First pass to scrub reference to Trelis

AUTHORS.rst

@@ -27,8 +27,8 @@ included contributions from the following:
 * Julie C. Zachman
 * Xiaokang Zhang
 
-The DAGMC project also relies heavily on the MOAB_ project and the Trelis_
+The DAGMC project also relies heavily on the MOAB_ project and the Coreform Cubit_
 software package.
 
 .. _MOAB: http://sigma.mcs.anl.gov/moab-library
-.. _Trelis: http://www.csimsoft.com/trelis.jsp
+.. _Cubit: https://coreform.com/products/coreform-cubit/

README.rst

@@ -12,10 +12,12 @@ including MCNP5_, MCNP6_, Geant4_, FLUKA_, Tripoli4_, and Shift_. There are also
 efforts planned to integrate DAGMC into other codes such as Serpent2_, OpenMC_,
 Phits_, and FRENSIE_.
 
-DAGMC currently relies on using the solid modeling software Cubit_ or its
-commercial counterpart, Trelis_, to prepare solid models. These packages can be
+DAGMC currently relies on using the commercial solid modeling software Cubit_ (or its
+`government-use counterpart <https://cubit.sandia.gov>`_ available from 
+Sandia National Laboratories)
+to prepare solid models. These packages can be
 used to import CAD models from other tools such as SolidWorks, CATIA, etc., or
-to create geometry from scratch. DAGMC also relies on Trelis/Cubit to assign
+to create geometry from scratch. DAGMC also relies on Cubit to assign
 materials and other geometry-related information.
 
 For more information, please visit the `DAGMC website <DAGMC_>`_.
@@ -27,8 +29,7 @@ Quick links:
 * `Contributors guide <https://svalinn.github.io/DAGMC/contribute/index.html>`_
 
 ..  _DAGMC: https://svalinn.github.io/DAGMC
-..  _Cubit: https://cubit.sandia.gov
-..  _Trelis: https://www.csimsoft.com/trelis
+..  _Cubit: https://coreform.com/products/coreform-cubit/
 ..  _MCNP5: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/mcnp5.shtml
 ..  _MCNP6: https://mcnp.lanl.gov
 ..  _Geant4: https://geant4.cern.ch

doc/index.rst

@@ -26,10 +26,12 @@ DAGMC has been integrated into a variety of Monte Carlo radiation codes
 including MCNP5_, MCNP6_, Geant4_, FLUKA_, Tripoli4_, OpenMC_, and Shift_. There are also
 efforts planned to integrate DAGMC into other codes such as Serpent2_, Phits_, and FRENSIE_.
 
-DAGMC currently relies on using the solid modeling software Cubit_ or its
-commercial counterpart, Trelis_, to prepare solid models. These packages can be
+DAGMC currently relies on using the commercial solid modeling software Cubit_ (or its
+`government-use counterpart <https://cubit.sandia.gov>`_ available from 
+Sandia National Laboratories)
+to prepare solid models. These packages can be
 used to import CAD models from other tools such as SolidWorks, CATIA, etc., or
-to create geometry from scratch. DAGMC also relies on Trelis/Cubit to assign
+to create geometry from scratch. DAGMC also relies on Cubit to assign
 materials and other geometry-related information.
 
 ..  toctree::
@@ -47,8 +49,7 @@ materials and other geometry-related information.
 
 ..  _CNERG: https://cnerg.github.io
 ..  _MOAB: https://press3.mcs.anl.gov/sigma/moab-library
-..  _Cubit: https://cubit.sandia.gov
-..  _Trelis: https://www.csimsoft.com/trelis
+..  _Cubit: https://coreform.com/products/coreform-cubit/
 ..  _MCNP5: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/mcnp5.shtml
 ..  _MCNP6: https://mcnp.lanl.gov
 ..  _Geant4: https://geant4.cern.ch

doc/install/index.rst

@@ -9,7 +9,7 @@ should know that the following will be required:
 2.  MCNP5_ or MCNP6_ source code, if you intend to install DAG-MCNP5 or
     DAG-MCNP6
 3.  FLUKA_, if you intend to install FluDAG
-4.  Cubit_ or Trelis_, for the creation of geometry
+4.  Coreform Cubit_ for the creation of geometry
 
 Once you have the basic pre-requisite peices in place you can proceed to the
 DAGMC installation. There are three main steps in the DAGMC installation:
@@ -29,5 +29,4 @@ options available to you.
 ..  _MCNP5: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/mcnp5.shtml
 ..  _MCNP6: https://mcnp.lanl.gov
 ..  _FLUKA: http://www.fluka.org/fluka.php
-..  _Cubit: https://cubit.sandia.gov
-..  _Trelis: https://www.csimsoft.com/trelis
+..  _Cubit: https://coreform.com/products/coreform-cubit/

doc/install/plugin.rst

@@ -1,4 +1,4 @@
-Installing the Cubit/Trelis plugin
+Installing the Cubit plugin
 ==================================
 
