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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -76.325809 0.0000000) to (38.162904 76.325809 4.0452598) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5743568 5.5743568 4.0452598 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.325809 0.0000000) to (38.162904 76.325809 4.0452598) create_atoms CPU = 0.001 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5743568 5.5743568 4.0452598 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.325809 0.0000000) to (38.162904 76.325809 4.0452598) create_atoms CPU = 0.001 seconds 714 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 36 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1420 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_106969701023_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.512 | 5.512 | 5.512 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4634.5125 0 -4634.5125 18168.049 151 0 -4833.7174 0 -4833.7174 1113.7422 Loop time of 3.53039 on 1 procs for 151 steps with 1420 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4634.51253034717 -4833.71378374702 -4833.71744097211 Force two-norm initial, final = 395.27598 0.12952364 Force max component initial, final = 133.78130 0.018413662 Final line search alpha, max atom move = 1.0000000 0.018413662 Iterations, force evaluations = 151 277 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4465 | 3.4465 | 3.4465 | 0.0 | 97.62 Neigh | 0.037619 | 0.037619 | 0.037619 | 0.0 | 1.07 Comm | 0.02519 | 0.02519 | 0.02519 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02111 | | | 0.60 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9965.00 ave 9965 max 9965 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: 200920.0 ave 200920 max 200920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200920 Ave neighs/atom = 141.49296 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 151 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.512 | 5.512 | 5.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 151 0 -4833.7174 0 -4833.7174 1113.7422 23566.183 155 0 -4833.7927 0 -4833.7927 -140.40109 23603.724 Loop time of 0.0737528 on 1 procs for 4 steps with 1420 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 = -4833.71744097215 -4833.79136236981 -4833.79267848965 Force two-norm initial, final = 43.530266 4.9112505 Force max component initial, final = 42.687633 4.5782614 Final line search alpha, max atom move = 0.00015338144 0.00070222034 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071363 | 0.071363 | 0.071363 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004345 | 0.0004345 | 0.0004345 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001956 | | | 2.65 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9960.00 ave 9960 max 9960 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: 199880.0 ave 199880 max 199880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199880 Ave neighs/atom = 140.76056 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.650 | 5.650 | 5.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4833.7927 0 -4833.7927 -140.40109 Loop time of 2.346e-06 on 1 procs for 0 steps with 1420 atoms 170.5% 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 | | 2.346e-06 | | |100.00 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9945.00 ave 9945 max 9945 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: 199776.0 ave 199776 max 199776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199776 Ave neighs/atom = 140.68732 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.650 | 5.650 | 5.650 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 -4833.7927 -4833.7927 38.158187 153.15931 4.0387725 -140.40109 -140.40109 -119.8983 8.9604689 -310.26544 2.5286415 587.22901 Loop time of 2.754e-06 on 1 procs for 0 steps with 1420 atoms 217.9% 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 | | 2.754e-06 | | |100.00 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9945.00 ave 9945 max 9945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99888.0 ave 99888 max 99888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199776.0 ave 199776 max 199776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199776 Ave neighs/atom = 140.68732 Neighbor list builds = 0 Dangerous builds = 0 1420 -4833.79267848965 eV 2.52864151373024 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03