feat(pythonInterface/eos): fast forward

2025-06-12 14:04:11 -04:00
parent b5980ea57a 353e2072e7
commit 54e408a4af
273 changed files with 42783 additions and 12196 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -67,6 +67,7 @@ subprojects/opat-core/
 subprojects/pybind11*/
 subprojects/packagecache/
 subprojects/hypre/
+subprojects/qhull/

 .vscode/

@@ -80,3 +81,5 @@ output/
 .last_build_flags

 .idea/
+
+scratch/
--- a/29
+++ b/29
@@ -42,7 +42,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.

-PROJECT_NAME           = "New 4DSSE Code"
+PROJECT_NAME           = SERiF

 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -54,7 +54,7 @@ PROJECT_NUMBER         = 0.0.1a
 # for a project that appears at the top of each page and should give viewers a
 # quick idea about the purpose of the project. Keep the description short.

-PROJECT_BRIEF          =
+PROJECT_BRIEF          = 3+1D Stellar Structure and Evolution

 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -349,7 +349,7 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 #
 # Note see also the list of default file extension mappings.

-EXTENSION_MAPPING      = py=C++
+EXTENSION_MAPPING      = md=markdown

 # If the MARKDOWN_SUPPORT tag is enabled then Doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
@@ -406,7 +406,7 @@ AUTOLINK_IGNORE_WORDS  =
 # collaboration diagrams that involve STL classes more complete and accurate.
 # The default value is: NO.

-BUILTIN_STL_SUPPORT    = NO
+BUILTIN_STL_SUPPORT    = YES

 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
@@ -540,13 +540,13 @@ EXTRACT_ALL            = YES
 # be included in the documentation.
 # The default value is: NO.

-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES

 # If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
 # methods of a class will be included in the documentation.
 # The default value is: NO.

-EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PRIV_VIRTUAL   = YES

 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -558,7 +558,7 @@ EXTRACT_PACKAGE        = NO
 # included in the documentation.
 # The default value is: NO.

-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES

 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -991,7 +991,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.

-INPUT                  = src tests utils/opatio
+INPUT                  = src tests docs/static/mainpage.md

 # This tag can be used to specify the character encoding of the source files
 # that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1207,7 +1207,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the Doxygen output.

-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = docs/static/mainpage.md

 # If the IMPLICIT_DIR_DOCS tag is set to YES, any README.md file found in sub-
 # directories of the project's root, is used as the documentation for that sub-
@@ -1238,7 +1238,7 @@ FORTRAN_COMMENT_AFTER  = 72
 # also VERBATIM_HEADERS is set to NO.
 # The default value is: NO.

-SOURCE_BROWSER         = NO
+SOURCE_BROWSER         = YES

 # Setting the INLINE_SOURCES tag to YES will include the body of functions,
 # multi-line macros, enums or list initialized variables directly into the
@@ -1416,7 +1416,10 @@ HTML_STYLESHEET        =
 # documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.

-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = docs/static/doxygen-awesome-css/doxygen-awesome.css \
+                         docs/static/doxygen-awesome-css/doxygen-awesome-sidebar-only.css
+
+

 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1439,7 +1442,7 @@ HTML_EXTRA_FILES       =
 # The default value is: AUTO_LIGHT.
 # This tag requires that the tag GENERATE_HTML is set to YES.

-HTML_COLORSTYLE        = AUTO_LIGHT
+HTML_COLORSTYLE        = LIGHT

 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
@@ -1750,7 +1753,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.

-DISABLE_INDEX          = YES
+DISABLE_INDEX          = NO

 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information. If the tag
--- a/Readme.md
+++ b/Readme.md
@@ -1,23 +1,278 @@
-# New implimentation of 3+1D SSE
-New (as yet unnamed) 4DSSE code. 
-We need an exciting name.
+<p style="display: flex; justify-content: center;">
+  <img src="assets/logo/serifLogo.png" width="300" alt="Logo">
+</p>

-This code is very early in development and should not be used for scientific purposes yet. 
+## Stellar Evolution and Rotation in Four dimensions.

+> ⚠️ This code is very early in development and should not be used for scientific purposes yet. 
+----
+
+## Introduction
+SERiF is a stellar structure and evolution program written in C++. This README will eventually provide guidance on how end users (i.e. non SERiF developers) can use the code. However, due
+to the early stage of development we are in, this README is currently intended only for developers. Its purpose is to provide an overview of the build system, development philosphy, development process,
+and current state of the code. Further, general information tasks which need doing will also be included (though for more detailed information on this please refer to the issue tracker or the
+4DSSE project board).

 ## Building
-In order to build you will need meson installed on your system. The easiest way to do this is to use the python package manager (pip)
+
+SERiF uses meson as its build system. It may be useful to understand why we selected meson before we dive into
+detailed build instructions. The headline for "why meson" is ease of use for us. A primary goal of SERiF is that it
+should be easier to use than many current generation SSE code bases. This effectively means that we are looking for a "1
+click" install process. Meson does not, out of the box, provide this. However, it does make it easier for us to build
+such an installation system around it. 
+
+In general all meson projects are built in a similar manner. The challenge, for end users, is often installation and linking
+of dependencies. Let us therefore first look at what depdendencies SERiF has.
+
+### Dependencies
+There are only a small number of dependencies which must be installed by the user
+1. pip
+2. clang/gcc (clang >= 16, gcc >= 13)
+3. ninja
+4. meson
+
+Further, if you use the `mk` script `ninja` and `meson` can even be installed for you!
+
+There are a number of dependencies which are automatically installed by our build system. These are all stored in the `subprojects`
+1. MFEM - MFEM is a finite element modeling library developed primarily by a team at Lawrence Livermore National Labs. MFEM is used as our primary solver.
+2. opat-core - opat-core is a library for I/O operations related to the opat file format. All tables used by SERiF are in the opat-format. opat-core is maintained by the 4D-STAR collaboration and is very well intergrated with a meson build system.
+3. boost - boost is a C++ library which provides a number of useful utilities. It is used in SERiF for a number of tasks including file I/O and string manipulation. We use the ode solver from boost. Boost is complex to install and is a potential pain point. We will address this in more detail below.
+4. pybind11 - pybind11 is a library which allows us to create python bindings for C++ code. This is used to allow us to use SERiF in python. 
+5. quill - quill is a C++ logging library. It is used to provide very fast logging functionality in SERiF.
+6. yaml-cpp - yaml-cpp is a C++ library for parsing YAML files. It is used to parse the configuration files used by SERiF.
+
+All of these could be installed using either the system package manager, built from source, or simply manually included (in the case of header only libraries). However, we have chosen to make extensive use of the `wrap` system which meson provides to automatically fetch and build as many dependencies as we can. This *significantly* simplifies the build process for end users. __Great care should be taken when adding any new dependencies to SERiF as we must maintain this ease of use.__
+
+##### Boost and other complex dependencies
+
+Certain dependencies are either too complex or expensive to reasonably build with SERiF, therefore these must be
+installed system-wide. It is perfectly acceptable that a user might have these installed already; however, we do still
+want to maintain this same "one click setup" where users do not need to think about dependencies. Therefore, we also
+include a series of scripts which will automatically detect the system the user is on and install dependencies, such as
+boost, for them. Meson is then capable of detecting and using these system installations.
+
+### Compiling
+
+For the moment let us assume that all "system" dependencies have been installed (i.e. boost. One can check if a
+dependency is a system dependency or not by looking for a .wrap file in the subprojects directory. If a .wrap file
+exists then meson will automatically handle this dependency and nothing need be done). In that case, we can use the 
+standard meson build commands.
+
 ```bash
-pip install meson
+meson setup build
+meson compile -C build
+meson test -C build
 ```
-You can then either use the mk script or meson commands automatically. When running either the script or meson commands manually `MFEM` will be pulled from github and built. As part of this a small patch will be applied to the MFEM `CMakeLists.txt` file. This process should only need to happen once as future builds will use the cached version of MFEM in `subprojects` and the cached build files of `MFEM` in `build`.
+
+meson uses an out of source build system so all build artifacts will be in the `build` directory. The first
+command above sets up the build directory and configures the build itself (if you are familar with cmake this is 
+similar to running the cmake command). The second command compiles the code, using the `ninja` backend by default.
+The third command runs the tests. Note that this will only run the tests which are in the `tests` directory.
+
+If you wish to run a test manually (i.e. without the meson test command) you must set the `MESON_SOURCE_ROOT`
+environment variable to the root directory of SERiF. Then you can navigate to `SERiF/build/tests/<module_name>/<test_name>`
+and run the test as you would any executable.
+
+Note that this will *automatically* build all dependencies defined in the meson wrap system. This is a key feature of
+meson and is one of the reasons we selected it as our build system.
+
+### Building with the mk script
+We also provide a `mk` script which is a wrapper around both the meson build system and the automatic dependency installation
+scripts we write. This is intended to be a "one click" install system. All the automatic installation scripts are stored
+in `SERiF/build-config/<dependency_name>`. You can then use the `mk` script to build SERiF. This will automatically check
+for all dependencies, try to install them if not found, fail over safely if they are not found, and then build the code
+if all dependencies are found. __The `mk` script is intended to be the method with end users will use to build SERiF.__
+
+To use `mk` it is as simple as running `mk` in a bash compatible shell (currently tested on `bash` and `zsh`)
 ```bash
 ./mk
 ```
-if you want to build with no test suite run
+if you want to build with no test suite run. Note that this will neither run nor build the tests (meaning you will not be
+able to run them manually).
 ```bash
 ./mk --noTest
 ```
+If you do not want to use the mk script you can also use the `4DSSEConsole` which is just a simple bash script can help with building and debugging
+```bash
+./4DSSEConsole.sh
+```
+
+Finally, if you just want to use meson directly you can do the following
+
+To not run tests
+```bash
+meson setup build
+meson compile -C build
+```
+If you want to run tests
+```bash
+meson test -C build
+```
+
+## Test Configuration
+Some tests use config variables setup in tests/testsConfig.yaml. Specifically for things like the GLVis host and port. You should configre those to point to whatever host you are running GLVis on. 
+
+## Development Philosophy
+A few core philosophies of SERiF development are
+
+1. Modularity
+2. Modernity
+3. Testability
+4. Usability
+5. Documentation
+
+To briefly summarize the importance of each of these
+
+### Modularity
+1. All code is organized into modules. We aim to maintain the minimum number of modules possible while still enforcing
+   that each module has a well-defined job. This is obviously somewhat nebulous so look at the current modules which
+   exist to get a sense for how we distribute things. When adding a feature to the code first think carefully if it can
+   or should exist in an already extant module.
+2. Within a module all code should maintain a very well documented and robust public interface. This can and will change
+   dramatically during development but keep in mind that eventually we will likely want to "lock" our public interface
+   so try to design it with that in mind.
+3. Careful thought should be given to what *kind* of module is being added. That is to say is it a: physics module,
+   utility module, I/O module, infrastructure module, or something else. This will determine how and when this module is
+   build during compilation. For example all physics modules should be built after all utility modules.
+
+### Modernity
+
+1. We use C++23 as the target language standard. This is a very intentional choice, and it means that code commited should
+   not be written in older C++ standards where possible. Certainly C++98 code should be avoided.
+2. Some effects of this are that, for example, we do not allow raw pointer allocation using `new` or `malloc`. C++
+   provides very powerful tools which are easy to use and dramatically increase memory saftey (such as
+   `std::unique_ptr<Type>()` or `std::shared_ptr<T>()`). If you *ever* find yourself wanting to allocate a raw pointer
+   on the heap consider smart pointers instead.
+3. All of that being said, we do interface with external libraries which will sometimes return raw, C style pointers. In
+   those cases, of course you need to do what needs be done. Just make sure to document things carefully and note in a
+   comment that there is an enhanced possibility of a memory leak at those locations.
+
+### Testability
+
+1. It is unrealistic, and likely unproductive, to expect fully test driven development or 100% code coverage. However,
+   we do want to maintain a high degree of testability. As such the recommended development approach is to develop
+   against tests first. That is to say, instead of a single entry point binary, we have a testing module for each
+   module. We run the code for each module through that testing module. Eventually, there will be entry points for
+   users. However, that is very far down the line.
+2. While we do not enforce any specific amount of code coverage we do require that all modules have some degree of
+   testing that a reasonable astronomer would look at and say "that looks well tested". This is a very subjective measure,
+   but we will be using this as a guideline for code reviews.
+3. Testing for all C++ code is done using gtest. Make sure to be cognizant that floating point values __will not__ be
+   the same from machine to machine and therefore using `EXPECT_EQ` for floating point values will likely result in test
+   failures. gtest provides tools for just this, use them.
+
+### Usability & Documentation
+
+1. SERiF is intended to be used by astronomers, not astronomers who are also developers. When developing new code or
+   refactoring existing code keep this in mind. This means that public interface methods and functions should have
+   *very* clear names (note that very clear __does not mean long__, it means clear). Every public method and function
+   should include a doxygen comment which describes, at minimum, its purpose, inputs, and outputs. Ideally any
+   exceptions which can be thrown should also be documented. Further, we *strongly* reccomend that every time a doxygen
+   comment is written an example for that method, function or class is also written. This will give us a clear example
+   set from the outset.
+2. There are times when complex code is required. In these cases that code should likely be private to the module.
+3. All modules will eventually be tied into the python interface. Write the public module with that in mind.

 ## Current Status
-Currently we are working on implimenting modules such as opacity, equation of state, polytrope, and meshing. Builds may not work on any branches at any time. 
+
+There are two primary modules currently under construction, many which need to be worked on, and a few which have either
+been finished or are at least at their minimum viable state (MVS). Modules where the current assigne is marked as N/A
+are currently not being worked on. This does not mean that they do not need work or will not be worked on in the future.
+But if a new developer wants somewhere to start, those are good places too.
+
+#### Name Key
+- A.D. : Aaron Dotter
+- E.B. : Emily Boudreaux
+
+| Module Name | Status   | Description                                                                                                                                                                                                                                  | Current Assigne |
+|-------------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------|
+| config      | Complete | This module handles all configuration files. It is responsible for parsing the YAML files                                                                                                                                                    | N/A             |
+| composition | MVS      | This module tracks a general composition object, allowing for arbitrary species tracking and mixing                                                                                                                                          | N/A             |
+| const       | Complete | This module contains all physical constants from the CODATA 2022 data release as well as some astronomical constants from IAU 2015                                                                                                           | N/A             |
+| eos         | MVS      | This module implements both a general interface for equation of states as well as specific equations of states. Currently the helmholtz equation of state is the only one implemented.                                                       | N/A             |
+| meshIO      | Complete | This module handles all I/O for the mesh. It is responsible for reading and writing the mesh to disk. This is used to interface with the resource manager which allows for easer configuration on the user end.                              | N/A             |
+| misc        | WIP      | This is a catch all module for misc things. Generally we should *avoid* putting stuff in here but sometimes (such as for debugging macros) it is useful.                                                                                     | N/A             |
+| network     | MVS      | This module handles the nuclear network and burning calculations. Currently only Frank Timmes' Approx8 network is implemented. It also implements a general interface for nuclear networks so that other networks can be added.              | N/A             |
+| opac        | WIP      | This module handles opacity calculation / interpolation.                                                                                                                                                                                     | A.D.            |
+| poly        | WIP      | This module computes polytropic models which are used as initial states for solving the structure equations.                                                                                                                                 | E.B.            |
+| probe       | Complete | This module implements the `probe` namespace which is used to hold functions for probing the current state of the code (stuff like `whydt` in `MESA`)                                                                                        | N/A             |
+| python      | WIP      | This module contains all code relevant to the python interface. All interface code is then organized in submodules within this (such as python/config)                                                                                       | E.B.            |
+| resource    | Complete | This module handles loading resource from disk in a clean fashion. The key justification here is to avoid users having to explicitly set environmental variables but also to make loading of resources any where in the code easer to handle | N/A             |
+| types       | Complete | This module implements custom datatypes for SERiF which do not cleanly fall into any other module (i.e. __datatypes should not__ go in `misc`)                                                                                               | N/A             |
+
+
+### Future Work
+This is a non-comprehensive list of things which still need to be done (and which are not being actively developed). If you pick up one of these projects go ahead and edit the README to mark these checkboxes as marked ([x])
+
+- [ ] Extended nuclear reaction network
+- [ ] Extend the equation of state module
+- [ ] Atmospheric boundary conditions
+- [ ] Mixing length
+- [ ] Magnetic fields
+- [ ] Rotation
+- [ ] Structure equations
+- [ ] Time stepping
+- [ ] Curvilinear finite elements
+- [ ] All sorts of details that I cannot even begin to enumerate at this stage
+
+When thinking about picking up new modules it is important to think first about: one, what that work would depend on,
+and two, what work dependency on that. For example there would be very little point in working on time stepping until
+there is a stable structure solver. Whereas extending the nuclear network and equation of state can be extended
+independent of the primary solver (as is the case with the microphysics in general). If you want to start work and 
+need some ideas about where to start reach out to Aaron or Emily.
+
+## Developing
+
+There is a detailed development document which all 4D-STAR collaboration members should have access to. First
+familiarize yourself with that. I will note that we do not treat that as a 100% hard and fast rule. However, we do try
+to stick to that as a general rule. I will summarize some best practices which I find particularly helpful (outside of
+the actual source code itself)
+
+#### git
+
+All development should be done on your own fork of the repository. You can organize these forks in whatever way you
+want, they are your fork after all. However, I find it helpful to organize my branches into a few categories
+
+- [feature/\<feature name\>] - This is a new feature which I am working on. (i.e. `git checkout -b feature/python/eos_interface`)
+- [bugfix/\<bug name\>] - This is a bug which I am working on. (i.e. `git checkout -b bugfix/python/eos_interface_memory_overflow`)
+- [perf/\<perf name\>] - This is a performance improvement which I am working on. (i.e. `git checkout -b perf/python/eos_interface_cache`)
+
+What I like about this is that it effectively creates a tree structure for my branches. However, as said before, on your own fork 
+use any organizational scheme you find effective for yourself. 
+
+When you have finished writing code, and you have tested it open a pull request (PR) to the main branch for SERiF in the
+4D-STAR organization. There is a template present for this which should automatically populate if you use the GitHub web interface.
+Not every PR will need to fill content in every field of the template, use your own judgment for this. Further, most PRs will,
+for sake of time, likely not be reviewed (major physics modules will be); however, the first PR by any new developer will
+need to be reviewed by one of the current experienced developers (Currently Aaron and Emily, though if and when new
+developers come on board with this part of the project that list will hopefully grow).
+
+#### Code Style
+Again for this primarily follow the style guide in the developer assets repository (owned by the 4D-STAR organization). In
+general though use clear and concise names for variables, functions, methods and classes. Adhear to consistent naming
+conventions (preferably also consistent with what is already in the code).
+
+Note that we take an Object-Oriented Programming (OOP) approach to much of the code, but this is a pragmatic not a
+dogmatic choice. That is to say that OOP is sometimes a good tool for a job and other times it is not. Because of this
+we do have a good number of objects floating around but you, as a developer, should not feel as if you need to use an
+OOP design if you do not think it would be best. One thing that we will enforce is that overly complicated inheritance
+hierarchies are not allowed. If you find yourself writing a class which has more than 2 levels of inheritance then you
+should probably consider using composition instead. 
+
+#### Environment
+The current team builds with both `clang` and `gcc`, we *will* maintain compatibility with both of these compilers. As such
+when developing new code you should, __before opening a PR__, test your compilation with gcc and clang. Meson makes this
+super easy as you can simply have two build directories (i.e. `build-gcc` and `build-clang`) and run the same commands in both. 
+```bash
+CXX=g++ meson setup build-gcc
+CXX=clang++ meson setup build-clang
+```
+
+Aside from this I find it useful to have the `MESON_SOURCE_ROOT` environmental variable set since this makes it easy to 
+run individual executables. Therefore in your shell profile file (`~/.bashrc`, `~/.zshrc`, etc.) add the following line
+```bash
+export MESON_SOURCE_ROOT=/path/to/SERiF
+```
+
+#### Other
+Should you have any questions not answered here or in the development guidelines please feel free to reach out to Emily.
--- a/assets/dynamic/index.yaml
+++ b/assets/dynamic/index.yaml
@@ -1,4 +1,4 @@
-eos:
-  helm: "eos/helm_table.dat"
+#eos:
+#  helm: "eos/helm_table.dat"
 mesh:
-  sphere: "mesh/sphere.msh"
+  polySphere: "mesh/core_midres.msh"
--- a/assets/logo/serifLogo.png
+++ b/assets/logo/serifLogo.png
--- a/assets/logo/serifLogo.svg
+++ b/assets/logo/serifLogo.svg
@@ -0,0 +1,100 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="500mm"
+   height="300mm"
+   viewBox="0 0 500 300"
+   version="1.1"
+   id="svg1"
+   sodipodi:docname="serifLogo.svg"
+   inkscape:version="1.4 (e7c3feb1, 2024-10-09)"
+   inkscape:export-filename="serifLogo.png"
+   inkscape:export-xdpi="300"
+   inkscape:export-ydpi="300"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
+     id="namedview1"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
+     inkscape:pageopacity="0.0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="mm"
+     inkscape:zoom="0.31892609"
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+     inkscape:cy="660.02753"
+     inkscape:window-width="1728"
+     inkscape:window-height="962"
+     inkscape:window-x="0"
+     inkscape:window-y="38"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="layer1">
+    <inkscape:page
+       x="0"
+       y="0"
+       width="500"
+       height="300"
+       id="page2"
+       margin="0"
+       bleed="0" />
+  </sodipodi:namedview>
+  <defs
+     id="defs1" />
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1">
+    <path
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+       transform="scale(0.93412862,1.0705164)"
+       id="text1" />
+  </g>
+</svg>
--- a/build-config/hypre/meson.build
+++ b/build-config/hypre/meson.build
@@ -1,2 +1,9 @@
-hypre_sp = cmake.subproject('hypre')
+hypre_cpp_cmake_options = cmake.subproject_options()
+hypre_cpp_cmake_options.add_cmake_defines({
+    'BUILD_SHARED_LIBS': 'ON',
+})
+hypre_sp = cmake.subproject(
+    'hypre',
+    options: hypre_cpp_cmake_options,
+)
 hypre_dep = hypre_sp.dependency('HYPRE')
--- a/build-config/meson.build
+++ b/build-config/meson.build
@@ -5,6 +5,8 @@ subdir('yaml-cpp')
 subdir('quill')
 subdir('boost')
 subdir('opatIO')
+subdir('mpi')
+subdir('hypre')
 subdir('pybind')
 subdir('mpi')
 subdir('hypre')
--- a/build-config/opatIO/meson.build
+++ b/build-config/opatIO/meson.build
@@ -1,3 +1,10 @@
-opatio_dep = dependency('opatio', fallback: ['opat-core', 'opatio_dep'])
-picosha2_dep = dependency('picosha2', fallback: ['opat-core', 'picosha2_dep'])
+# Get the subproject object first
+opat_sub = subproject(
+    'opat-core',
+    default_options: {
+        'generate_pc': false
+    }
+)

+# Get the dependency variable from that subproject
+opatio_dep = opat_sub.get_variable('opatio_dep')
--- a/build-python/meson.build
+++ b/build-python/meson.build
@@ -2,7 +2,7 @@
 py_installation = import('python').find_installation('python3')

 py_mod = py_installation.extension_module(
-    'fourdsse_bindings', # Name of the generated .so/.pyd file (without extension)
+    'serif', # Name of the generated .so/.pyd file (without extension)
    sources: [
        meson.project_source_root() + '/src/python/bindings.cpp',
        meson.project_source_root() + '/src/python/composition/bindings.cpp',
@@ -20,5 +20,4 @@ py_mod = py_installation.extension_module(
    ],
    cpp_args : ['-UNDEBUG'], # Example: Ensure assertions are enabled if needed
    install : true,
-    subdir: 'fourdstar' # Optional: Install the module inside a 'fourdsse' Python package directory
 )
--- a/commit-config/hooks/formatHeader.py
+++ b/commit-config/hooks/formatHeader.py
@@ -120,6 +120,10 @@ if __name__ == "__main__":
    args = parser.parse_args()

    absPath = os.path.abspath(args.file)
+    fileName = os.path.basename(args.file)
+    if fileName == "formatHeader.py":
+        print(f"{BLUECOLOR}NOTE! Cannot format the formatHeader script{RESETCOLOR}")
+        exit(0)

    assert os.path.exists(absPath), f"{REDCOLOR}ERROR! The file {absPath} does not exist{RESETCOLOR}"

--- a/docs/derivations/laneEmdenVariationalForm/laneEmdenVariationalBlockForm.pdf
+++ b/docs/derivations/laneEmdenVariationalForm/laneEmdenVariationalBlockForm.pdf
--- a/docs/derivations/laneEmdenVariationalForm/laneEmdenVariationalBlockForm.tex
+++ b/docs/derivations/laneEmdenVariationalForm/laneEmdenVariationalBlockForm.tex
@@ -84,7 +84,7 @@ Now we exploit the linearity of summation and integration to move the sums out o
 \end{align}
 We will now define $M_{kj}$, $D_{\ell j}$, and $Q_{\ell i}$ such that
 \begin{align}
-    M_{kj} &\equiv \int_{\Omega}\nabla \psi_{k}^{\theta}\cdot \vec{N}_{j}^{\phi}dV \\
+    M_{kj} &\equiv -\int_{\Omega}\nabla \psi_{k}^{\theta}\cdot \vec{N}_{j}^{\phi}dV \\
    D_{\ell j} &\equiv \int_{\Omega}\vec{\psi}_{\ell}^{\phi}\cdot\vec{N}_{j}^{\phi}dV \\
    Q_{\ell i} &\equiv \int_{\Omega}\vec{\psi}_{\ell}^{\phi}\cdot\nabla N_{i}^{\theta} dV
 \end{align}
@@ -96,18 +96,18 @@ f(\bar{\theta}) \equiv \int_{\Omega}\psi_{k}^{\theta}\left(\theta_{h}\right)^{n}
 \end{align}
 We can write the variational form of our system of equations as
 \begin{align}
-\sum_{j=1}^{N_{dof}^{\phi}}\phi_{j}M_{kj} + f(\bar{\theta)} &= 0 \\
+\sum_{j=1}^{N_{dof}^{\phi}}\phi_{j}M_{kj} + f(\bar{\theta)} &= 0 \\
 \sum_{j=1}^{N^{\phi}_{dof}}\phi_{j}D_{\ell j} - \sum_{i=1}^{N_{dof}^{\theta}}\theta_{i}Q_{\ell i} &= 0
 \end{align}
 Or using the notation we defined
 \begin{align}
-\mathbf{M}\bar{\phi} + f(\bar{\theta}) &= 0 \\
+\mathbf{M}\bar{\phi} + f(\bar{\theta}) &= 0 \\
 \mathbf{D}\bar{\phi} - \mathbf{Q}\bar{\theta} &= 0
 \end{align}
 We can then set this up as a matrix operation
 \begin{align}
    \begin{bmatrix}
-        0 & -\mathbf{M} \\
+        0 & \mathbf{M} \\
        -\mathbf{Q} & \mathbf{D}
    \end{bmatrix}
    \begin{bmatrix}
@@ -126,7 +126,7 @@ From this form we can easily see that the residual matrix is

 \begin{align}
    R &= \begin{bmatrix}
-        f(\bar{\theta}) - M\bar{\phi} \\
+        f(\bar{\theta}) + M\bar{\phi} \\
        D\bar{\phi} - Q\bar{\theta}
    \end{bmatrix}
 \end{align}
@@ -144,11 +144,11 @@ in our Newton-Raphson method. Generally the Jacobian is the matrix of partial de
 So then the Jacobian is
 \begin{align}
    J &= \begin{bmatrix}
-        \frac{\partial}{\partial \theta}\left(f(\theta) - M\phi\right) & \frac{\partial}{\partial \phi}\left(f(\theta) - M\phi\right) \\
+        \frac{\partial}{\partial \theta}\left(f(\theta) + M\phi\right) & \frac{\partial}{\partial \phi}\left(f(\theta) + M\phi\right) \\
        \frac{\partial}{\partial \theta}\left(D\phi - Q\theta\right) & \frac{\partial}{\partial \phi}\left(D\phi - Q\theta\right)
    \end{bmatrix} \\
    J &= \begin{bmatrix}
-        \frac{df}{d\theta} - \phi\frac{\partial M}{\partial \theta} & -M-\phi\frac{\partial M}{\partial \phi} \\
+        \frac{df}{d\theta} + \phi\frac{\partial M}{\partial \theta} & M+\phi\frac{\partial M}{\partial \phi} \\
        -Q - \theta\frac{\partial Q}{\partial \theta} & D + \phi\frac{\partial D}{\partial \phi} - \theta\frac{\partial Q}{\partial \phi}
    \end{bmatrix}
 \end{align}
@@ -156,7 +156,7 @@ So then the Jacobian is
 Finally, we know that the matrices $M$, $D$, and $Q$ are constant with respect to $\theta$ and $\phi$. Therefore, we can drop the partial derivatives with respect to $\theta$ and $\phi$ from the Jacobian. This gives us
 \begin{align}
  \mathbf{J} &= \begin{bmatrix}
-        \frac{df}{d\theta} & -M \\
+        \frac{df}{d\theta} & M \\
        -Q & D
    \end{bmatrix}
 \end{align}
@@ -164,9 +164,9 @@ Finally, we know that the matrices $M$, $D$, and $Q$ are constant with respect t
 \noindent In a fully assembled, distritized form this will look like

 \begin{align}
-  \mathbf{J} = \begin{bmatrix} \frac{df}{d\theta}_{00}          & \dots  & \frac{df}{d\theta}_{0n_{\theta}}          & -M_{00}                  & \dots            & -M_{0n_{\phi}} \\
+  \mathbf{J} = \begin{bmatrix} \frac{df}{d\theta}_{00}          & \dots  & \frac{df}{d\theta}_{0n_{\theta}}          & M_{00}                  & \dots            & M_{0n_{\phi}} \\
  \vdots          & \ddots &                          & \vdots                   & \ddots           & \\
-    \frac{df}{d\theta}_{n_{\theta}0} &        & \frac{df}{d\theta}_{n_{\theta}n_{\theta}} & -M_{n_{\theta}0}         &                  & -M_{n_{\theta}n_{\phi}} \\
+    \frac{df}{d\theta}_{n_{\theta}0} &        & \frac{df}{d\theta}_{n_{\theta}n_{\theta}} & M_{n_{\theta}0}         &                  & M_{n_{\theta}n_{\phi}} \\
  -Q_{00}         & \dots  & -Q_{0n_{\theta}}         & D_{00}                   & \dots            & D_{0n_{\phi}} \\
  \vdots          & \ddots &                          & \vdots                   & \ddots           & \\
  -Q_{n_{\phi}0}  &        & -Q_{n_{\phi}n_{\theta}}  & D_{n_{\phi}0}            &                  & D_{n_{\phi}n_{\phi}}
--- a/docs/html/_d_object_8cpp.html
+++ b/docs/html/_d_object_8cpp.html
@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: src/dobj/private/DObject.cpp File Reference</title>
+<title>SERiF: src/dobj/private/DObject.cpp File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
@@ -18,12 +18,9 @@
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <span id="MSearchSelect"                onmouseover="return searchBox.OnSearchSelectShow()"                onmouseout="return searchBox.OnSearchSelectHide()">&#160;</span>
-          <input type="text" id="MSearchField" value="" placeholder="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
-               onkeyup="searchBox.OnSearchFieldChange(event)"/>
-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -102,6 +99,8 @@ $(function(){initNavTree('_d_object_8cpp.html',''); initResizable(true); });
 </div>

