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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -69.774257 0.0000000) to (42.725674 69.774257 8.6318896) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9410643 4.9836238 5.7545931 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.774257 0.0000000) to (42.725674 69.774257 8.6318896) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9410643 4.9836238 5.7545931 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.774257 0.0000000) to (42.725674 69.774257 8.6318896) create_atoms CPU = 0.002 seconds 2358 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 37 3 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 4668 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 12.33 | 12.33 | 12.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20597.104 0 -20597.104 299.31936 20 0 -20632.497 0 -20632.497 -5019.3883 Loop time of 1.28671 on 1 procs for 20 steps with 4668 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 = -20597.1043070331 -20632.4775702929 -20632.4967500149 Force two-norm initial, final = 34.801093 0.44749418 Force max component initial, final = 6.3042561 0.056916503 Final line search alpha, max atom move = 1.0000000 0.056916503 Iterations, force evaluations = 20 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2751 | 1.2751 | 1.2751 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046929 | 0.0046929 | 0.0046929 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006964 | | | 0.54 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14690.0 ave 14690 max 14690 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: 815412.0 ave 815412 max 815412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815412 Ave neighs/atom = 174.68123 Neighbor list builds = 0 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.33 | 12.33 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -20632.497 0 -20632.497 -5019.3883 51465.953 22 0 -20632.644 0 -20632.644 -1174.9108 51357.06 Loop time of 0.145615 on 1 procs for 2 steps with 4668 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 = -20632.4967500148 -20632.6428782422 -20632.643980159 Force two-norm initial, final = 199.16894 5.2280686 Force max component initial, final = 143.86240 5.1847708 Final line search alpha, max atom move = 6.6968134e-05 0.00034721443 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1429 | 0.1429 | 0.1429 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042655 | 0.00042655 | 0.00042655 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002285 | | | 1.57 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14690.0 ave 14690 max 14690 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: 816504.0 ave 816504 max 816504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816504 Ave neighs/atom = 174.91517 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 11.84 | 11.84 | 11.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20632.644 0 -20632.644 -1174.9108 Loop time of 2e-06 on 1 procs for 0 steps with 4668 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14690.0 ave 14690 max 14690 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: 816624.0 ave 816624 max 816624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816624 Ave neighs/atom = 174.94087 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 11.84 | 11.84 | 11.84 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 -20632.644 -20632.644 42.676714 139.54851 8.6235078 -1174.9108 -1174.9108 -15.476662 -3670.847 161.59125 2.1798581 1701.1972 Loop time of 2.099e-06 on 1 procs for 0 steps with 4668 atoms 238.2% 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 | | 2.099e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14690.0 ave 14690 max 14690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 408312.0 ave 408312 max 408312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 816624.0 ave 816624 max 816624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816624 Ave neighs/atom = 174.94087 Neighbor list builds = 0 Dangerous builds = 0 4668 -20632.643980159 eV 2.17985810750234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02