 There is a common location that stores all the plugins that are available for
@@ -9,20 +9,20 @@ Linux install
 ~~~~~~~~~~~~~
 
 Obtain the Linux plugin from the link above. These instructions assume that you
-have installed Trelis in ``/opt/Trelis-16.0``. If you installed it somewhere
+have installed Cubit in ``/opt/Coreform-Cubit-2020.2``. If you installed it somewhere
 else, modify these instructions appropriately.
 
 These operations may need to be performed as the root user (sudo).
 
-1.  Unpack the tarball in ``/opt/Trelis-16.0/bin/plugins``.
-2.  Change directory to ``/opt/Trelis-16.0/bin/plugins/dagmc``.
+1.  Unpack the tarball in ``/opt/Coreform-Cubit-2020.2/bin/plugins``.
+2.  Change directory to ``/opt/Coreform-Cubit-2020.2/bin/plugins/dagmc``.
 3.  Run the install script: ``./install.sh``.
 
 OS/X install
 ~~~~~~~~~~~~
 
 Obtain the OS/X plugin from the link above. These instructions assume that you
-have installed Trelis in ``/Applications/Trelis-16.0``. If you installed it
+have installed Cubit in ``/Applications/Trelis-16.0``. If you installed it
 somewhere else, modify these instructions appropriately.
 
 These operations may need to be performed as the root user (sudo).
@@ -40,4 +40,4 @@ Windows install
 A plugin for Windows is currently being developed; it will be posted to the
 DAGMC plugins page when it is ready.
 
-..  _DAGMC_plugins: http://go.wisc.edu/dagmc-trelis
+..  _DAGMC_plugins: https://go.wisc.edu/svalinn-cubit-plugin

doc/usersguide/codes/dag-mcnp.rst

@@ -6,7 +6,7 @@ the term "DAG-MCNP" refers to both.
 
 There are three varieties of code-specific steps for DAG-MCNP:
 
-1.  Defining attributes of the geometry using Cubit/Trelis groups
+1.  Defining attributes of the geometry using Cubit groups
 2.  Defining DAGMC runtime parameters using the DAGMC input file
 3.  Specifying additional parameters on the command line
 
@@ -75,7 +75,7 @@ geometric shape can be used for this, but a cubic shell is preferred. The
 graveyard represents the outside world, and any particle that enters it will be
 terminated.
 
-To create a graveyard volume, create two volumes in Cubit/Trelis with the same shape
+To create a graveyard volume, create two volumes in Cubit with the same shape
 and same center with one slightly larger than the other, making sure that both
 bound the entire problem geometry. Then, subtract the smaller one from the
 larger one. The remaining volume is the graveyard.

doc/usersguide/codes/dag-mcnp_specific.txt

@@ -31,7 +31,7 @@ keywords have been added to the command line to specify the necessary files.
 
 :``gcad=<geom_file>`` (required): Specify the filename of the input geometry
     file. It can be in one of two formats: the MOAB (\*.h5m) format (this is the
-    format produced by ``export dagmc`` in Trelis/Cubit), or a facet file
+    format produced by ``export dagmc`` in Cubit), or a facet file
     produced by DAGMC. If this entry is not present, DAG-MCNP will assume that
     it is running in native MCNP mode.
 

doc/usersguide/codes/dag-tripoli4.rst

@@ -3,7 +3,7 @@ Code-specific steps for DAG-Tripoli4
 
 There are three varieties of code-specific steps:
 
-1.  defining attributes of the geometry using groups in Cubit/Trelis
+1.  defining attributes of the geometry using groups in Cubit
 2.  defining DAGMC runtime parameters using input file syntax
 3.  changes to the command-line
 

doc/usersguide/codes/fludag.rst

@@ -3,7 +3,7 @@ Code-specific steps for FluDAG
 
 There are several varieties of code-specific steps:
 
-1.  Defining attributes of the geometry using groups in Cubit/Trelis
+1.  Defining attributes of the geometry using groups in Cubit
 2.  Producing material assignments in FLUKA input format from the h5m file, with
     the help of FluDAG
 3.  Preparing the FLUKA input file for running with DAGMC
@@ -142,7 +142,7 @@ Running FluDAG
 Running FluDAG bears some similarity to running ``FLUGG``. The first step is to
 create the CAD geometry of the problem you wish to run. In order to produce the
 material assignment data from the CAD geometry we must first
-:ref:`facet the file <geom_production>` using the Cubit/Trelis plugin. Using the
+:ref:`facet the file <geom_production>` using the Cubit plugin. Using the
 subsequently-defined geometry file, the user must produce the ``mat.inp`` file.
 ::
 

doc/usersguide/codes/openmc.rst

@@ -9,7 +9,7 @@ Code-Specific steps for OpenMC
 
 There are two varieties of code-specific steps for OpenMC_:
 