 <div class="header">
+  <div class="summary">
+<a href="#func-members">Functions</a>  </div>
  <div class="headertitle"><div class="title">DObject.cpp File Reference</div></div>
 </div><!--header-->
 <div class="contents">
@@ -111,10 +110,56 @@ $(function(){initNavTree('_d_object_8cpp.html',''); initResizable(true); });
 <div class="textblock"><code>#include &quot;<a class="el" href="_d_object_8h_source.html">DObject.h</a>&quot;</code><br />
 <code>#include &lt;iostream&gt;</code><br />
 <code>#include &lt;stdexcept&gt;</code><br />
-</div><a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+</div>
+<p><a href="_d_object_8cpp_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:aa54e75574f0302a2ca7252f9f0f0b3f1" id="r_aa54e75574f0302a2ca7252f9f0f0b3f1"><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa54e75574f0302a2ca7252f9f0f0b3f1">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="class_d_object.html">DObject</a> &amp;obj)</td></tr>
+<tr class="memdesc:aa54e75574f0302a2ca7252f9f0f0b3f1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Provides a human-readable summary of the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
+<tr class="separator:aa54e75574f0302a2ca7252f9f0f0b3f1"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Implementation of the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> class. </p>
 <p>Provides the implementation for a universal data container with plugin support. </p>
-</div></div><!-- contents -->
+
+<p class="definition">Definition in file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="aa54e75574f0302a2ca7252f9f0f0b3f1" name="aa54e75574f0302a2ca7252f9f0f0b3f1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aa54e75574f0302a2ca7252f9f0f0b3f1">&#9670;&#160;</a></span>operator&lt;&lt;()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::ostream &amp; operator&lt;&lt; </td>
+          <td>(</td>
+          <td class="paramtype">std::ostream &amp;</td>          <td class="paramname"><span class="paramname"><em>os</em></span>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="class_d_object.html">DObject</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>obj</em></span>&#160;)</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Provides a human-readable summary of the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
+<p>Useful for quick inspection or logging during debugging sessions.</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">os</td><td>The output stream to write to. </td></tr>
+    <tr><td class="paramname">obj</td><td>The <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> to summarize. </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>A reference to the output stream. </dd></dl>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00126">126</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
+</div>
+</div>
+</div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->
 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
--- a/docs/html/_d_object_8h.html
+++ b/docs/html/_d_object_8h.html
@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: src/dobj/public/DObject.h File Reference</title>
+<title>SERiF: src/dobj/public/DObject.h File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
@@ -18,12 +18,9 @@
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <span id="MSearchSelect"                onmouseover="return searchBox.OnSearchSelectShow()"                onmouseout="return searchBox.OnSearchSelectHide()">&#160;</span>
-          <input type="text" id="MSearchField" value="" placeholder="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
-               onkeyup="searchBox.OnSearchFieldChange(event)"/>
-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -110,8 +107,7 @@ $(function(){initNavTree('_d_object_8h.html',''); initResizable(true); });

