This tool can be used to generate an isosurface geometry from any 3D mesh tagged with scalar values (eg, a Cartesian weight window mesh used for Monte Carlo particle transport). The tool will create a meshed surface geometry (DAGMC-compliant) using specified isosurface values.

1. Installation

2. Python Module

3. Command Line Tool

• Python 2.7
• VisIt
• MOAB v5.1+ with PyMOAB enabled

From the source directory, run the following to install:

  pip install . --user

To use, import the Python module with from IsogeomGenerator import vol.

To generate a full geometry from a starting Cartesian mesh file, run the following steps in order:

1. Set contour levels values: This will assign the values that will be used for the isosurface selections in the mesh file. The values can be set using one of three methods:

   • assign_levels(levels): User defines the contour levels to be used as the isosurfaces.

     Input: levels, list of floats, list of user-defined values

   • read_levels(levelfile): Read level values from a file. One value per line only.

     Input: levelfile, string, relative path to file with level information.

   • generate_levels(N, minN, maxN, mode='lin'): Auto-generate evenly-spaced level values between the min and max value.

     Input:

     • N: int or float, number of levels (int) to generate ('lin' or 'log' mode); or the ratio (float) to use to separate levels ('ratio' mode).
     • minN: float, minimum level value
     • maxN: float, maximum level value
     • mode (optional): string, options are 'lin' (default), 'log', or 'ratio'.
       • 'lin': N linearly spaced values between minN and maxN
       • 'log': N logarithmically spaced values between minN and maxN
       • ratio: levels that are spaced by a constant ratio N. minN will be used as minimum level value and the maximum level value is less than or equal to maxN.

2. Generate the isovolume database: This step will use the level values assigned in step 1 to create isovolumes in the mesh file using VisIt. Two consecutive level values are used to generate an isovolume in the meshfile and the surface of that volume is exported as a meshed surface. Each isovolume is exported as one file in the database.

   • generate_volumes(self, filename, data, dbname='/tmp/'): Creates an STL file for each isovolume. Files are generated in the dbname folder.

     Input:

     • filename: string, path to vtk file with the mesh file
     • data: string, name of the data whose values exist on the mesh (will be used to generate the isovolumes)
     • dbname: (optional), string, Absolute path to the folder to store created surface files. Default: a folder called tmp/ in the current directory.

3. Create the DAGMC isosurface geometry:

   • create_geometry(tag_for_viz=False, norm=1.0, merge_tol=1e-5, dbname='/tmp/', tags=None, sname=None, sdir=None): Creates a DAGMC-compliant isosurface geometry from the isovolume files in the database created in step 2 using MOAB.

     Input:

     • tag_for_viz: bool (optional), True to tag each triangle on every surface with the data value. Needed to visualize values in VisIt. Default=False.
     • norm: float (optional), default=1. All data values will be multiplied by the normalization factor.
     • merge_tol: float (option), default=1e-5 cm. Merge tolerance for mesh based merge of coincident surfaces.
     • dbname: string (optional), name of folder to store created surface files. Must be absolute path. default: a folder called 'tmp' in the current directory
     • tags: dict (optional), set of names and values to tag on the geometry root set. Dictionary should be structured with each key as a tag name (str) and with a single value (float) for the tag. Example: {'NAME1':1.0, 'NAME2': 2.0}
     • sname: string (optional), name of file (including extension) for the written geometry file. Acceptable file types are VTK and H5M. Default name: isogeom.h5m

The steps for creating an isosurface geometry can be done on the command line with the generate_isogeom command. This tool can be run in three different modes:

• full: this will run both the visit step then the moab step (described below). Command:

  generate_isogeom full <meshfile> <dataname> [options]
  

• visit: starting from a Cartesian mesh file, this will generate only a database of separate isosurface files from VisIt (step 2 above). Command:

  generate_isogeom visit <meshfile> <dataname> [options]
  

• moab: this will start from the database (generated in the visit step) to create a DAGMC-compliant isosurface geometry using PyMOAB (step 3 above). Command:

  generate_isogeom moab [options]
  

To view the three different modes, run generate_isogeom --help.

Each mode has different required or optional arguments needed at run time. Below is a table summary of those options. This information is also available via terminal help message: (generate_isogeom [mode] --help).

• X = required
• O = optional
• - = Not allowed

All of these examples will assume a starting Cartesian mesh file called cw_mesh with the desired data called wwn.

• Run all the steps start to finish, defining 3 values for the level information at runtime, and tag for visualization:

  generate_isogeom full cw_mesh wwn -lv 0.1 5.2 12.3 --viz
  

• Generate a geometry start to finish, with 5 levels logarithmically spaced from 1e-5 to 1e+3. Also tag the geometry two metadata tags called E1 and E2 with values of 1.0 and 10.0, respectively:

  generate_isogeom full cw_mesh wwn -gl log -lx 1e-5 1e+3 -N 5 -t E1 1.0 -t E2 10.0
  

• Generate only the isovolume database using levels that logarithmically spaced between 0.1 and 1e+14 and specifying where to write the generated database:

  generate_isogeom visit cw_mesh wwn -gl log -lx 0.1 1e+14 -db my_database/
  

• Generate an isovolume database in the default location using levels between 1.0 2e+4 that are spaced with a ratio of 20:

  generate_isogeom visit cw_mesh wwn -gl ratio -lx 1.0 2.e4 -N 20
  

• Generate an isosurface geometry using the levelfile and database located in my_database/, specifying a file name for file produced:

  generate_isogeom moab -lf my_database/levelfile -db my_database -g geom1.h5m
  

• Generate a geometry from a database located in my_isogeom/, read the level info from a file called levelinfo, mutliply all data by a factor of 2e4, and save the file as my_isogeom.vtk in a new folder called output_folder/:

  generate_isogeom moab -db my_isogeom/ -lf levelinfo -n 2e4 -g my_isogeom.vtk -sp output_folder/