! This code is not commented with as much detail as PackLSD.nml ! It does however contain all of the available options. ! Become familiar with PackLSD.nml first! &HPPPackingSize hpp_n_types=1, ! Number of species ptp_n_points=100, ! Total number of particles / ! For spheres: &HPPParticleShapes_HS radii_pdf="U U", ! Probability distribution for radii (polydisperse) type_proportions_="0.5", ! Molar composition ratios radii_="1.0 1.4" ! The relative radii of different species / ! For ellipsoids: &HPPParticleShapes_HE axes_pdf="U", ! Probability distribution for axes (polydisperse) type_proportions_="0.5", ! Molar composition ratios axes_="1.0 2.0", ! The semiaxes (aspect ratios) / ! For lattice boundary conditions: &HPPBoundaryShape_LB lb_lattice_vectors=1.0 0.0 0.0 1.0, ! Lattice matrix lb_periodic=T T, ! Periodic or hard wall / ! For spheres: &DHPPVelocities_HS masses_="1 1", ! Species masses (-1 for frozen particles) equipartition_speeds=F, ! Initialize via equipartition to kT=1, or speeds_="0", ! Use these initial speeds for each specie / ! For ellipsoids: &DHPPVelocities_HE masses_="1", ! Species masses (-1 for frozen particles) inertias_="", ! Moments of inertia (empty for default I~mR^2, -1 for fixed orientations) equipartition_speeds=F, ! Initialize via equipartition to kT=1, or equipartition_angular_speeds=T, ! For rotational motion speeds_="0", ! Use these initial speeds for each specie angular_speeds_="0" ! For rotational motion / ! For spheres: &DHPPParticleDeformations_HS one_expansion_rate=T, ! Keep particle shapes in a certain proportion or ! let each grow/shrink independently? expansions_="0.01", ! Expansion rate(s) hpn_cutoff_expansion=0 ! When using the BCMD algorithm, the rate of change of bounding neighborhood / ! For ellipsoids: &DHPPParticleDeformations_HE one_expansion_rate=T, ! Keep particle shapes in a certain proportion or ! let each grow/shrink independently? expansions_="0.01", hpn_cutoff_expansion=0 ! When using the BCMD algorithm, the rate of change of bounding neighborhood / ! For periodic BCs with deformable unit cell: &DHPPBoundaryDeformation_LB strain_rate=0.0 0.0 0.0 0.0 ! A matrix of strain rate (does not have to be symmetric) / ! For near neighbor lists (NNLs) &HPPNNLParameters hpn_cutoff=0.1, ! Cutoff mu=1+hpn_cutoff hpn_safety_cushion=0.0, ! Add a safety cushion to the NNLs as well max_neighbours_="20 20", ! Maximum space allocated in NNLs per particle for each specie bounding_refinements_="-1.0 -1.0 -1.0 -1.0", ! When using bounding cell complexes (complicated!) !hpp_neighbourhood_correction=0, ! For spheres, it can be set to 0 for maximal precision in BCMD / &LSDPackingOptions lsd_options%lsd_monitor_stress=T, ! Monitor the collisional stress (momentum exchange) lsd_rebuild_nnl_from_scratch=F, ! Method for updating NNLs (see papers) hpp_preserve_interactions=T, ! Preserve old interactions upon updating the NNLs of a particle nnl_infinite_priority=1E16, ! Do not remove interactions with higher priority (sticky interactions) lsd_display_n_collisions=T, ! Color each particle according to number of collisions lsd_display_stress=T, ! Render the collisional stress lsd_options%lsd_largest_hpp_type=-1, ! Largest of all species (if known) lsd_options%lsd_collision_tolerance=1E-6, ! The precision used in predicing time-of-collision for ellipsoids lsd_options%lsd_max_time=-1, ! Stop at a given time (if positive) ! Elastic moduli---this does not work yet, so don't even try! lsd_options%lsd_record_stress_correlations=F, ! Keep at FALSE