-1.  Defining attributes of the geometry using Cubit/Trelis groups
+1.  Defining attributes of the geometry using Cubit groups
 2.  Defining DAGMC runtime parameters using the OpenMC input files
 
 Geometry metadata
@@ -105,7 +105,7 @@ boundary between the problem and the outside world.  This volume should surround
 the entire geometry with a shell of finite thickness. Any geometric shape can be
 used, but a cubic shell is recommended to maximize performance.
 
-To create a containing volume, make two volumes in Cubit/Trelis with the same
+To create a containing volume, make two volumes in Cubit with the same
 shape and same center with one slightly larger than the other, making sure that
 both bound the entire problem geometry. Then, subtract the smaller one from the
 larger one. The result is a containing volume for the problem.

doc/usersguide/trelis_basics.rst → doc/usersguide/cubit_basics.rst

@@ -1,7 +1,7 @@
-Cubit/Trelis basics
+Cubit basics
 ===================
 
-Pre-processing solid models using Cubit/Trelis
+Pre-processing solid models using Cubit
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This section focuses on steps that are independent of the Monte Carlo code used
@@ -12,10 +12,10 @@ needed.
 Importing the solid model
 -------------------------
 
-The first step in Cubit/Trelis is to import the generated solid model. Depending
+The first step in Cubit is to import the generated solid model. Depending
 on the complexity of the model, this step can take several seconds up to a half
 an hour. As an initial user, it is recommend to start with simple models and
-geometries to obtain a better understanding of Cubit/Trelis.
+geometries to obtain a better understanding of Cubit.
 
 Imprint and merge
 -----------------
@@ -97,7 +97,7 @@ Production of the DAGMC geometry
 --------------------------------
 
 Now that the geometry is ready for DAGMC we must export it. Using the
-Cubit/Trelis plugin make this very straightforward, assuming that the user has
+Cubit plugin make this very straightforward, assuming that the user has
 proceeded through the previous steps then all one must do is use the export
 dagmc command.
 ::
@@ -130,7 +130,7 @@ length tolerances of 1.0e-4 cm and 5.0 cm respectively
 The time taken to perform this step depends upon the complexity of the model, it
 could  take seconds for very simple models to hours for very complex models. It
 is also possible that faceting artifacts or failures could occur at this point,
-so monitor the output of this command in the Cubit/Trelis command line. If
+so monitor the output of this command in the Cubit command line. If
 issues due occurs, these should be addressed following the workflow listed
 above.
 
@@ -146,15 +146,15 @@ Roadmap for the future
 ~~~~~~~~~~~~~~~~~~~~~~
 
 Currently we have a number of standalone command line tools that are run sequentially
-on a model following faceting using Cubit/Trelis. We run `make_watertight` to seal
+on a model following faceting using Cubit. We run `make_watertight` to seal
 models to ensure no topological weaknesses exist and we run `uwuw_preproc` to add
 materials into analysis geometries. It is envisioned that at some point in the
-near future that we will integrate these as options within the Cubit/Trelis plugin.
+near future that we will integrate these as options within the Cubit plugin.
 
 ..  image:: plugin_infrastructure.png
     :height: 350
     :width:  800
-    :alt: The future infrastructure for the Cubit/Trelis plugin
+    :alt: The future infrastructure for the Cubit plugin
 
 This will allow you to add additional options if you want the model to be made
 watertight and/or if you want to add materials to the resultant geometry. There will

doc/usersguide/trelis_workflow.rst → doc/usersguide/cubit_workflow.rst

@@ -1,4 +1,4 @@
-Producing solid models for DAGMC using Cubit/Trelis
+Producing solid models for DAGMC using Cubit
 ===================================================
 
 The general workflow for the production of models for analysis using DAGMC
@@ -76,7 +76,7 @@ Preparing solid models
 In theory, solid models can be prepared in any modeling software
 system (e.g. SolidWorks, Pro/E, Catia, etc).  What is most important
 about the choice of solid modeling system is the ability to export to
-a format that can be imported by Trelis or Cubit, in particular:
+a format that can be imported by Cubit, in particular:
 
     * ACIS (\*.sat)
     * STEP (\*.stp, \*.step, etc)
@@ -224,7 +224,7 @@ Finishing up and final notes
 Having prepared your model to completion with the appropriate groups created
 , you can choose to save your model in various formats. Previously
 we recommended ACIS \*.sat files, but any format that reliably retains
-imprortant metadata will suffice.  Recommended storage formats are ACIS, \*.Trelis or
+imprortant metadata will suffice.  Recommended storage formats are ACIS or
 \*.cub files.
 
 One should also use the :ref:`make_watertight`. tool on the

doc/usersguide/index.rst

@@ -46,10 +46,10 @@ creation.
 ..  toctree::
     :maxdepth: 1
 
-    trelis_basics
+    cubit_basics
     uw2
     codes/index
-    trelis_workflow
+    cubit_workflow
     tally
     tools
     postprocessing

doc/usersguide/tally.rst

@@ -8,14 +8,14 @@ an unstructured mesh.
 Mesh production workflow
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-Cubit/Trelis can be used to generate the unstructured meshes needed for tallies.
+Cubit can be used to generate the unstructured meshes needed for tallies.
 To do so, use the following steps.
 
-1.  Load the geometry you wish to mesh into Cubit/Trelis.
+1.  Load the geometry you wish to mesh into Cubit.
 2.  Use the mesh tools to produce the meshes you want.
-3.  Save the file as a .trelis or .cub file. Remember to check the "Use Legacy
-    .cub file Format" option in Trelis or Cubit.
-4.  Use MOAB's ``mbconvert`` executable to convert from the Cubit/Trelis format
+3.  Save the file as a .cub file. Remember to check the "Use Legacy
+    .cub file Format" option in Cubit.
+4.  Use MOAB's ``mbconvert`` executable to convert from the Cubit format
     to a faceted .h5m file that DAGMC can use.
 
 Here is an example of how to use ``mbconvert``:

doc/usersguide/tools.rst

@@ -11,7 +11,7 @@ make_watertight
 ~~~~~~~~~~~~~~~
 
