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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -51.634794 0.0000000) to (36.511313 51.634794 5.7021090) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2336387 6.9266186 5.7021090 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.634794 0.0000000) to (36.511313 51.634794 5.7021090) create_atoms CPU = 0.003 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2336387 6.9266186 5.7021090 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.634794 0.0000000) to (36.511313 51.634794 5.7021090) create_atoms CPU = 0.002 seconds 660 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4254.3836 0 -4254.3836 16677.149 79 0 -4400.124 0 -4400.124 2972.623 Loop time of 1.76137 on 1 procs for 79 steps with 1312 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 = -4254.38361017306 -4400.12040503059 -4400.12403048622 Force two-norm initial, final = 183.68649 0.14200390 Force max component initial, final = 43.526407 0.020274491 Final line search alpha, max atom move = 1.0000000 0.020274491 Iterations, force evaluations = 79 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7269 | 1.7269 | 1.7269 | 0.0 | 98.04 Neigh | 0.013284 | 0.013284 | 0.013284 | 0.0 | 0.75 Comm | 0.011603 | 0.011603 | 0.011603 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009562 | | | 0.54 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8422.00 ave 8422 max 8422 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: 231160.0 ave 231160 max 231160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231160 Ave neighs/atom = 176.18902 Neighbor list builds = 1 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.478 | 5.478 | 5.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -4400.124 0 -4400.124 2972.623 21499.849 85 0 -4400.3293 0 -4400.3293 -74.544213 21580.037 Loop time of 0.101754 on 1 procs for 6 steps with 1312 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 = -4400.12403048622 -4400.328993109 -4400.32931553079 Force two-norm initial, final = 88.233285 2.2018549 Force max component initial, final = 84.639017 2.0914050 Final line search alpha, max atom move = 0.00038420917 0.00080353698 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.098489 | 0.098489 | 0.098489 | 0.0 | 96.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053842 | 0.00053842 | 0.00053842 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002727 | | | 2.68 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8379.00 ave 8379 max 8379 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: 230216.0 ave 230216 max 230216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230216 Ave neighs/atom = 175.46951 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.616 | 5.616 | 5.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4400.3293 0 -4400.3293 -74.544213 Loop time of 2.571e-06 on 1 procs for 0 steps with 1312 atoms 194.5% 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 | | 2.571e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8352.00 ave 8352 max 8352 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: 229976.0 ave 229976 max 229976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229976 Ave neighs/atom = 175.28659 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.616 | 5.616 | 5.616 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 -4400.3293 -4400.3293 36.468934 103.80115 5.700684 -74.544213 -74.544213 -155.09291 -30.032361 -38.507371 2.6524935 773.78809 Loop time of 2.536e-06 on 1 procs for 0 steps with 1312 atoms 236.6% 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 | | 2.536e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8352.00 ave 8352 max 8352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114988.0 ave 114988 max 114988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229976.0 ave 229976 max 229976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229976 Ave neighs/atom = 175.28659 Neighbor list builds = 0 Dangerous builds = 0 1312 -4400.32931553079 eV 2.65249352921532 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02