 <p>Defines the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> class, a universal data container for the project.  
 <a href="#details">More...</a></p>
-<div class="textblock"><code>#include &quot;<a class="el" href="_metadata_8h_source.html">Metadata.h</a>&quot;</code><br />
-<code>#include &lt;variant&gt;</code><br />
+<div class="textblock"><code>#include &lt;variant&gt;</code><br />
 <code>#include &lt;memory&gt;</code><br />
 <code>#include &lt;vector&gt;</code><br />
 <code>#include &lt;string&gt;</code><br />
@@ -130,6 +126,8 @@ Classes</h2></td></tr>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Defines the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> class, a universal data container for the project. </p>
 <p>The <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> class encapsulates arbitrary data and its associated metadata, providing a consistent interface for public-facing functions. It includes support for dynamically registered plugins. </p>
+
+<p class="definition">Definition in file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
 </div></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->
--- a/docs/html/_d_object_8h_source.html
+++ b/docs/html/_d_object_8h_source.html
@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: src/dobj/public/DObject.h Source File</title>
+<title>SERiF: src/dobj/public/DObject.h Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
@@ -18,12 +18,9 @@
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <span id="MSearchSelect"                onmouseover="return searchBox.OnSearchSelectShow()"                onmouseout="return searchBox.OnSearchSelectHide()">&#160;</span>
-          <input type="text" id="MSearchField" value="" placeholder="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
-               onkeyup="searchBox.OnSearchFieldChange(event)"/>
-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -105,79 +102,135 @@ $(function(){initNavTree('_d_object_8h_source.html',''); initResizable(true); })
  <div class="headertitle"><div class="title">DObject.h</div></div>
 </div><!--header-->
 <div class="contents">
-<a href="_d_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="preprocessor">#ifndef DOBJECT_H</span></div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="preprocessor">#define DOBJECT_H</span></div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span> </div>
-<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="preprocessor">#include &quot;<a class="code" href="_metadata_8h.html">Metadata.h</a>&quot;</span></div>
-<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="preprocessor">#include &lt;variant&gt;</span></div>
-<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="preprocessor">#include &lt;memory&gt;</span></div>
-<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
-<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="preprocessor">#include &lt;string&gt;</span></div>
-<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span><span class="preprocessor">#include &lt;mutex&gt;</span></div>
-<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="preprocessor">#include &lt;map&gt;</span></div>
-<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
-<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span></div>
-<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span></div>
-<div class="foldopen" id="foldopen00029" data-start="{" data-end="};">
-<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="class_d_object.html">   29</a></span><span class="keyword">class </span><a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a> {</div>
-<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span><span class="keyword">public</span>:</div>
-<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"><a class="line" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">   37</a></span>    <span class="keyword">using </span><a class="code hl_typedef" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a> = std::variant&lt;</div>
-<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        int, float, double, std::string, std::monostate,</div>
-<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>        std::vector&lt;int&gt;, std::vector&lt;float&gt;, std::vector&lt;double&gt;</div>
-<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    &gt;;</div>
-<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span></div>
-<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"><a class="line" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">   47</a></span>    <span class="keyword">using </span><a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> = std::function&lt;void(<a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>&amp;)&gt;;</div>
-<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span></div>
-<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>    <a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>();</div>
-<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span></div>
-<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>    <a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a>&amp; data, <span class="keyword">const</span> <a class="code hl_class" href="class_metadata.html">Metadata</a>&amp; metadata);</div>
-<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span></div>
-<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>    <span class="keyword">const</span> <a class="code hl_typedef" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a>&amp; <a class="code hl_function" href="class_d_object.html#a4862655c3634d019b0a45b811d6f7235">getData</a>() const noexcept;</div>
-<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span></div>
-<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#ab1718571434e84e90f1ec463e4786a8a">setData</a>(const <a class="code hl_typedef" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a>&amp; data);</div>
-<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span></div>
-<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span>    const <a class="code hl_class" href="class_metadata.html">Metadata</a>&amp; <a class="code hl_function" href="class_d_object.html#a157b31e881aac6dd40782d3abc561d4e">getMetadata</a>() const noexcept;</div>
-<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span></div>
-<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a296b1519249fdc1f6c7b4ab62d5421bc">setMetadata</a>(const <a class="code hl_class" href="class_metadata.html">Metadata</a>&amp; metadata);</div>
-<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span></div>
-<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a6f0023aee463e71d92442dcf61b6ed47">setDebugging</a>(<span class="keywordtype">bool</span> enableDebug);</div>
-<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span></div>
-<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>    [[nodiscard]] <span class="keywordtype">bool</span> <a class="code hl_function" href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">isDebuggingEnabled</a>() const noexcept;</div>
-<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span></div>
-<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a15afffdf339150fc872bf63bdd08d581">registerPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>, <a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> plugin);</div>
-<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span></div>
-<div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a99b8688849e11501033a25f61efb8356">unregisterPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>);</div>
-<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span></div>
-<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a99072eb52bb22745f0248f273fbf28fb">runPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>);</div>
-<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span></div>
-<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a1223275dcbbf20334ea11707346acb93">runAllPlugins</a>();</div>
-<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span></div>
-<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"><a class="line" href="class_d_object.html#aa54e75574f0302a2ca7252f9f0f0b3f1">  161</a></span>    friend std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const <a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>&amp; obj);</div>
-<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span> </div>
-<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span>private:</div>
-<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>    <a class="code hl_typedef" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a> data_;                              </div>
-<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span>    <a class="code hl_class" href="class_metadata.html">Metadata</a> metadata_;                          </div>
-<div class="line"><a id="l00166" name="l00166"></a><span class="lineno">  166</span>    <span class="keywordtype">bool</span> debugEnabled_ = false;                  </div>
-<div class="line"><a id="l00167" name="l00167"></a><span class="lineno">  167</span>    std::map&lt;std::<span class="keywordtype">string</span>, <a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a>&gt; plugins_;      </div>
-<div class="line"><a id="l00168" name="l00168"></a><span class="lineno">  168</span>};</div>
+<a href="_d_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="comment">/* ***********************************************************************</span></div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="comment">//</span></div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span><span class="comment">//   Copyright (C) 2025 -- The 4D-STAR Collaboration</span></div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="comment">//   File Author: Emily Boudreaux</span></div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="comment">//   Last Modified: March 17, 2025</span></div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="comment">//</span></div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="comment">//   4DSSE is free software; you can use it and/or modify</span></div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="comment">//   it under the terms and restrictions the GNU General Library Public</span></div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span><span class="comment">//   License version 3 (GPLv3) as published by the Free Software Foundation.</span></div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="comment">//</span></div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="comment">//   4DSSE is distributed in the hope that it will be useful,</span></div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="comment">//   See the GNU Library General Public License for more details.</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="comment">//</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="comment">//   You should have received a copy of the GNU Library General Public License</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="comment">//   along with this software; if not, write to the Free Software</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="comment">//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span><span class="comment">//</span></div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="comment">// *********************************************************************** */</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#ifndef DOBJECT_H</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span><span class="preprocessor">#define DOBJECT_H</span></div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#include &lt;variant&gt;</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#include &lt;memory&gt;</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span><span class="preprocessor">#include &lt;mutex&gt;</span></div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span><span class="preprocessor">#include &lt;map&gt;</span></div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span></div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span></div>
+<div class="foldopen" id="foldopen00089" data-start="{" data-end="};">
+<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"><a class="line" href="class_d_object.html">   89</a></span><span class="keyword">class </span><a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a> {</div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span><span class="keyword">public</span>:</div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"><a class="line" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">   97</a></span>    <span class="keyword">using </span><a class="code hl_typedef" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> = std::variant&lt;</div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span>        bool, <span class="keywordtype">short</span> int, int, <span class="keywordtype">long</span> int, float, double, </div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>        <span class="keywordtype">long</span> double, std::string, std::monostate, std::vector&lt;int&gt;,</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span>        std::vector&lt;float&gt;, std::vector&lt;double&gt;, std::vector&lt;std::string&gt;,</div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>        std::vector&lt;std::vector&lt;int&gt;&gt;, std::vector&lt;std::vector&lt;float&gt;&gt;,</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>        std::vector&lt;std::vector&lt;double&gt;&gt;,</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span>        std::vector&lt;std::vector&lt;std::vector&lt;int&gt;&gt;&gt;,</div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span>        std::vector&lt;std::vector&lt;std::vector&lt;float&gt;&gt;&gt;,</div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>        std::vector&lt;std::vector&lt;std::vector&lt;double&gt;&gt;&gt;</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>    &gt;;</div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span> </div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    <span class="comment">// Mapping of data types to their string representations</span></div>
+<div class="foldopen" id="foldopen00109" data-start="{" data-end="};">
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"><a class="line" href="class_d_object.html#a358d5f015da09ae5f0cbb46f3fd9e401">  109</a></span>    std::map&lt;int, std::string&gt; <a class="code hl_variable" href="class_d_object.html#a358d5f015da09ae5f0cbb46f3fd9e401">dataTypeMap</a> = {</div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span>        {0, <span class="stringliteral">&quot;bool&quot;</span>}, {1, <span class="stringliteral">&quot;short int&quot;</span>}, {2, <span class="stringliteral">&quot;int&quot;</span>}, {3, <span class="stringliteral">&quot;long int&quot;</span>}, {4, <span class="stringliteral">&quot;float&quot;</span>},</div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span>        {5, <span class="stringliteral">&quot;double&quot;</span>}, {6, <span class="stringliteral">&quot;long double&quot;</span>}, {7, <span class="stringliteral">&quot;string&quot;</span>}, {8, <span class="stringliteral">&quot;std::monostate&quot;</span>},</div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span>        {9, <span class="stringliteral">&quot;vector&lt;int&gt;&quot;</span>}, {10, <span class="stringliteral">&quot;vector&lt;float&gt;&quot;</span>}, {11, <span class="stringliteral">&quot;vector&lt;double&gt;&quot;</span>},</div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>        {12, <span class="stringliteral">&quot;vector&lt;string&gt;&quot;</span>}, {13, <span class="stringliteral">&quot;vector&lt;vector&lt;int&gt;&quot;</span>},</div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span>        {14, <span class="stringliteral">&quot;vector&lt;vector&lt;float&gt;&quot;</span>}, {15, <span class="stringliteral">&quot;vector&lt;vector&lt;double&gt;&quot;</span>},</div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>        {16, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;int&gt;&gt;&quot;</span>}, {17, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;float&gt;&gt;&quot;</span>},</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span>        {18, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;double&gt;&gt;&quot;</span>}</div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>    };</div>
 </div>
-<div class="line"><a id="l00169" name="l00169"></a><span class="lineno">  169</span> </div>
-<div class="line"><a id="l00170" name="l00170"></a><span class="lineno">  170</span><span class="preprocessor">#endif </span><span class="comment">// DOBJECT_H</span></div>
-<div class="ttc" id="a_metadata_8h_html"><div class="ttname"><a href="_metadata_8h.html">Metadata.h</a></div><div class="ttdoc">Public interface for the Metadata class used in the dobj module.</div></div>
-<div class="ttc" id="aclass_d_object_html_a0ae54853e18265657296bfb5ac3bf9d0"><div class="ttname"><a href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject::DObject</a></div><div class="ttdeci">DObject()</div><div class="ttdoc">Default constructor.</div><div class="ttdef"><b>Definition</b> DObject.cpp:13</div></div>
-<div class="ttc" id="aclass_d_object_html_a1223275dcbbf20334ea11707346acb93"><div class="ttname"><a href="class_d_object.html#a1223275dcbbf20334ea11707346acb93">DObject::runAllPlugins</a></div><div class="ttdeci">void runAllPlugins()</div><div class="ttdoc">Executes all registered plugins in the registry.</div><div class="ttdef"><b>Definition</b> DObject.cpp:99</div></div>
-<div class="ttc" id="aclass_d_object_html_a157b31e881aac6dd40782d3abc561d4e"><div class="ttname"><a href="class_d_object.html#a157b31e881aac6dd40782d3abc561d4e">DObject::getMetadata</a></div><div class="ttdeci">const Metadata &amp; getMetadata() const noexcept</div><div class="ttdoc">Retrieves the metadata associated with the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:41</div></div>
-<div class="ttc" id="aclass_d_object_html_a15afffdf339150fc872bf63bdd08d581"><div class="ttname"><a href="class_d_object.html#a15afffdf339150fc872bf63bdd08d581">DObject::registerPlugin</a></div><div class="ttdeci">void registerPlugin(const std::string &amp;id, Plugin plugin)</div><div class="ttdoc">Registers a plugin with the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:69</div></div>
-<div class="ttc" id="aclass_d_object_html_a296b1519249fdc1f6c7b4ab62d5421bc"><div class="ttname"><a href="class_d_object.html#a296b1519249fdc1f6c7b4ab62d5421bc">DObject::setMetadata</a></div><div class="ttdeci">void setMetadata(const Metadata &amp;metadata)</div><div class="ttdoc">Updates the metadata for the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:48</div></div>
-<div class="ttc" id="aclass_d_object_html_a4862655c3634d019b0a45b811d6f7235"><div class="ttname"><a href="class_d_object.html#a4862655c3634d019b0a45b811d6f7235">DObject::getData</a></div><div class="ttdeci">const DataType &amp; getData() const noexcept</div><div class="ttdoc">Retrieves the data stored in the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:26</div></div>
-<div class="ttc" id="aclass_d_object_html_a6f0023aee463e71d92442dcf61b6ed47"><div class="ttname"><a href="class_d_object.html#a6f0023aee463e71d92442dcf61b6ed47">DObject::setDebugging</a></div><div class="ttdeci">void setDebugging(bool enableDebug)</div><div class="ttdoc">Enables or disables debugging and tracing for the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:55</div></div>
-<div class="ttc" id="aclass_d_object_html_a99072eb52bb22745f0248f273fbf28fb"><div class="ttname"><a href="class_d_object.html#a99072eb52bb22745f0248f273fbf28fb">DObject::runPlugin</a></div><div class="ttdeci">void runPlugin(const std::string &amp;id)</div><div class="ttdoc">Executes a plugin by its identifier.</div><div class="ttdef"><b>Definition</b> DObject.cpp:88</div></div>
-<div class="ttc" id="aclass_d_object_html_a99b8688849e11501033a25f61efb8356"><div class="ttname"><a href="class_d_object.html#a99b8688849e11501033a25f61efb8356">DObject::unregisterPlugin</a></div><div class="ttdeci">void unregisterPlugin(const std::string &amp;id)</div><div class="ttdoc">Unregisters a plugin by its identifier.</div><div class="ttdef"><b>Definition</b> DObject.cpp:79</div></div>
-<div class="ttc" id="aclass_d_object_html_ab1718571434e84e90f1ec463e4786a8a"><div class="ttname"><a href="class_d_object.html#ab1718571434e84e90f1ec463e4786a8a">DObject::setData</a></div><div class="ttdeci">void setData(const DataType &amp;data)</div><div class="ttdoc">Sets the data for the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:33</div></div>
-<div class="ttc" id="aclass_d_object_html_ad6fc2e29eae70cf94a2d241527857573"><div class="ttname"><a href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DObject::DataType</a></div><div class="ttdeci">std::variant&lt; int, float, double, std::string, std::monostate, std::vector&lt; int &gt;, std::vector&lt; float &gt;, std::vector&lt; double &gt; &gt; DataType</div><div class="ttdoc">Supported data types for the DObject.</div><div class="ttdef"><b>Definition</b> DObject.h:37</div></div>
-<div class="ttc" id="aclass_d_object_html_ae47bf220fbe2173cf6933c2380035dbd"><div class="ttname"><a href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">DObject::isDebuggingEnabled</a></div><div class="ttdeci">bool isDebuggingEnabled() const noexcept</div><div class="ttdoc">Checks if debugging is enabled for the DObject.</div><div class="ttdef"><b>Definition</b> DObject.cpp:62</div></div>
-<div class="ttc" id="aclass_d_object_html_af11334d08ef85c68b3aae7554548e5a7"><div class="ttname"><a href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">DObject::Plugin</a></div><div class="ttdeci">std::function&lt; void(DObject &amp;)&gt; Plugin</div><div class="ttdoc">Placeholder type for plugins.</div><div class="ttdef"><b>Definition</b> DObject.h:47</div></div>
-<div class="ttc" id="aclass_metadata_html"><div class="ttname"><a href="class_metadata.html">Metadata</a></div><div class="ttdoc">Represents metadata information for data objects in the dobj module.</div><div class="ttdef"><b>Definition</b> Metadata.h:31</div></div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span> </div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span></div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"><a class="line" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">  125</a></span>    <span class="keyword">using </span><a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> = std::function&lt;void(<a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>&amp;)&gt;;</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span></div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>    <a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>();</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span></div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno">  139</span>    <a class="code hl_function" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a>&amp; data);</div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span></div>
+<div class="line"><a id="l00148" name="l00148"></a><span class="lineno">  148</span>    <span class="keyword">const</span> <a class="code hl_typedef" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a>&amp; <a class="code hl_function" href="class_d_object.html#a4862655c3634d019b0a45b811d6f7235">getData</a>() const noexcept;</div>
+<div class="line"><a id="l00149" name="l00149"></a><span class="lineno">  149</span></div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span>    template &lt;typename T&gt;</div>
+<div class="foldopen" id="foldopen00156" data-start="{" data-end="}">
+<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"><a class="line" href="class_d_object.html#aca2db093c1c8c6f7893de07544aed619">  156</a></span>    T <a class="code hl_function" href="class_d_object.html#aca2db093c1c8c6f7893de07544aed619">getDataAs</a>()<span class="keyword"> const </span>{</div>
+<div class="line"><a id="l00157" name="l00157"></a><span class="lineno">  157</span>        <span class="keywordflow">if</span> (std::holds_alternative&lt;T&gt;(<a class="code hl_variable" href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">data_</a>)) {</div>
+<div class="line"><a id="l00158" name="l00158"></a><span class="lineno">  158</span>            <span class="keywordflow">return</span> std::get&lt;T&gt;(<a class="code hl_variable" href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">data_</a>);</div>
+<div class="line"><a id="l00159" name="l00159"></a><span class="lineno">  159</span>        } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00160" name="l00160"></a><span class="lineno">  160</span>            <span class="keywordflow">throw</span> std::bad_variant_access();</div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>        }</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span>    }</div>
+</div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span></div>
+<div class="line"><a id="l00171" name="l00171"></a><span class="lineno">  171</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#ab1718571434e84e90f1ec463e4786a8a">setData</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a>&amp; data);</div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span></div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a6f0023aee463e71d92442dcf61b6ed47">setDebugging</a>(<span class="keywordtype">bool</span> enableDebug);</div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span></div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span>    <span class="keywordtype">bool</span> <a class="code hl_function" href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">isDebuggingEnabled</a>() const noexcept;</div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span></div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>    <span class="keywordtype">int</span> <a class="code hl_function" href="class_d_object.html#a3dce47a519f9da5085c0c5ac1eea4f38">setErrorCode</a>(<span class="keywordtype">int</span> code) noexcept;</div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span></div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno">  201</span>    <span class="keywordtype">int</span> <a class="code hl_function" href="class_d_object.html#afa8926d916081de72478cb8813c25e98">getErrorCode</a>() const noexcept;</div>
+<div class="line"><a id="l00202" name="l00202"></a><span class="lineno">  202</span> </div>
+<div class="line"><a id="l00203" name="l00203"></a><span class="lineno">  203</span></div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a15afffdf339150fc872bf63bdd08d581">registerPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>, <a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> plugin);</div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span></div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a99b8688849e11501033a25f61efb8356">unregisterPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>);</div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span></div>
+<div class="line"><a id="l00230" name="l00230"></a><span class="lineno">  230</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a99072eb52bb22745f0248f273fbf28fb">runPlugin</a>(const std::<span class="keywordtype">string</span>&amp; <span class="keywordtype">id</span>);</div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span></div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_d_object.html#a1223275dcbbf20334ea11707346acb93">runAllPlugins</a>();</div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span></div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span>    friend std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const <a class="code hl_class" href="class_d_object.html">DObject</a>&amp; obj);</div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span> </div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span>private:</div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"><a class="line" href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">  251</a></span>    <a class="code hl_typedef" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> <a class="code hl_variable" href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">data_</a>;                              </div>
+<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"><a class="line" href="class_d_object.html#accf5c10d4afc3969607e11b0055312d5">  252</a></span>    <span class="keywordtype">bool</span> <a class="code hl_variable" href="class_d_object.html#accf5c10d4afc3969607e11b0055312d5">debugEnabled_</a> = false;                  </div>
+<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"><a class="line" href="class_d_object.html#ad8de5890e8dae5fc7e72fabca2520fc3">  253</a></span>    <span class="keywordtype">int</span> <a class="code hl_variable" href="class_d_object.html#ad8de5890e8dae5fc7e72fabca2520fc3">errorCode_</a> = 0;                          </div>
+<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"><a class="line" href="class_d_object.html#ae9f7e4d2fbabc076961a40185676e208">  254</a></span>    std::map&lt;std::<span class="keywordtype">string</span>, <a class="code hl_typedef" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a>&gt; <a class="code hl_variable" href="class_d_object.html#ae9f7e4d2fbabc076961a40185676e208">plugins_</a>;      </div>
+<div class="line"><a id="l00255" name="l00255"></a><span class="lineno">  255</span>};</div>
+</div>
+<div class="line"><a id="l00256" name="l00256"></a><span class="lineno">  256</span> </div>
+<div class="line"><a id="l00257" name="l00257"></a><span class="lineno">  257</span><span class="preprocessor">#endif </span><span class="comment">// DOBJECT_H</span></div>
+<div class="ttc" id="aclass_d_object_html"><div class="ttname"><a href="class_d_object.html">DObject</a></div><div class="ttdoc">A universal data container class.</div><div class="ttdef"><b>Definition</b> <a href="#l00089">DObject.h:89</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a0ae54853e18265657296bfb5ac3bf9d0"><div class="ttname"><a href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject::DObject</a></div><div class="ttdeci">DObject()</div><div class="ttdoc">Default constructor.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00033">DObject.cpp:33</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a1223275dcbbf20334ea11707346acb93"><div class="ttname"><a href="class_d_object.html#a1223275dcbbf20334ea11707346acb93">DObject::runAllPlugins</a></div><div class="ttdeci">void runAllPlugins()</div><div class="ttdoc">Executes all registered plugins in the registry.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00117">DObject.cpp:117</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a15afffdf339150fc872bf63bdd08d581"><div class="ttname"><a href="class_d_object.html#a15afffdf339150fc872bf63bdd08d581">DObject::registerPlugin</a></div><div class="ttdeci">void registerPlugin(const std::string &amp;id, Plugin plugin)</div><div class="ttdoc">Registers a plugin with the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00087">DObject.cpp:87</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a358d5f015da09ae5f0cbb46f3fd9e401"><div class="ttname"><a href="class_d_object.html#a358d5f015da09ae5f0cbb46f3fd9e401">DObject::dataTypeMap</a></div><div class="ttdeci">std::map&lt; int, std::string &gt; dataTypeMap</div><div class="ttdef"><b>Definition</b> <a href="#l00109">DObject.h:109</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a3dce47a519f9da5085c0c5ac1eea4f38"><div class="ttname"><a href="class_d_object.html#a3dce47a519f9da5085c0c5ac1eea4f38">DObject::setErrorCode</a></div><div class="ttdeci">int setErrorCode(int code) noexcept</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00074">DObject.cpp:74</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a4862655c3634d019b0a45b811d6f7235"><div class="ttname"><a href="class_d_object.html#a4862655c3634d019b0a45b811d6f7235">DObject::getData</a></div><div class="ttdeci">const DataType &amp; getData() const noexcept</div><div class="ttdoc">Retrieves the data stored in the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00046">DObject.cpp:46</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a55b7cdac36a3a518ba6e1ecef0e25dcd"><div class="ttname"><a href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DObject::DataType</a></div><div class="ttdeci">std::variant&lt; bool, short int, int, long int, float, double, long double, std::string, std::monostate, std::vector&lt; int &gt;, std::vector&lt; float &gt;, std::vector&lt; double &gt;, std::vector&lt; std::string &gt;, std::vector&lt; std::vector&lt; int &gt; &gt;, std::vector&lt; std::vector&lt; float &gt; &gt;, std::vector&lt; std::vector&lt; double &gt; &gt;, std::vector&lt; std::vector&lt; std::vector&lt; int &gt; &gt; &gt;, std::vector&lt; std::vector&lt; std::vector&lt; float &gt; &gt; &gt;, std::vector&lt; std::vector&lt; std::vector&lt; double &gt; &gt; &gt; &gt; DataType</div><div class="ttdoc">Supported data types for the DObject.</div><div class="ttdef"><b>Definition</b> <a href="#l00097">DObject.h:97</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a6f0023aee463e71d92442dcf61b6ed47"><div class="ttname"><a href="class_d_object.html#a6f0023aee463e71d92442dcf61b6ed47">DObject::setDebugging</a></div><div class="ttdeci">void setDebugging(bool enableDebug)</div><div class="ttdoc">Enables or disables debugging and tracing for the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00060">DObject.cpp:60</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a99072eb52bb22745f0248f273fbf28fb"><div class="ttname"><a href="class_d_object.html#a99072eb52bb22745f0248f273fbf28fb">DObject::runPlugin</a></div><div class="ttdeci">void runPlugin(const std::string &amp;id)</div><div class="ttdoc">Executes a plugin by its identifier.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00106">DObject.cpp:106</a></div></div>
+<div class="ttc" id="aclass_d_object_html_a99b8688849e11501033a25f61efb8356"><div class="ttname"><a href="class_d_object.html#a99b8688849e11501033a25f61efb8356">DObject::unregisterPlugin</a></div><div class="ttdeci">void unregisterPlugin(const std::string &amp;id)</div><div class="ttdoc">Unregisters a plugin by its identifier.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00097">DObject.cpp:97</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ab1718571434e84e90f1ec463e4786a8a"><div class="ttname"><a href="class_d_object.html#ab1718571434e84e90f1ec463e4786a8a">DObject::setData</a></div><div class="ttdeci">void setData(const DataType &amp;data)</div><div class="ttdoc">Sets the data for the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00053">DObject.cpp:53</a></div></div>
+<div class="ttc" id="aclass_d_object_html_aca2db093c1c8c6f7893de07544aed619"><div class="ttname"><a href="class_d_object.html#aca2db093c1c8c6f7893de07544aed619">DObject::getDataAs</a></div><div class="ttdeci">T getDataAs() const</div><div class="ttdoc">Retrieves the data stored in the DObject as a typed object so that std::get&lt;T&gt;() is not needed.</div><div class="ttdef"><b>Definition</b> <a href="#l00156">DObject.h:156</a></div></div>
+<div class="ttc" id="aclass_d_object_html_accf5c10d4afc3969607e11b0055312d5"><div class="ttname"><a href="class_d_object.html#accf5c10d4afc3969607e11b0055312d5">DObject::debugEnabled_</a></div><div class="ttdeci">bool debugEnabled_</div><div class="ttdoc">Indicates whether debugging is enabled.</div><div class="ttdef"><b>Definition</b> <a href="#l00252">DObject.h:252</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ad7ba02f6d87ce64792149096f3310b21"><div class="ttname"><a href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">DObject::data_</a></div><div class="ttdeci">DataType data_</div><div class="ttdoc">The main data stored in the DObject.</div><div class="ttdef"><b>Definition</b> <a href="#l00251">DObject.h:251</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ad8de5890e8dae5fc7e72fabca2520fc3"><div class="ttname"><a href="class_d_object.html#ad8de5890e8dae5fc7e72fabca2520fc3">DObject::errorCode_</a></div><div class="ttdeci">int errorCode_</div><div class="ttdoc">Error code tracked by the DObject.</div><div class="ttdef"><b>Definition</b> <a href="#l00253">DObject.h:253</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ae47bf220fbe2173cf6933c2380035dbd"><div class="ttname"><a href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">DObject::isDebuggingEnabled</a></div><div class="ttdeci">bool isDebuggingEnabled() const noexcept</div><div class="ttdoc">Checks if debugging is enabled for the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00067">DObject.cpp:67</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ae9f7e4d2fbabc076961a40185676e208"><div class="ttname"><a href="class_d_object.html#ae9f7e4d2fbabc076961a40185676e208">DObject::plugins_</a></div><div class="ttdeci">std::map&lt; std::string, Plugin &gt; plugins_</div><div class="ttdoc">Registry for dynamically registered plugins.</div><div class="ttdef"><b>Definition</b> <a href="#l00254">DObject.h:254</a></div></div>
+<div class="ttc" id="aclass_d_object_html_af11334d08ef85c68b3aae7554548e5a7"><div class="ttname"><a href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">DObject::Plugin</a></div><div class="ttdeci">std::function&lt; void(DObject &amp;)&gt; Plugin</div><div class="ttdoc">Placeholder type for plugins.</div><div class="ttdef"><b>Definition</b> <a href="#l00125">DObject.h:125</a></div></div>
+<div class="ttc" id="aclass_d_object_html_afa8926d916081de72478cb8813c25e98"><div class="ttname"><a href="class_d_object.html#afa8926d916081de72478cb8813c25e98">DObject::getErrorCode</a></div><div class="ttdeci">int getErrorCode() const noexcept</div><div class="ttdoc">Get the error code tracked by the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00080">DObject.cpp:80</a></div></div>
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-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
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+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
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+/* @license-end */
+</script>
+<div id="main-nav"></div>
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@@ -124,6 +121,8 @@ Classes</h2></td></tr>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>A lightweight wrapper for <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> that adds locking capabilities. </p>
 <p>This class allows safe concurrent access to a <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> by providing locking and unlocking methods. </p>
+
+<p class="definition">Definition in file <a class="el" href="_lockable_d_object_8h_source.html">LockableDObject.h</a>.</p>
 </div></div><!-- contents -->
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-<title>New 4DSSE Code: src/dobj/public/LockableDObject.h Source File</title>
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-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
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+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
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+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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@@ -105,36 +102,58 @@ $(function(){initNavTree('_lockable_d_object_8h_source.html',''); initResizable(
  <div class="headertitle"><div class="title">LockableDObject.h</div></div>
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-<a href="_lockable_d_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="preprocessor">#ifndef LOCKABLE_DOBJECT_H</span></div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="preprocessor">#define LOCKABLE_DOBJECT_H</span></div>
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-<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span></div>
-<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span></div>
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-<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span></div>
-<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    <a class="code hl_class" href="class_d_object.html">DObject</a>&amp; <a class="code hl_function" href="class_lockable_d_object.html#adcfe201fc728cc1c6fcf638a566ba9a1">get</a>();</div>
-<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span></div>
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-<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span></div>
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-<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>};</div>
+<a href="_lockable_d_object_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="comment">/* ***********************************************************************</span></div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="comment">//</span></div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span><span class="comment">//   Copyright (C) 2025 -- The 4D-STAR Collaboration</span></div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="comment">//   File Author: Emily Boudreaux</span></div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="comment">//   Last Modified: March 17, 2025</span></div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="comment">//</span></div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="comment">//   4DSSE is free software; you can use it and/or modify</span></div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="comment">//   it under the terms and restrictions the GNU General Library Public</span></div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span><span class="comment">//   License version 3 (GPLv3) as published by the Free Software Foundation.</span></div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="comment">//</span></div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="comment">//   4DSSE is distributed in the hope that it will be useful,</span></div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="comment">//   See the GNU Library General Public License for more details.</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="comment">//</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="comment">//   You should have received a copy of the GNU Library General Public License</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="comment">//   along with this software; if not, write to the Free Software</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="comment">//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span><span class="comment">//</span></div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="comment">// *********************************************************************** */</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#ifndef LOCKABLE_DOBJECT_H</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span><span class="preprocessor">#define LOCKABLE_DOBJECT_H</span></div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#include &quot;<a class="code" href="_d_object_8h.html">DObject.h</a>&quot;</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#include &lt;mutex&gt;</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span></div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span></div>
+<div class="foldopen" id="foldopen00039" data-start="{" data-end="};">
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="class_lockable_d_object.html">   39</a></span><span class="keyword">class </span><a class="code hl_function" href="class_lockable_d_object.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a> {</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span><span class="keyword">public</span>:</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"><a class="line" href="class_lockable_d_object.html#ae1a174a2740fa053626fe2820ee0efee">   44</a></span>    <a class="code hl_function" href="class_lockable_d_object.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a>() = <span class="keywordflow">default</span>;</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span></div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>    <a class="code hl_class" href="class_d_object.html">DObject</a>&amp; <a class="code hl_function" href="class_lockable_d_object.html#adcfe201fc728cc1c6fcf638a566ba9a1">get</a>();</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span></div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_lockable_d_object.html#ade38ca54703913359fc3b4366f6e292a">lock</a>();</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span></div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_lockable_d_object.html#a1481ed99dcd837490bf28309aadaedfb">unlock</a>();</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span> </div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span><span class="keyword">private</span>:</div>
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+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"><a class="line" href="class_lockable_d_object.html#a712cd3ea0c565f7e9089a651ef79b7bd">   64</a></span>    std::mutex <a class="code hl_variable" href="class_lockable_d_object.html#a712cd3ea0c565f7e9089a651ef79b7bd">mutex_</a>;      </div>
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+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span> </div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</span><span class="preprocessor">#endif </span><span class="comment">// LOCKABLE_DOBJECT_H</span></div>
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-<div class="ttc" id="aclass_lockable_d_object_html_a1481ed99dcd837490bf28309aadaedfb"><div class="ttname"><a href="class_lockable_d_object.html#a1481ed99dcd837490bf28309aadaedfb">LockableDObject::unlock</a></div><div class="ttdeci">void unlock()</div><div class="ttdoc">Unlocks the mutex after thread-safe access.</div><div class="ttdef"><b>Definition</b> LockableDObject.cpp:20</div></div>
-<div class="ttc" id="aclass_lockable_d_object_html_adcfe201fc728cc1c6fcf638a566ba9a1"><div class="ttname"><a href="class_lockable_d_object.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject::get</a></div><div class="ttdeci">DObject &amp; get()</div><div class="ttdoc">Access the underlying DObject.</div><div class="ttdef"><b>Definition</b> LockableDObject.cpp:6</div></div>
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+<div class="ttc" id="aclass_d_object_html"><div class="ttname"><a href="class_d_object.html">DObject</a></div><div class="ttdoc">A universal data container class.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8h_source.html#l00089">DObject.h:89</a></div></div>
+<div class="ttc" id="aclass_lockable_d_object_html_a1481ed99dcd837490bf28309aadaedfb"><div class="ttname"><a href="class_lockable_d_object.html#a1481ed99dcd837490bf28309aadaedfb">LockableDObject::unlock</a></div><div class="ttdeci">void unlock()</div><div class="ttdoc">Unlocks the mutex after thread-safe access.</div><div class="ttdef"><b>Definition</b> <a href="_lockable_d_object_8cpp_source.html#l00040">LockableDObject.cpp:40</a></div></div>
+<div class="ttc" id="aclass_lockable_d_object_html_a1eb1ca1d9cf979dcb9eead96054b89bb"><div class="ttname"><a href="class_lockable_d_object.html#a1eb1ca1d9cf979dcb9eead96054b89bb">LockableDObject::object_</a></div><div class="ttdeci">DObject object_</div><div class="ttdoc">The underlying DObject instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00063">LockableDObject.h:63</a></div></div>
+<div class="ttc" id="aclass_lockable_d_object_html_a712cd3ea0c565f7e9089a651ef79b7bd"><div class="ttname"><a href="class_lockable_d_object.html#a712cd3ea0c565f7e9089a651ef79b7bd">LockableDObject::mutex_</a></div><div class="ttdeci">std::mutex mutex_</div><div class="ttdoc">Mutex for thread-safe access.</div><div class="ttdef"><b>Definition</b> <a href="#l00064">LockableDObject.h:64</a></div></div>
+<div class="ttc" id="aclass_lockable_d_object_html_adcfe201fc728cc1c6fcf638a566ba9a1"><div class="ttname"><a href="class_lockable_d_object.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject::get</a></div><div class="ttdeci">DObject &amp; get()</div><div class="ttdoc">Access the underlying DObject.</div><div class="ttdef"><b>Definition</b> <a href="_lockable_d_object_8cpp_source.html#l00026">LockableDObject.cpp:26</a></div></div>
+<div class="ttc" id="aclass_lockable_d_object_html_ade38ca54703913359fc3b4366f6e292a"><div class="ttname"><a href="class_lockable_d_object.html#ade38ca54703913359fc3b4366f6e292a">LockableDObject::lock</a></div><div class="ttdeci">void lock()</div><div class="ttdoc">Locks the mutex to ensure thread-safe access.</div><div class="ttdef"><b>Definition</b> <a href="_lockable_d_object_8cpp_source.html#l00033">LockableDObject.cpp:33</a></div></div>
 <div class="ttc" id="aclass_lockable_d_object_html_ae1a174a2740fa053626fe2820ee0efee"><div class="ttname"><a href="class_lockable_d_object.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject::LockableDObject</a></div><div class="ttdeci">LockableDObject()=default</div><div class="ttdoc">Default constructor.</div></div>
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-</script>
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-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
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 <div id="side-nav" class="ui-resizable side-nav-resizable">
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@@ -111,7 +108,9 @@ $(function(){initNavTree('_metadata_8cpp.html',''); initResizable(true); });
 <p>Implementation of the <a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a> class used in the dobj module.  
 <a href="#details">More...</a></p>
 <div class="textblock"><code>#include &quot;<a class="el" href="_metadata_8h_source.html">Metadata.h</a>&quot;</code><br />
-</div><table class="memberdecls">
+</div>
+<p><a href="_metadata_8cpp_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
 Functions</h2></td></tr>
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 <div class="textblock"><p>Implementation of the <a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a> class used in the dobj module. </p>
 <p>Provides methods to manage metadata for data objects, including size, type, dimensions, and debugging flags. </p>
+
+<p class="definition">Definition in file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
 </div><h2 class="groupheader">Function Documentation</h2>
 <a id="a12949a1ea26c4ff1afeb97101c0493c5" name="a12949a1ea26c4ff1afeb97101c0493c5"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#a12949a1ea26c4ff1afeb97101c0493c5">&#9670;&#160;</a></span>operator&lt;&lt;()</h2>
@@ -152,6 +153,8 @@ Functions</h2></td></tr>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>A reference to the output stream. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00146">146</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 </div><!-- contents -->
--- a/docs/html/_metadata_8h.html
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@@ -5,7 +5,7 @@
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 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: src/dobj/public/Metadata.h File Reference</title>
+<title>SERiF: src/dobj/public/Metadata.h File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
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-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
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@@ -32,20 +29,9 @@
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-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
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-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
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@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
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 <div id="side-nav" class="ui-resizable side-nav-resizable">
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+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="define-members" name="define-members"></a>
+Macros</h2></td></tr>
+<tr class="memitem:ab57c319c35ea0fbacf781f2ecb3a4339" id="r_ab57c319c35ea0fbacf781f2ecb3a4339"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab57c319c35ea0fbacf781f2ecb3a4339">EXPORT_SYMBOL</a></td></tr>
+<tr class="separator:ab57c319c35ea0fbacf781f2ecb3a4339"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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 <p>The <a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a> class provides descriptive information about the data encapsulated within a dobj, including size, type, dimensions, and debugging flags. </p>
-</div></div><!-- contents -->
+
+<p class="definition">Definition in file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+</div><h2 class="groupheader">Macro Definition Documentation</h2>
+<a id="ab57c319c35ea0fbacf781f2ecb3a4339" name="ab57c319c35ea0fbacf781f2ecb3a4339"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ab57c319c35ea0fbacf781f2ecb3a4339">&#9670;&#160;</a></span>EXPORT_SYMBOL</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define EXPORT_SYMBOL</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00027">27</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+
+</div>
+</div>
+</div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->
 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
--- a/docs/html/_metadata_8h.js
+++ b/docs/html/_metadata_8h.js
@@ -1,4 +1,5 @@
 var _metadata_8h =
 [
-    [ "Metadata", "class_metadata.html", "class_metadata" ]
+    [ "Metadata", "class_metadata.html", "class_metadata" ],
+    [ "EXPORT_SYMBOL", "_metadata_8h.html#ab57c319c35ea0fbacf781f2ecb3a4339", null ]
 ];
--- a/docs/html/_metadata_8h_source.html
+++ b/docs/html/_metadata_8h_source.html
@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: src/dobj/public/Metadata.h Source File</title>
+<title>SERiF: src/dobj/public/Metadata.h Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
@@ -18,12 +18,9 @@
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <span id="MSearchSelect"                onmouseover="return searchBox.OnSearchSelectShow()"                onmouseout="return searchBox.OnSearchSelectHide()">&#160;</span>
-          <input type="text" id="MSearchField" value="" placeholder="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
-               onkeyup="searchBox.OnSearchFieldChange(event)"/>
-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -105,64 +102,89 @@ $(function(){initNavTree('_metadata_8h_source.html',''); initResizable(true); })
  <div class="headertitle"><div class="title">Metadata.h</div></div>
 </div><!--header-->
 <div class="contents">
-<a href="_metadata_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="preprocessor">#ifndef METADATA_H</span></div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="preprocessor">#define METADATA_H</span></div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span> </div>
-<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="preprocessor">#if defined(__APPLE__) || defined(__linux__)</span></div>
-<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="preprocessor">#define EXPORT_SYMBOL __attribute__((visibility(&quot;default&quot;)))</span></div>
-<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="preprocessor">#else</span></div>
-<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="preprocessor">#define EXPORT_SYMBOL</span></div>
-<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="preprocessor">#endif</span></div>
-<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span> </div>
-<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="preprocessor">#include &lt;string&gt;</span></div>
-<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
-<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="preprocessor">#include &lt;cstddef&gt;</span></div>
-<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &lt;iostream&gt;</span></div>
-<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span></div>
-<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span></div>
-<div class="foldopen" id="foldopen00031" data-start="{" data-end="};">
-<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"><a class="line" href="class_metadata.html">   31</a></span><span class="keyword">class </span>EXPORT_SYMBOL <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a> {</div>
-<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span><span class="keyword">public</span>:</div>
-<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"><a class="line" href="class_metadata.html#ae849560667461008cb72e83919c20be0">   36</a></span>    <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>() = <span class="keywordflow">default</span>;</div>
-<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span></div>
-<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>(std::size_t byteSize, std::string dataType, std::vector&lt;std::size_t&gt; dimensions, <span class="keywordtype">bool</span> debugFlag = <span class="keyword">false</span>);</div>
-<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span></div>
-<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>    [[nodiscard]] std::size_t <a class="code hl_function" href="class_metadata.html#ac7980d1efdd6ae434f0115f83d08348e">getByteSize</a>() const noexcept;</div>
-<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span></div>
-<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a07035de7b0c780ef340e1a11c60a4d2b">setByteSize</a>(std::<span class="keywordtype">size_t</span> byteSize) noexcept;</div>
-<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span></div>
-<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>    [[nodiscard]] const std::<span class="keywordtype">string</span>&amp; <a class="code hl_function" href="class_metadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">getDataType</a>() const noexcept;</div>
-<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span></div>
-<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">setDataType</a>(const std::<span class="keywordtype">string</span>&amp; dataType);</div>
-<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span></div>
-<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    [[nodiscard]] const std::vector&lt;std::<span class="keywordtype">size_t</span>&gt;&amp; <a class="code hl_function" href="class_metadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">getDimensions</a>() const noexcept;</div>
-<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span></div>
-<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#af5264d1666839e69c192b565b5cfa606">setDimensions</a>(const std::vector&lt;std::<span class="keywordtype">size_t</span>&gt;&amp; dimensions);</div>
-<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span></div>
-<div class="line"><a id="l00088" name="l00088"></a><span class="lineno">   88</span>    [[nodiscard]] <span class="keywordtype">bool</span> <a class="code hl_function" href="class_metadata.html#abe52c81e04665628666b4140cd346b69">isDebugEnabled</a>() const noexcept;</div>
-<div class="line"><a id="l00089" name="l00089"></a><span class="lineno">   89</span></div>
-<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">setDebugEnabled</a>(<span class="keywordtype">bool</span> debugFlag) noexcept;</div>
-<div class="line"><a id="l00095" name="l00095"></a><span class="lineno">   95</span></div>
-<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span>    friend std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>&amp; metadata);</div>
-<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span> </div>
-<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>private:</div>
-<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>    std::<span class="keywordtype">size_t</span> byteSize_ = 0;                      </div>
-<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span>    std::<span class="keywordtype">string</span> dataType_;                          </div>
-<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    std::vector&lt;std::<span class="keywordtype">size_t</span>&gt; dimensions_;           </div>
-<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span>    <span class="keywordtype">bool</span> debugFlag_ = false;                        </div>
-<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span>};</div>
+<a href="_metadata_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span><span class="comment">/* ***********************************************************************</span></div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span><span class="comment">//</span></div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span><span class="comment">//   Copyright (C) 2025 -- The 4D-STAR Collaboration</span></div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="comment">//   File Author: Emily Boudreaux</span></div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span><span class="comment">//   Last Modified: March 17, 2025</span></div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span><span class="comment">//</span></div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span><span class="comment">//   4DSSE is free software; you can use it and/or modify</span></div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span><span class="comment">//   it under the terms and restrictions the GNU General Library Public</span></div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span><span class="comment">//   License version 3 (GPLv3) as published by the Free Software Foundation.</span></div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span><span class="comment">//</span></div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="comment">//   4DSSE is distributed in the hope that it will be useful,</span></div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="comment">//   See the GNU Library General Public License for more details.</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="comment">//</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="comment">//   You should have received a copy of the GNU Library General Public License</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="comment">//   along with this software; if not, write to the Free Software</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="comment">//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span><span class="comment">//</span></div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="comment">// *********************************************************************** */</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#ifndef METADATA_H</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span><span class="preprocessor">#define METADATA_H</span></div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#if defined(__APPLE__) || defined(__linux__)</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#define EXPORT_SYMBOL __attribute__((visibility(&quot;default&quot;)))</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span><span class="preprocessor">#else</span></div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="_metadata_8h.html#ab57c319c35ea0fbacf781f2ecb3a4339">   27</a></span><span class="preprocessor">#define EXPORT_SYMBOL</span></div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span><span class="preprocessor">#endif</span></div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span> </div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span><span class="preprocessor">#include &lt;cstddef&gt;</span></div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span></div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span></div>
+<div class="foldopen" id="foldopen00051" data-start="{" data-end="};">
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"><a class="line" href="class_metadata.html">   51</a></span><span class="keyword">class </span><a class="code hl_define" href="_metadata_8h.html#ab57c319c35ea0fbacf781f2ecb3a4339">EXPORT_SYMBOL</a> <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a> {</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span><span class="keyword">public</span>:</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"><a class="line" href="class_metadata.html#ae849560667461008cb72e83919c20be0">   56</a></span>    <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>() = <span class="keywordflow">default</span>;</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span></div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span>    <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>(std::size_t byteSize, std::string dataType, std::vector&lt;std::size_t&gt; dimensions, <span class="keywordtype">bool</span> debugFlag = <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</span></div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>    [[nodiscard]] std::size_t <a class="code hl_function" href="class_metadata.html#ac7980d1efdd6ae434f0115f83d08348e">getByteSize</a>() const noexcept;</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span></div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a07035de7b0c780ef340e1a11c60a4d2b">setByteSize</a>(std::<span class="keywordtype">size_t</span> byteSize) noexcept;</div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span></div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span>    [[nodiscard]] const std::<span class="keywordtype">string</span>&amp; <a class="code hl_function" href="class_metadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">getDataType</a>() const noexcept;</div>
+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span></div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">setDataType</a>(const std::<span class="keywordtype">string</span>&amp; dataType);</div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span></div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span>    [[nodiscard]] const std::vector&lt;std::<span class="keywordtype">size_t</span>&gt;&amp; <a class="code hl_function" href="class_metadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">getDimensions</a>() const noexcept;</div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span></div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#af5264d1666839e69c192b565b5cfa606">setDimensions</a>(const std::vector&lt;std::<span class="keywordtype">size_t</span>&gt;&amp; dimensions);</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span></div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    [[nodiscard]] <span class="keywordtype">bool</span> <a class="code hl_function" href="class_metadata.html#abe52c81e04665628666b4140cd346b69">isDebugEnabled</a>() const noexcept;</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span></div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="class_metadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">setDebugEnabled</a>(<span class="keywordtype">bool</span> debugFlag) noexcept;</div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span></div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span>    friend std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const <a class="code hl_function" href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>&amp; metadata);</div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span> </div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>private:</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"><a class="line" href="class_metadata.html#ac73a509797c98c0d52fb32e1f93e38bc">  126</a></span>    <span class="keywordtype">int</span> <a class="code hl_variable" href="class_metadata.html#ac73a509797c98c0d52fb32e1f93e38bc">byteSize_</a> = 0;                      </div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"><a class="line" href="class_metadata.html#a290205e5f46416dd0f48bd6ff62888ac">  127</a></span>    std::<span class="keywordtype">string</span> <a class="code hl_variable" href="class_metadata.html#a290205e5f46416dd0f48bd6ff62888ac">dataType_</a>;                          </div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"><a class="line" href="class_metadata.html#a163f74d4ef9ecd13a34e7e9cab2e21ce">  128</a></span>    std::vector&lt;std::<span class="keywordtype">size_t</span>&gt; <a class="code hl_variable" href="class_metadata.html#a163f74d4ef9ecd13a34e7e9cab2e21ce">dimensions_</a>;           </div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"><a class="line" href="class_metadata.html#a65fd506f1bd41699d9cd19bc0dfc9701">  129</a></span>    <span class="keywordtype">bool</span> <a class="code hl_variable" href="class_metadata.html#a65fd506f1bd41699d9cd19bc0dfc9701">debugFlag_</a> = false;                        </div>
+<div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span>};</div>
 </div>
-<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span> </div>
-<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span><span class="preprocessor">#endif </span><span class="comment">// METADATA_H</span></div>
-<div class="ttc" id="aclass_metadata_html_a07035de7b0c780ef340e1a11c60a4d2b"><div class="ttname"><a href="class_metadata.html#a07035de7b0c780ef340e1a11c60a4d2b">Metadata::setByteSize</a></div><div class="ttdeci">void setByteSize(std::size_t byteSize) noexcept</div><div class="ttdoc">Sets the total size of the data in bytes.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:42</div></div>
-<div class="ttc" id="aclass_metadata_html_a365c4594ad65c3b10b40a1cf4f4aea26"><div class="ttname"><a href="class_metadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">Metadata::setDebugEnabled</a></div><div class="ttdeci">void setDebugEnabled(bool debugFlag) noexcept</div><div class="ttdoc">Sets the debugging flag.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:112</div></div>
-<div class="ttc" id="aclass_metadata_html_a412c0c0b8754d85f9edbbdcd637f3b20"><div class="ttname"><a href="class_metadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">Metadata::getDimensions</a></div><div class="ttdeci">const std::vector&lt; std::size_t &gt; &amp; getDimensions() const noexcept</div><div class="ttdoc">Gets the dimensions of the data.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:78</div></div>
-<div class="ttc" id="aclass_metadata_html_a88f4f57d443e2b7664e75e57a29dfbf0"><div class="ttname"><a href="class_metadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">Metadata::setDataType</a></div><div class="ttdeci">void setDataType(const std::string &amp;dataType)</div><div class="ttdoc">Sets the type of the data.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:66</div></div>
-<div class="ttc" id="aclass_metadata_html_abe52c81e04665628666b4140cd346b69"><div class="ttname"><a href="class_metadata.html#abe52c81e04665628666b4140cd346b69">Metadata::isDebugEnabled</a></div><div class="ttdeci">bool isDebugEnabled() const noexcept</div><div class="ttdoc">Checks if debugging information is enabled.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:100</div></div>
-<div class="ttc" id="aclass_metadata_html_ac7980d1efdd6ae434f0115f83d08348e"><div class="ttname"><a href="class_metadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata::getByteSize</a></div><div class="ttdeci">std::size_t getByteSize() const noexcept</div><div class="ttdoc">Gets the total size of the data in bytes.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:30</div></div>
+<div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span> </div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span><span class="preprocessor">#endif </span><span class="comment">// METADATA_H</span></div>
+<div class="ttc" id="a_metadata_8h_html_ab57c319c35ea0fbacf781f2ecb3a4339"><div class="ttname"><a href="_metadata_8h.html#ab57c319c35ea0fbacf781f2ecb3a4339">EXPORT_SYMBOL</a></div><div class="ttdeci">#define EXPORT_SYMBOL</div><div class="ttdef"><b>Definition</b> <a href="#l00027">Metadata.h:27</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a07035de7b0c780ef340e1a11c60a4d2b"><div class="ttname"><a href="class_metadata.html#a07035de7b0c780ef340e1a11c60a4d2b">Metadata::setByteSize</a></div><div class="ttdeci">void setByteSize(std::size_t byteSize) noexcept</div><div class="ttdoc">Sets the total size of the data in bytes.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00062">Metadata.cpp:62</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a163f74d4ef9ecd13a34e7e9cab2e21ce"><div class="ttname"><a href="class_metadata.html#a163f74d4ef9ecd13a34e7e9cab2e21ce">Metadata::dimensions_</a></div><div class="ttdeci">std::vector&lt; std::size_t &gt; dimensions_</div><div class="ttdoc">Dimensions of the data (e.g., {3, 4} for a 3x4 matrix).</div><div class="ttdef"><b>Definition</b> <a href="#l00128">Metadata.h:128</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a290205e5f46416dd0f48bd6ff62888ac"><div class="ttname"><a href="class_metadata.html#a290205e5f46416dd0f48bd6ff62888ac">Metadata::dataType_</a></div><div class="ttdeci">std::string dataType_</div><div class="ttdoc">Type of the data (e.g., &quot;float&quot;, &quot;double&quot;).</div><div class="ttdef"><b>Definition</b> <a href="#l00127">Metadata.h:127</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a365c4594ad65c3b10b40a1cf4f4aea26"><div class="ttname"><a href="class_metadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">Metadata::setDebugEnabled</a></div><div class="ttdeci">void setDebugEnabled(bool debugFlag) noexcept</div><div class="ttdoc">Sets the debugging flag.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00132">Metadata.cpp:132</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a412c0c0b8754d85f9edbbdcd637f3b20"><div class="ttname"><a href="class_metadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">Metadata::getDimensions</a></div><div class="ttdeci">const std::vector&lt; std::size_t &gt; &amp; getDimensions() const noexcept</div><div class="ttdoc">Gets the dimensions of the data.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00098">Metadata.cpp:98</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a65fd506f1bd41699d9cd19bc0dfc9701"><div class="ttname"><a href="class_metadata.html#a65fd506f1bd41699d9cd19bc0dfc9701">Metadata::debugFlag_</a></div><div class="ttdeci">bool debugFlag_</div><div class="ttdoc">Indicates whether debugging is enabled.</div><div class="ttdef"><b>Definition</b> <a href="#l00129">Metadata.h:129</a></div></div>
+<div class="ttc" id="aclass_metadata_html_a88f4f57d443e2b7664e75e57a29dfbf0"><div class="ttname"><a href="class_metadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">Metadata::setDataType</a></div><div class="ttdeci">void setDataType(const std::string &amp;dataType)</div><div class="ttdoc">Sets the type of the data.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00086">Metadata.cpp:86</a></div></div>
+<div class="ttc" id="aclass_metadata_html_abe52c81e04665628666b4140cd346b69"><div class="ttname"><a href="class_metadata.html#abe52c81e04665628666b4140cd346b69">Metadata::isDebugEnabled</a></div><div class="ttdeci">bool isDebugEnabled() const noexcept</div><div class="ttdoc">Checks if debugging information is enabled.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00120">Metadata.cpp:120</a></div></div>
+<div class="ttc" id="aclass_metadata_html_ac73a509797c98c0d52fb32e1f93e38bc"><div class="ttname"><a href="class_metadata.html#ac73a509797c98c0d52fb32e1f93e38bc">Metadata::byteSize_</a></div><div class="ttdeci">int byteSize_</div><div class="ttdoc">Total size of the data in bytes.</div><div class="ttdef"><b>Definition</b> <a href="#l00126">Metadata.h:126</a></div></div>
+<div class="ttc" id="aclass_metadata_html_ac7980d1efdd6ae434f0115f83d08348e"><div class="ttname"><a href="class_metadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata::getByteSize</a></div><div class="ttdeci">std::size_t getByteSize() const noexcept</div><div class="ttdoc">Gets the total size of the data in bytes.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00050">Metadata.cpp:50</a></div></div>
 <div class="ttc" id="aclass_metadata_html_ae849560667461008cb72e83919c20be0"><div class="ttname"><a href="class_metadata.html#ae849560667461008cb72e83919c20be0">Metadata::Metadata</a></div><div class="ttdeci">Metadata()=default</div><div class="ttdoc">Default constructor for Metadata.</div></div>
-<div class="ttc" id="aclass_metadata_html_aeed7f22ccc61d9a3d6425441d381dcdc"><div class="ttname"><a href="class_metadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">Metadata::getDataType</a></div><div class="ttdeci">const std::string &amp; getDataType() const noexcept</div><div class="ttdoc">Gets the type of the data.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:54</div></div>
-<div class="ttc" id="aclass_metadata_html_af5264d1666839e69c192b565b5cfa606"><div class="ttname"><a href="class_metadata.html#af5264d1666839e69c192b565b5cfa606">Metadata::setDimensions</a></div><div class="ttdeci">void setDimensions(const std::vector&lt; std::size_t &gt; &amp;dimensions)</div><div class="ttdoc">Sets the dimensions of the data.</div><div class="ttdef"><b>Definition</b> Metadata.cpp:89</div></div>
+<div class="ttc" id="aclass_metadata_html_aeed7f22ccc61d9a3d6425441d381dcdc"><div class="ttname"><a href="class_metadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">Metadata::getDataType</a></div><div class="ttdeci">const std::string &amp; getDataType() const noexcept</div><div class="ttdoc">Gets the type of the data.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00074">Metadata.cpp:74</a></div></div>
+<div class="ttc" id="aclass_metadata_html_af5264d1666839e69c192b565b5cfa606"><div class="ttname"><a href="class_metadata.html#af5264d1666839e69c192b565b5cfa606">Metadata::setDimensions</a></div><div class="ttdeci">void setDimensions(const std::vector&lt; std::size_t &gt; &amp;dimensions)</div><div class="ttdoc">Sets the dimensions of the data.</div><div class="ttdef"><b>Definition</b> <a href="_metadata_8cpp_source.html#l00109">Metadata.cpp:109</a></div></div>
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+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+<script type="text/javascript">
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+/* @license-end */
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 <div class="header">
-  <div class="headertitle">
-<div class="title">Class List</div>  </div>
+  <div class="headertitle"><div class="title">Class List</div></div>
 </div><!--header-->
 <div class="contents">
 <div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
-<table class="directory">
-<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classBilinearIntegratorWrapper.html" target="_self">BilinearIntegratorWrapper</a></td><td class="desc">A wrapper class for bilinear integrator </td></tr>
-<tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classCompositeNonlinearIntegrator.html" target="_self">CompositeNonlinearIntegrator</a></td><td class="desc">A class for composite nonlinear integrator </td></tr>
-<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classConfig.html" target="_self">Config</a></td><td class="desc">Singleton class to manage configuration settings loaded from a YAML file </td></tr>
-<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classconfigTest.html" target="_self">configTest</a></td><td class="desc">Test suite for the <a class="el" href="classConfig.html" title="Singleton class to manage configuration settings loaded from a YAML file.">Config</a> class </td></tr>
-<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classconfigTestPrivateAccessor.html" target="_self">configTestPrivateAccessor</a></td><td class="desc"></td></tr>
-<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structConstant.html" target="_self">Constant</a></td><td class="desc">Structure to hold a constant's details </td></tr>
-<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classConstants.html" target="_self">Constants</a></td><td class="desc">Class to manage a collection of constants </td></tr>
-<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classconstTest.html" target="_self">constTest</a></td><td class="desc">Test suite for the const class </td></tr>
-<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classDObject.html" target="_self">DObject</a></td><td class="desc">A universal data container class </td></tr>
-<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classDObjectTest.html" target="_self">DObjectTest</a></td><td class="desc">Test suite for the <a class="el" href="classDObject.html" title="A universal data container class.">DObject</a> class </td></tr>
-<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structHeader.html" target="_self">Header</a></td><td class="desc">Structure to hold the header information of an OPAT file </td></tr>
-<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classLockableDObject.html" target="_self">LockableDObject</a></td><td class="desc">Wrapper for <a class="el" href="classDObject.html" title="A universal data container class.">DObject</a> with thread-safe access </td></tr>
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--- a/docs/html/annotated_dup.js
+++ b/docs/html/annotated_dup.js
@@ -1,25 +1,68 @@
 var annotated_dup =
 [
-    [ "BilinearIntegratorWrapper", "classBilinearIntegratorWrapper.html", "classBilinearIntegratorWrapper" ],
-    [ "CompositeNonlinearIntegrator", "classCompositeNonlinearIntegrator.html", "classCompositeNonlinearIntegrator" ],
-    [ "Config", "classConfig.html", null ],
-    [ "configTest", "classconfigTest.html", null ],
-    [ "configTestPrivateAccessor", "classconfigTestPrivateAccessor.html", null ],
-    [ "Constant", "structConstant.html", "structConstant" ],
-    [ "Constants", "classConstants.html", "classConstants" ],
-    [ "constTest", "classconstTest.html", "classconstTest" ],
-    [ "DObject", "classDObject.html", "classDObject" ],
-    [ "DObjectTest", "classDObjectTest.html", "classDObjectTest" ],
-    [ "Header", "structHeader.html", "structHeader" ],
-    [ "LockableDObject", "classLockableDObject.html", "classLockableDObject" ],
-    [ "LockableDObjectTest", "classLockableDObjectTest.html", "classLockableDObjectTest" ],
-    [ "MeshIO", "classMeshIO.html", "classMeshIO" ],
-    [ "meshIOTest", "classmeshIOTest.html", null ],
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-    [ "MetadataTest", "classMetadataTest.html", "classMetadataTest" ],
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-    [ "OpatIO", "classOpatIO.html", "classOpatIO" ],
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-    [ "OPATTable", "structOPATTable.html", "structOPATTable" ],
-    [ "TableIndex", "structTableIndex.html", "structTableIndex" ]
+    [ "serif", "namespaceserif.html", [
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+        [ "Composition", "classserif_1_1composition_1_1_composition.html", "classserif_1_1composition_1_1_composition" ],
+        [ "CompositionEntry", "structserif_1_1composition_1_1_composition_entry.html", "structserif_1_1composition_1_1_composition_entry" ],
+        [ "GlobalComposition", "structserif_1_1composition_1_1_global_composition.html", "structserif_1_1composition_1_1_global_composition" ]
+      ] ],
+      [ "constant", "namespaceserif_1_1constant.html", [
+        [ "Constant", "structserif_1_1constant_1_1_constant.html", "structserif_1_1constant_1_1_constant" ],
+        [ "Constants", "classserif_1_1constant_1_1_constants.html", "classserif_1_1constant_1_1_constants" ]
+      ] ],
+      [ "eos", "namespaceserif_1_1eos.html", [
+        [ "helmholtz", "namespaceserif_1_1eos_1_1helmholtz.html", [
+          [ "EOS", "structserif_1_1eos_1_1helmholtz_1_1_e_o_s.html", "structserif_1_1eos_1_1helmholtz_1_1_e_o_s" ],
+          [ "EOSInput", "structserif_1_1eos_1_1helmholtz_1_1_e_o_s_input.html", "structserif_1_1eos_1_1helmholtz_1_1_e_o_s_input" ],
+          [ "HELMTable", "structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html", "structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table" ]
+        ] ],
+        [ "EosIO", "classserif_1_1eos_1_1_eos_i_o.html", "classserif_1_1eos_1_1_eos_i_o" ]
+      ] ],
+      [ "mesh", "namespaceserif_1_1mesh.html", [
+        [ "MeshIO", "classserif_1_1mesh_1_1_mesh_i_o.html", "classserif_1_1mesh_1_1_mesh_i_o" ]
+      ] ],
+      [ "network", "namespaceserif_1_1network.html", [
+        [ "approx8", "namespaceserif_1_1network_1_1approx8.html", [
+          [ "Approx8Network", "classserif_1_1network_1_1approx8_1_1_approx8_network.html", "classserif_1_1network_1_1approx8_1_1_approx8_network" ],
+          [ "Jacobian", "structserif_1_1network_1_1approx8_1_1_jacobian.html", "structserif_1_1network_1_1approx8_1_1_jacobian" ],
+          [ "Net", "structserif_1_1network_1_1approx8_1_1_net.html", "structserif_1_1network_1_1approx8_1_1_net" ],
+          [ "ODE", "structserif_1_1network_1_1approx8_1_1_o_d_e.html", "structserif_1_1network_1_1approx8_1_1_o_d_e" ]
+        ] ],
+        [ "NetIn", "structserif_1_1network_1_1_net_in.html", "structserif_1_1network_1_1_net_in" ],
+        [ "NetOut", "structserif_1_1network_1_1_net_out.html", "structserif_1_1network_1_1_net_out" ],
+        [ "Network", "classserif_1_1network_1_1_network.html", "classserif_1_1network_1_1_network" ]
+      ] ],
+      [ "polytrope", "namespaceserif_1_1polytrope.html", [
+        [ "polycoeff", "namespaceserif_1_1polytrope_1_1polycoeff.html", [
+          [ "dThetaInterpCoeff", "structserif_1_1polytrope_1_1polycoeff_1_1d_theta_interp_coeff.html", "structserif_1_1polytrope_1_1polycoeff_1_1d_theta_interp_coeff" ],
+          [ "x1InterpCoeff", "structserif_1_1polytrope_1_1polycoeff_1_1x1_interp_coeff.html", "structserif_1_1polytrope_1_1polycoeff_1_1x1_interp_coeff" ]
+        ] ],
+        [ "polyMFEMUtils", "namespaceserif_1_1polytrope_1_1poly_m_f_e_m_utils.html", [
+          [ "NonlinearPowerIntegrator", "classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html", "classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator" ]
+        ] ],
+        [ "formBundle", "structserif_1_1polytrope_1_1form_bundle.html", "structserif_1_1polytrope_1_1form_bundle" ],
+        [ "GMRESInverter", "classserif_1_1polytrope_1_1_g_m_r_e_s_inverter.html", "classserif_1_1polytrope_1_1_g_m_r_e_s_inverter" ],
+        [ "PolySolver", "classserif_1_1polytrope_1_1_poly_solver.html", "classserif_1_1polytrope_1_1_poly_solver" ],
+        [ "PolytropeOperator", "classserif_1_1polytrope_1_1_polytrope_operator.html", "classserif_1_1polytrope_1_1_polytrope_operator" ],
+        [ "SchurCompliment", "classserif_1_1polytrope_1_1_schur_compliment.html", "classserif_1_1polytrope_1_1_schur_compliment" ],
+        [ "solverBundle", "structserif_1_1polytrope_1_1solver_bundle.html", "structserif_1_1polytrope_1_1solver_bundle" ]
+      ] ],
+      [ "probe", "namespaceserif_1_1probe.html", [
+        [ "LogManager", "classserif_1_1probe_1_1_log_manager.html", "classserif_1_1probe_1_1_log_manager" ]
+      ] ],
+      [ "resource", "namespaceserif_1_1resource.html", [
+        [ "ResourceManager", "classserif_1_1resource_1_1_resource_manager.html", "classserif_1_1resource_1_1_resource_manager" ]
+      ] ]
+    ] ],
+    [ "approx8Test", "classapprox8_test.html", null ],
+    [ "compositionTest", "classcomposition_test.html", null ],
+    [ "configTest", "classconfig_test.html", null ],
+    [ "configTestPrivateAccessor", "classconfig_test_private_accessor.html", "classconfig_test_private_accessor" ],
+    [ "constTest", "classconst_test.html", "classconst_test" ],
+    [ "eosTest", "classeos_test.html", null ],
+    [ "meshIOTest", "classmesh_i_o_test.html", null ],
+    [ "polyTest", "classpoly_test.html", null ],
+    [ "probeTest", "classprobe_test.html", null ],
+    [ "ResourceManager", "class_resource_manager.html", null ],
+    [ "resourceManagerTest", "classresource_manager_test.html", null ]
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@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: Member List</title>
+<title>SERiF: Member List</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
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-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
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-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
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-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
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+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -108,20 +105,26 @@ $(function(){initNavTree('class_d_object.html',''); initResizable(true); });

