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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -33.980653 0.0000000) to (16.990327 33.980653 2.6534432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7295839 3.7295839 2.6534432 Created 164 atoms using lattice units in orthogonal box = (0.0000000 -33.980653 0.0000000) to (16.990327 33.980653 2.6534432) create_atoms CPU = 0.001 seconds 164 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7295839 3.7295839 2.6534432 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -33.980653 0.0000000) to (16.990327 33.980653 2.6534432) create_atoms CPU = 0.000 seconds 165 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 325 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_201919462778_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2375.3039 0 -2375.3039 309830.65 77 0 -2704.7035 0 -2704.7035 3852.1191 Loop time of 1.70105 on 1 procs for 77 steps with 325 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 = -2375.30387991315 -2704.70125176712 -2704.70349970015 Force two-norm initial, final = 1407.4893 0.33453001 Force max component initial, final = 693.51290 0.059634940 Final line search alpha, max atom move = 0.92600755 0.055222404 Iterations, force evaluations = 77 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6878 | 1.6878 | 1.6878 | 0.0 | 99.22 Neigh | 0.0038896 | 0.0038896 | 0.0038896 | 0.0 | 0.23 Comm | 0.005869 | 0.005869 | 0.005869 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003533 | | | 0.21 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4925.00 ave 4925 max 4925 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: 57588.0 ave 57588 max 57588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57588 Ave neighs/atom = 177.19385 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -2704.7035 0 -2704.7035 3852.1191 3063.8905 83 0 -2704.9365 0 -2704.9365 74.410387 3066.396 Loop time of 0.0913862 on 1 procs for 6 steps with 325 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2704.70349970015 -2704.93511656247 -2704.93648789975 Force two-norm initial, final = 70.742256 0.79523046 Force max component initial, final = 57.722862 0.34122168 Final line search alpha, max atom move = 0.00025165442 8.5869946e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090055 | 0.090055 | 0.090055 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027052 | 0.00027052 | 0.00027052 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001061 | | | 1.16 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4925.00 ave 4925 max 4925 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: 57434.0 ave 57434 max 57434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57434 Ave neighs/atom = 176.72000 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2704.9365 0 -2704.9365 74.410387 Loop time of 1.801e-06 on 1 procs for 0 steps with 325 atoms 166.6% 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 | | 1.801e-06 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918.00 ave 4918 max 4918 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: 57362.0 ave 57362 max 57362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57362 Ave neighs/atom = 176.49846 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.598 | 4.598 | 4.598 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 -2704.9365 -2704.9365 17.016338 68.258449 2.6400109 74.410387 74.410387 -64.405394 179.06613 108.57043 2.1766278 160.14726 Loop time of 1.353e-06 on 1 procs for 0 steps with 325 atoms 147.8% 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 | | 1.353e-06 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918.00 ave 4918 max 4918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28681.0 ave 28681 max 28681 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57362.0 ave 57362 max 57362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57362 Ave neighs/atom = 176.49846 Neighbor list builds = 0 Dangerous builds = 0 325 -2704.93648789975 eV 2.17662777873222 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01