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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -81.196164 0.0000000) to (46.878627 81.196164 7.0142802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2971290 6.4633762 7.0142802 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.196164 0.0000000) to (46.878627 81.196164 7.0142802) create_atoms CPU = 0.014 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2971290 6.4633762 7.0142802 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.196164 0.0000000) to (46.878627 81.196164 7.0142802) create_atoms CPU = 0.012 seconds 1610 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_284963179498_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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.626 | 6.626 | 6.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10261.051 0 -10261.051 29071.693 174 0 -10818.374 0 -10818.374 3126.5654 Loop time of 12.7995 on 1 procs for 174 steps with 3216 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 = -10261.0509218834 -10818.3638129813 -10818.3736164389 Force two-norm initial, final = 593.94368 0.25670019 Force max component initial, final = 161.84473 0.057872750 Final line search alpha, max atom move = 1.0000000 0.057872750 Iterations, force evaluations = 174 331 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.397 | 12.397 | 12.397 | 0.0 | 96.85 Neigh | 0.21206 | 0.21206 | 0.21206 | 0.0 | 1.66 Comm | 0.08528 | 0.08528 | 0.08528 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1056 | | | 0.83 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10752.0 ave 10752 max 10752 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: 417032.0 ave 417032 max 417032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417032 Ave neighs/atom = 129.67413 Neighbor list builds = 4 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 174 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.626 | 6.626 | 6.626 Mbytes Step Temp E_pair E_mol TotEng Press Volume 174 0 -10818.374 0 -10818.374 3126.5654 53397.817 181 0 -10818.925 0 -10818.925 7.6242197 53634.309 Loop time of 0.426311 on 1 procs for 7 steps with 3216 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 = -10818.3736164389 -10818.9219958109 -10818.9247234131 Force two-norm initial, final = 215.05243 1.6616827 Force max component initial, final = 196.29750 1.3683412 Final line search alpha, max atom move = 5.7392629e-05 7.8532698e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3612 | 0.3612 | 0.3612 | 0.0 | 84.73 Neigh | 0.05134 | 0.05134 | 0.05134 | 0.0 | 12.04 Comm | 0.0030637 | 0.0030637 | 0.0030637 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0107 | | | 2.51 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10728.0 ave 10728 max 10728 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: 417240.0 ave 417240 max 417240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417240 Ave neighs/atom = 129.73881 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.764 | 6.764 | 6.764 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10818.925 0 -10818.925 7.6242197 Loop time of 6.776e-06 on 1 procs for 0 steps with 3216 atoms 191.9% 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 | | 6.776e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10728.0 ave 10728 max 10728 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: 416820.0 ave 416820 max 416820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416820 Ave neighs/atom = 129.60821 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.764 | 6.764 | 6.764 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 -10818.925 -10818.925 46.882587 163.38067 7.0021346 7.6242197 7.6242197 -25.185292 7.253324 40.804627 2.6110374 1420.1779 Loop time of 6.795e-06 on 1 procs for 0 steps with 3216 atoms 309.1% 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 | | 6.795e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10728.0 ave 10728 max 10728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 208410.0 ave 208410 max 208410 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 416820.0 ave 416820 max 416820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 416820 Ave neighs/atom = 129.60821 Neighbor list builds = 0 Dangerous builds = 0 3216 -10818.9247234131 eV 2.61103739851998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14