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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -72.750039 0.0000000) to (42.002255 72.750039 6.2846462) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6420939 5.7910479 6.2846462 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.750039 0.0000000) to (42.002255 72.750039 6.2846462) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6420939 5.7910479 6.2846462 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.750039 0.0000000) to (42.002255 72.750039 6.2846462) create_atoms CPU = 0.004 seconds 1610 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 12 39 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.663 | 6.663 | 6.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12028.393 0 -12028.393 95522.14 311 0 -13590.49 0 -13590.49 -11226.714 Loop time of 13.4923 on 1 procs for 311 steps with 3216 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12028.3927175668 -13590.4772877581 -13590.489684747 Force two-norm initial, final = 2146.9470 0.39610139 Force max component initial, final = 580.79062 0.050456486 Final line search alpha, max atom move = 1.0000000 0.050456486 Iterations, force evaluations = 311 542 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.814 | 12.814 | 12.814 | 0.0 | 94.97 Neigh | 0.4886 | 0.4886 | 0.4886 | 0.0 | 3.62 Comm | 0.095968 | 0.095968 | 0.095968 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09344 | | | 0.69 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13149.0 ave 13149 max 13149 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: 499096.0 ave 499096 max 499096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 499096 Ave neighs/atom = 155.19154 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 311 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.80 | 10.80 | 10.80 Mbytes Step Temp E_pair E_mol TotEng Press Volume 311 0 -13590.49 0 -13590.49 -11226.714 38407.555 324 0 -13595.887 0 -13595.887 1.8993927 38127.7 Loop time of 0.407155 on 1 procs for 13 steps with 3216 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 = -13590.489684747 -13595.8792949748 -13595.8872306552 Force two-norm initial, final = 734.04984 2.4443997 Force max component initial, final = 592.35574 0.37554002 Final line search alpha, max atom move = 5.2721350e-05 1.9798977e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36236 | 0.36236 | 0.36236 | 0.0 | 89.00 Neigh | 0.032278 | 0.032278 | 0.032278 | 0.0 | 7.93 Comm | 0.0020412 | 0.0020412 | 0.0020412 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01047 | | | 2.57 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13131.0 ave 13131 max 13131 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: 502712.0 ave 502712 max 502712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502712 Ave neighs/atom = 156.31592 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 10.31 | 10.31 | 10.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13595.887 0 -13595.887 1.8993927 Loop time of 1.8333e-05 on 1 procs for 0 steps with 3216 atoms 0.0% 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 | | 1.833e-05 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13118.0 ave 13118 max 13118 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: 503540.0 ave 503540 max 503540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503540 Ave neighs/atom = 156.57338 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 10.31 | 10.31 | 10.31 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 -13595.887 -13595.887 41.775575 143.83712 6.3452272 1.8993927 1.8993927 15.695524 -0.35869983 -9.6386455 2.291511 6480.3767 Loop time of 2.828e-06 on 1 procs for 0 steps with 3216 atoms 247.5% 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 | | 2.828e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13118.0 ave 13118 max 13118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251770.0 ave 251770 max 251770 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 503540.0 ave 503540 max 503540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503540 Ave neighs/atom = 156.57338 Neighbor list builds = 0 Dangerous builds = 0 3216 -13595.8872306552 eV 2.29151099336923 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14