 A model is considered watertight if the faceting of all topologically linked
-surfaces are coincident. Models produced by Cubit/Trelis are not guarenteed to
+surfaces are coincident. Models produced by Cubit are not guaranteed to
 be watertight, and as a general rule, the more complicated the model, the less
 likely it is to be completely watertight.
 
@@ -23,14 +23,14 @@ before ``make_watertight`` and the black lines show the geometry after its use.
 ..  image:: watertight.png
     :height: 500
     :width:  600
-    :alt: An example of the use of make_wateright: the red lines show the
+    :alt: An example of the use of make_watertight: the red lines show the
           geometry before ``make_watertight`` and the black lines show the
           geometry after its use.
 
 ``make_watertight`` can be run with:
 ::
 
-    $ make_wateright <filename>
+    $ make_watertight <filename>
 
 The product will be a file named, `filename_zip.h5m`, and a summary is provided
 of what operations were done to seal the model.
@@ -45,7 +45,7 @@ given model is. It should be used as a post-processing step after
 ``check_watertight`` can be run  with:
 ::
 
-    $ check_wateright <filename>
+    $ check_watertight <filename>
 
 Both ``make_watertight``and ``check_watertight`` are built during the main DAGMC
 build procedure and can be found in DAGMC's `bin` directory.
@@ -69,7 +69,7 @@ The options which control mbconvert are:
     -s  <int> - extract a specific surface or range of surfaces
     -c  <int> - extract a specific curve or range of curves
     -1  - extract edges only
-    -2  - extract two dimensional entites only e.g. Tri, Quad, etc.
+    -2  - extract two dimensional entities only e.g. Tri, Quad, etc.
     -3  - extract three dimensional entities only, e.g. tet, hex, etc.
     -h  - print help
     -f  - list available read/write formats
@@ -79,7 +79,7 @@ mklostvis
 
 Sometimes either poor quality CAD, incorrect imprinting & merging or overlapping
 volumes; particles are regarded as lost by the Monte Carlo code. It is therefore
-neccessary to be able to examine where the particles were lost and in which
+necessary to be able to examine where the particles were lost and in which
 direction they were travelling in. The tool mklostvis_ is designed for this
 purpose, reading the output of the MCNP lost particle information and producing
 a Cubit or journal file which will draw the lost particles as vertices and their

doc/usersguide/uw2.rst

@@ -25,7 +25,7 @@ code, since each MC code specifies materials in a different way. Instead, we tag
 groups of volumes with a name and syntax that corresponds to material
 compositions in a predefined material library.
 
-The group naming syntax for describing materials in Cubit/Trelis is:
+The group naming syntax for describing materials in Cubit is:
 ::
 
     CUBIT> group "mat:<Name of Material>"
@@ -187,7 +187,7 @@ and the number of particles to simulate. The problem is then run with
 Worked example
 ~~~~~~~~~~~~~~
 
-Open Cubit/Trelis, and let's place some volumes to create our first problem. We
+Open Cubit, and let's place some volumes to create our first problem. We
 will create 4 cubes of side 10 cm, shifting each in a different direction.
 ::