lsd_options%lsd_n_bins=1000, lsd_options%lsd_collision_history_length=1000, lsd_n_relaxation_collisions=5, ! Per particle lsd_bin_dt_factor=0.5, ! To ensure no unbinned collisions ! Verification of program (do additional checks to make sure collisions are not missed etc.) lsd_verify=F, lsd_overlap_tolerance=1E-6, lsd_lambda_tolerance=1E-3, ! Sticky particles (keep particles close to one another using permanent/sticky NNLs) lsd_options%lsd_sticky_particles=F, lsd_options%lsd_sticky_cutoff=0.001, ! Length of sticky tether lsd_sticky_stretch_tolerance=1E16, ! When to let the tether go lsd_sticky_n_collisions=100, ! Minimal number of collisions before desolving tether ! Entropy measurement: lsd_options%lsd_cell_model=F, ! Use the BCMD algorithm or not / &LSDGenerationOptions lsdpg_options%lsdpg_animate_compression=T, ! Animate the packing process lsdpg_options%lsdpg_save_animation=F, ! Safe frames to disk lsdpg_options%lsdpg_save_static_stages=T, ! Save each stage lsdpg_options%lsdpg_save_dynamic_stages=F, ! Also save velocities lsdpg_options%lsdpg_average_g2=F, ! Average g2 during the MD run lsdpg_options%lsdpg_save_statistics=T, ! Report useful statistics lsdpg_options%lsdpg_density_stepsize=-1, ! Report statistics every density increment (if positive) lsdpg_save_static_snapshots=F, ! Save backup .stage files for recovery in case of crash lsdpg_save_dynamic_snapshots=F, ! Also save the velocities lsdpg_reset_stress_tensor=T, ! Reset the stress tensor to zero every stage or do long-term averaging lsdpg_reset_velocities=T, ! Reset the velocities every cycle lsdpg_reset_NNL_stresses=F, ! Reset the collisional stresses or keep a long-term average ! Statistics: lsdpg_save_lsdpg_log=F, ! Save a log of the progress to a file (can be large!) lsdpg_options%lsdpg_Q6_cutoff=0.1, ! Cutoff for Q6 ! Compression parameters: lsdpg_options%lsdpg_initial_density=0.6, ! Density at which to start cooling (of positive) lsdpg_options%lsdpg_n_stages=1000, ! Number of stages lsdpg_options%lsdpg_n_cycles=-1, ! Number of re-jamming cycles (if positive) lsdpg_options%lsdpg_n_events=1000, ! Number of events per stage lsdpg_options%lsdpg_cool_down=-1, ! Cool down if non-negative (0-velocity rescaling, 1-reinitialize velocities) lsdpg_jamming_stage_factor=0.1, ! Even I don't know what this is lsdpg_relaxation_stages=2, ! If n_cycles>0, how many stages to relax the packing before re-jamming ! Adaptive expansion rates (does not really work!) lsdpg_options%lsdpg_adjust_expansion=F, ! Try to automatically adjust the expansion lsdpg_options%lsdpg_max_abs_expansion=1E-3, ! But do not go beyond this expansion rate hpp_convert_to_polydisperse=F, ! Convert from mono to polydisperse packing for densification lsdpg_optimal_collision_time=1E-12, ! Target time-between-collisions lsdpg_max_expansion_reduction=1E6, ! Do not reduce expansion too much ! Termination criteria lsdpg_options%lsdpg_density_tolerance=0, ! Stop if density changes less than this after a whole stage elapsed (if positive) lsdpg_options%lsdpg_pressure_tolerance=1E3, ! Stop if pressure exceeds this lsdpg_options%lsdpg_stress_tolerance=0.0, ! Stop if self-stress becomes very balanced (if positive) ! Parinello-Rahman MD (deforming lattice): lsdpg_options%lsdpg_lattice_mass=1E6, ! Unit cell mass lsdpg_cell_inertia=0, ! Unit cell inertia ! If positive, use damped dynamics, or, ! if 0, use Newton-law type dynamics for the lattice strain rate ! NNLs: lsdpg_options%lsdpg_use_nnl=T, ! Use NNLs lsdpg_options%lsdpg_compact_nnl=F, ! Compact the NNLs near jamming lsdpg_options%lsdpg_min_nnl_cutoff=-0.075, ! If compacting, do not shrink NNLs too small