! This code is not commented with as much detail as ProcessPacking.nml ! It does however contain all of the available options. ! Become familiar with ProcessPacking.nml first! &HPPProcessOptions ! This info is repetetive, but this is not saved in the input file so it must be re-entered, sorry hpp_spherical_boundary=F, ! Is the packing inside a hard-wall spherical container frozen_particles=F, ! Treat species 2 and higher as frozen particles? hpp_density=-1 ! Initial density (-1 to keep the same as in the file) ! Basic controls: common_namelist=T, ! Read all namelists from a common file (namely THIS file), or ! read them from an nml file named after the packing (say MyPacking.nml) scale_packing=F, ! Scale the particles to make the packing overlap free or keep as is contact_cutoff=1E-6, ! Can be negative, if -1 no new contacts will be added hpp_convert_to_polydisperse=F, ! Convert and save the input file to polydisperse format ! Contact networks: ! Further controls are provided below in namelist HPPNNLParameters ptp_use_nnl=F, ! Use NNLs or not (does not work for superellipsoids!) read_contacts=F, read_forces=2, ! 0=none, 1=read contact forces as priorities from file, 2=read contact forces from separate file nnl_infinite_priority=-1E16, ! Keep all read interactions with higher priority even if below cutoff hpp_io_nni_numbering=T, ! Keep at TRUE (F is only used for old files) gaps_as_priorities=F, ! Give highest priorities to smallest gaps) ! Operations on the contact network: hpp_histogram_forces=F, ! Output all the contact forces to a file (for histogramming) process_coordination=F, ! Output the coordination number distribution to file hpp_histogram_coordinations=F, ! Output all individual particle coordinations to a file ! Backbone extraction write_backbone=F, ! Extract and save the backbone of the packing write_rattlers=F, ! Save just the rattlers as a (sub)packing Z_cutoff=2, ! Coordination cutoff for rattlers ! Rendering via OpenGL: render_packing=T, ! Render the packing to screen plot_packing=F, ! Save it to an EPS file (disks and ellipses only), or VRML (spheres and ellipsoids) plot_type="EPS", ! DISLIN file format (EPS is best in 2D) ! Correlation function calculation: ! Further controls are provided below compute_g2=F, ! Computer pair correlation compute_OPs=F, ! Compute additional order parameters ! Transforming the packing: rewrite_packing=F, ! Save the rescaled and modified packing to a file, as described below write_ampl=F, ! Write an AMPL file from the NNLs to be used to test for jamming for spheres n_replications=1 1, ! Replicate the unit cell several times to make a larger packing (for lattices) transform_affinely=F, ! Apply an affine transformation, as below affine_transformation=1.0 0 0 2 ! Matrix of transformation stretch_affinely=F, ! A special case of transformation---apply a sequence of n_stretches stretches n_stretches=1, stretch_directions=1.0001 0.0, ! Process the interparticle gap distribution count_contacts=F, ! Write a file with the PDF of interparticle gaps Z_gap_range=-10 0, ! The range for the PDF hpp_histogram_gaps=F, ! Write all gaps to a file for external processing write_contact_network=F, ! Write the contact network to a file for MATLAB processing write_contact_hessians=F, ! Also write the Hessians in MATLAB format hpp_histogram_Q6_local=F, ! Write the local particle Q6 for separate processing ! Additional functions density_profile=F, ! Compute radial or planar density profile density_fluctuations=F, ! Compute density fluctuations inside a moving window pore_sizes=F, ! Compute pore-size distribution histogram_pore_sizes=F, ! Write all pore sizes to a file (don't remember what exactly this is) ! If computing the pore-size distribution, use: !n_windows=1250, ! Number of pore bins !n_samples=2000000000, ! Number of trial spheres ! If computing density fluctuations, use: n_windows=50, ! Number of window sizes n_samples=10000, ! Or number of window samples window_cutoff=-1, ! The largest window to look at ! Structure factor: fourier_analyze=F, ! Compute S(k) grid_size=100, ! If positive FFT is used, otherwise NFFT or DFT (see below) window_size=10, ! How much of the S(k) cube to write to a VTK file. ! If negative DFT is used, otherwise NFFT centroids_only=T, ! DFT of delta functions at centroids only normalize_structure_factor=T, write_digitized_packing=F, ! Write a 0/1 digitized version of the packings (as in MRI experiments) write_structure_factor_points=F, ! Output the whole structure factor S(k_vector) ! Shell analyzis for contact network of packing (uses graph algorithms, see g2 PRE paper) process_shells=F, shell_cutoff=0 0.01 0.1, second_shell=F, ! Process also second-neighbor shells histogram_bond_angles=F, hpp_histogram_Q6_local=F, ! Voronoi tesselation voronoi_tessellatation=F ! Compute the NNL neighbors using Voronoi/Delanay tesselation delanay_cutoff=2 ! The maximum possible distance to Delanay neighbor (user guess) / ! For NNLs: &HPPNNLParameters max_neighbours_="30 30 30 30", ! Max number of neighbors for each specie bounding_refinements_="-1.0 -1.0 -1 -1", ! If using bounding complexes (see papers) / ! For computing g2: &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