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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -59.890668 0.0000000) to (42.349098 59.890668 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3207608 5.8102887 5.1737657 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.890668 0.0000000) to (42.349098 59.890668 5.1737657) create_atoms CPU = 0.002 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3207608 5.8102887 5.1737657 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.890668 0.0000000) to (42.349098 59.890668 5.1737657) create_atoms CPU = 0.002 seconds 1080 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 = 12 33 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 0 atoms, new total = 2152 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_884343146310_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 = 12 33 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6007.5086 0 -6007.5086 219475.83 583 0 -8460.0488 0 -8460.0488 -60031.374 Loop time of 18.3932 on 1 procs for 583 steps with 2152 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 = -6007.50863153059 -8460.04222186376 -8460.04883341573 Force two-norm initial, final = 3356.8344 0.23198148 Force max component initial, final = 468.26764 0.018514161 Final line search alpha, max atom move = 1.0000000 0.018514161 Iterations, force evaluations = 583 1135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.946 | 17.946 | 17.946 | 0.0 | 97.57 Neigh | 0.1948 | 0.1948 | 0.1948 | 0.0 | 1.06 Comm | 0.13279 | 0.13279 | 0.13279 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1197 | | | 0.65 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10196.0 ave 10196 max 10196 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: 294472.0 ave 294472 max 294472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294472 Ave neighs/atom = 136.83643 Neighbor list builds = 9 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 = 12 33 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 : 583 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.642 | 5.642 | 5.642 Mbytes Step Temp E_pair E_mol TotEng Press Volume 583 0 -8460.0488 0 -8460.0488 -60031.374 26244.607 620 0 -8494.6986 0 -8494.6986 60.012719 25107.569 Loop time of 0.677142 on 1 procs for 37 steps with 2152 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 = -8460.04883341567 -8494.69722729013 -8494.698647294 Force two-norm initial, final = 1828.0824 7.8801418 Force max component initial, final = 1404.3485 6.2172264 Final line search alpha, max atom move = 0.00044863993 0.0027892961 Iterations, force evaluations = 37 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63219 | 0.63219 | 0.63219 | 0.0 | 93.36 Neigh | 0.020484 | 0.020484 | 0.020484 | 0.0 | 3.03 Comm | 0.0038645 | 0.0038645 | 0.0038645 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0206 | | | 3.04 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 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: 304944.0 ave 304944 max 304944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304944 Ave neighs/atom = 141.70260 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 = 12 34 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) = 6.165 | 6.165 | 6.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8494.6986 0 -8494.6986 60.012719 Loop time of 2.397e-06 on 1 procs for 0 steps with 2152 atoms 166.9% 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 | | 2.397e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10637.0 ave 10637 max 10637 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: 304928.0 ave 304928 max 304928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304928 Ave neighs/atom = 141.69517 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 = 12 34 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) = 6.165 | 6.165 | 6.165 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 -8494.6986 -8494.6986 41.672165 120.6853 4.9923406 60.012719 60.012719 390.39503 -63.789709 -146.56717 2.3061715 5215.3639 Loop time of 2.803e-06 on 1 procs for 0 steps with 2152 atoms 249.7% 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 | | 2.803e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10637.0 ave 10637 max 10637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152464.0 ave 152464 max 152464 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 304928.0 ave 304928 max 304928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304928 Ave neighs/atom = 141.69517 Neighbor list builds = 0 Dangerous builds = 0 2152 -8494.698647294 eV 2.30617153493161 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19