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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -50.170751 0.0000000) to (25.083417 50.170751 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5061159 5.5061159 3.9173716 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -50.170751 0.0000000) to (25.083417 50.170751 3.9173716) create_atoms CPU = 0.002 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5061159 5.5061159 3.9173716 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -50.170751 0.0000000) to (25.083417 50.170751 3.9173716) create_atoms CPU = 0.001 seconds 329 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 652 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_020840179467_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3691.3923 0 -3691.3923 19745.015 73 0 -3748.2511 0 -3748.2511 -2608.7077 Loop time of 3.3005 on 1 procs for 73 steps with 652 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 = -3691.39233455783 -3748.24772977611 -3748.25106590391 Force two-norm initial, final = 59.850717 0.23425478 Force max component initial, final = 18.560438 0.080216417 Final line search alpha, max atom move = 1.0000000 0.080216417 Iterations, force evaluations = 73 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2763 | 3.2763 | 3.2763 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01239 | 0.01239 | 0.01239 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01178 | | | 0.36 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4353.00 ave 4353 max 4353 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: 50460.0 ave 50460 max 50460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50460 Ave neighs/atom = 77.392638 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -3748.2511 0 -3748.2511 -2608.7077 9859.6628 75 0 -3748.2601 0 -3748.2601 -527.96099 9847.8997 Loop time of 0.140163 on 1 procs for 2 steps with 652 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3748.25106590391 -3748.26013616758 -3748.26014983073 Force two-norm initial, final = 21.694058 0.38451544 Force max component initial, final = 16.862708 0.30159163 Final line search alpha, max atom move = 0.0054584787 0.0016462315 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13824 | 0.13824 | 0.13824 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045379 | 0.00045379 | 0.00045379 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001466 | | | 1.05 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4384.00 ave 4384 max 4384 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: 50444.0 ave 50444 max 50444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50444 Ave neighs/atom = 77.368098 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3748.2601 0 -3748.2601 -527.96099 Loop time of 6.495e-06 on 1 procs for 0 steps with 652 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 | | 6.495e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4384.00 ave 4384 max 4384 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: 50452.0 ave 50452 max 50452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50452 Ave neighs/atom = 77.380368 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.648 | 4.648 | 4.648 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 -3748.2601 -3748.2601 25.067874 100.3415 3.9151239 -527.96099 -527.96099 -2.6532247 -1630.2682 49.038454 2.4943885 200.26027 Loop time of 6.696e-06 on 1 procs for 0 steps with 652 atoms 283.8% 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 | | 6.696e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4384.00 ave 4384 max 4384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25226.0 ave 25226 max 25226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50452.0 ave 50452 max 50452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50452 Ave neighs/atom = 77.380368 Neighbor list builds = 0 Dangerous builds = 0 652 -3748.26014983073 eV 2.49438853252236 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03