mesh2vtk

Command line tool to convert MCNP mesh tallies to Visual ToolKit (VTK) formats.

Generalised conversion of meshtal files to visual toolkit formats

Usage: mesh2vtk <file> <id> [options]

Arguments:
  <file>    Path to input meshtal file
  <number>  Mesh tally identifier

Options:
  -v, --verbose...        Verbose logging (-v, -vv)
  -q, --quiet             Supress all log output (overrules --verbose)
  -h, --help              Print help (see more with '--help')

Mesh options:
  -t, --total             Only extract 'Total' energy/time groups
  -e, --errors            Include errors mesh in output files
  -s, --scale <num>       Multiply all results by a constant
      --energy <list>...  Filter energy group(s)
      --time <list>...    Filter time group(s)
  -a, --absolute          Interpret filter values as MeV/shakes

Vtk options:
  -o, --output <name>     Name of output file (excl. extension)
  -f, --format <fmt>      VTK output format
      --resolution <res>  Cylindrical mesh resolution
      --endian <end>      Byte ordering (endian)
      --compressor <cmp>  Comression method for xml

Note: --help shows more information and examples

Help is printed with the -h flag, and --help will show default values, examples, and any important behaviour.

Install

Direct from github:

cargo install --git https://github.com/repositony/mesh2vtk.git

All executables are under ~/.cargo/bin/, which should already be in your path after installing Rust.

Click here if you have never used Rust

If you have never used the Rust programming language, the toolchain is easily installed from the official website

curl https://sh.rustup.rs -sSf | sh

This should have added source $HOME/.cargo/env to the bash profile, so update your environment with source ~/.bashrc.

Overview

Supported output formats

For more detail, see the OUT keyword for the FMESH card definition in the MCNPv6.2 or MCNPv6.3 user manuals.

Output format	Supported?	Description
COL	Yes	Column data (MCNP default)
CF	Yes	Column data including voxel volume
IJ	Yes	2D matrix of I (col) and J (row) data, grouped by K
IK	Yes	2D matrix of I (col) and K (row) data, grouped by J
JK	Yes	2D matrix of J (col) and K (row) data, grouped by I
CUV (UKAEA)	Yes	UKAEA Cell-under-Voxel column data
NONE	N/A	`NONE` or unknown output format

Once I get my paws on MCNPv6.3 this will be extended to include the new COLSCI, CFSCI, and XDMF/HDF5 formats.

Supported mesh geometries

All functionality is fully supported for both rectangular and cylindrical meshes.

Mesh geometry	Supported?	MCNP designators
Rectangular	Yes	rec, xyz
Cylindrical	Yes	cyl, rzt
Spherical	No	sph, rpt

Currently spherical meshes are not supported because barely anyone knows about them, let alone uses them. They are therefore a low priority, but raise an issue if anyone needs it.

Examples

Including uncertainty meshes

Corresponding uncertainty meshes are optional in case of large meshtal files.

# Extract every energy and time group, with corresponding error meshes
mesh2vtk /path/to/meshtal.msht 104 --errors

Only use the 'Total' energy/time groups

Often only the Total energy/time bins are of interest, and a quick way of only converting this subset is provided.

# Extract only the 'Total' energy and time groups
mesh2vtk /path/to/meshtal.msht 104 --total

Choose specific energy/time groups

If specific energy or time groups are required they can be filtered by group index.

# Extract specific energy and time groups by index
mesh2vtk /path/to/meshtal.msht 104  \
            --energy 0 2 6          \
            --time 1 total

The keyword total can be used for the 'Total' energy/time groups for convenience.

Filtering by index avoids the precision issues that accompany the extremely limited MCNPv6.2 output formatting. However, if you really want to use absolute values in units of MeV and shakes then include the --absolute flag.

# Extract specific energy and time groups by MeV/shakes values
mesh2vtk /path/to/meshtal.msht 104  \
            --energy 1.0 20.0 1e2   \
            --time 1e12 total       \
            --absolute

For intuitive use, the groups correspond with values defined on the EMESH and TMESH cards.

Note: mesh tallies label groups by the upper bounds defined on EMESH/TMESH cards. i.e the energy group 1.0 corresponds to the 0.0>=E<1.0 bin, though in reality 1 MeV particle would end up in the next group up.

Rescale all results

MCNP normalises everything so it is often the case that the results must be rescaled to provide physical values.

# Rescale the result by a constant multiplier, e.g 6.50E+18 neutrons/s
mesh2vtk /path/to/meshtal.msht 104 --scale 6.50E+18

Mesh rotations are a work in progress.

Change the output file name

By default the file prefix is fmesh, so the output files will be fmesh_<number>.vtk. This may be changed as needed.

# Change the output name to `myvtk_104.vtr`
mesh2vtk /path/to/meshtal.msht 104 --output myvtk

Change the Vtk format

Most useful may be the ability to decide on output formats. XML and legacy formats are supported, with both ascii and binary variants.

# Output as a binary vtk with legacy formatting
mesh2vtk /path/to/meshtal.msht 104 --format legacy-binary

Specify XML compression and binary byte order

For more advanced usage, things like byte ordering and xml compression methods are also configurable.

# Output as an xml using lzma and setting the byte order to big endian
mesh2vtk /path/to/meshtal.msht 104      \
        --format xml                    \
        --compresser lzma               \
        --endian big-endian

Note - VisIt only reads big-endian, but most sytems are natively little-endian. For personal convenience the default is big, but I am open to arguments for little endian as the default.

Plotting cylindrical meshes

There is no VTK representation of cylindrical meshes, so an unstructured mesh is generated from verticies based on the RZT bounds.

Unfortunately, this can result in "low-resolution" plots for meshes with few theta bins. The number of theta bins can be increased to round off these edges. This simply subdivides the voxels by an integer number of theta bins.

# Subdivide voxels into 3 to round off cylindrical unstructured mesh
mesh2vtk /path/to/meshtal.msht 104 --resolution 3

Note that this will increase the file size and memory usage significantly in some cases.