lsdpg_monitor_NNL_activity=F, ! Monitor (and report) how many neighbor pairs are colliding during a stage hpp_io_nni_numbering=T ! Keep this at T (F is used only for compatibility with old files) hpn_cutoff_adaptiveness=0.25, ! If using the BCMD algorithm, how to adaptively change the rate of shrinking of the bounding cells (see paper) ! Elastic constants (does not work!) lsdpg_options%lsdpg_elastic_symmetry='I', / ! Monitor g2(r) during the run: One can monitor several different kinds of g2 (say both logarithmic and linear-scale in r): &HPPDistributionParameters_1 hpp_g2_options%hpp_g2_nonoverlapping=T, ! If T, then r starts at 1 instead of 0 hpp_g2_options%hpp_g2_logarithmic=F, ! Use a logarithmic or linear scale hpp_g2_options%hpp_g2_n_r_bins=100, ! Number of bins hpp_g2_options%hpp_g2_cutoff=2.0, ! Maximum radius hpp_g2_options%hpp_g2_n_theta_bins=10, ! If also processing hpp_g2_options%hpp_g2_dmu=0.1, ! If logarithmic scale, the multiplier in the log scale / ! These control the execution options, such as level of verbosity, profiling, etc. ! Some of these options are too hard to explain without knowing my execution handling library &ExecutionHandlerOptions log_type="FO" monitor_log_type="FO" log_default="D" log_execution="D" log_procedure_execution="M" ! "N" for normal, "M" for monitoring (more output), "E" for little to no output to screen terminate_execution="W" ! Terminate at warnings execution_options%execution_random_seed=0 ! If zero than clock will be used to seed the random number generator execution_options%register_execution=F ! Register every executed procedure execution_options%register_procedure_execution=T execution_options%trace_execution=T ! If register_execution=T, print out execution stack trace execution_options%timestamp_execution=F execution_options%profile_execution=F execution_options%profile_TAU=F execution_options%trace_allocation=F ! Hardware performance profiling using PAPI: PAPI_multiplex=F PAPI_events_names="TOT_INS FP_INS L1_DCM RES_STL" report_profile_cutoff=1 / OpenGL general rendering options (I do not document most of them) &OpenGLOptions glw_options%glw_name="" ! Name of OpenGL window glw_options%glw_filename="" ! The filenames used for image snapshots (blank for default) glw_options%glw_file_type="TIFF" ! "EPS" for eps (large files), or "TIFF" (better) glw_options%glw_width=600 ! Window width glw_options%glw_height=600 ! Window height glw_options%glw_offscreen=F ! If T then only images are saved without outputing to screen ! If you want to tune the look: !glw_options%glw_lookat=0 0 0, !glw_options%glw_lookfrom=0 0 5, glut_default_menu=T, glut_mouse_sensitivity=1, gl_clear_color=0 0 0 1, gl_diffuse_color=1 1 1 1, gl_ambient_color=0 0 0 1, gl_specular_color=1 1 1 1 / &HPPRenderingOptions hpr_line_width=5, hpr_transparency=0, hpr_virtual_transparency=0.5, hpr_brightness=1, hpr_specularity=0.0, hpr_shininess=0.0, hpr_emissivity=0.0, hpr_render_bidirectional=F, !hpr_plot_scaling=1.0, hpr_options%hpr_ball_resolution=25, hpr_options%hpr_cylinder_resolution=6, hpr_options%hpr_render_particles=T, hpr_options%hpr_render_boundary=T, hpr_options%hpr_render_virtual=F, hpr_options%hpr_render_contacts=F, hpr_options%hpr_render_neighbourhoods=T, hpr_options%hpr_rerender=F, hpr_options%hpr_display_invisible=T, hpr_options%hpr_render_grid=F, hpr_options%hpr_particle_colors=1 0 0 1 0 0 1 1, hpr_options%hpr_neighbourhood_colors=0 1 0 0.25 0 1 0 0.25, hpr_options%hpr_contact_colors=0 0 0 1 0 0 1 1, hpr_options%hpr_virtual_colors=1 1 1 0.25 0 1 0 0.5, hpr_options%hpr_misc_colors=0 0 0 0.5 1 1 1 0.5, / ! EOF