 <p>This is the complete list of members for <a class="el" href="class_d_object.html">DObject</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#ad6fc2e29eae70cf94a2d241527857573">DataType</a> typedef</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>()</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#ab0c940fa193a42158c6726bf1a2ef54d">DObject</a>(const DataType &amp;data, const Metadata &amp;metadata)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#ad7ba02f6d87ce64792149096f3310b21">data_</a></td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> typedef</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a358d5f015da09ae5f0cbb46f3fd9e401">dataTypeMap</a></td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#accf5c10d4afc3969607e11b0055312d5">debugEnabled_</a></td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>()</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a598321f3b8524b98df72393c04d7470c">DObject</a>(const DataType &amp;data)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#ad8de5890e8dae5fc7e72fabca2520fc3">errorCode_</a></td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a4862655c3634d019b0a45b811d6f7235">getData</a>() const noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a157b31e881aac6dd40782d3abc561d4e">getMetadata</a>() const noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">isDebuggingEnabled</a>() const noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#aa54e75574f0302a2ca7252f9f0f0b3f1">operator&lt;&lt;</a>(std::ostream &amp;os, const DObject &amp;obj)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> typedef</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#aca2db093c1c8c6f7893de07544aed619">getDataAs</a>() const</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#afa8926d916081de72478cb8813c25e98">getErrorCode</a>() const noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#ae47bf220fbe2173cf6933c2380035dbd">isDebuggingEnabled</a>() const noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#aa54e75574f0302a2ca7252f9f0f0b3f1">operator&lt;&lt;</a>(std::ostream &amp;os, const DObject &amp;obj)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> typedef</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#ae9f7e4d2fbabc076961a40185676e208">plugins_</a></td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a15afffdf339150fc872bf63bdd08d581">registerPlugin</a>(const std::string &amp;id, Plugin plugin)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a1223275dcbbf20334ea11707346acb93">runAllPlugins</a>()</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a99072eb52bb22745f0248f273fbf28fb">runPlugin</a>(const std::string &amp;id)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#ab1718571434e84e90f1ec463e4786a8a">setData</a>(const DataType &amp;data)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a6f0023aee463e71d92442dcf61b6ed47">setDebugging</a>(bool enableDebug)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a296b1519249fdc1f6c7b4ab62d5421bc">setMetadata</a>(const Metadata &amp;metadata)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_d_object.html#a3dce47a519f9da5085c0c5ac1eea4f38">setErrorCode</a>(int code) noexcept</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_d_object.html#a99b8688849e11501033a25f61efb8356">unregisterPlugin</a>(const std::string &amp;id)</td><td class="entry"><a class="el" href="class_d_object.html">DObject</a></td><td class="entry"></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
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 <meta http-equiv="X-UA-Compatible" content="IE=11"/>
 <meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: DObject Class Reference</title>
+<title>SERiF: DObject Class Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
@@ -18,12 +18,9 @@
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
-  $(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
@@ -32,20 +29,9 @@
 <tbody>
 <tr id="projectrow">
  <td id="projectalign">
-   <div id="projectname">New 4DSSE Code<span id="projectnumber">&#160;0.0.1a</span>
-   </div>
-  </td>
-    <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <span id="MSearchSelect"                onmouseover="return searchBox.OnSearchSelectShow()"                onmouseout="return searchBox.OnSearchSelectHide()">&#160;</span>
-          <input type="text" id="MSearchField" value="" placeholder="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
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-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
@@ -63,6 +49,17 @@ var searchBox = new SearchBox("searchBox", "search/",'.html');
 $(function() { codefold.init(0); });
 /* @license-end */
 </script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
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@@ -105,6 +102,8 @@ $(function(){initNavTree('class_d_object.html',''); initResizable(true); });
  <div class="summary">
 <a href="#pub-types">Public Types</a> &#124;
 <a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-attribs">Public Attributes</a> &#124;
+<a href="#pri-attribs">Private Attributes</a> &#124;
 <a href="#friends">Friends</a> &#124;
 <a href="class_d_object-members.html">List of all members</a>  </div>
  <div class="headertitle"><div class="title">DObject Class Reference</div></div>
@@ -118,9 +117,9 @@ $(function(){initNavTree('class_d_object.html',''); initResizable(true); });
 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-types" name="pub-types"></a>
 Public Types</h2></td></tr>
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-<tr class="separator:ad6fc2e29eae70cf94a2d241527857573"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memdesc:a55b7cdac36a3a518ba6e1ecef0e25dcd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Supported data types for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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@@ -130,27 +129,30 @@ Public Member Functions</h2></td></tr>
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+<tr class="memdesc:a598321f3b8524b98df72393c04d7470c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor to initialize a <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> with data.  <br /></td></tr>
+<tr class="separator:a598321f3b8524b98df72393c04d7470c"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memitem:aca2db093c1c8c6f7893de07544aed619" id="r_aca2db093c1c8c6f7893de07544aed619"><td class="memTemplParams" colspan="2">template&lt;typename T&gt; </td></tr>
+<tr class="memitem:aca2db093c1c8c6f7893de07544aed619"><td class="memTemplItemLeft" align="right" valign="top">T&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="#aca2db093c1c8c6f7893de07544aed619">getDataAs</a> () const</td></tr>
+<tr class="memdesc:aca2db093c1c8c6f7893de07544aed619"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieves the data stored in the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> as a typed object so that std::get&lt;T&gt;() is not needed.  <br /></td></tr>
+<tr class="separator:aca2db093c1c8c6f7893de07544aed619"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab1718571434e84e90f1ec463e4786a8a" id="r_ab1718571434e84e90f1ec463e4786a8a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab1718571434e84e90f1ec463e4786a8a">setData</a> (const <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> &amp;data)</td></tr>
 <tr class="memdesc:ab1718571434e84e90f1ec463e4786a8a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the data for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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-<tr class="memdesc:a157b31e881aac6dd40782d3abc561d4e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieves the metadata associated with the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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-<tr class="memdesc:a296b1519249fdc1f6c7b4ab62d5421bc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Updates the metadata for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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 <tr class="memdesc:a6f0023aee463e71d92442dcf61b6ed47"><td class="mdescLeft">&#160;</td><td class="mdescRight">Enables or disables debugging and tracing for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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 <tr class="separator:ae47bf220fbe2173cf6933c2380035dbd"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3dce47a519f9da5085c0c5ac1eea4f38" id="r_a3dce47a519f9da5085c0c5ac1eea4f38"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3dce47a519f9da5085c0c5ac1eea4f38">setErrorCode</a> (int code) noexcept</td></tr>
+<tr class="separator:a3dce47a519f9da5085c0c5ac1eea4f38"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afa8926d916081de72478cb8813c25e98" id="r_afa8926d916081de72478cb8813c25e98"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afa8926d916081de72478cb8813c25e98">getErrorCode</a> () const noexcept</td></tr>
+<tr class="memdesc:afa8926d916081de72478cb8813c25e98"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the error code tracked by the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
+<tr class="separator:afa8926d916081de72478cb8813c25e98"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a15afffdf339150fc872bf63bdd08d581" id="r_a15afffdf339150fc872bf63bdd08d581"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a15afffdf339150fc872bf63bdd08d581">registerPlugin</a> (const std::string &amp;id, <a class="el" href="#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> plugin)</td></tr>
 <tr class="memdesc:a15afffdf339150fc872bf63bdd08d581"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a plugin with the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
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@@ -164,6 +166,26 @@ Public Member Functions</h2></td></tr>
 <tr class="memdesc:a1223275dcbbf20334ea11707346acb93"><td class="mdescLeft">&#160;</td><td class="mdescRight">Executes all registered plugins in the registry.  <br /></td></tr>
 <tr class="separator:a1223275dcbbf20334ea11707346acb93"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-attribs" name="pub-attribs"></a>
+Public Attributes</h2></td></tr>
+<tr class="memitem:a358d5f015da09ae5f0cbb46f3fd9e401" id="r_a358d5f015da09ae5f0cbb46f3fd9e401"><td class="memItemLeft" align="right" valign="top">std::map&lt; int, std::string &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a358d5f015da09ae5f0cbb46f3fd9e401">dataTypeMap</a></td></tr>
+<tr class="separator:a358d5f015da09ae5f0cbb46f3fd9e401"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
+Private Attributes</h2></td></tr>
+<tr class="memitem:ad7ba02f6d87ce64792149096f3310b21" id="r_ad7ba02f6d87ce64792149096f3310b21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad7ba02f6d87ce64792149096f3310b21">data_</a></td></tr>
+<tr class="memdesc:ad7ba02f6d87ce64792149096f3310b21"><td class="mdescLeft">&#160;</td><td class="mdescRight">The main data stored in the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
+<tr class="separator:ad7ba02f6d87ce64792149096f3310b21"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:accf5c10d4afc3969607e11b0055312d5" id="r_accf5c10d4afc3969607e11b0055312d5"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#accf5c10d4afc3969607e11b0055312d5">debugEnabled_</a> = false</td></tr>
+<tr class="memdesc:accf5c10d4afc3969607e11b0055312d5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Indicates whether debugging is enabled.  <br /></td></tr>
+<tr class="separator:accf5c10d4afc3969607e11b0055312d5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad8de5890e8dae5fc7e72fabca2520fc3" id="r_ad8de5890e8dae5fc7e72fabca2520fc3"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad8de5890e8dae5fc7e72fabca2520fc3">errorCode_</a> = 0</td></tr>
+<tr class="memdesc:ad8de5890e8dae5fc7e72fabca2520fc3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Error code tracked by the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>.  <br /></td></tr>
+<tr class="separator:ad8de5890e8dae5fc7e72fabca2520fc3"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ae9f7e4d2fbabc076961a40185676e208" id="r_ae9f7e4d2fbabc076961a40185676e208"><td class="memItemLeft" align="right" valign="top">std::map&lt; std::string, <a class="el" href="#af11334d08ef85c68b3aae7554548e5a7">Plugin</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae9f7e4d2fbabc076961a40185676e208">plugins_</a></td></tr>
+<tr class="memdesc:ae9f7e4d2fbabc076961a40185676e208"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registry for dynamically registered plugins.  <br /></td></tr>
+<tr class="separator:ae9f7e4d2fbabc076961a40185676e208"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="friends" name="friends"></a>
 Friends</h2></td></tr>
 <tr class="memitem:aa54e75574f0302a2ca7252f9f0f0b3f1" id="r_aa54e75574f0302a2ca7252f9f0f0b3f1"><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa54e75574f0302a2ca7252f9f0f0b3f1">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="class_d_object.html">DObject</a> &amp;obj)</td></tr>
@@ -173,26 +195,66 @@ Friends</h2></td></tr>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>A universal data container class. </p>
 <p>The <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> class is designed to store arbitrary data alongside descriptive metadata. It supports plugin registration to allow extensible functionality.</p>
+<p>The general purpose of this is to simplify memory managment, function interfaces, and interoperability with other languages by wrapping all of that up inside of one location (<a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>). There are still a limited number of types that DOBject can represent these include</p><ul>
+<li>bool</li>
+<li>short int</li>
+<li>int</li>
+<li>long int</li>
+<li>float</li>
+<li>double</li>
+<li>long double</li>
+<li>std::string</li>
+<li>std::monostate</li>
+<li>std::vector&lt;int&gt;</li>
+<li>std::vector&lt;float&gt;</li>
+<li>std::vector&lt;double&gt;</li>
+<li>std::vector&lt;std::string&gt;</li>
+<li>std::vector&lt;std::vector&lt;int&gt;&gt;</li>
+<li>std::vector&lt;std::vector&lt;float&gt;&gt;</li>
+<li>std::vector&lt;std::vector&lt;double&gt;&gt;</li>
+<li>std::vector&lt;std::vector&lt;std::vector&lt;int&gt;&gt;&gt;</li>
+<li>std::vector&lt;std::vector&lt;std::vector&lt;float&gt;&gt;&gt;</li>
+<li>std::vector&lt;std::vector&lt;std::vector&lt;double&gt;&gt;</li>
+</ul>
+<p>If more types are needed, they can be added to the <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd" title="Supported data types for the DObject.">DataType</a> variant.</p>
+<p>In general the usage of this might look like </p><div class="fragment"><div class="line"><a class="code hl_function" href="#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a> obj;</div>
+<div class="line">std::vector&lt;int&gt; data = {1, 2, 3, 4, 5};</div>
+<div class="line">obj.<a class="code hl_function" href="#ab1718571434e84e90f1ec463e4786a8a">setData</a>(data);</div>
+<div class="line">std::cout &lt;&lt; <span class="stringliteral">&quot;Data is &quot;</span> &lt;&lt; obj &lt;&lt; std::end;</div>
+<div class="line">someFunction(&amp;obj);</div>
+<div class="ttc" id="aclass_d_object_html_a0ae54853e18265657296bfb5ac3bf9d0"><div class="ttname"><a href="#a0ae54853e18265657296bfb5ac3bf9d0">DObject::DObject</a></div><div class="ttdeci">DObject()</div><div class="ttdoc">Default constructor.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00033">DObject.cpp:33</a></div></div>
+<div class="ttc" id="aclass_d_object_html_ab1718571434e84e90f1ec463e4786a8a"><div class="ttname"><a href="#ab1718571434e84e90f1ec463e4786a8a">DObject::setData</a></div><div class="ttdeci">void setData(const DataType &amp;data)</div><div class="ttdoc">Sets the data for the DObject.</div><div class="ttdef"><b>Definition</b> <a href="_d_object_8cpp_source.html#l00053">DObject.cpp:53</a></div></div>
+</div><!-- fragment --><p>All memory managment should be taken care of as all datatypes accepted by the varient are either primatives or include their own built in memory managment (i.e. this means that wherever possible vectors should be used in place of raw arrays). </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00089">89</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
 </div><h2 class="groupheader">Member Typedef Documentation</h2>
-<a id="ad6fc2e29eae70cf94a2d241527857573" name="ad6fc2e29eae70cf94a2d241527857573"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ad6fc2e29eae70cf94a2d241527857573">&#9670;&#160;</a></span>DataType</h2>
+<a id="a55b7cdac36a3a518ba6e1ecef0e25dcd" name="a55b7cdac36a3a518ba6e1ecef0e25dcd"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">&#9670;&#160;</a></span>DataType</h2>

 <div class="memitem">
 <div class="memproto">
      <table class="memname">
        <tr>
-          <td class="memname">using <a class="el" href="#ad6fc2e29eae70cf94a2d241527857573">DObject::DataType</a></td>
+          <td class="memname">using <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DObject::DataType</a></td>
        </tr>
      </table>
 </div><div class="memdoc">
 <b>Initial value:</b><div class="fragment"><div class="line"> std::variant&lt;</div>
-<div class="line">        int, float, double, std::string, std::monostate,</div>
-<div class="line">        std::vector&lt;int&gt;, std::vector&lt;float&gt;, std::vector&lt;double&gt;</div>
+<div class="line">        bool, <span class="keywordtype">short</span> int, int, <span class="keywordtype">long</span> int, float, double, </div>
+<div class="line">        <span class="keywordtype">long</span> double, std::string, std::monostate, std::vector&lt;int&gt;,</div>
+<div class="line">        std::vector&lt;float&gt;, std::vector&lt;double&gt;, std::vector&lt;std::string&gt;,</div>
+<div class="line">        std::vector&lt;std::vector&lt;int&gt;&gt;, std::vector&lt;std::vector&lt;float&gt;&gt;,</div>
+<div class="line">        std::vector&lt;std::vector&lt;double&gt;&gt;,</div>
+<div class="line">        std::vector&lt;std::vector&lt;std::vector&lt;int&gt;&gt;&gt;,</div>
+<div class="line">        std::vector&lt;std::vector&lt;std::vector&lt;float&gt;&gt;&gt;,</div>
+<div class="line">        std::vector&lt;std::vector&lt;std::vector&lt;double&gt;&gt;&gt;</div>
 <div class="line">    &gt;</div>
 </div><!-- fragment -->
 <p>Supported data types for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
 <p>This type alias uses <code>std::variant</code> to store different types of data, ensuring type safety and flexibility. </p>

+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00097">97</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
 </div>
 </div>
 <a id="af11334d08ef85c68b3aae7554548e5a7" name="af11334d08ef85c68b3aae7554548e5a7"></a>
@@ -210,6 +272,8 @@ Friends</h2></td></tr>
 <p>Placeholder type for plugins. </p>
 <p>In the future, this will be replaced with a concrete interface. </p>

+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00125">125</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
 </div>
 </div>
 <h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
@@ -229,12 +293,14 @@ Friends</h2></td></tr>
 </div><div class="memdoc">

 <p>Default constructor. </p>
-<p>Creates an empty <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> with default metadata. </p>
+<p>Creates an empty <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00033">33</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>

 </div>
 </div>
-<a id="ab0c940fa193a42158c6726bf1a2ef54d" name="ab0c940fa193a42158c6726bf1a2ef54d"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ab0c940fa193a42158c6726bf1a2ef54d">&#9670;&#160;</a></span>DObject() <span class="overload">[2/2]</span></h2>
+<a id="a598321f3b8524b98df72393c04d7470c" name="a598321f3b8524b98df72393c04d7470c"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a598321f3b8524b98df72393c04d7470c">&#9670;&#160;</a></span>DObject() <span class="overload">[2/2]</span></h2>

 <div class="memitem">
 <div class="memproto">
@@ -242,25 +308,22 @@ Friends</h2></td></tr>
        <tr>
          <td class="memname">DObject::DObject </td>
          <td>(</td>
-          <td class="paramtype">const <a class="el" href="#ad6fc2e29eae70cf94a2d241527857573">DataType</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>data</em></span>, </td>
-        </tr>
-        <tr>
-          <td class="paramkey"></td>
+          <td class="paramtype">const <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>data</em></span></td><td>)</td>
          <td></td>
-          <td class="paramtype">const <a class="el" href="class_metadata.html">Metadata</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>metadata</em></span>&#160;)</td>
        </tr>
      </table>
 </div><div class="memdoc">

