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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) create_atoms CPU = 0.003 seconds 2358 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 32 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 4692 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20718.337 0 -20718.337 2031.7631 71 0 -20816.251 0 -20816.251 2824.7223 Loop time of 9.0936 on 1 procs for 71 steps with 4692 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20718.3369208896 -20816.2312898146 -20816.2506872531 Force two-norm initial, final = 39.755180 0.48710171 Force max component initial, final = 4.4800271 0.019910675 Final line search alpha, max atom move = 1.0000000 0.019910675 Iterations, force evaluations = 71 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8719 | 8.8719 | 8.8719 | 0.0 | 97.56 Neigh | 0.1514 | 0.1514 | 0.1514 | 0.0 | 1.66 Comm | 0.032531 | 0.032531 | 0.032531 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03775 | | | 0.42 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17649.0 ave 17649 max 17649 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: 1.15748e+06 ave 1.15748e+06 max 1.15748e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1157484 Ave neighs/atom = 246.69309 Neighbor list builds = 2 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.64 | 13.64 | 13.64 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -20816.251 0 -20816.251 2824.7223 51290.308 74 0 -20816.409 0 -20816.409 -124.0193 51375.25 Loop time of 0.424508 on 1 procs for 3 steps with 4692 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20816.2506872531 -20816.4074999949 -20816.4088329935 Force two-norm initial, final = 184.31646 8.9819668 Force max component initial, final = 166.88955 8.2362395 Final line search alpha, max atom move = 8.5911188e-05 0.00070758512 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41799 | 0.41799 | 0.41799 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097923 | 0.00097923 | 0.00097923 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005537 | | | 1.30 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18155.0 ave 18155 max 18155 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: 1.15932e+06 ave 1.15932e+06 max 1.15932e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1159320 Ave neighs/atom = 247.08440 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 13.15 | 13.15 | 13.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20816.409 0 -20816.409 -124.0193 Loop time of 2.334e-06 on 1 procs for 0 steps with 4692 atoms 171.4% 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 | | 2.334e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18158.0 ave 18158 max 18158 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: 1.15894e+06 ave 1.15894e+06 max 1.15894e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1158936 Ave neighs/atom = 247.00256 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 13.15 | 13.15 | 13.15 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 -20816.409 -20816.409 42.677504 139.66575 8.6191612 -124.0193 -124.0193 -256.85207 -110.69404 -4.5117995 2.1859007 1695.3757 Loop time of 2.421e-06 on 1 procs for 0 steps with 4692 atoms 289.1% 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 | | 2.421e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18158.0 ave 18158 max 18158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 579468.0 ave 579468 max 579468 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.15894e+06 ave 1.15894e+06 max 1.15894e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1158936 Ave neighs/atom = 247.00256 Neighbor list builds = 0 Dangerous builds = 0 4692 -20816.4088329935 eV 2.18590065877686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10