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README_vol2planeTransfer.md

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vol2planeTransfer

vol2planeTransfer is a utility to transfer data on a 3D mesh (output from RocLB) to an arbitrary planar cross-section of the 3D mesh. For each cell in the cross-section, a nearest neighbor search filtered by a user defined radius is performed in the 3D mesh. The data at these neighbors is then averaged, weighted by the inverse of their distance from the query point on the cross-section, and the result is assigned to the query point.

The driver for the utility is utils/vol2planeTransfer.C

The following classes were modified or added during development:

  • vtkAnalyzer
  • baseInterp
  • spheres (added)

I didn't modify the original interfaces, only overloaded and added members.

The executable 'vol2planeTransfer' is placed in Nemosys/build/bin. Append this path to $PATH so the executable name is within scope of the shell.

Building

All utilities, including vol2planeTransfer will be built if cmake is invoked as follows from within the build directory:

$ CMAKE_PREFIX_PATH=../install/madlib:../install/gmsh:../install/cgns cmake ..
$ make -j8 (change number of cores if needed)

To turn off (or turn back on) utility building, pass the 'BUILD_UTILS' option:

$ CMAKE_PREFIX_PATH=../install/madlib:../install/gmsh:../install/cgns cmake -DBUILD_UTILS=OFF ..
$ make -j8

To test the utility, run:

$ make test

This executes a test case found in Nemosys/testing/test_data/vol2planeTransfer_test. This directory also contains a python script for plotting the resulting points with values of 0 for crosslink density, colored by material. It can be run with:

$ python plot_points.py

Usage

After the utility has been compiled, it can be executed from the command line with an input file, below named "file.inp" as the only argument.

$ vol2planeTransfer file.inp

Input File Specification

The name of the input file is the only argument passed to the utility. Below is an example of the required specifications in the file with descriptions of each option:


  Vol_vti_File          =   {vtk_diff1_002000.vti}    // 3D mesh file
  Vol_geo_File          =   {TEST.geo}                // 2D geo file (with inclusion definitions)
  Plane_vtk_File        =   {TEST.vtk}                // 2D mesh file
  mask_file             =   {vtk_bbmask_diff1.vti}    // 3D bbmask outupt with RocLB
  outputFile            =   {has_sphere_has_coord1}   // output file name
  material_names        =   {sphere_1.00,sphere_2.00} // names of physical surfaces
  cross_link_name       =   {species3_conc}           // name of crosslink array in 3D mesh file
  write_coords          =   {1}                       // option to write coordinates
  has_spheres           =   {1}                       // option to consider spherical inclusions
  youngs_inc_default    =   {70,-1}                   // youngs moduli defaults for each physical surface 
  shear_inc_default     =   {26,36}                   // shear moduli defaults for each physical surface
  poisson_inc_default   =   {-1,100}                  // poisson ratio defaults for each physical surcace
  youngs_dom_default    =   {-1}                      // youngs modulus default for domain (non-inclusions)
  poisson_dom_default   =   {105}                     // poisson ratio default for domain (non-inclusions)
  M_weight              =   {1}                       // Molecular weight of primary polymer before cross linking
  Mc_weight             =   {0}                       // Molecular weight of polymer chain between cross links
  NN_TOL                =   {.01}                     // Multiplier of min-extent to define radius in k-NN search
  Temperature           =   {300}                     // Temperature in which RocLB sim was conducted

NOTES:

  • The order of the options matters and MUST be as given above.
  • DO NOT put spaces between elements in a list.
  • The order of default values MUST correspond to the order of the physical names listed in material_names.
  • A default value of "-1" indicates an unknown parameter that will be calculated by the utility and requires non-negative values for the other two defaults.

Output Specification

The output file will have at most 7 columns, as in:

id    X    Y    Z    rho    E    V
 |    |    |    |     |     |    |
  • id - index of cell on cross-section
  • X - X coordinate of cell center
  • Y - Y coordinate of cell center
  • Z - Z coordinate of cell center
  • rho - cross-link density at cell center
  • E - Young's modulus at cell center
  • V - Poisson ratio at cell center

If write_coords is set to 0 in the input file, the output will exclude the X, Y and Z columns.

An example case can be found in testing/test_data/vol2planeTransfer_test

Unit Specification

Currently, unit specifications are as follows:

  • Gas constant R is in units of (m^3 * GPa)/(K * mol) and is specified in the driver source file: utils/vol2planeTransfer.C
  • Temperature is in Kelvin and is specified in the input file
  • All moduli are in GPa and are specified in the input file

Notes to user

During the interpolation and subsequent writing of data, the following checks are performed:

  • If a point on the cross-section is inside of an inclusion, the properties of the material of the inclusion are used for Young's modulus and Poisson ratio; the crosslink density at the point is set to 0. This determination is made with the analytic equation describing a given spherical inclusion.
  • Neighbors of a point on the cross-section that are outside of the radius of the search (% of extent passed by user) or inside of inclusions are given 0 weight in the interpolation. The latter determination is made using the bbmask output by RocLB.
  • If all neighbors of a non-inclusion point on the cross-section are inside of inclusions, an error is thrown and the program halts with non-zero exit status. This determination is made using the bbmask output by RocLB.