-<p>Constructor to initialize a <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> with data and metadata. </p>
+<p>Constructor to initialize a <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> with data. </p>
 <dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">data</td><td>The data to be stored in the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </td></tr>
-    <tr><td class="paramname">metadata</td><td><a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a> describing the stored data. </td></tr>
  </table>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00040">40</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <h2 class="groupheader">Member Function Documentation</h2>
@@ -274,7 +337,7 @@ Friends</h2></td></tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
-          <td class="memname">const <a class="el" href="#ad6fc2e29eae70cf94a2d241527857573">DObject::DataType</a> &amp; DObject::getData </td>
+          <td class="memname">const <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DObject::DataType</a> &amp; DObject::getData </td>
          <td>(</td>
          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
          <td> const</td>
@@ -291,10 +354,44 @@ Friends</h2></td></tr>
 <p>Use the appropriate type (matching the stored data) with <code>std::get&lt;T&gt;()</code>.</p>
 <dl class="section return"><dt>Returns</dt><dd>A constant reference to the stored data. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00046">46</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
-<a id="a157b31e881aac6dd40782d3abc561d4e" name="a157b31e881aac6dd40782d3abc561d4e"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a157b31e881aac6dd40782d3abc561d4e">&#9670;&#160;</a></span>getMetadata()</h2>
+<a id="aca2db093c1c8c6f7893de07544aed619" name="aca2db093c1c8c6f7893de07544aed619"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aca2db093c1c8c6f7893de07544aed619">&#9670;&#160;</a></span>getDataAs()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;typename T&gt; </div>
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">T DObject::getDataAs </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel inline">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Retrieves the data stored in the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> as a typed object so that std::get&lt;T&gt;() is not needed. </p>
+<dl class="section return"><dt>Returns</dt><dd>Data as type T </dd></dl>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00156">156</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
+</div>
+</div>
+<a id="afa8926d916081de72478cb8813c25e98" name="afa8926d916081de72478cb8813c25e98"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#afa8926d916081de72478cb8813c25e98">&#9670;&#160;</a></span>getErrorCode()</h2>

 <div class="memitem">
 <div class="memproto">
@@ -303,7 +400,7 @@ Friends</h2></td></tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
-          <td class="memname">const <a class="el" href="class_metadata.html">Metadata</a> &amp; DObject::getMetadata </td>
+          <td class="memname">int DObject::getErrorCode </td>
          <td>(</td>
          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
          <td> const</td>
@@ -316,9 +413,10 @@ Friends</h2></td></tr>
 </table>
 </div><div class="memdoc">

-<p>Retrieves the metadata associated with the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
-<p>The metadata provides essential information about the stored data, such as its type, size, and dimensions.</p>
-<dl class="section return"><dt>Returns</dt><dd>A constant reference to the metadata. </dd></dl>
+<p>Get the error code tracked by the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
+<dl class="section return"><dt>Returns</dt><dd>The error code </dd></dl>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00080">80</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>

 </div>
 </div>
@@ -340,7 +438,7 @@ Friends</h2></td></tr>
      </table>
  </td>
  <td class="mlabels-right">
-<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel noexcept">noexcept</span></span>  </td>
+<span class="mlabels"><span class="mlabel noexcept">noexcept</span></span>  </td>
  </tr>
 </table>
 </div><div class="memdoc">
@@ -348,6 +446,8 @@ Friends</h2></td></tr>
 <p>Checks if debugging is enabled for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
 <dl class="section return"><dt>Returns</dt><dd>True if debugging is enabled, false otherwise. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00067">67</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a15afffdf339150fc872bf63bdd08d581" name="a15afffdf339150fc872bf63bdd08d581"></a>
@@ -379,6 +479,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00087">87</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a1223275dcbbf20334ea11707346acb93" name="a1223275dcbbf20334ea11707346acb93"></a>
@@ -399,6 +501,8 @@ Friends</h2></td></tr>
 <p>Executes all registered plugins in the registry. </p>
 <p>Iterates through all plugins and invokes them on the current <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00117">117</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a99072eb52bb22745f0248f273fbf28fb" name="a99072eb52bb22745f0248f273fbf28fb"></a>
@@ -425,6 +529,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00106">106</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <a id="ab1718571434e84e90f1ec463e4786a8a" name="ab1718571434e84e90f1ec463e4786a8a"></a>
@@ -436,7 +542,7 @@ Friends</h2></td></tr>
        <tr>
          <td class="memname">void DObject::setData </td>
          <td>(</td>
-          <td class="paramtype">const <a class="el" href="#ad6fc2e29eae70cf94a2d241527857573">DataType</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>data</em></span></td><td>)</td>
+          <td class="paramtype">const <a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>data</em></span></td><td>)</td>
          <td></td>
        </tr>
      </table>
@@ -451,6 +557,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00053">53</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a6f0023aee463e71d92442dcf61b6ed47" name="a6f0023aee463e71d92442dcf61b6ed47"></a>
@@ -477,31 +585,37 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00060">60</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
-<a id="a296b1519249fdc1f6c7b4ab62d5421bc" name="a296b1519249fdc1f6c7b4ab62d5421bc"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a296b1519249fdc1f6c7b4ab62d5421bc">&#9670;&#160;</a></span>setMetadata()</h2>
+<a id="a3dce47a519f9da5085c0c5ac1eea4f38" name="a3dce47a519f9da5085c0c5ac1eea4f38"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a3dce47a519f9da5085c0c5ac1eea4f38">&#9670;&#160;</a></span>setErrorCode()</h2>

 <div class="memitem">
 <div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
      <table class="memname">
        <tr>
-          <td class="memname">void DObject::setMetadata </td>
+          <td class="memname">int DObject::setErrorCode </td>
          <td>(</td>
-          <td class="paramtype">const <a class="el" href="class_metadata.html">Metadata</a> &amp;</td>          <td class="paramname"><span class="paramname"><em>metadata</em></span></td><td>)</td>
+          <td class="paramtype">int</td>          <td class="paramname"><span class="paramname"><em>code</em></span></td><td>)</td>
          <td></td>
        </tr>
      </table>
-</div><div class="memdoc">
-
-<p>Updates the metadata for the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
-<p>Use this function carefully to ensure consistency between the data and metadata.</p>
-<dl class="params"><dt>Parameters</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">metadata</td><td>The new metadata to associate with the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </td></tr>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel noexcept">noexcept</span></span>  </td>
+  </tr>
 </table>
-  </dd>
-</dl>
+</div><div class="memdoc">
+<p>@breif Set error code tracked by the DOBject</p>
+<dl class="section return"><dt>Returns</dt><dd>The previous error code</dd></dl>
+<p>@breif Sets an error code and returns the old one </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00074">74</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>

 </div>
 </div>
@@ -529,6 +643,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00097">97</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
 </div>
 </div>
 <h2 class="groupheader">Friends And Related Symbol Documentation</h2>
@@ -570,11 +686,143 @@ Friends</h2></td></tr>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>A reference to the output stream. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_d_object_8cpp_source.html#l00126">126</a> of file <a class="el" href="_d_object_8cpp_source.html">DObject.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="ad7ba02f6d87ce64792149096f3310b21" name="ad7ba02f6d87ce64792149096f3310b21"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad7ba02f6d87ce64792149096f3310b21">&#9670;&#160;</a></span>data_</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="#a55b7cdac36a3a518ba6e1ecef0e25dcd">DataType</a> DObject::data_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>The main data stored in the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00251">251</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
+</div>
+</div>
+<a id="a358d5f015da09ae5f0cbb46f3fd9e401" name="a358d5f015da09ae5f0cbb46f3fd9e401"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a358d5f015da09ae5f0cbb46f3fd9e401">&#9670;&#160;</a></span>dataTypeMap</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::map&lt;int, std::string&gt; DObject::dataTypeMap</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line">= {</div>
+<div class="line">        {0, <span class="stringliteral">&quot;bool&quot;</span>}, {1, <span class="stringliteral">&quot;short int&quot;</span>}, {2, <span class="stringliteral">&quot;int&quot;</span>}, {3, <span class="stringliteral">&quot;long int&quot;</span>}, {4, <span class="stringliteral">&quot;float&quot;</span>},</div>
+<div class="line">        {5, <span class="stringliteral">&quot;double&quot;</span>}, {6, <span class="stringliteral">&quot;long double&quot;</span>}, {7, <span class="stringliteral">&quot;string&quot;</span>}, {8, <span class="stringliteral">&quot;std::monostate&quot;</span>},</div>
+<div class="line">        {9, <span class="stringliteral">&quot;vector&lt;int&gt;&quot;</span>}, {10, <span class="stringliteral">&quot;vector&lt;float&gt;&quot;</span>}, {11, <span class="stringliteral">&quot;vector&lt;double&gt;&quot;</span>},</div>
+<div class="line">        {12, <span class="stringliteral">&quot;vector&lt;string&gt;&quot;</span>}, {13, <span class="stringliteral">&quot;vector&lt;vector&lt;int&gt;&quot;</span>},</div>
+<div class="line">        {14, <span class="stringliteral">&quot;vector&lt;vector&lt;float&gt;&quot;</span>}, {15, <span class="stringliteral">&quot;vector&lt;vector&lt;double&gt;&quot;</span>},</div>
+<div class="line">        {16, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;int&gt;&gt;&quot;</span>}, {17, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;float&gt;&gt;&quot;</span>},</div>
+<div class="line">        {18, <span class="stringliteral">&quot;vector&lt;vector&lt;vector&lt;double&gt;&gt;&quot;</span>}</div>
+<div class="line">    }</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00109">109</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
+</div>
+</div>
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+<h2 class="memtitle"><span class="permalink"><a href="#accf5c10d4afc3969607e11b0055312d5">&#9670;&#160;</a></span>debugEnabled_</h2>
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+      <table class="memname">
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+          <td class="memname">bool DObject::debugEnabled_ = false</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Indicates whether debugging is enabled. </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00252">252</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
+</div>
+</div>
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+<h2 class="memtitle"><span class="permalink"><a href="#ad8de5890e8dae5fc7e72fabca2520fc3">&#9670;&#160;</a></span>errorCode_</h2>
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+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">int DObject::errorCode_ = 0</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Error code tracked by the <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00253">253</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
+</div>
+</div>
+<a id="ae9f7e4d2fbabc076961a40185676e208" name="ae9f7e4d2fbabc076961a40185676e208"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae9f7e4d2fbabc076961a40185676e208">&#9670;&#160;</a></span>plugins_</h2>
+
+<div class="memitem">
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+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::map&lt;std::string, <a class="el" href="#af11334d08ef85c68b3aae7554548e5a7">Plugin</a>&gt; DObject::plugins_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Registry for dynamically registered plugins. </p>
+
+<p class="definition">Definition at line <a class="el" href="_d_object_8h_source.html#l00254">254</a> of file <a class="el" href="_d_object_8h_source.html">DObject.h</a>.</p>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
 <li>src/dobj/public/<a class="el" href="_d_object_8h_source.html">DObject.h</a></li>
-<li>src/dobj/private/<a class="el" href="_d_object_8cpp.html">DObject.cpp</a></li>
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+<tr class="memdesc:a712cd3ea0c565f7e9089a651ef79b7bd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mutex for thread-safe access.  <br /></td></tr>
+<tr class="separator:a712cd3ea0c565f7e9089a651ef79b7bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Wrapper for <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> with thread-safe access. </p>
-</div><h2 class="groupheader">Member Function Documentation</h2>
+
+<p class="definition">Definition at line <a class="el" href="_lockable_d_object_8h_source.html#l00039">39</a> of file <a class="el" href="_lockable_d_object_8h_source.html">LockableDObject.h</a>.</p>
+</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="ae1a174a2740fa053626fe2820ee0efee" name="ae1a174a2740fa053626fe2820ee0efee"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae1a174a2740fa053626fe2820ee0efee">&#9670;&#160;</a></span>LockableDObject()</h2>
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+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">LockableDObject::LockableDObject </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel default">default</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Default constructor. </p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Function Documentation</h2>
 <a id="adcfe201fc728cc1c6fcf638a566ba9a1" name="adcfe201fc728cc1c6fcf638a566ba9a1"></a>
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 <dl class="section return"><dt>Returns</dt><dd>A reference to the wrapped <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a>. </dd></dl>

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+
+</div>
+</div>
+<a id="ade38ca54703913359fc3b4366f6e292a" name="ade38ca54703913359fc3b4366f6e292a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ade38ca54703913359fc3b4366f6e292a">&#9670;&#160;</a></span>lock()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void LockableDObject::lock </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Locks the mutex to ensure thread-safe access. </p>
+
+<p class="definition">Definition at line <a class="el" href="_lockable_d_object_8cpp_source.html#l00033">33</a> of file <a class="el" href="_lockable_d_object_8cpp_source.html">LockableDObject.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a1481ed99dcd837490bf28309aadaedfb" name="a1481ed99dcd837490bf28309aadaedfb"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a1481ed99dcd837490bf28309aadaedfb">&#9670;&#160;</a></span>unlock()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void LockableDObject::unlock </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Unlocks the mutex after thread-safe access. </p>
+
+<p class="definition">Definition at line <a class="el" href="_lockable_d_object_8cpp_source.html#l00040">40</a> of file <a class="el" href="_lockable_d_object_8cpp_source.html">LockableDObject.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="a712cd3ea0c565f7e9089a651ef79b7bd" name="a712cd3ea0c565f7e9089a651ef79b7bd"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a712cd3ea0c565f7e9089a651ef79b7bd">&#9670;&#160;</a></span>mutex_</h2>
+
+<div class="memitem">
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+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::mutex LockableDObject::mutex_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Mutex for thread-safe access. </p>
+
+<p class="definition">Definition at line <a class="el" href="_lockable_d_object_8h_source.html#l00064">64</a> of file <a class="el" href="_lockable_d_object_8h_source.html">LockableDObject.h</a>.</p>
+
+</div>
+</div>
+<a id="a1eb1ca1d9cf979dcb9eead96054b89bb" name="a1eb1ca1d9cf979dcb9eead96054b89bb"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a1eb1ca1d9cf979dcb9eead96054b89bb">&#9670;&#160;</a></span>object_</h2>
+
+<div class="memitem">
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+          <td class="memname"><a class="el" href="class_d_object.html">DObject</a> LockableDObject::object_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>The underlying <a class="el" href="class_d_object.html" title="A universal data container class.">DObject</a> instance. </p>
+
+<p class="definition">Definition at line <a class="el" href="_lockable_d_object_8h_source.html#l00063">63</a> of file <a class="el" href="_lockable_d_object_8h_source.html">LockableDObject.h</a>.</p>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
 <li>src/dobj/public/<a class="el" href="_lockable_d_object_8h_source.html">LockableDObject.h</a></li>
-<li>src/dobj/private/<b>LockableDObject.cpp</b></li>
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+    [ "mutex_", "class_lockable_d_object.html#a712cd3ea0c565f7e9089a651ef79b7bd", null ],
+    [ "object_", "class_lockable_d_object.html#a1eb1ca1d9cf979dcb9eead96054b89bb", null ]
 ];
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+  <tr class="even"><td class="entry"><a class="el" href="class_metadata.html#ac73a509797c98c0d52fb32e1f93e38bc">byteSize_</a></td><td class="entry"><a class="el" href="class_metadata.html">Metadata</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_metadata.html#a290205e5f46416dd0f48bd6ff62888ac">dataType_</a></td><td class="entry"><a class="el" href="class_metadata.html">Metadata</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="class_metadata.html#a65fd506f1bd41699d9cd19bc0dfc9701">debugFlag_</a></td><td class="entry"><a class="el" href="class_metadata.html">Metadata</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="class_metadata.html#a163f74d4ef9ecd13a34e7e9cab2e21ce">dimensions_</a></td><td class="entry"><a class="el" href="class_metadata.html">Metadata</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
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+  $(function() { init_search(); });
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+<tr class="memdesc:a163f74d4ef9ecd13a34e7e9cab2e21ce"><td class="mdescLeft">&#160;</td><td class="mdescRight">Dimensions of the data (e.g., {3, 4} for a 3x4 matrix).  <br /></td></tr>
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+<tr class="memitem:a65fd506f1bd41699d9cd19bc0dfc9701" id="r_a65fd506f1bd41699d9cd19bc0dfc9701"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a65fd506f1bd41699d9cd19bc0dfc9701">debugFlag_</a> = false</td></tr>
+<tr class="memdesc:a65fd506f1bd41699d9cd19bc0dfc9701"><td class="mdescLeft">&#160;</td><td class="mdescRight">Indicates whether debugging is enabled.  <br /></td></tr>
+<tr class="separator:a65fd506f1bd41699d9cd19bc0dfc9701"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="friends" name="friends"></a>
 Friends</h2></td></tr>
 <tr class="memitem:a12949a1ea26c4ff1afeb97101c0493c5" id="r_a12949a1ea26c4ff1afeb97101c0493c5"><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a12949a1ea26c4ff1afeb97101c0493c5">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="class_metadata.html">Metadata</a> &amp;metadata)</td></tr>
@@ -158,9 +170,38 @@ Friends</h2></td></tr>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Represents metadata information for data objects in the dobj module. </p>
 <p>The <a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a> class encapsulates details such as data size, type, dimensions, and optional debugging flags. It is designed to provide descriptive attributes in a lightweight and efficient manner. </p>
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00051">51</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
 </div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
+<a id="ae849560667461008cb72e83919c20be0" name="ae849560667461008cb72e83919c20be0"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae849560667461008cb72e83919c20be0">&#9670;&#160;</a></span>Metadata() <span class="overload">[1/2]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">Metadata::Metadata </td>
+          <td>(</td>
+          <td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel default">default</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Default constructor for <a class="el" href="class_metadata.html" title="Represents metadata information for data objects in the dobj module.">Metadata</a>. </p>
+
+</div>
+</div>
 <a id="a3d56c8c5adee4b8c7d2089802211522b" name="a3d56c8c5adee4b8c7d2089802211522b"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a3d56c8c5adee4b8c7d2089802211522b">&#9670;&#160;</a></span>Metadata()</h2>
+<h2 class="memtitle"><span class="permalink"><a href="#a3d56c8c5adee4b8c7d2089802211522b">&#9670;&#160;</a></span>Metadata() <span class="overload">[2/2]</span></h2>

 <div class="memitem">
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@@ -199,6 +240,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00040">40</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <h2 class="groupheader">Member Function Documentation</h2>
@@ -230,6 +273,8 @@ Friends</h2></td></tr>
 <p>The size is often required for memory allocation and validation in numerical routines.</p>
 <dl class="section return"><dt>Returns</dt><dd>The total byte size of the data. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00050">50</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="aeed7f22ccc61d9a3d6425441d381dcdc" name="aeed7f22ccc61d9a3d6425441d381dcdc"></a>
@@ -260,6 +305,8 @@ Friends</h2></td></tr>
 <p>The type (e.g., "float", "double") is critical for casting raw data or interfacing with libraries that require specific types.</p>
 <dl class="section return"><dt>Returns</dt><dd>A string representing the data type. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00074">74</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a412c0c0b8754d85f9edbbdcd637f3b20" name="a412c0c0b8754d85f9edbbdcd637f3b20"></a>
@@ -290,6 +337,8 @@ Friends</h2></td></tr>
 <p>Dimensions define the shape of the data (e.g., 2D arrays, 3D matrices). This is essential for ensuring that operations (e.g., matrix multiplication) are performed correctly.</p>
 <dl class="section return"><dt>Returns</dt><dd>A vector representing the size of each dimension. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00098">98</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="abe52c81e04665628666b4140cd346b69" name="abe52c81e04665628666b4140cd346b69"></a>
@@ -320,6 +369,8 @@ Friends</h2></td></tr>
 <p>Debugging flags can be useful for tracking performance metrics or error provenance.</p>
 <dl class="section return"><dt>Returns</dt><dd>True if debugging is enabled, false otherwise. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00120">120</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
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@@ -360,6 +411,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00062">62</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a88f4f57d443e2b7664e75e57a29dfbf0" name="a88f4f57d443e2b7664e75e57a29dfbf0"></a>
@@ -392,6 +445,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00086">86</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="a365c4594ad65c3b10b40a1cf4f4aea26" name="a365c4594ad65c3b10b40a1cf4f4aea26"></a>
@@ -432,6 +487,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00132">132</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <a id="af5264d1666839e69c192b565b5cfa606" name="af5264d1666839e69c192b565b5cfa606"></a>
@@ -464,6 +521,8 @@ Friends</h2></td></tr>
  </dd>
 </dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00109">109</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
 </div>
 </div>
 <h2 class="groupheader">Friends And Related Symbol Documentation</h2>
@@ -513,11 +572,118 @@ Friends</h2></td></tr>
 </dl>
 <dl class="section return"><dt>Returns</dt><dd>A reference to the output stream. </dd></dl>

+<p class="definition">Definition at line <a class="el" href="_metadata_8cpp_source.html#l00146">146</a> of file <a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Member Data Documentation</h2>
+<a id="ac73a509797c98c0d52fb32e1f93e38bc" name="ac73a509797c98c0d52fb32e1f93e38bc"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ac73a509797c98c0d52fb32e1f93e38bc">&#9670;&#160;</a></span>byteSize_</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
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+          <td class="memname">int Metadata::byteSize_ = 0</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Total size of the data in bytes. </p>
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00126">126</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+
+</div>
+</div>
+<a id="a290205e5f46416dd0f48bd6ff62888ac" name="a290205e5f46416dd0f48bd6ff62888ac"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a290205e5f46416dd0f48bd6ff62888ac">&#9670;&#160;</a></span>dataType_</h2>
+
+<div class="memitem">
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+  <td class="mlabels-left">
+      <table class="memname">
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+          <td class="memname">std::string Metadata::dataType_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Type of the data (e.g., "float", "double"). </p>
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00127">127</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+
+</div>
+</div>
+<a id="a65fd506f1bd41699d9cd19bc0dfc9701" name="a65fd506f1bd41699d9cd19bc0dfc9701"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a65fd506f1bd41699d9cd19bc0dfc9701">&#9670;&#160;</a></span>debugFlag_</h2>
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+          <td class="memname">bool Metadata::debugFlag_ = false</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
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+</table>
+</div><div class="memdoc">
+
+<p>Indicates whether debugging is enabled. </p>
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00129">129</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+
+</div>
+</div>
+<a id="a163f74d4ef9ecd13a34e7e9cab2e21ce" name="a163f74d4ef9ecd13a34e7e9cab2e21ce"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a163f74d4ef9ecd13a34e7e9cab2e21ce">&#9670;&#160;</a></span>dimensions_</h2>
+
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+          <td class="memname">std::vector&lt;std::size_t&gt; Metadata::dimensions_</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel private">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Dimensions of the data (e.g., {3, 4} for a 3x4 matrix). </p>
+
+<p class="definition">Definition at line <a class="el" href="_metadata_8h_source.html#l00128">128</a> of file <a class="el" href="_metadata_8h_source.html">Metadata.h</a>.</p>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
 <li>src/dobj/public/<a class="el" href="_metadata_8h_source.html">Metadata.h</a></li>
-<li>src/dobj/private/<a class="el" href="_metadata_8cpp.html">Metadata.cpp</a></li>
+<li>src/dobj/private/<a class="el" href="_metadata_8cpp_source.html">Metadata.cpp</a></li>
 </ul>
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--- a/docs/html/class_metadata.js
+++ b/docs/html/class_metadata.js
@@ -10,5 +10,9 @@ var class_metadata =
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    [ "setDebugEnabled", "class_metadata.html#a365c4594ad65c3b10b40a1cf4f4aea26", null ],
    [ "setDimensions", "class_metadata.html#af5264d1666839e69c192b565b5cfa606", null ],
-    [ "operator<<", "class_metadata.html#a12949a1ea26c4ff1afeb97101c0493c5", null ]
+    [ "operator<<", "class_metadata.html#a12949a1ea26c4ff1afeb97101c0493c5", null ],
+    [ "byteSize_", "class_metadata.html#ac73a509797c98c0d52fb32e1f93e38bc", null ],
+    [ "dataType_", "class_metadata.html#a290205e5f46416dd0f48bd6ff62888ac", null ],
+    [ "debugFlag_", "class_metadata.html#a65fd506f1bd41699d9cd19bc0dfc9701", null ],
+    [ "dimensions_", "class_metadata.html#a163f74d4ef9ecd13a34e7e9cab2e21ce", null ]
 ];
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 </div><!--header-->
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- var summary = $('#'+base+'-summary');
- var content = $('#'+base+'-content');
- var trigger = $('#'+base+'-trigger');
- var src=$(trigger).attr('src');
+
+function toggleVisibility(linkObj) {
+  return dynsection.toggleVisibility(linkObj);
+}
+
+let dynsection = {
+
+  // helper function
+  updateStripes : function() {
+    $('table.directory tr').
+      removeClass('even').filter(':visible:even').addClass('even');
+    $('table.directory tr').
+      removeClass('odd').filter(':visible:odd').addClass('odd');
+  },
+
+  toggleVisibility : function(linkObj) {
+    const base = $(linkObj).attr('id');
+    const summary = $('#'+base+'-summary');
+    const content = $('#'+base+'-content');
+    const trigger = $('#'+base+'-trigger');
+    const src=$(trigger).attr('src');
    if (content.is(':visible')===true) {
      content.hide();
      summary.show();
@@ -41,20 +55,13 @@ function toggleVisibility(linkObj)
      $(trigger).attr('src',src.substring(0,src.length-10)+'open.png');
    }
    return false;
-}
+  },

-function updateStripes()
-{
-  $('table.directory tr').
-       removeClass('even').filter(':visible:even').addClass('even');
-}
-
-function toggleLevel(level)
-{
+  toggleLevel : function(level) {
    $('table.directory tr').each(function() {
-    var l = this.id.split('_').length-1;
-    var i = $('#img'+this.id.substring(3));
-    var a = $('#arr'+this.id.substring(3));
+      const l = this.id.split('_').length-1;
+      const i = $('#img'+this.id.substring(3));
+      const a = $('#arr'+this.id.substring(3));
      if (l<level+1) {
        i.removeClass('iconfopen iconfclosed').addClass('iconfopen');
        a.html('&#9660;');
@@ -67,49 +74,46 @@ function toggleLevel(level)
        $(this).hide();
      }
    });
-  updateStripes();
-}
+    this.updateStripes();
+  },

-function toggleFolder(id)
-{
+  toggleFolder : function(id) {
    // the clicked row
-  var currentRow = $('#row_'+id);
+    const currentRow = $('#row_'+id);

    // all rows after the clicked row
-  var rows = currentRow.nextAll("tr");
+    const rows = currentRow.nextAll("tr");

-  var re = new RegExp('^row_'+id+'\\d+_$', "i"); //only one sub
+    const re = new RegExp('^row_'+id+'\\d+_$', "i"); //only one sub

    // only match elements AFTER this one (can't hide elements before)
-  var childRows = rows.filter(function() { return this.id.match(re); });
+    const childRows = rows.filter(function() { return this.id.match(re); });

    // first row is visible we are HIDING
    if (childRows.filter(':first').is(':visible')===true) {
      // replace down arrow by right arrow for current row
-    var currentRowSpans = currentRow.find("span");
+      const currentRowSpans = currentRow.find("span");
      currentRowSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed");
      currentRowSpans.filter(".arrow").html('&#9658;');
      rows.filter("[id^=row_"+id+"]").hide(); // hide all children
    } else { // we are SHOWING
      // replace right arrow by down arrow for current row
-    var currentRowSpans = currentRow.find("span");
+      const currentRowSpans = currentRow.find("span");
      currentRowSpans.filter(".iconfclosed").removeClass("iconfclosed").addClass("iconfopen");
      currentRowSpans.filter(".arrow").html('&#9660;');
      // replace down arrows by right arrows for child rows
-    var childRowsSpans = childRows.find("span");
+      const childRowsSpans = childRows.find("span");
      childRowsSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed");
      childRowsSpans.filter(".arrow").html('&#9658;');
      childRows.show(); //show all children
    }
-  updateStripes();
-}
+    this.updateStripes();
+  },

