.001 seconds 324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7765874 4.9537507 4.0530688 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -36.477619 0.0000000) to (25.793572 36.477619 4.0530688) create_atoms CPU = 0.001 seconds 326 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 7 20 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 642 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.913 | 4.913 | 4.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2410.5324 0 -2410.5324 112151.76 79 0 -2736.1679 0 -2736.1679 -2623.8371 Loop time of 0.741698 on 1 procs for 79 steps with 642 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 = -2410.53235057286 -2736.16549097756 -2736.16789129928 Force two-norm initial, final = 849.41487 0.16601999 Force max component initial, final = 294.48473 0.026566665 Final line search alpha, max atom move = 1.0000000 0.026566665 Iterations, force evaluations = 79 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70773 | 0.70773 | 0.70773 | 0.0 | 95.42 Neigh | 0.0203 | 0.0203 | 0.0203 | 0.0 | 2.74 Comm | 0.0076652 | 0.0076652 | 0.0076652 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005999 | | | 0.81 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471.00 ave 5471 max 5471 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: 105504.0 ave 105504 max 105504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105504 Ave neighs/atom = 164.33645 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.913 | 4.913 | 4.913 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2736.1679 0 -2736.1679 -2623.8371 7626.9682 81 0 -2736.1843 0 -2736.1843 -0.08441792 7614.5873 Loop time of 0.0276037 on 1 procs for 2 steps with 642 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 = -2736.16789129927 -2736.18266019008 -2736.18432578572 Force two-norm initial, final = 24.488271 0.54320510 Force max component initial, final = 20.088471 0.40955534 Final line search alpha, max atom move = 0.00017505911 7.1696393e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026484 | 0.026484 | 0.026484 | 0.0 | 95.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020837 | 0.00020837 | 0.00020837 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009113 | | | 3.30 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5488.00 ave 5488 max 5488 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: 105796.0 ave 105796 max 105796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105796 Ave neighs/atom = 164.79128 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2736.1843 0 -2736.1843 -0.08441792 Loop time of 2.488e-06 on 1 procs for 0 steps with 642 atoms 120.6% 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 | | 2.488e-06 | | |100.00 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5488.00 ave 5488 max 5488 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: 105864.0 ave 105864 max 105864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105864 Ave neighs/atom = 164.89720 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.051 | 5.051 | 5.051 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 -2736.1843 -2736.1843 25.800892 72.863968 4.0504085 -0.08441792 -0.08441792 28.729771 57.134479 -86.117504 2.2762022 479.40193 Loop time of 3.08e-06 on 1 procs for 0 steps with 642 atoms 194.8% 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 | | 3.08e-06 | | |100.00 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5488.00 ave 5488 max 5488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52932.0 ave 52932 max 52932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105864.0 ave 105864 max 105864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105864 Ave neighs/atom = 164.89720 Neighbor list builds = 0 Dangerous builds = 0 642 -2736.18432578572 eV 2.27620224682606 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01