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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -48.533715 0.0000000) to (29.720709 48.533715 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4037653 5.5151948 5.9740873 Created 1047 atoms using lattice units in orthogonal box = (0.0000000 -48.533715 0.0000000) to (29.720709 48.533715 8.9611309) create_atoms CPU = 0.002 seconds 1047 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4037653 5.5151948 5.9740873 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -48.533715 0.0000000) to (29.720709 48.533715 8.9611309) create_atoms CPU = 0.001 seconds 1071 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 27 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2108 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.574 | 5.574 | 5.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8409.253 0 -8409.253 32.304116 826 0 -8524.0123 0 -8524.0123 -67260.911 Loop time of 23.068 on 1 procs for 826 steps with 2108 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8409.25297363673 -8524.00413978452 -8524.01225368259 Force two-norm initial, final = 21.490095 0.33220750 Force max component initial, final = 5.7077010 0.097872008 Final line search alpha, max atom move = 1.0000000 0.097872008 Iterations, force evaluations = 826 1618 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.536 | 22.536 | 22.536 | 0.0 | 97.69 Neigh | 0.29147 | 0.29147 | 0.29147 | 0.0 | 1.26 Comm | 0.10554 | 0.10554 | 0.10554 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1348 | | | 0.58 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7375.00 ave 7375 max 7375 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: 286716.0 ave 286716 max 286716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286716 Ave neighs/atom = 136.01328 Neighbor list builds = 15 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 826 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 826 0 -8524.0123 0 -8524.0123 -67260.911 25852.081 869 0 -8571.7778 0 -8571.7778 -17.178806 24647.883 Loop time of 0.657802 on 1 procs for 43 steps with 2108 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 = -8524.01225368256 -8571.77473349558 -8571.77780162439 Force two-norm initial, final = 2121.9150 7.7910841 Force max component initial, final = 1669.3688 3.9688940 Final line search alpha, max atom move = 0.00017686585 0.00070196180 Iterations, force evaluations = 43 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61871 | 0.61871 | 0.61871 | 0.0 | 94.06 Neigh | 0.020069 | 0.020069 | 0.020069 | 0.0 | 3.05 Comm | 0.0028606 | 0.0028606 | 0.0028606 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01616 | | | 2.46 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7669.00 ave 7669 max 7669 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: 303124.0 ave 303124 max 303124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303124 Ave neighs/atom = 143.79696 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.095 | 6.095 | 6.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8571.7778 0 -8571.7778 -17.178806 Loop time of 2.129e-06 on 1 procs for 0 steps with 2108 atoms 187.9% 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 | | 2.129e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 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: 302194.0 ave 302194 max 302194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302194 Ave neighs/atom = 143.35579 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.095 | 6.095 | 6.095 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 -8571.7778 -8571.7778 29.025375 98.736175 8.6005351 -17.178806 -17.178806 25.121891 -262.42368 185.76537 2.2673113 4866.2313 Loop time of 2.028e-06 on 1 procs for 0 steps with 2108 atoms 246.5% 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 | | 2.028e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 151097.0 ave 151097 max 151097 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 302194.0 ave 302194 max 302194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302194 Ave neighs/atom = 143.35579 Neighbor list builds = 0 Dangerous builds = 0 2108 -8571.77780162439 eV 2.26731132710401 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24