-
-function toggleInherit(id)
-{
-  var rows = $('tr.inherit.'+id);
-  var img = $('tr.inherit_header.'+id+' img');
-  var src = $(img).attr('src');
+  toggleInherit : function(id) {
+    const rows = $('tr.inherit.'+id);
+    const img = $('tr.inherit_header.'+id+' img');
+    const src = $(img).attr('src');
    if (rows.filter(':first').is(':visible')===true) {
      rows.css('display','none');
      $(img).attr('src',src.substring(0,src.length-8)+'closed.png');
@@ -117,5 +121,85 @@ function toggleInherit(id)
      rows.css('display','table-row'); // using show() causes jump in firefox
      $(img).attr('src',src.substring(0,src.length-10)+'open.png');
    }
+  },
+};
+
+let codefold = {
+  opened : true,
+
+  // in case HTML_COLORSTYLE is LIGHT or DARK the vars will be replaced, so we write them out explicitly and use double quotes
+  plusImg:  [ "url('plus.svg')",  "url('../../plus.svg')" ],
+  minusImg: [ "url('minus.svg')", "url('../../minus.svg')" ],
+
+  // toggle all folding blocks
+  toggle_all : function(relPath) {
+    if (this.opened) {
+      $('#fold_all').css('background-image',this.plusImg[relPath]);
+      $('div[id^=foldopen]').hide();
+      $('div[id^=foldclosed]').show();
+    } else {
+      $('#fold_all').css('background-image',this.minusImg[relPath]);
+      $('div[id^=foldopen]').show();
+      $('div[id^=foldclosed]').hide();
    }
+    this.opened=!this.opened;
+  },
+
+  // toggle single folding block
+  toggle : function(id) {
+    $('#foldopen'+id).toggle();
+    $('#foldclosed'+id).toggle();
+  },
+
+  init : function(relPath) {
+    $('span[class=lineno]').css({
+      'padding-right':'4px',
+      'margin-right':'2px',
+      'display':'inline-block',
+      'width':'54px',
+      'background':'linear-gradient(#808080,#808080) no-repeat 46px/2px 100%'
+    });
+    // add global toggle to first line
+    $('span[class=lineno]:first').append('<span class="fold" id="fold_all" '+
+      'onclick="javascript:codefold.toggle_all('+relPath+');" '+
+      'style="background-image:'+this.minusImg[relPath]+';"></span>');
+    // add vertical lines to other rows
+    $('span[class=lineno]').not(':eq(0)').append('<span class="fold"></span>');
+    // add toggle controls to lines with fold divs
+    $('div[class=foldopen]').each(function() {
+      // extract specific id to use
+      const id    = $(this).attr('id').replace('foldopen','');
+      // extract start and end foldable fragment attributes
+      const start = $(this).attr('data-start');
+      const end   = $(this).attr('data-end');
+      // replace normal fold span with controls for the first line of a foldable fragment
+      $(this).find('span[class=fold]:first').replaceWith('<span class="fold" '+
+                   'onclick="javascript:codefold.toggle(\''+id+'\');" '+
+                   'style="background-image:'+codefold.minusImg[relPath]+';"></span>');
+      // append div for folded (closed) representation
+      $(this).after('<div id="foldclosed'+id+'" class="foldclosed" style="display:none;"></div>');
+      // extract the first line from the "open" section to represent closed content
+      const line = $(this).children().first().clone();
+      // remove any glow that might still be active on the original line
+      $(line).removeClass('glow');
+      if (start) {
+        // if line already ends with a start marker (e.g. trailing {), remove it
+        $(line).html($(line).html().replace(new RegExp('\\s*'+start+'\\s*$','g'),''));
+      }
+      // replace minus with plus symbol
+      $(line).find('span[class=fold]').css('background-image',codefold.plusImg[relPath]);
+      // append ellipsis
+      $(line).append(' '+start+'<a href="javascript:codefold.toggle(\''+id+'\')">&#8230;</a>'+end);
+      // insert constructed line into closed div
+      $('#foldclosed'+id).html(line);
+    });
+  },
+};
 /* @license-end */
+$(function() {
+  $('.code,.codeRef').each(function() {
+    $(this).data('powertip',$('#a'+$(this).attr('href').replace(/.*\//,'').replace(/[^a-z_A-Z0-9]/g,'_')).html());
+    $.fn.powerTip.smartPlacementLists.s = [ 's', 'n', 'ne', 'se' ];
+    $(this).powerTip({ placement: 's', smartPlacement: true, mouseOnToPopup: true });
+  });
+});
--- a/docs/html/files.html
+++ b/docs/html/files.html
@@ -1,65 +1,65 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
-<meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.9.1"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.13.2"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>New 4DSSE Code: File List</title>
+<title>SERiF: File List</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
+<script type="text/javascript" src="clipboard.js"></script>
 <link href="navtree.css" rel="stylesheet" type="text/css"/>
-<script type="text/javascript" src="resize.js"></script>
 <script type="text/javascript" src="navtreedata.js"></script>
 <script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="cookie.js"></script>
 <link href="search/search.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="search/searchdata.js"></script>
 <script type="text/javascript" src="search/search.js"></script>
-<script type="text/javascript">
-/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
-  $(document).ready(function() { init_search(); });
-/* @license-end */
-</script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen-awesome-sidebar-only.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 <div id="titlearea">
 <table cellspacing="0" cellpadding="0">
 <tbody>
- <tr style="height: 56px;">
-  <td id="projectalign" style="padding-left: 0.5em;">
-   <div id="projectname">New 4DSSE Code
-   &#160;<span id="projectnumber">0.0.1a</span>
-   </div>
-  </td>
-   <td>        <div id="MSearchBox" class="MSearchBoxInactive">
-        <span class="left">
-          <img id="MSearchSelect" src="search/mag_sel.svg"
-               onmouseover="return searchBox.OnSearchSelectShow()"
-               onmouseout="return searchBox.OnSearchSelectHide()"
-               alt=""/>
-          <input type="text" id="MSearchField" value="Search" accesskey="S"
-               onfocus="searchBox.OnSearchFieldFocus(true)" 
-               onblur="searchBox.OnSearchFieldFocus(false)" 
-               onkeyup="searchBox.OnSearchFieldChange(event)"/>
-          </span><span class="right">
-            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.svg" alt=""/></a>
-          </span>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
   </div>
+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
  </td>
 </tr>
 </tbody>
 </table>
 </div>
 <!-- end header part -->
-<!-- Generated by Doxygen 1.9.1 -->
+<!-- Generated by Doxygen 1.13.2 -->
 <script type="text/javascript">
-/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
-var searchBox = new SearchBox("searchBox", "search",false,'Search','.html');
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
 /* @license-end */
 </script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() { codefold.init(0); });
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search',true);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
  <div id="nav-tree">
@@ -72,8 +72,8 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search','.html');
  </div>
 </div>
 <script type="text/javascript">
-/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
-$(document).ready(function(){initNavTree('files.html',''); initResizable(); });
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('files.html',''); initResizable(true); });
 /* @license-end */
 </script>
 <div id="doc-content">
@@ -86,96 +86,121 @@ $(document).ready(function(){initNavTree('files.html',''); initResizable(); });

 <!-- iframe showing the search results (closed by default) -->
 <div id="MSearchResultsWindow">
-<iframe src="javascript:void(0)" frameborder="0" 
-        name="MSearchResults" id="MSearchResults">
-</iframe>
+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
 </div>

 <div class="header">
-  <div class="headertitle">
-<div class="title">File List</div>  </div>
+  <div class="headertitle"><div class="title">File List</div></div>
 </div><!--header-->
 <div class="contents">
 <div class="textblock">Here is a list of all files with brief descriptions:</div><div class="directory">
-<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span><span onclick="javascript:toggleLevel(5);">5</span><span onclick="javascript:toggleLevel(6);">6</span><span onclick="javascript:toggleLevel(7);">7</span>]</div><table class="directory">
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('functions.html',''); initResizable(true); });
 /* @license-end */
 </script>
 <div id="doc-content">
@@ -86,407 +86,35 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();

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 <div id="MSearchResultsWindow">
-<iframe src="javascript:void(0)" frameborder="0" 
-        name="MSearchResults" id="MSearchResults">
-</iframe>
+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
 </div>

 <div class="contents">
 <div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>

-<h3><a id="index_a"></a>- a -</h3><ul>
-<li>add_integrator()
-: <a class="el" href="classCompositeNonlinearIntegrator.html#af336df4849e99a3bc95161f03868efc4">CompositeNonlinearIntegrator</a>
-</li>
-<li>AssembleElementGrad()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a19b6facddeba8256619981e6276f5815">BilinearIntegratorWrapper</a>
-, <a class="el" href="classCompositeNonlinearIntegrator.html#a2b466f6e16a5797f5ed50621fc4818a0">CompositeNonlinearIntegrator</a>
-, <a class="el" href="classNonlinearPowerIntegrator.html#a5d8116206e35119fbee20540f5bd3157">NonlinearPowerIntegrator</a>
-</li>
-<li>AssembleElementVector()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a10c3ac5bb62c91c3a437924e33a527d8">BilinearIntegratorWrapper</a>
-, <a class="el" href="classCompositeNonlinearIntegrator.html#a0a3c6ccf134c4566218eb3a33861214c">CompositeNonlinearIntegrator</a>
-, <a class="el" href="classNonlinearPowerIntegrator.html#a23b79c0ab632824ffda9b43928a00504">NonlinearPowerIntegrator</a>
-</li>
-</ul>
-
-
-<h3><a id="index_b"></a>- b -</h3><ul>
-<li>BilinearIntegratorWrapper()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a72155007095c629dfca4f349739e4a18">BilinearIntegratorWrapper</a>
-</li>
-<li>byteEnd
-: <a class="el" href="structTableIndex.html#a69c87fd1cb0b7a64a82c52c54193e5e6">TableIndex</a>
-</li>
-<li>byteStart
-: <a class="el" href="structTableIndex.html#ad899cf13056eb17b33e1c5e303e10132">TableIndex</a>
-</li>
-</ul>
-
-
-<h3><a id="index_c"></a>- c -</h3><ul>
-<li>callAddToCache()
-: <a class="el" href="classconfigTestPrivateAccessor.html#adf7f5c651bdd5ca8c12f18a6a0f8a8e9">configTestPrivateAccessor</a>
-</li>
-<li>callCacheSize()
-: <a class="el" href="classconfigTestPrivateAccessor.html#aaa9517067ef84ab7fb6365536180ce13">configTestPrivateAccessor</a>
-</li>
-<li>callIsKeyInCache()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a6d7d0e1bf82c1917dde20167697a03b1">configTestPrivateAccessor</a>
-</li>
-<li>callRegisterKeyNotFound()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a447eb550ff20700e31bd530b7ca01592">configTestPrivateAccessor</a>
-</li>
-<li>CheckIfKeyUnknown()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a4de7c133e8e296d7f9e713aa0b2c4329">configTestPrivateAccessor</a>
-</li>
-<li>comment
-: <a class="el" href="structHeader.html#a122331824871070af2c6cebc9698abd8">Header</a>
-</li>
-<li>CompositeNonlinearIntegrator()
-: <a class="el" href="classCompositeNonlinearIntegrator.html#aba931cf9d57170b7483eed0ade6cd459">CompositeNonlinearIntegrator</a>
-</li>
-<li>computeChecksum()
-: <a class="el" href="classOpatIO.html#af5c52b5d862f5b94ee847c6c791998db">OpatIO</a>
-</li>
-<li>Constant()
-: <a class="el" href="structConstant.html#a84ca5b6951cc8a8eccd083894302a857">Constant</a>
-</li>
-<li>creationDate
-: <a class="el" href="structHeader.html#a83f52dffac0449704ef1a50a5e787e92">Header</a>
-</li>
-</ul>
-
-
-<h3><a id="index_d"></a>- d -</h3><ul>
-<li>DataType
-: <a class="el" href="classDObject.html#a79a2ecac4130ef3df272bdfeed26a620">DObject</a>
-</li>
-<li>dataTypeMap
-: <a class="el" href="classDObject.html#a358d5f015da09ae5f0cbb46f3fd9e401">DObject</a>
-</li>
-<li>defaultObject
-: <a class="el" href="classDObjectTest.html#ac753942590ae6ee456e6f3dd8b205df2">DObjectTest</a>
-</li>
-<li>DObject()
-: <a class="el" href="classDObject.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>
-</li>
-</ul>
-
-
-<h3><a id="index_g"></a>- g -</h3><ul>
-<li>get()
-: <a class="el" href="classConstants.html#a36ddd7fe6857d1bbf6d1c84d4ed7bc19">Constants</a>
-, <a class="el" href="classLockableDObject.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject</a>
-</li>
-<li>getByteSize()
-: <a class="el" href="classMetadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata</a>
-</li>
-<li>getData()
-: <a class="el" href="classDObject.html#a4862655c3634d019b0a45b811d6f7235">DObject</a>
-</li>
-<li>getDataAs()
-: <a class="el" href="classDObject.html#aca2db093c1c8c6f7893de07544aed619">DObject</a>
-</li>
-<li>getDataType()
-: <a class="el" href="classMetadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">Metadata</a>
-</li>
-<li>getDimensions()
-: <a class="el" href="classMetadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">Metadata</a>
-</li>
-<li>getErrorCode()
-: <a class="el" href="classDObject.html#afa8926d916081de72478cb8813c25e98">DObject</a>
-</li>
-<li>getHeader()
-: <a class="el" href="classOpatIO.html#afe725b647bc5bb802f6d711fc5dca3ab">OpatIO</a>
-</li>
-<li>getInstance()
-: <a class="el" href="classConstants.html#aaa6f3af20fa563cf22df71a987923065">Constants</a>
-</li>
-<li>getMaxQDepth()
-: <a class="el" href="classOpatIO.html#a48cd5e4f3fdb221bc1b6253e149e8e01">OpatIO</a>
-</li>
-<li>GetMesh()
-: <a class="el" href="classMeshIO.html#a3e4bccff08abf9a28b3d64c8fb9f7317">MeshIO</a>
-</li>
-<li>getNumIndex()
-: <a class="el" href="classOpatIO.html#a8f7cc9a4ec8845c22df330678afd29c6">OpatIO</a>
-</li>
-<li>getOPATVersion()
-: <a class="el" href="classOpatIO.html#a2894437c09f4cdb06c9b06d6aad4bd2f">OpatIO</a>
-</li>
-<li>getTable()
-: <a class="el" href="classOpatIO.html#a5c35b863873239e023427864ed016f58">OpatIO</a>
-</li>
-<li>getTableIndex()
-: <a class="el" href="classOpatIO.html#af0bc6bb210c4ff74bc1e043aeb252e1a">OpatIO</a>
-</li>
-</ul>
-
-
-<h3><a id="index_h"></a>- h -</h3><ul>
-<li>has()
-: <a class="el" href="classConstants.html#a2aa041fd223f259e55bf098c90581039">Constants</a>
-</li>
-<li>headerSize
-: <a class="el" href="structHeader.html#af0bdf31defd5888cc8d2f7537e687917">Header</a>
-</li>
-</ul>
-
-
-<h3><a id="index_i"></a>- i -</h3><ul>
-<li>index
-: <a class="el" href="structTableIndex.html#a5abb8638b94f778674d999db0f506ecc">TableIndex</a>
-</li>
-<li>indexOffset
-: <a class="el" href="structHeader.html#a31039c09176a479defcbe38597eb9957">Header</a>
-</li>
-<li>initializedObject
-: <a class="el" href="classDObjectTest.html#a2150dd7881a4d1c68ce51344f174738e">DObjectTest</a>
-</li>
-<li>isDebugEnabled()
-: <a class="el" href="classMetadata.html#abe52c81e04665628666b4140cd346b69">Metadata</a>
-</li>
-<li>isDebuggingEnabled()
-: <a class="el" href="classDObject.html#ae47bf220fbe2173cf6933c2380035dbd">DObject</a>
-</li>
-<li>isLoaded()
-: <a class="el" href="classConstants.html#ae276dfdc0ffe75a53e3842e33ab52630">Constants</a>
-</li>
-<li>IsLoaded()
-: <a class="el" href="classMeshIO.html#a12495fc814254021d44e0509ac760672">MeshIO</a>
-</li>
-<li>isLoaded()
-: <a class="el" href="classOpatIO.html#aba1be05d51d4b0b9e4581b95ad0e1890">OpatIO</a>
-</li>
-</ul>
-
-
-<h3><a id="index_k"></a>- k -</h3><ul>
-<li>keys()
-: <a class="el" href="classConstants.html#ab9de36fa145552a3e7964e7e85a67149">Constants</a>
-</li>
-</ul>
-
-
-<h3><a id="index_l"></a>- l -</h3><ul>
-<li>load()
-: <a class="el" href="classOpatIO.html#a3578ac9bad40dd45ada3459f92a93b56">OpatIO</a>
-</li>
-<li>lock()
-: <a class="el" href="classLockableDObject.html#ade38ca54703913359fc3b4366f6e292a">LockableDObject</a>
-</li>
-<li>LockableDObject()
-: <a class="el" href="classLockableDObject.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a>
-</li>
-<li>lockableObject
-: <a class="el" href="classLockableDObjectTest.html#a6f639c0023311b7900595ab11c40cd59">LockableDObjectTest</a>
-</li>
-<li>logKappa
-: <a class="el" href="structOPATTable.html#aee4e3713cffa0ed0a5bd79e2dec97d6e">OPATTable</a>
-</li>
-<li>logR
-: <a class="el" href="structOPATTable.html#afaf11794675d27e75de5233b947fced9">OPATTable</a>
-</li>
-<li>logT
-: <a class="el" href="structOPATTable.html#a237ed50cee8df2144a2c47b5ffa443d3">OPATTable</a>
-</li>
-<li>lookupClosestTableID()
-: <a class="el" href="classOpatIO.html#a82715d95a5ddd1e78470b90fbd005c4d">OpatIO</a>
-</li>
-<li>lookupTableID()
-: <a class="el" href="classOpatIO.html#a1a4456b7745c0dd559eca72d5d744fc0">OpatIO</a>
-</li>
-</ul>
-
-
-<h3><a id="index_m"></a>- m -</h3><ul>
-<li>magic
-: <a class="el" href="structHeader.html#a87c9fc5b27c41fe65698f8538c23b182">Header</a>
-</li>
-<li>MeshIO()
-: <a class="el" href="classMeshIO.html#a8fe43b55b7851c805c276517b0aacac5">MeshIO</a>
-</li>
-<li>Metadata()
-: <a class="el" href="classMetadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>
-</li>
-</ul>
-
-
-<h3><a id="index_n"></a>- n -</h3><ul>
-<li>N_R
-: <a class="el" href="structOPATTable.html#a70b70699726b2f77b486702e913a164b">OPATTable</a>
-</li>
-<li>N_T
-: <a class="el" href="structOPATTable.html#a87cc2d8e225e5e9c567602d779aec88f">OPATTable</a>
-</li>
-<li>name
-: <a class="el" href="structConstant.html#a8d8d2a81e9a8f36dfa02b4d23a5be55c">Constant</a>
-</li>
-<li>NonlinearPowerIntegrator()
-: <a class="el" href="classNonlinearPowerIntegrator.html#a0578e900c8e95cfa1161362c98fd3d31">NonlinearPowerIntegrator</a>
-</li>
-<li>numIndex
-: <a class="el" href="structHeader.html#a2ab1f0eeaadd3be76f253a71d06e2b39">Header</a>
-</li>
-<li>numTables
-: <a class="el" href="structHeader.html#a162ced3913c3373d6d54c32274b99d72">Header</a>
-</li>
-</ul>
-
-
-<h3><a id="index_o"></a>- o -</h3><ul>
-<li>OpatIO()
-: <a class="el" href="classOpatIO.html#a7f3436b3ac0dbe141b08d8064550f1b3">OpatIO</a>
-</li>
-<li>operator&lt;&lt;
-: <a class="el" href="structConstant.html#ad298f7af7cdfd2e2267fd9e464558e2b">Constant</a>
-, <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
-, <a class="el" href="classMetadata.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata</a>
-</li>
-<li>operator[]()
-: <a class="el" href="classConstants.html#ad75620743b867fc20d4a05027d1a1c01">Constants</a>
-</li>
-</ul>
-
-
-<h3><a id="index_p"></a>- p -</h3><ul>
-<li>Plugin
-: <a class="el" href="classDObject.html#af11334d08ef85c68b3aae7554548e5a7">DObject</a>
-</li>
-<li>printHeader()
-: <a class="el" href="classOpatIO.html#a117f7e1f45d6c410c21d0644e447bbb1">OpatIO</a>
-</li>
-<li>printTable()
-: <a class="el" href="classOpatIO.html#afae90144930f190ed4018fbf328bf8ea">OpatIO</a>
-</li>
-<li>printTableIndex()
-: <a class="el" href="classOpatIO.html#afa623ba10f188097e555a682a4c69a9f">OpatIO</a>
-</li>
-</ul>
-
-
-<h3><a id="index_r"></a>- r -</h3><ul>
-<li>reference
-: <a class="el" href="structConstant.html#a1c7e6c5a1d2316c98e59e04a234754d1">Constant</a>
-</li>
-<li>registerPlugin()
-: <a class="el" href="classDObject.html#a15afffdf339150fc872bf63bdd08d581">DObject</a>
-</li>
-<li>reserved
-: <a class="el" href="structHeader.html#a40ba18cda24aa3bb788555a209dd1bad">Header</a>
-</li>
-<li>runAllPlugins()
-: <a class="el" href="classDObject.html#a1223275dcbbf20334ea11707346acb93">DObject</a>
-</li>
-<li>runPlugin()
-: <a class="el" href="classDObject.html#a99072eb52bb22745f0248f273fbf28fb">DObject</a>
-</li>
-</ul>
-
-
-<h3><a id="index_s"></a>- s -</h3><ul>
-<li>setByteSize()
-: <a class="el" href="classMetadata.html#a07035de7b0c780ef340e1a11c60a4d2b">Metadata</a>
-</li>
-<li>setData()
-: <a class="el" href="classDObject.html#ab1718571434e84e90f1ec463e4786a8a">DObject</a>
-</li>
-<li>setDataType()
-: <a class="el" href="classMetadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">Metadata</a>
-</li>
-<li>setDebugEnabled()
-: <a class="el" href="classMetadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">Metadata</a>
-</li>
-<li>setDebugging()
-: <a class="el" href="classDObject.html#a6f0023aee463e71d92442dcf61b6ed47">DObject</a>
-</li>
-<li>setDimensions()
-: <a class="el" href="classMetadata.html#af5264d1666839e69c192b565b5cfa606">Metadata</a>
-</li>
-<li>setErrorCode()
-: <a class="el" href="classDObject.html#a3dce47a519f9da5085c0c5ac1eea4f38">DObject</a>
-</li>
-<li>setFilename()
-: <a class="el" href="classOpatIO.html#ad189e0f239bc4184fecf7daef7923272">OpatIO</a>
-</li>
-<li>setMaxQDepth()
-: <a class="el" href="classOpatIO.html#ab0edd41690b8d5c1775f87439cf82cb5">OpatIO</a>
-</li>
-<li>SetUp()
-: <a class="el" href="classconstTest.html#af4753885bf401953202f89d455a2702f">constTest</a>
-, <a class="el" href="classDObjectTest.html#a95ba0f78c44e0bd46603de32028b7be6">DObjectTest</a>
-, <a class="el" href="classLockableDObjectTest.html#a4ca643fb176141b51f4761dd3df64769">LockableDObjectTest</a>
-, <a class="el" href="classMetadataTest.html#a6273a370a10b42155af951a8fc2c47fa">MetadataTest</a>
-</li>
-<li>sha256
-: <a class="el" href="structTableIndex.html#a0c4826e48839977fa2bfaa1bf51b6cdb">TableIndex</a>
-</li>
-<li>sourceInfo
-: <a class="el" href="structHeader.html#ac1a0c67ed5bd4021581fc00c2d79dba3">Header</a>
-</li>
-</ul>
-
-
-<h3><a id="index_t"></a>- t -</h3><ul>
-<li>TearDown()
-: <a class="el" href="classMetadataTest.html#a24075d61d37dceacd353ecde16a1ac71">MetadataTest</a>
-</li>
-</ul>
-
-
-<h3><a id="index_u"></a>- u -</h3><ul>
-<li>uncertainty
-: <a class="el" href="structConstant.html#a0ae09f22af150a41aa4169a4a60933be">Constant</a>
-</li>
-<li>unit
-: <a class="el" href="structConstant.html#a2c46956a2d2b0ebf78ff99c5971130d2">Constant</a>
-</li>
-<li>unload()
-: <a class="el" href="classOpatIO.html#ac1c1a6159f82462fedf9b526ddcc19a6">OpatIO</a>
-</li>
-<li>unlock()
-: <a class="el" href="classLockableDObject.html#a1481ed99dcd837490bf28309aadaedfb">LockableDObject</a>
-</li>
-<li>unregisterPlugin()
-: <a class="el" href="classDObject.html#a99b8688849e11501033a25f61efb8356">DObject</a>
-</li>
-</ul>
-
-
-<h3><a id="index_v"></a>- v -</h3><ul>
-<li>validateAll()
-: <a class="el" href="classOpatIO.html#aafb5941c4c93104af8ba06f2271a3dc7">OpatIO</a>
-</li>
-<li>value
-: <a class="el" href="structConstant.html#a3bda8d7fadd6fb2510fd39962a065a02">Constant</a>
-</li>
-<li>version
-: <a class="el" href="structHeader.html#ac55e763f9e96050f4dab115a4a1c2356">Header</a>
-</li>
-</ul>
-
-
-<h3><a id="index__7E"></a>- ~ -</h3><ul>
-<li>~BilinearIntegratorWrapper()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a6f550f0cb8d39c5ebc6e712762eb8504">BilinearIntegratorWrapper</a>
-</li>
-<li>~CompositeNonlinearIntegrator()
-: <a class="el" href="classCompositeNonlinearIntegrator.html#a93b4496295c20d461b971c65633570d8">CompositeNonlinearIntegrator</a>
-</li>
-<li>~MeshIO()
-: <a class="el" href="classMeshIO.html#abf2d0986e73b920c71c03dc61730846c">MeshIO</a>
-</li>
-<li>~OpatIO()
-: <a class="el" href="classOpatIO.html#ac34f611a9eab458329553d27e8bffec6">OpatIO</a>
-</li>
+<h3><a id="index_a" name="index_a"></a>- a -</h3><ul>
+<li>abar&#160;:&#160;<a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_e_o_s_input.html#a4974e4e163e9ff60aa1c4d4a1ebd426c">serif::eos::helmholtz::EOSInput</a></li>
+<li>aion&#160;:&#160;<a class="el" href="structserif_1_1network_1_1approx8_1_1_net.html#ae4d6bfb7bee80e80dc7947648d755e6c">serif::network::approx8::Net</a></li>
+<li>assembleAndFinalizeForm()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a3d7ed2ad970e24927cb13ea2e4ae572f">serif::polytrope::PolySolver</a></li>
+<li>assembleBlockSystem()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a8b6283e2d865e2941d314e6155c558b8">serif::polytrope::PolySolver</a></li>
+<li>AssembleElementGrad()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html#a3ff176719caad168f9e72011a9468370">serif::polytrope::polyMFEMUtils::NonlinearPowerIntegrator</a></li>
+<li>AssembleElementVector()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html#a370aeb5312191abc5bf8cb07d5993d87">serif::polytrope::polyMFEMUtils::NonlinearPowerIntegrator</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->
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 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
  <ul>
-    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.1 </li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.13.2 </li>
  </ul>
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-<html xmlns="http://www.w3.org/1999/xhtml">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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-<meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.9.1"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.13.2"/>
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-<title>New 4DSSE Code: Class Members - Functions</title>
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+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
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+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">SERiF<span id="projectnumber">&#160;0.0.1a</span>
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+   <div id="projectbrief">3+1D Stellar Structure and Evolution</div>
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+<script type="text/javascript">
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+/* @license-end */
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
 </div>

 <div class="contents">
-&#160;
+<div class="textblock">Here is a list of all functions with links to the classes they belong to:</div>

-<h3><a id="index_a"></a>- a -</h3><ul>
-<li>add_integrator()
-: <a class="el" href="classCompositeNonlinearIntegrator.html#af336df4849e99a3bc95161f03868efc4">CompositeNonlinearIntegrator</a>
-</li>
-<li>AssembleElementGrad()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a19b6facddeba8256619981e6276f5815">BilinearIntegratorWrapper</a>
-, <a class="el" href="classCompositeNonlinearIntegrator.html#a2b466f6e16a5797f5ed50621fc4818a0">CompositeNonlinearIntegrator</a>
-, <a class="el" href="classNonlinearPowerIntegrator.html#a5d8116206e35119fbee20540f5bd3157">NonlinearPowerIntegrator</a>
-</li>
-<li>AssembleElementVector()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a10c3ac5bb62c91c3a437924e33a527d8">BilinearIntegratorWrapper</a>
-, <a class="el" href="classCompositeNonlinearIntegrator.html#a0a3c6ccf134c4566218eb3a33861214c">CompositeNonlinearIntegrator</a>
-, <a class="el" href="classNonlinearPowerIntegrator.html#a23b79c0ab632824ffda9b43928a00504">NonlinearPowerIntegrator</a>
-</li>
+<h3><a id="index_a" name="index_a"></a>- a -</h3><ul>
+<li>assembleAndFinalizeForm()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a3d7ed2ad970e24927cb13ea2e4ae572f">serif::polytrope::PolySolver</a></li>
+<li>assembleBlockSystem()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a8b6283e2d865e2941d314e6155c558b8">serif::polytrope::PolySolver</a></li>
+<li>AssembleElementGrad()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html#a3ff176719caad168f9e72011a9468370">serif::polytrope::polyMFEMUtils::NonlinearPowerIntegrator</a></li>
+<li>AssembleElementVector()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html#a370aeb5312191abc5bf8cb07d5993d87">serif::polytrope::polyMFEMUtils::NonlinearPowerIntegrator</a></li>
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-<h3><a id="index_b"></a>- b -</h3><ul>
-<li>BilinearIntegratorWrapper()
-: <a class="el" href="classBilinearIntegratorWrapper.html#a72155007095c629dfca4f349739e4a18">BilinearIntegratorWrapper</a>
-</li>
+<h3><a id="index_b" name="index_b"></a>- b -</h3><ul>
+<li>buildIndividualForms()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#aa39b58a2afbb203ea2e30c3dcda3d2d5">serif::polytrope::PolySolver</a></li>
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-<h3><a id="index_c"></a>- c -</h3><ul>
-<li>callAddToCache()
-: <a class="el" href="classconfigTestPrivateAccessor.html#adf7f5c651bdd5ca8c12f18a6a0f8a8e9">configTestPrivateAccessor</a>
-</li>
-<li>callCacheSize()
-: <a class="el" href="classconfigTestPrivateAccessor.html#aaa9517067ef84ab7fb6365536180ce13">configTestPrivateAccessor</a>
-</li>
-<li>callIsKeyInCache()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a6d7d0e1bf82c1917dde20167697a03b1">configTestPrivateAccessor</a>
-</li>
-<li>callRegisterKeyNotFound()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a447eb550ff20700e31bd530b7ca01592">configTestPrivateAccessor</a>
-</li>
-<li>CheckIfKeyUnknown()
-: <a class="el" href="classconfigTestPrivateAccessor.html#a4de7c133e8e296d7f9e713aa0b2c4329">configTestPrivateAccessor</a>
-</li>
-<li>CompositeNonlinearIntegrator()
-: <a class="el" href="classCompositeNonlinearIntegrator.html#aba931cf9d57170b7483eed0ade6cd459">CompositeNonlinearIntegrator</a>
-</li>
-<li>computeChecksum()
-: <a class="el" href="classOpatIO.html#af5c52b5d862f5b94ee847c6c791998db">OpatIO</a>
-</li>
-<li>Constant()
-: <a class="el" href="structConstant.html#a84ca5b6951cc8a8eccd083894302a857">Constant</a>
-</li>
+<h3><a id="index_c" name="index_c"></a>- c -</h3><ul>
+<li>callAddToCache()&#160;:&#160;<a class="el" href="classconfig_test_private_accessor.html#a17b572a5d4c9d980d0a8cc59aafd4a7d">configTestPrivateAccessor</a></li>
+<li>callCacheSize()&#160;:&#160;<a class="el" href="classconfig_test_private_accessor.html#ad255c2b4d2ed83c38ddb3b01bfc7699e">configTestPrivateAccessor</a></li>
+<li>callIsKeyInCache()&#160;:&#160;<a class="el" href="classconfig_test_private_accessor.html#a9ed85386d1877a4c842a1e4de6ca94c4">configTestPrivateAccessor</a></li>
+<li>callRegisterKeyNotFound()&#160;:&#160;<a class="el" href="classconfig_test_private_accessor.html#a5de5045126d1a03e462556e7bc314503">configTestPrivateAccessor</a></li>
+<li>CheckIfKeyUnknown()&#160;:&#160;<a class="el" href="classconfig_test_private_accessor.html#a2e64c804b2c7a25f250e8e178e479550">configTestPrivateAccessor</a></li>
+<li>Composition()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a4d6440dcd749d9f8e5d83ca85878311c">serif::composition::Composition</a></li>
+<li>CompositionEntry()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#ab19c35239824ec2e6b8fedd4f93fe59e">serif::composition::CompositionEntry</a></li>
+<li>computeBlockOffsets()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a3e23e4843b735dcf23782e5273004930">serif::polytrope::PolySolver</a></li>
+<li>Constant()&#160;:&#160;<a class="el" href="structserif_1_1constant_1_1_constant.html#a065affdd5f1deef4c743a9fd2075e869">serif::constant::Constant</a></li>
+<li>Constants()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#af27bfe943a6d02ea9a4740e1c015c705">serif::constant::Constants</a></li>
+<li>construct_jacobian_constant_terms()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#ad0f1686571720135c2bd6bf7c906de9c">serif::polytrope::PolytropeOperator</a></li>
+<li>construct_matrix_representations()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a9b8a2515a9cd420823b8783565457554">serif::polytrope::PolytropeOperator</a></li>
+<li>construct_reduced_block_offsets()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a44dd22d256274552a4e2a062a556607a">serif::polytrope::PolytropeOperator</a></li>
+<li>convert_netIn()&#160;:&#160;<a class="el" href="classserif_1_1network_1_1approx8_1_1_approx8_network.html#a2578a3fa5f1ad880d8bede87ed6b8460">serif::network::approx8::Approx8Network</a></li>
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-<h3><a id="index_d"></a>- d -</h3><ul>
-<li>DObject()
-: <a class="el" href="classDObject.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>
-</li>
+<h3><a id="index_e" name="index_e"></a>- e -</h3><ul>
+<li>EosIO()&#160;:&#160;<a class="el" href="classserif_1_1eos_1_1_eos_i_o.html#afd7bfc464ba6dfdbc15750f500656e0a">serif::eos::EosIO</a></li>
+<li>evaluate()&#160;:&#160;<a class="el" href="classserif_1_1network_1_1approx8_1_1_approx8_network.html#a1b592b4dd76a2a0a62dbc21a66869cef">serif::network::approx8::Approx8Network</a>, <a class="el" href="classserif_1_1network_1_1_network.html#a1fbbd504511f4e20074f47063d99db59">serif::network::Network</a></li>
 </ul>


