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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -34.980673 0.0000000) to (30.294152 34.980673 5.9411719) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4374118 5.3816420 5.9411719 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -34.980673 0.0000000) to (30.294152 34.980673 5.9411719) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4374118 5.3816420 5.9411719 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -34.980673 0.0000000) to (30.294152 34.980673 5.9411719) create_atoms CPU = 0.001 seconds 628 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 ghost atom cutoff = 8 binsize = 4, bins = 8 18 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1245 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_044341472608_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 ghost atom cutoff = 8 binsize = 4, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4139.1324 0 -4139.1324 183523.87 106 0 -4951.9743 0 -4951.9743 50057.457 Loop time of 2.80481 on 1 procs for 106 steps with 1245 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 = -4139.13241118482 -4951.9706737246 -4951.97429123031 Force two-norm initial, final = 1977.9663 0.24367119 Force max component initial, final = 721.06727 0.054804374 Final line search alpha, max atom move = 1.0000000 0.054804374 Iterations, force evaluations = 106 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7377 | 2.7377 | 2.7377 | 0.0 | 97.61 Neigh | 0.033392 | 0.033392 | 0.033392 | 0.0 | 1.19 Comm | 0.019064 | 0.019064 | 0.019064 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01463 | | | 0.52 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 256122.0 ave 256122 max 256122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256122 Ave neighs/atom = 205.72048 Neighbor list builds = 2 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 ghost atom cutoff = 8 binsize = 4, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -4951.9743 0 -4951.9743 50057.457 12591.836 118 0 -4955.6298 0 -4955.6298 -262.10851 12749.477 Loop time of 0.197989 on 1 procs for 12 steps with 1245 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 = -4951.97429123033 -4955.62736616263 -4955.62978150351 Force two-norm initial, final = 735.00309 4.0030043 Force max component initial, final = 617.52353 2.5096788 Final line search alpha, max atom move = 8.7839939e-05 0.00022045003 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19232 | 0.19232 | 0.19232 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089801 | 0.00089801 | 0.00089801 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004774 | | | 2.41 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7438.00 ave 7438 max 7438 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: 255772.0 ave 255772 max 255772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255772 Ave neighs/atom = 205.43936 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 ghost atom cutoff = 8 binsize = 4, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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 -4955.6298 0 -4955.6298 -262.10851 Loop time of 2.215e-06 on 1 procs for 0 steps with 1245 atoms 135.4% 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 | | 2.215e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7416.00 ave 7416 max 7416 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: 248758.0 ave 248758 max 248758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248758 Ave neighs/atom = 199.80562 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 ghost atom cutoff = 8 binsize = 4, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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 -4955.6298 -4955.6298 30.314461 70.754779 5.9441085 -262.10851 -262.10851 -315.59288 -221.40766 -249.32499 2.2325582 1065.683 Loop time of 2.626e-06 on 1 procs for 0 steps with 1245 atoms 266.6% 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 | | 2.626e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7416.00 ave 7416 max 7416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124379.0 ave 124379 max 124379 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248758.0 ave 248758 max 248758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248758 Ave neighs/atom = 199.80562 Neighbor list builds = 0 Dangerous builds = 0 1245 -4955.62978150351 eV 2.23255816911875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03