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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -38.018842 0.0000000) to (26.883381 38.018842 5.1737091) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9740847 4.9283684 5.1737091 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -38.018842 0.0000000) to (26.883381 38.018842 5.1737091) create_atoms CPU = 0.001 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9740847 4.9283684 5.1737091 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -38.018842 0.0000000) to (26.883381 38.018842 5.1737091) create_atoms CPU = 0.001 seconds 439 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 = 8 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 864 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_769582363439_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 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) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3283.3379 0 -3283.3379 63379.507 568 0 -3492.1168 0 -3492.1168 -59454.21 Loop time of 7.69973 on 1 procs for 568 steps with 864 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3283.33790403897 -3492.11333426411 -3492.11675703826 Force two-norm initial, final = 305.58710 0.17252194 Force max component initial, final = 51.203761 0.027311066 Final line search alpha, max atom move = 1.0000000 0.027311066 Iterations, force evaluations = 568 1113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.514 | 7.514 | 7.514 | 0.0 | 97.59 Neigh | 0.063958 | 0.063958 | 0.063958 | 0.0 | 0.83 Comm | 0.066875 | 0.066875 | 0.066875 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05494 | | | 0.71 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5229.00 ave 5229 max 5229 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: 118100.0 ave 118100 max 118100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118100 Ave neighs/atom = 136.68981 Neighbor list builds = 8 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 = 8 21 2 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 : 568 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 568 0 -3492.1168 0 -3492.1168 -59454.21 10575.838 606 0 -3506.1543 0 -3506.1543 5.097124 10122.35 Loop time of 0.290439 on 1 procs for 38 steps with 864 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3492.11675703826 -3506.15149285055 -3506.15428821814 Force two-norm initial, final = 726.88127 2.9411398 Force max component initial, final = 585.15226 1.3229781 Final line search alpha, max atom move = 0.00016905945 0.00022366195 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27853 | 0.27853 | 0.27853 | 0.0 | 95.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019156 | 0.0019156 | 0.0019156 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009994 | | | 3.44 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5239.00 ave 5239 max 5239 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: 117864.0 ave 117864 max 117864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117864 Ave neighs/atom = 136.41667 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 21 2 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3506.1543 0 -3506.1543 5.097124 Loop time of 2.542e-06 on 1 procs for 0 steps with 864 atoms 196.7% 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 | | 2.542e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5413.00 ave 5413 max 5413 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: 122760.0 ave 122760 max 122760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122760 Ave neighs/atom = 142.08333 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 21 2 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) = 5.105 | 5.105 | 5.105 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 -3506.1543 -3506.1543 26.614402 76.349053 4.9815099 5.097124 5.097124 -101.25349 -85.078403 201.62326 2.2710076 2738.434 Loop time of 2.691e-06 on 1 procs for 0 steps with 864 atoms 260.1% 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 | | 2.691e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5413.00 ave 5413 max 5413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61380.0 ave 61380 max 61380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122760.0 ave 122760 max 122760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122760 Ave neighs/atom = 142.08333 Neighbor list builds = 0 Dangerous builds = 0 864 -3506.15428821814 eV 2.27100760952468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08