-<h3><a id="index_g"></a>- g -</h3><ul>
-<li>get()
-: <a class="el" href="classConstants.html#a36ddd7fe6857d1bbf6d1c84d4ed7bc19">Constants</a>
-, <a class="el" href="classLockableDObject.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject</a>
-</li>
-<li>getByteSize()
-: <a class="el" href="classMetadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata</a>
-</li>
-<li>getData()
-: <a class="el" href="classDObject.html#a4862655c3634d019b0a45b811d6f7235">DObject</a>
-</li>
-<li>getDataAs()
-: <a class="el" href="classDObject.html#aca2db093c1c8c6f7893de07544aed619">DObject</a>
-</li>
-<li>getDataType()
-: <a class="el" href="classMetadata.html#aeed7f22ccc61d9a3d6425441d381dcdc">Metadata</a>
-</li>
-<li>getDimensions()
-: <a class="el" href="classMetadata.html#a412c0c0b8754d85f9edbbdcd637f3b20">Metadata</a>
-</li>
-<li>getErrorCode()
-: <a class="el" href="classDObject.html#afa8926d916081de72478cb8813c25e98">DObject</a>
-</li>
-<li>getHeader()
-: <a class="el" href="classOpatIO.html#afe725b647bc5bb802f6d711fc5dca3ab">OpatIO</a>
-</li>
-<li>getInstance()
-: <a class="el" href="classConstants.html#aaa6f3af20fa563cf22df71a987923065">Constants</a>
-</li>
-<li>getMaxQDepth()
-: <a class="el" href="classOpatIO.html#a48cd5e4f3fdb221bc1b6253e149e8e01">OpatIO</a>
-</li>
-<li>GetMesh()
-: <a class="el" href="classMeshIO.html#a3e4bccff08abf9a28b3d64c8fb9f7317">MeshIO</a>
-</li>
-<li>getNumIndex()
-: <a class="el" href="classOpatIO.html#a8f7cc9a4ec8845c22df330678afd29c6">OpatIO</a>
-</li>
-<li>getOPATVersion()
-: <a class="el" href="classOpatIO.html#a2894437c09f4cdb06c9b06d6aad4bd2f">OpatIO</a>
-</li>
-<li>getTable()
-: <a class="el" href="classOpatIO.html#a5c35b863873239e023427864ed016f58">OpatIO</a>
-</li>
-<li>getTableIndex()
-: <a class="el" href="classOpatIO.html#af0bc6bb210c4ff74bc1e043aeb252e1a">OpatIO</a>
-</li>
+<h3><a id="index_f" name="index_f"></a>- f -</h3><ul>
+<li>finalize()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a8308d68b06dd878c88b2b811583b506a">serif::composition::Composition</a>, <a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a25e32d09fd447b067a6d4eafbce7b855">serif::polytrope::PolytropeOperator</a></li>
+<li>finalizeMassFracMode()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a452328138249daff620a1456492053bf">serif::composition::Composition</a></li>
+<li>finalizeNumberFracMode()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a93ef21072ce2c887dee25a98ef62f392">serif::composition::Composition</a></li>
+<li>findCenterElement()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#aa6c616ae4ea0dafd3dc92860ae2bf247">serif::polytrope::PolySolver</a></li>
 </ul>


-<h3><a id="index_h"></a>- h -</h3><ul>
-<li>has()
-: <a class="el" href="classConstants.html#a2aa041fd223f259e55bf098c90581039">Constants</a>
-</li>
+<h3><a id="index_g" name="index_g"></a>- g -</h3><ul>
+<li>get()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#af31ca8c845765f54641735316f36b4b5">serif::constant::Constants</a></li>
+<li>get_block_offsets()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a99a7d2d6631344c04e18068c0fa8cc5b">serif::polytrope::PolytropeOperator</a></li>
+<li>get_essential_true_dofs()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a845cae6df0e574657fb7b15496fd2ade">serif::polytrope::PolytropeOperator</a></li>
+<li>get_free_dofs()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a637dbe63b37d5a6089c39830eec7e488">serif::polytrope::PolytropeOperator</a></li>
+<li>get_jacobian_operator()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a7b968c4dc7d338e36b75fc3efd1114b2">serif::polytrope::PolytropeOperator</a></li>
+<li>get_preconditioner()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#ac323a14e8f4bf5afcd85a0b802ca72cf">serif::polytrope::PolytropeOperator</a></li>
+<li>get_reduced_block_offsets()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#aa3ac1b125083008e5a465caa6db4bd04">serif::polytrope::PolytropeOperator</a></li>
+<li>get_reduced_system_size()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a94e582b0aeac97aff16b63db0a8137b2">serif::polytrope::PolytropeOperator</a></li>
+<li>getAvaliableResources()&#160;:&#160;<a class="el" href="classserif_1_1resource_1_1_resource_manager.html#a77243baf9aa96d5f3c1635f8a34b48b5">serif::resource::ResourceManager</a></li>
+<li>getComposition()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a7fb0a21428bd55ce156f17d19d10a557">serif::composition::Composition</a></li>
+<li>GetDofCoordinates()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a3d70b1098484fa1b0b384d291610d07c">serif::polytrope::PolySolver</a></li>
+<li>getEssentialTrueDof()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a26e30f4424c746dbda63b387674dbf26">serif::polytrope::PolySolver</a></li>
+<li>getFormat()&#160;:&#160;<a class="el" href="classserif_1_1eos_1_1_eos_i_o.html#a58c3fd6063593fa14eaad85340b82d3d">serif::eos::EosIO</a></li>
+<li>GetGradient()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a55d3e6dd6037eed30f3ebf52ca2d2a80">serif::polytrope::PolytropeOperator</a></li>
+<li>getInstance()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#a9f5ea958e59c0cc3a09760d65199a3d8">serif::constant::Constants</a>, <a class="el" href="classserif_1_1probe_1_1_log_manager.html#a78db97bdbb72254855501677b18bc67e">serif::probe::LogManager</a>, <a class="el" href="classserif_1_1resource_1_1_resource_manager.html#a70b5ce13f2b169ccdaa23f73ad070bf0">serif::resource::ResourceManager</a></li>
+<li>getLogger()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a1dba1bc242c599c42c4882e5ab35c431">serif::probe::LogManager</a></li>
+<li>getLoggerNames()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a98d6bf86e6d7e6948f91ae4786b94940">serif::probe::LogManager</a></li>
+<li>getLoggers()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a64dc9652f8e060750c3f6c97d9d62047">serif::probe::LogManager</a></li>
+<li>getMassFracMode()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#af7e046098066c0f3a6372eee3cd459a2">serif::composition::CompositionEntry</a></li>
+<li>getMassFraction()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a063176b2e4ff9f29111f08f74e21c14c">serif::composition::Composition</a></li>
+<li>GetMesh()&#160;:&#160;<a class="el" href="classserif_1_1mesh_1_1_mesh_i_o.html#ae46a00d0a57e0f67f3dd7f57b9685b9c">serif::mesh::MeshIO</a></li>
+<li>getMesh()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#adacb9b9ca63bf49956accb36e182f148">serif::polytrope::PolySolver</a></li>
+<li>getN()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#aace004c231e8ec057714fbca9fa8caae">serif::polytrope::PolySolver</a></li>
+<li>getNumberFraction()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a0020ef34d2e4170495f36074af391e6c">serif::composition::Composition</a></li>
+<li>getOrder()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#adbf0f08417551b87c93b9ad864460d81">serif::polytrope::PolySolver</a></li>
+<li>getRegisteredSymbols()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a45b3ee396daad93e44387c71b0929ddd">serif::composition::Composition</a></li>
+<li>getResource()&#160;:&#160;<a class="el" href="classserif_1_1resource_1_1_resource_manager.html#a0c187f9ef3abc3200d992ef008cfb40a">serif::resource::ResourceManager</a></li>
+<li>getSolution()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a33ae7fcf09e558949f34eaf2df1388a1">serif::polytrope::PolySolver</a></li>
+<li>getTable()&#160;:&#160;<a class="el" href="classserif_1_1eos_1_1_eos_i_o.html#ae5dff85fb847d0c284997dfb75ccf327">serif::eos::EosIO</a></li>
+<li>GMRESInverter()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_g_m_r_e_s_inverter.html#a26e52db2e259ceb0efc74a188a0626df">serif::polytrope::GMRESInverter</a></li>
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-<h3><a id="index_i"></a>- i -</h3><ul>
-<li>isDebugEnabled()
-: <a class="el" href="classMetadata.html#abe52c81e04665628666b4140cd346b69">Metadata</a>
-</li>
-<li>isDebuggingEnabled()
-: <a class="el" href="classDObject.html#ae47bf220fbe2173cf6933c2380035dbd">DObject</a>
-</li>
-<li>isLoaded()
-: <a class="el" href="classConstants.html#ae276dfdc0ffe75a53e3842e33ab52630">Constants</a>
-</li>
-<li>IsLoaded()
-: <a class="el" href="classMeshIO.html#a12495fc814254021d44e0509ac760672">MeshIO</a>
-</li>
-<li>isLoaded()
-: <a class="el" href="classOpatIO.html#aba1be05d51d4b0b9e4581b95ad0e1890">OpatIO</a>
-</li>
+<h3><a id="index_h" name="index_h"></a>- h -</h3><ul>
+<li>has()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#a71aa21de5e8ee9f5fc23169df28f9a4e">serif::constant::Constants</a></li>
+<li>hasSymbol()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a01e00a40385ebc61c93dba8064733f7f">serif::composition::Composition</a></li>
+<li>HELMTable()&#160;:&#160;<a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html#a884959cf006a38fdad597724891f88b3">serif::eos::helmholtz::HELMTable</a></li>
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-<h3><a id="index_k"></a>- k -</h3><ul>
-<li>keys()
-: <a class="el" href="classConstants.html#ab9de36fa145552a3e7964e7e85a67149">Constants</a>
-</li>
+<h3><a id="index_i" name="index_i"></a>- i -</h3><ul>
+<li>initialize()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#a88578dd2dc433c5c862b01a1539862fe">serif::constant::Constants</a></li>
+<li>isFinalized()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a99b59a8f7cf8ac1f6106ee9cb014c931">serif::polytrope::PolytropeOperator</a></li>
+<li>IsLoaded()&#160;:&#160;<a class="el" href="classserif_1_1mesh_1_1_mesh_i_o.html#aa685c3f323d5189edfa326c866f552d6">serif::mesh::MeshIO</a></li>
+<li>isLoaded()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#abaebbd4df3f8ce0162b1f6014f2420ac">serif::constant::Constants</a></li>
+<li>isotope()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#a17eb67ef1c07528295db845150c32615">serif::composition::CompositionEntry</a></li>
+<li>isStiff()&#160;:&#160;<a class="el" href="classserif_1_1network_1_1approx8_1_1_approx8_network.html#a2e1f6e00bd622d2186724680dce7184f">serif::network::approx8::Approx8Network</a></li>
+<li>isValidComposition()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a14d19ec7ff396768bfe553522abc44db">serif::composition::Composition</a></li>
+<li>isValidSymbol()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a753bcffca93a4dd8a0f38afc00cf05fb">serif::composition::Composition</a></li>
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-<h3><a id="index_l"></a>- l -</h3><ul>
-<li>load()
-: <a class="el" href="classOpatIO.html#a3578ac9bad40dd45ada3459f92a93b56">OpatIO</a>
-</li>
-<li>lock()
-: <a class="el" href="classLockableDObject.html#ade38ca54703913359fc3b4366f6e292a">LockableDObject</a>
-</li>
-<li>LockableDObject()
-: <a class="el" href="classLockableDObject.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a>
-</li>
-<li>lookupClosestTableID()
-: <a class="el" href="classOpatIO.html#a82715d95a5ddd1e78470b90fbd005c4d">OpatIO</a>
-</li>
-<li>lookupTableID()
-: <a class="el" href="classOpatIO.html#a1a4456b7745c0dd559eca72d5d744fc0">OpatIO</a>
-</li>
+<h3><a id="index_k" name="index_k"></a>- k -</h3><ul>
+<li>keys()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#a74dd8438a0f96ef5ee4f0d97c5a83f21">serif::constant::Constants</a></li>
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-<h3><a id="index_m"></a>- m -</h3><ul>
-<li>MeshIO()
-: <a class="el" href="classMeshIO.html#a8fe43b55b7851c805c276517b0aacac5">MeshIO</a>
-</li>
-<li>Metadata()
-: <a class="el" href="classMetadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>
-</li>
+<h3><a id="index_l" name="index_l"></a>- l -</h3><ul>
+<li>LinearRescale()&#160;:&#160;<a class="el" href="classserif_1_1mesh_1_1_mesh_i_o.html#a059c3c5dbabff0d175a6dccfbe8819f6">serif::mesh::MeshIO</a></li>
+<li>load()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#aa9c956328b38dc37136afa98cc5edc49">serif::constant::Constants</a>, <a class="el" href="classserif_1_1eos_1_1_eos_i_o.html#ae7defa9a9e1b4a05f5220faf24ee2810">serif::eos::EosIO</a>, <a class="el" href="classserif_1_1resource_1_1_resource_manager.html#ad27100286a53042182fe6c2315dc32c6">serif::resource::ResourceManager</a></li>
+<li>loadAllResources()&#160;:&#160;<a class="el" href="classserif_1_1resource_1_1_resource_manager.html#ace59a058090680691c1d5fdc1c3d9896">serif::resource::ResourceManager</a></li>
+<li>loadHelm()&#160;:&#160;<a class="el" href="classserif_1_1eos_1_1_eos_i_o.html#a01213c94ceed0860810411288f185a02">serif::eos::EosIO</a></li>
+<li>loadResource()&#160;:&#160;<a class="el" href="classserif_1_1resource_1_1_resource_manager.html#ae50d8cd6e967d02ca9e04220778d4b57">serif::resource::ResourceManager</a></li>
+<li>LoadSolverUserParams()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a9054799327ed6752e33bf88e0722ebfc">serif::polytrope::PolySolver</a></li>
+<li>LogManager()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a0b6ca6d6064efb3d7b0d05d222238fed">serif::probe::LogManager</a></li>
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-<h3><a id="index_n"></a>- n -</h3><ul>
-<li>NonlinearPowerIntegrator()
-: <a class="el" href="classNonlinearPowerIntegrator.html#a0578e900c8e95cfa1161362c98fd3d31">NonlinearPowerIntegrator</a>
-</li>
+<h3><a id="index_m" name="index_m"></a>- m -</h3><ul>
+<li>mass_fraction()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#a8dc5fd664434eed80c9a476bc36978f1">serif::composition::CompositionEntry</a></li>
+<li>MeshIO()&#160;:&#160;<a class="el" href="classserif_1_1mesh_1_1_mesh_i_o.html#aa08d33bc551cc289002cda7c9628bcce">serif::mesh::MeshIO</a></li>
+<li>mix()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a5b493cbd3219704d7eca1f276e79c4ce">serif::composition::Composition</a></li>
+<li>Mult()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_g_m_r_e_s_inverter.html#a698ccfa71e87e381b6c0a4d7a081a776">serif::polytrope::GMRESInverter</a>, <a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a3967768a154ffd53cae54e1b69ef32a5">serif::polytrope::PolytropeOperator</a>, <a class="el" href="classserif_1_1polytrope_1_1_schur_compliment.html#a697f3d788eaac9124e17c905b4b3d19f">serif::polytrope::SchurCompliment</a></li>
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-<h3><a id="index_o"></a>- o -</h3><ul>
-<li>OpatIO()
-: <a class="el" href="classOpatIO.html#a7f3436b3ac0dbe141b08d8064550f1b3">OpatIO</a>
-</li>
-<li>operator[]()
-: <a class="el" href="classConstants.html#ad75620743b867fc20d4a05027d1a1c01">Constants</a>
-</li>
+<h3><a id="index_n" name="index_n"></a>- n -</h3><ul>
+<li>Network()&#160;:&#160;<a class="el" href="classserif_1_1network_1_1_network.html#a24e5233caa58d04a3064783be69c6011">serif::network::Network</a></li>
+<li>newFileLogger()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a74964777715ea748c3c88491f4d0697f">serif::probe::LogManager</a></li>
+<li>NonlinearPowerIntegrator()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1poly_m_f_e_m_utils_1_1_nonlinear_power_integrator.html#a1755c6ed93aa9aa09b54254b16f38b69">serif::polytrope::polyMFEMUtils::NonlinearPowerIntegrator</a></li>
+<li>number_fraction()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#a74a1d1362ee06e0414d96542be64036d">serif::composition::CompositionEntry</a></li>
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-<h3><a id="index_p"></a>- p -</h3><ul>
-<li>printHeader()
-: <a class="el" href="classOpatIO.html#a117f7e1f45d6c410c21d0644e447bbb1">OpatIO</a>
-</li>
-<li>printTable()
-: <a class="el" href="classOpatIO.html#afae90144930f190ed4018fbf328bf8ea">OpatIO</a>
-</li>
-<li>printTableIndex()
-: <a class="el" href="classOpatIO.html#afa623ba10f188097e555a682a4c69a9f">OpatIO</a>
-</li>
+<h3><a id="index_o" name="index_o"></a>- o -</h3><ul>
+<li>operator()()&#160;:&#160;<a class="el" href="structserif_1_1network_1_1approx8_1_1_jacobian.html#a8b2b6104944902f9ae737fd7a2aac7c9">serif::network::approx8::Jacobian</a>, <a class="el" href="structserif_1_1network_1_1approx8_1_1_o_d_e.html#a040a8c59f79d7b890076e7f0eb1f94de">serif::network::approx8::ODE</a></li>
+<li>operator+()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#aa53bed008cfde8ff4f2e51a352c52afe">serif::composition::Composition</a></li>
+<li>operator=()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#a5bf06167fb1e8da5248fe2cb0385ad53">serif::probe::LogManager</a>, <a class="el" href="classserif_1_1resource_1_1_resource_manager.html#ae82262af7c49d6a9d0158514a9e5a572">serif::resource::ResourceManager</a></li>
+<li>operator[]()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#a11a887b54836c00beecd14b110bc0d5d">serif::constant::Constants</a></li>
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-<h3><a id="index_r"></a>- r -</h3><ul>
-<li>registerPlugin()
-: <a class="el" href="classDObject.html#a15afffdf339150fc872bf63bdd08d581">DObject</a>
-</li>
-<li>runAllPlugins()
-: <a class="el" href="classDObject.html#a1223275dcbbf20334ea11707346acb93">DObject</a>
-</li>
-<li>runPlugin()
-: <a class="el" href="classDObject.html#a99072eb52bb22745f0248f273fbf28fb">DObject</a>
-</li>
+<h3><a id="index_p" name="index_p"></a>- p -</h3><ul>
+<li>PolySolver()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a2c11412977ffbd57ccc85a2a38c0343e">serif::polytrope::PolySolver</a></li>
+<li>PolytropeOperator()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a667449268dd8e49bce15d870c5c06a34">serif::polytrope::PolytropeOperator</a></li>
+<li>populate_free_dof_array()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a3e41f4a3cb8c34cc1ffcb531d4b7bf18">serif::polytrope::PolytropeOperator</a></li>
+<li>prepareMesh()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#aa5ff308c9a7cce691e2c03e2b8ebc7ee">serif::polytrope::PolySolver</a></li>
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-<h3><a id="index_s"></a>- s -</h3><ul>
-<li>setByteSize()
-: <a class="el" href="classMetadata.html#a07035de7b0c780ef340e1a11c60a4d2b">Metadata</a>
-</li>
-<li>setData()
-: <a class="el" href="classDObject.html#ab1718571434e84e90f1ec463e4786a8a">DObject</a>
-</li>
-<li>setDataType()
-: <a class="el" href="classMetadata.html#a88f4f57d443e2b7664e75e57a29dfbf0">Metadata</a>
-</li>
-<li>setDebugEnabled()
-: <a class="el" href="classMetadata.html#a365c4594ad65c3b10b40a1cf4f4aea26">Metadata</a>
-</li>
-<li>setDebugging()
-: <a class="el" href="classDObject.html#a6f0023aee463e71d92442dcf61b6ed47">DObject</a>
-</li>
-<li>setDimensions()
-: <a class="el" href="classMetadata.html#af5264d1666839e69c192b565b5cfa606">Metadata</a>
-</li>
-<li>setErrorCode()
-: <a class="el" href="classDObject.html#a3dce47a519f9da5085c0c5ac1eea4f38">DObject</a>
-</li>
-<li>setFilename()
-: <a class="el" href="classOpatIO.html#ad189e0f239bc4184fecf7daef7923272">OpatIO</a>
-</li>
-<li>setMaxQDepth()
-: <a class="el" href="classOpatIO.html#ab0edd41690b8d5c1775f87439cf82cb5">OpatIO</a>
-</li>
-<li>SetUp()
-: <a class="el" href="classconstTest.html#af4753885bf401953202f89d455a2702f">constTest</a>
-, <a class="el" href="classDObjectTest.html#a95ba0f78c44e0bd46603de32028b7be6">DObjectTest</a>
-, <a class="el" href="classLockableDObjectTest.html#a4ca643fb176141b51f4761dd3df64769">LockableDObjectTest</a>
-, <a class="el" href="classMetadataTest.html#a6273a370a10b42155af951a8fc2c47fa">MetadataTest</a>
-</li>
+<h3><a id="index_r" name="index_r"></a>- r -</h3><ul>
+<li>reconstruct_full_block_state_vector()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a254f390119cfb84ddb0f422c5a5d7d40">serif::polytrope::PolytropeOperator</a></li>
+<li>reconstruct_full_state_vector()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a8a0fe3f8e5a477d2e33aaed29fb22dd0">serif::polytrope::PolytropeOperator</a></li>
+<li>registerSymbol()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a66fde1b9ae6724aefb8eb98800a0ae2b">serif::composition::Composition</a></li>
+<li>rel_abundance()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#a061453b8c21234b8f05d7093bf1998fc">serif::composition::CompositionEntry</a></li>
+<li>ResourceManager()&#160;:&#160;<a class="el" href="classserif_1_1resource_1_1_resource_manager.html#a3b32babd2e81909bbd90d7f2d566fadb">serif::resource::ResourceManager</a></li>
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-<h3><a id="index_t"></a>- t -</h3><ul>
-<li>TearDown()
-: <a class="el" href="classMetadataTest.html#a24075d61d37dceacd353ecde16a1ac71">MetadataTest</a>
-</li>
+<h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
+<li>saveAndViewSolution()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a0a5356ef1625fcd41e7b04ad22884366">serif::polytrope::PolySolver</a></li>
+<li>scatter_boundary_conditions()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a8b394c9ed626714a49f4212aa17f454c">serif::polytrope::PolytropeOperator</a></li>
+<li>SchurCompliment()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_schur_compliment.html#a213cf397b1fd4e46891937ab1d2b738b">serif::polytrope::SchurCompliment</a></li>
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+<li>setCompositionMode()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#adbaf8124e91249b78943231fc0be4c04">serif::composition::Composition</a></li>
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+<li>setMassFracMode()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#aa204680bddf81496f2fa5aefd6992c88">serif::composition::CompositionEntry</a></li>
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+<li>SetUp()&#160;:&#160;<a class="el" href="classconst_test.html#af4753885bf401953202f89d455a2702f">constTest</a></li>
+<li>setupNewtonSolver()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a582ff9bdcfaeac3ad3497aadb5064990">serif::polytrope::PolySolver</a></li>
+<li>solve()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a275f62a8b6a473ba0fe700692be561b0">serif::polytrope::PolySolver</a></li>
+<li>subset()&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a7acbc7f61d6c68dec03f3866d2c53daf">serif::composition::Composition</a></li>
+<li>symbol()&#160;:&#160;<a class="el" href="structserif_1_1composition_1_1_composition_entry.html#a03afb05a401736976348003bc465a561">serif::composition::CompositionEntry</a></li>
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-<li>unregisterPlugin()
-: <a class="el" href="classDObject.html#a99b8688849e11501033a25f61efb8356">DObject</a>
-</li>
+<h3><a id="index_t" name="index_t"></a>- t -</h3><ul>
+<li>trim()&#160;:&#160;<a class="el" href="classserif_1_1constant_1_1_constants.html#afc1fc624ed4be1fe31a581d7a211df8d">serif::constant::Constants</a></li>
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-: <a class="el" href="classOpatIO.html#aafb5941c4c93104af8ba06f2271a3dc7">OpatIO</a>
-</li>
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-: <a class="el" href="classOpatIO.html#ac34f611a9eab458329553d27e8bffec6">OpatIO</a>
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+
+
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+<li>~HELMTable()&#160;:&#160;<a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html#ae324718638916a18cf505cdcb21ff9cd">serif::eos::helmholtz::HELMTable</a></li>
+<li>~LogManager()&#160;:&#160;<a class="el" href="classserif_1_1probe_1_1_log_manager.html#aa54e2c1cc121707bfc20d24674078d4a">serif::probe::LogManager</a></li>
+<li>~MeshIO()&#160;:&#160;<a class="el" href="classserif_1_1mesh_1_1_mesh_i_o.html#a141be1b68e64421b76a7627d0b5c9546">serif::mesh::MeshIO</a></li>
+<li>~Network()&#160;:&#160;<a class="el" href="classserif_1_1network_1_1_network.html#a1073c0e19c11da221b60916343dbd6e4">serif::network::Network</a></li>
+<li>~PolySolver()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_poly_solver.html#a0fb680aba815bf4f409d9c07a16a0c16">serif::polytrope::PolySolver</a></li>
+<li>~PolytropeOperator()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_polytrope_operator.html#a30894180acd8d2226675cc7e697ac988">serif::polytrope::PolytropeOperator</a></li>
+<li>~SchurCompliment()&#160;:&#160;<a class="el" href="classserif_1_1polytrope_1_1_schur_compliment.html#a3a725e360438516bdca280da31bbfc08">serif::polytrope::SchurCompliment</a></li>
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+ <tr id="projectrow">
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+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
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+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
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-&#160;<ul>
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-: <a class="el" href="structConstant.html#ad298f7af7cdfd2e2267fd9e464558e2b">Constant</a>
-, <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
-, <a class="el" href="classMetadata.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata</a>
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+<li>operator&lt;&lt;&#160;:&#160;<a class="el" href="classserif_1_1composition_1_1_composition.html#a36c2525d21cd932065bb2bb30bc57fb4">serif::composition::Composition</a>, <a class="el" href="structserif_1_1composition_1_1_composition_entry.html#ae7a6a113fc5914248eff5629716d6eb2">serif::composition::CompositionEntry</a>, <a class="el" href="structserif_1_1composition_1_1_global_composition.html#a3c072a749c3648607771ac9105181f26">serif::composition::GlobalComposition</a>, <a class="el" href="structserif_1_1constant_1_1_constant.html#a387b3e0a55788b0ea04c77ba040c5aaa">serif::constant::Constant</a>, <a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_e_o_s.html#a8071bdc90dec68ba933eb59c902a0b7b">serif::eos::helmholtz::EOS</a>, <a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_e_o_s_input.html#ae6bc0662e64e05608593df6129ab8edb">serif::eos::helmholtz::EOSInput</a>, <a class="el" href="structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html#a65eea84782fc9b5b69b6f7f2ebf57940">serif::eos::helmholtz::HELMTable</a></li>
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-</li><li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a>
-</li><li><a href="functions.html"><span>Class&#160;Members</span></a>
-</li></ul>
-</li><li><a href="files.html"><span>Files</span></a>
-<ul><li><a href="files.html"><span>File&#160;List</span></a>
-</li><li><a href="globals.html"><span>File&#160;Members</span></a>
-</li></ul>
-</li></ul>
+<div class="textblock"><h1><a class="anchor" id="intro_sec"></a>
+Introduction</h1>
+<p>Welcome to the documentation for 4DSSE (4D Stellar Structure and Evolution), a new code designed for simulating stellar phenomena in three spatial dimensions plus time. This project is currently under active development.</p>
+<p>The primary goal of 4DSSE is to provide a flexible and extensible framework for advanced stellar modeling, incorporating modern numerical techniques and physics modules.</p>
+<h1><a class="anchor" id="build_sec"></a>
+Building 4DSSE</h1>
+<p>The project uses Meson as its build system. MFEM is a core dependency and will be automatically downloaded and built if not found.</p>
+<p><b>Prerequisites:</b></p><ul>
+<li>A C++ compiler (supporting C++17 or later)</li>
+<li>Meson (Install via pip: <code>pip install meson</code>)</li>
+<li>Python 3</li>
+</ul>
+<p><b>Build Steps:</b></p>
+<ol type="1">
+<li><b>Clone the repository (if you haven't already):</b> <code>bash git clone &lt;repository-url&gt; cd 4dsse </code></li>
+<li><b>Using the <code>mk</code> script (recommended for ease of use):</b><ul>
+<li>To build the project: <code>bash ./mk </code></li>
+<li>To build without tests: <code>bash ./mk --noTest </code></li>
+</ul>
+</li>
+<li><b>Using the <code>4DSSEConsole.sh</code> script:</b> This script provides a simple interface for building and debugging. <code>bash ./4DSSEConsole.sh </code> Follow the on-screen prompts.</li>
+<li><b>Manual Meson build:</b><ul>
+<li>Setup the build directory (e.g., <code>build</code>): <code>bash meson setup build </code></li>
+<li>Compile the project: <code>bash meson compile -C build </code></li>
+<li>To run tests (if built with tests enabled): <code>bash meson test -C build </code></li>
+</ul>
+</li>
+</ol>
+<p>The compiled executables and libraries will typically be found in the <code>build</code> directory.</p>
+<h1><a class="anchor" id="usage_sec"></a>
+High-Level Usage Examples</h1>
+<p>Below are some high-level examples of how to use key components of 4DSSE.</p>
+<h2><a class="anchor" id="usage_polysolver"></a>
+Solving for a Polytrope</h2>
+<p>The <code>PolySolver</code> class handles the setup and solution of the Lane-Emden equation for polytropic stellar models.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="poly_solver_8h.html">polySolver.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="config_8h.html">config.h</a>&quot;</span> <span class="comment">// For global configuration</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="probe_8h.html">probe.h</a>&quot;</span>  <span class="comment">// For logging</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    <span class="comment">// Initialize configuration and logging</span></div>
+<div class="line">    Config::getInstance().loadConfig(<span class="stringliteral">&quot;path/to/your/config.yaml&quot;</span>);</div>
+<div class="line">    Probe::LogManager::getInstance().getLogger(<span class="stringliteral">&quot;main_log&quot;</span>); <span class="comment">// Initialize a logger</span></div>
+<div class="line"> </div>
+<div class="line">    <span class="keywordflow">try</span> {</div>
+<div class="line">        <span class="comment">// Create a PolySolver for polytropic index n=1.5 and FE order 2</span></div>
+<div class="line">        PolySolver solver(1.5, 2);</div>
+<div class="line">        solver.solve(); <span class="comment">// Solve the system</span></div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Access the solution</span></div>
+<div class="line">        mfem::GridFunction&amp; theta_solution = solver.getSolution();</div>
+<div class="line">        <span class="comment">// ... process or visualize theta_solution ...</span></div>
+<div class="line"> </div>
+<div class="line">    } <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::exception&amp; e) {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;An error occurred: &quot;</span> &lt;&lt; e.what() &lt;&lt; std::endl;</div>
+<div class="line">        <span class="keywordflow">return</span> 1;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="acomp_8cpp_html_ac4c0f8a8146b128f1b8f920e3a9c3b1e"><div class="ttname"><a href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a></div><div class="ttdeci">int main(int argv, char *argc[])</div><div class="ttdef"><b>Definition</b> <a href="comp_8cpp_source.html#l00005">comp.cpp:5</a></div></div>
+<div class="ttc" id="aconfig_8h_html"><div class="ttname"><a href="config_8h.html">config.h</a></div></div>
+<div class="ttc" id="apoly_solver_8h_html"><div class="ttname"><a href="poly_solver_8h.html">polySolver.h</a></div></div>
+<div class="ttc" id="aprobe_8h_html"><div class="ttname"><a href="probe_8h.html">probe.h</a></div></div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_composition"></a>
+Managing Chemical Compositions</h2>
+<p>The <code>Composition</code> class allows for defining and managing chemical compositions.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="composition_8h.html">composition.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    <span class="keywordflow">try</span> {</div>
+<div class="line">        <span class="comment">// Define symbols and their mass fractions</span></div>
+<div class="line">        std::vector&lt;std::string&gt; symbols = {<span class="stringliteral">&quot;H-1&quot;</span>, <span class="stringliteral">&quot;He-4&quot;</span>}; <span class="comment">// Use specific isotopes</span></div>
+<div class="line">        std::vector&lt;double&gt; mass_fractions = {0.75, 0.25};</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Create and finalize the composition</span></div>
+<div class="line">        composition::Composition comp(symbols, mass_fractions);</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Get mass fraction of a specific element</span></div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Mass fraction of H-1: &quot;</span> &lt;&lt; comp.getMassFraction(<span class="stringliteral">&quot;H-1&quot;</span>) &lt;&lt; std::endl;</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Get global properties</span></div>
+<div class="line">        <span class="keyword">auto</span> global_props = comp.getComposition().second;</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Mean particle mass: &quot;</span> &lt;&lt; global_props.meanParticleMass &lt;&lt; std::endl;</div>
+<div class="line"> </div>
+<div class="line">    } <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::exception&amp; e) {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;Composition error: &quot;</span> &lt;&lt; e.what() &lt;&lt; std::endl;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="acomposition_8h_html"><div class="ttname"><a href="composition_8h.html">composition.h</a></div></div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_network"></a>
+Nuclear Reaction Networks</h2>
+<p>The <code>Network</code> and <code>Approx8Network</code> classes provide interfaces for nuclear reaction network calculations.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="network_8h.html">network.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="approx8_8h.html">approx8.h</a>&quot;</span> <span class="comment">// Specific network implementation</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    nnApprox8::Approx8Network approx8_net; <span class="comment">// Using the Approx8 network</span></div>
+<div class="line">    approx8_net.setStiff(<span class="keyword">true</span>); <span class="comment">// Example: use stiff solver</span></div>
+<div class="line"> </div>
+<div class="line">    nuclearNetwork::NetIn input;</div>
+<div class="line">    input.composition = {0.7, 0.0, 0.28, 0.01, 0.005, 0.004, 0.0005, 0.0005}; <span class="comment">// H1, He3, He4, C12, N14, O16, Ne20, Mg24</span></div>
+<div class="line">    input.temperature = 1.5e7; <span class="comment">// K</span></div>
+<div class="line">    input.density = 150.0;     <span class="comment">// g/cm^3</span></div>
+<div class="line">    input.tmax = 1.0e10;   <span class="comment">// s</span></div>
+<div class="line">    input.dt0 = 1.0e6;     <span class="comment">// s</span></div>
+<div class="line">    <span class="comment">// input.energy can also be set if needed</span></div>
+<div class="line"> </div>
+<div class="line">    <span class="keywordflow">try</span> {</div>
+<div class="line">        nuclearNetwork::NetOut output = approx8_net.evaluate(input);</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Number of steps: &quot;</span> &lt;&lt; output.num_steps &lt;&lt; std::endl;</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Final H-1 mass fraction (approx): &quot;</span> &lt;&lt; output.composition[nnApprox8::Net::ih1] &lt;&lt; std::endl;</div>
+<div class="line">    } <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::exception&amp; e) {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;Network evaluation error: &quot;</span> &lt;&lt; e.what() &lt;&lt; std::endl;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="aapprox8_8h_html"><div class="ttname"><a href="approx8_8h.html">approx8.h</a></div><div class="ttdoc">Header file for the Approx8 nuclear reaction network.</div></div>
+<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_constants"></a>
+Accessing Physical Constants</h2>
+<p>The <code>Constants</code> singleton provides access to a database of physical constants.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="const_8h.html">const.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    Constants&amp; consts = Constants::getInstance();</div>
+<div class="line">    <span class="keywordflow">if</span> (consts.isLoaded()) {</div>
+<div class="line">        Constant G = consts.get(<span class="stringliteral">&quot;Gravitational constant&quot;</span>);</div>
+<div class="line">        std::cout &lt;&lt; G.name &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; G.value &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; G.unit &lt;&lt; std::endl;</div>
+<div class="line"> </div>
+<div class="line">        Constant c = consts[<span class="stringliteral">&quot;Speed of light in vacuum&quot;</span>]; <span class="comment">// Can also use operator[]</span></div>
+<div class="line">        std::cout &lt;&lt; c.name &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; c.value &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; c.unit &lt;&lt; std::endl;</div>
+<div class="line">    } <span class="keywordflow">else</span> {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;Failed to load constants.&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="aconst_8h_html"><div class="ttname"><a href="const_8h.html">const.h</a></div></div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_config"></a>
+Configuration Management</h2>
+<p>The <code>Config</code> singleton manages settings from a YAML configuration file.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="config_8h.html">config.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    Config&amp; config = Config::getInstance();</div>
+<div class="line">    <span class="keywordflow">if</span> (config.loadConfig(<span class="stringliteral">&quot;path/to/your/config.yaml&quot;</span>)) {</div>
+<div class="line">        <span class="comment">// Get a string value, with a default if not found</span></div>
+<div class="line">        std::string outputPath = config.get&lt;std::string&gt;(<span class="stringliteral">&quot;Output:Path&quot;</span>, <span class="stringliteral">&quot;./output/&quot;</span>);</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Output path: &quot;</span> &lt;&lt; outputPath &lt;&lt; std::endl;</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Get an integer value</span></div>
+<div class="line">        <span class="keywordtype">int</span> maxIter = config.get&lt;<span class="keywordtype">int</span>&gt;(<span class="stringliteral">&quot;Solver:MaxIterations&quot;</span>, 100);</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Max iterations: &quot;</span> &lt;&lt; maxIter &lt;&lt; std::endl;</div>
+<div class="line">    } <span class="keywordflow">else</span> {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;Failed to load configuration.&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_logging"></a>
+Logging</h2>
+<p>The <code>Probe::LogManager</code> provides a way to manage and use loggers.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="probe_8h.html">probe.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="config_8h.html">config.h</a>&quot;</span> <span class="comment">// Often used to configure logging</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    <span class="comment">// Assuming config is loaded and might define log file, level etc.</span></div>
+<div class="line">    <span class="comment">// Config::getInstance().loadConfig(&quot;config.yaml&quot;);</span></div>
+<div class="line"> </div>
+<div class="line">    Probe::LogManager&amp; logManager = Probe::LogManager::getInstance();</div>
+<div class="line">    quill::Logger* mainLogger = logManager.getLogger(<span class="stringliteral">&quot;main_app_log&quot;</span>); <span class="comment">// Get or create logger</span></div>
+<div class="line"> </div>
+<div class="line">    <span class="comment">// Example: Create a new file logger if not configured through a central mechanism</span></div>
+<div class="line">    <span class="comment">// quill::Logger* fileLogger = logManager.newFileLogger(&quot;app_trace.log&quot;, &quot;trace_log&quot;);</span></div>
+<div class="line"> </div>
+<div class="line">    LOG_INFO(mainLogger, <span class="stringliteral">&quot;Application started. Version: {}&quot;</span>, <span class="stringliteral">&quot;1.0.0&quot;</span>);</div>
+<div class="line">    <span class="comment">// ... application logic ...</span></div>
+<div class="line">    LOG_ERROR(mainLogger, <span class="stringliteral">&quot;An unexpected error occurred in module X.&quot;</span>);</div>
+<div class="line"> </div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_eos"></a>
+Equation of State (EOS)</h2>
+<p>The <code>EosIO</code> class loads EOS tables, and the <code>helmholtz</code> namespace provides functions to use them, for example, the Helmholtz EOS.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="eos_i_o_8h.html">eosIO.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;<a class="code" href="helm_8h.html">helm.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    <span class="keywordflow">try</span> {</div>
+<div class="line">        <span class="comment">// Load the Helmholtz EOS table</span></div>
+<div class="line">        EosIO helm_eos_io(<span class="stringliteral">&quot;path/to/helm_table.dat&quot;</span>); <span class="comment">// Replace with actual path</span></div>
+<div class="line">        EOSTable&amp; table_variant = helm_eos_io.getTable();</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Assuming it&#39;s a HELMTable, get it (add error checking in real code)</span></div>
+<div class="line">        <span class="keyword">auto</span>* helm_table_ptr = std::get_if&lt;std::unique_ptr&lt;helmholtz::HELMTable&gt;&gt;(&amp;table_variant);</div>
+<div class="line">        <span class="keywordflow">if</span> (!helm_table_ptr || !(*helm_table_ptr) || !(*helm_table_ptr)-&gt;loaded) {</div>
+<div class="line">            std::cerr &lt;&lt; <span class="stringliteral">&quot;Failed to load or access HELM table.&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">            <span class="keywordflow">return</span> 1;</div>
+<div class="line">        }</div>
+<div class="line">        <span class="keyword">const</span> helmholtz::HELMTable&amp; table = **helm_table_ptr;</div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Define input conditions</span></div>
+<div class="line">        helmholtz::EOSInput input;</div>
+<div class="line">        input.T = 1.0e7;    <span class="comment">// Temperature in K</span></div>
+<div class="line">        input.rho = 100.0;  <span class="comment">// Density in g/cm^3</span></div>
+<div class="line">        input.abar = 1.0;   <span class="comment">// Mean atomic mass (e.g., for pure hydrogen)</span></div>
+<div class="line">        input.zbar = 1.0;   <span class="comment">// Mean atomic number (e.g., for pure hydrogen)</span></div>
+<div class="line"> </div>
+<div class="line">        <span class="comment">// Get EOS results</span></div>
+<div class="line">        helmholtz::EOS results = helmholtz::get_helm_EOS(input, table);</div>
+<div class="line"> </div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Total Pressure (Ptot): &quot;</span> &lt;&lt; results.ptot &lt;&lt; <span class="stringliteral">&quot; dyne/cm^2&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">        std::cout &lt;&lt; <span class="stringliteral">&quot;Total Energy (Etot): &quot;</span> &lt;&lt; results.etot &lt;&lt; <span class="stringliteral">&quot; erg/g&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"> </div>
+<div class="line">    } <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::exception&amp; e) {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;EOS error: &quot;</span> &lt;&lt; e.what() &lt;&lt; std::endl;</div>
+<div class="line">        <span class="keywordflow">return</span> 1;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="aeos_i_o_8h_html"><div class="ttname"><a href="eos_i_o_8h.html">eosIO.h</a></div></div>
+<div class="ttc" id="ahelm_8h_html"><div class="ttname"><a href="helm_8h.html">helm.h</a></div></div>
+</div><!-- fragment --><h2><a class="anchor" id="usage_meshio"></a>
+Mesh Handling</h2>
+<p>The <code>MeshIO</code> class facilitates loading and managing computational meshes.</p>
+<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="mesh_i_o_8h.html">meshIO.h</a>&quot;</span></div>
+<div class="line"><span class="preprocessor">#include &quot;mfem.hpp&quot;</span> <span class="comment">// For mfem::Mesh</span></div>
+<div class="line"><span class="preprocessor">#include &lt;iostream&gt;</span></div>
+<div class="line"> </div>
+<div class="line"><span class="keywordtype">int</span> <a class="code hl_function" href="comp_8cpp.html#ac4c0f8a8146b128f1b8f920e3a9c3b1e">main</a>() {</div>
+<div class="line">    <span class="keywordflow">try</span> {</div>
+<div class="line">        <span class="comment">// Initialize MeshIO with a mesh file and a scale factor</span></div>
+<div class="line">        MeshIO mesh_handler(<span class="stringliteral">&quot;path/to/your/mesh.msh&quot;</span>, 1.0); <span class="comment">// Replace with actual path</span></div>
+<div class="line"> </div>
+<div class="line">        <span class="keywordflow">if</span> (mesh_handler.IsLoaded()) {</div>
+<div class="line">            mfem::Mesh&amp; mesh = mesh_handler.GetMesh();</div>
+<div class="line">            std::cout &lt;&lt; <span class="stringliteral">&quot;Mesh loaded successfully with &quot;</span> &lt;&lt; mesh.GetNE() &lt;&lt; <span class="stringliteral">&quot; elements.&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">            </div>
+<div class="line">            <span class="comment">// Optionally, rescale the mesh</span></div>
+<div class="line">            <span class="comment">// mesh_handler.LinearRescale(2.0);</span></div>
+<div class="line">            <span class="comment">// std::cout &lt;&lt; &quot;Mesh rescaled. New bounding box: &quot;;</span></div>
+<div class="line">            <span class="comment">// mfem::Vector min, max;</span></div>
+<div class="line">            <span class="comment">// mesh.GetBoundingBox(min, max);</span></div>
+<div class="line">            <span class="comment">// min.Print(std::cout); max.Print(std::cout);</span></div>
+<div class="line">        } <span class="keywordflow">else</span> {</div>
+<div class="line">            std::cerr &lt;&lt; <span class="stringliteral">&quot;Failed to load mesh.&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line">        }</div>
+<div class="line">    } <span class="keywordflow">catch</span> (<span class="keyword">const</span> std::exception&amp; e) {</div>
+<div class="line">        std::cerr &lt;&lt; <span class="stringliteral">&quot;MeshIO error: &quot;</span> &lt;&lt; e.what() &lt;&lt; std::endl;</div>
+<div class="line">    }</div>
+<div class="line">    <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+<div class="ttc" id="amesh_i_o_8h_html"><div class="ttname"><a href="mesh_i_o_8h.html">meshIO.h</a></div></div>
+</div><!-- fragment --><h1><a class="anchor" id="modules_sec"></a>
+Key Modules and Components</h1>
+<p>4DSSE is organized into several key modules:</p>
+<ul>
+<li><b>Polytrope Solver (<code><a class="el" href="poly_solver_8h.html">polySolver.h</a></code>, <code><a class="el" href="polytrope_operator_8h.html">polytropeOperator.h</a></code>):</b> Provides tools to solve the Lane-Emden equation for polytropic stellar structures using a mixed finite element method. <code>PolytropeOperator</code> defines the nonlinear system and its Jacobian, while <code>PolySolver</code> orchestrates the solution process. The <code>SchurCompliment</code> and <code>GMRESInverter</code> classes are helper components for the linear algebra involved.</li>
+<li><b>Equation of State (EOS) (<code><a class="el" href="helm_8h.html">helm.h</a></code>, <code><a class="el" href="eos_i_o_8h.html">eosIO.h</a></code>):</b> Manages Equation of State data. <code><a class="el" href="helm_8h.html">helm.h</a></code> provides an implementation of the Helmholtz EOS (Timmes &amp; Swesty 2000), including structures for table data (<code>HELMTable</code>), input parameters (<code>EOSInput</code>), and output results (<code>EOS</code>). It also defines functions for reading tables and calculating EOS quantities. <code><a class="el" href="eos_i_o_8h.html">eosIO.h</a></code> provides the <code>EosIO</code> class for loading EOS tables from files, currently supporting the HELM table format.</li>
+<li><b>Chemical Composition (<code><a class="el" href="composition_8h.html">composition.h</a></code>, <code>atomicSpecies.h</code>):</b> Manages chemical compositions, allowing representation in mass or number fractions. It interfaces with <code>atomicSpecies.h</code> which provides a database of atomic species properties (based on AME2020).</li>
+<li><b>Nuclear Reaction Networks (<code><a class="el" href="network_8h.html">network.h</a></code>, <code><a class="el" href="approx8_8h.html" title="Header file for the Approx8 nuclear reaction network.">approx8.h</a></code>):</b> Defines a base <code>Network</code> class for nuclear reaction network calculations. <code><a class="el" href="approx8_8h.html" title="Header file for the Approx8 nuclear reaction network.">approx8.h</a></code> provides a specific implementation, <code>Approx8Network</code>, for an 8-isotope network (H1, He3, He4, C12, N14, O16, Ne20, Mg24) based on Frank Timmes' "aprox8". It includes functions for individual reaction rates and uses Boost.Numeric.Odeint for solving the ODE system.</li>
+<li><b>Physical Constants (<code><a class="el" href="const_8h.html">const.h</a></code>):</b> A singleton class <code>Constants</code> that loads and provides access to a wide range of physical constants with their values, uncertainties, units, and references.</li>
+<li><b>Configuration Management (<code><a class="el" href="config_8h.html">config.h</a></code>):</b> A singleton class <code>Config</code> for loading and accessing application settings from YAML configuration files.</li>
+<li><b>Probing and Logging (<code><a class="el" href="probe_8h.html">probe.h</a></code>):</b> The <code>Probe</code> namespace offers utility functions for debugging, such as GLVis visualization (<code>glVisView</code>), and a <code>LogManager</code> for handling application-wide logging using the Quill library.</li>
+<li><b>Mesh I/O (<code><a class="el" href="mesh_i_o_8h.html">meshIO.h</a></code>):</b> The <code>MeshIO</code> class handles loading and basic manipulation (e.g., scaling) of computational meshes using MFEM's <code>mfem::Mesh</code>. It ensures that meshes are correctly loaded and accessible.</li>
+<li><b>Integrators (<code><a class="el" href="integrators_8h.html" title="A collection of utilities for working with MFEM and solving the lane-emden equation.">integrators.h</a></code>):</b> (Details inferred) Likely contains custom MFEM integrators or coefficients used in the finite element formulations.</li>
+<li><b>Custom Types (<code><a class="el" href="4_d_s_t_a_r_types_8h.html">4DSTARTypes.h</a></code>):</b> Defines project-specific data type aliases within the <code>SSE</code> namespace, primarily for simplifying common <code>std::pair</code> combinations involving <code>mfem::Array&lt;int&gt;</code> and <code>mfem::Array&lt;double&gt;</code>. These include <code>SSE::MFEMArrayPair</code> and <code>SSE::MFEMArrayPairSet</code>, often used for managing collections of MFEM degree-of-freedom lists and their corresponding values, especially for boundary conditions.</li>
+</ul>
+<h1><a class="anchor" id="future_dev"></a>
+Future Development</h1>
+<p>Future work will focus on expanding the physics modules (e.g., equation of state, opacity), improving numerical solvers, and enhancing the parallelization capabilities for large-scale simulations.</p>
+<h1><a class="anchor" id="contact_sec"></a>
+Contact and Contributions</h1>
+<p>For questions, bug reports, or contributions, please refer to the project's repository or contact the development team. (Details to be added) </p>
+</div></div><!-- PageDoc -->
+<a href="doxygen_crawl.html"></a>
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+#nav-tree .selected .arrow {
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+  width: $width;
+  overflow : hidden;
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+  background-image:url('splitbar.png');
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@@ -117,7 +121,6 @@
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--- a/docs/html/navtree.js
+++ b/docs/html/navtree.js
@@ -22,82 +22,59 @@

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-{
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-  var n = i>=0 ? varName.substring(i+1) : varName;
-  return eval(n.replace(/\-/g,'_'));
+function initNavTree(toroot,relpath) {
+  let navTreeSubIndices = [];
+  const ARROW_DOWN = '&#9660;';
+  const ARROW_RIGHT = '&#9658;';
+  const NAVPATH_COOKIE_NAME = ''+'navpath';
+
+  const getData = function(varName) {
+    const i = varName.lastIndexOf('/');
+    const n = i>=0 ? varName.substring(i+1) : varName;
+    return eval(n.replace(/-/g,'_'));
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-function stripPath(uri)
-{
+  const stripPath = function(uri) {
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-function stripPath2(uri)
-{
-  var i = uri.lastIndexOf('/');
-  var s = uri.substring(i+1);
-  var m = uri.substring(0,i+1).match(/\/d\w\/d\w\w\/$/);
+  const stripPath2 = function(uri) {
+    const i = uri.lastIndexOf('/');
+    const s = uri.substring(i+1);
+    const m = uri.substring(0,i+1).match(/\/d\w\/d\w\w\/$/);
    return m ? uri.substring(i-6) : s;
  }

-function hashValue()
-{
-  return $(location).attr('hash').substring(1).replace(/[^\w\-]/g,'');
+  const hashValue = function() {
+    return $(location).attr('hash').substring(1).replace(/[^\w-]/g,'');
  }

-function hashUrl()
-{
+  const hashUrl = function() {
    return '#'+hashValue();
  }

-function pathName()
-{
-  return $(location).attr('pathname').replace(/[^-A-Za-z0-9+&@#/%?=~_|!:,.;\(\)]/g, '');
+  const pathName = function() {
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  }

-function localStorageSupported()
-{
-  try {
-    return 'localStorage' in window && window['localStorage'] !== null && window.localStorage.getItem;
-  }
-  catch(e) {
-    return false;
+  const storeLink = function(link) {
+    if (!$("#nav-sync").hasClass('sync')) {
+      Cookie.writeSetting(NAVPATH_COOKIE_NAME,link,0);
    }
  }

-function storeLink(link)
-{
-  if (!$("#nav-sync").hasClass('sync') && localStorageSupported()) {
-      window.localStorage.setItem('navpath',link);
-  }
+  const deleteLink = function() {
+    Cookie.eraseSetting(NAVPATH_COOKIE_NAME);
  }

-function deleteLink()
-{
-  if (localStorageSupported()) {
-    window.localStorage.setItem('navpath','');
-  }
+  const cachedLink = function() {
+    return Cookie.readSetting(NAVPATH_COOKIE_NAME,'');
  }

-function cachedLink()
-{
-  if (localStorageSupported()) {
-    return window.localStorage.getItem('navpath');
-  } else {
-    return '';
-  }
-}
-
-function getScript(scriptName,func,show)
-{
-  var head = document.getElementsByTagName("head")[0];
-  var script = document.createElement('script');
+  const getScript = function(scriptName,func) {
+    const head = document.getElementsByTagName("head")[0];
+    const script = document.createElement('script');
    script.id = scriptName;
    script.type = 'text/javascript';
    script.onload = func;
@@ -105,32 +82,31 @@ function getScript(scriptName,func,show)
    head.appendChild(script);
  }

-function createIndent(o,domNode,node,level)
-{
-  var level=-1;
-  var n = node;
+  const createIndent = function(o,domNode,node) {
+    let level=-1;
+    let n = node;
    while (n.parentNode) { level++; n=n.parentNode; }
    if (node.childrenData) {
-    var imgNode = document.createElement("span");
+      const imgNode = document.createElement("span");
      imgNode.className = 'arrow';
      imgNode.style.paddingLeft=(16*level).toString()+'px';
-    imgNode.innerHTML=arrowRight;
+      imgNode.innerHTML=ARROW_RIGHT;
      node.plus_img = imgNode;
      node.expandToggle = document.createElement("a");
      node.expandToggle.href = "javascript:void(0)";
      node.expandToggle.onclick = function() {
        if (node.expanded) {
          $(node.getChildrenUL()).slideUp("fast");
-        node.plus_img.innerHTML=arrowRight;
+          node.plus_img.innerHTML=ARROW_RIGHT;
          node.expanded = false;
        } else {
-        expandNode(o, node, false, false);
+          expandNode(o, node, false, true);
        }
      }
      node.expandToggle.appendChild(imgNode);
      domNode.appendChild(node.expandToggle);
    } else {
-    var span = document.createElement("span");
+      let span = document.createElement("span");
      span.className = 'arrow';
      span.style.width   = 16*(level+1)+'px';
      span.innerHTML = '&#160;';
@@ -138,166 +114,31 @@ function createIndent(o,domNode,node,level)
    }
  }

-var animationInProgress = false;
+  let animationInProgress = false;

-function gotoAnchor(anchor,aname,updateLocation)
-{
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-  var ancParent = $(anchor.parent());
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-      ancParent.hasClass('fieldname') ||
-      ancParent.hasClass('fieldtype') ||
-      ancParent.is(':header'))
-  {
-    pos = ancParent.position().top;
+  const gotoAnchor = function(anchor,aname) {
+    let pos, docContent = $('#doc-content');
+    let ancParent = $(anchor.parent());
+    if (ancParent.hasClass('memItemLeft') || ancParent.hasClass('memtitle')  ||
+        ancParent.hasClass('fieldname')   || ancParent.hasClass('fieldtype') ||
+        ancParent.is(':header')) {
+      pos = ancParent.offset().top;
    } else if (anchor.position()) {
-    pos = anchor.position().top;
+      pos = anchor.offset().top;
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    if (pos) {
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-               pos-docContent.offset().top,
-               docContent[0].scrollHeight-
-               docContent.height()-docContent.scrollTop()));
+      const dcOffset    = docContent.offset().top;
+      const dcHeight    = docContent.height();
+      const dcScrHeight = docContent[0].scrollHeight
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+        scrollTop: pos + dcScrTop - dcOffset
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-{
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-{
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-  var anchor = $(aname);
        if (anchor.parent().attr('class')=='memItemLeft') {
-    var rows = $('.memberdecls tr[class$="'+hashValue()+'"]');
+          let rows = $('.memberdecls tr[class$="'+hashValue()+'"]');
          glowEffect(rows.children(),300); // member without details
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          glowEffect(anchor.parent().parent(),1000); // enum value
@@ -308,13 +149,135 @@ function highlightAnchor()
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+      a.href = "javascript:void(0)";
+      a.onclick = node.expandToggle.onclick;
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+    return node;
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+    const headerHeight = $("#top").height();
+    const footerHeight = $("#nav-path").height();
+    const windowHeight = $(window).height() - headerHeight - footerHeight;
+    (function() { // retry until we can scroll to the selected item
+      try {
+        const navtree=$('#nav-tree');
+        navtree.scrollTo('#selected',100,{offset:-windowHeight/2});
+      } catch (err) {
+        setTimeout(arguments.callee, 0);
+      }
+    })();
+  }
+
+  const expandNode = function(o, node, imm, setFocus) {
+    if (node.childrenData && !node.expanded) {
+      if (typeof(node.childrenData)==='string') {
+        const varName = node.childrenData;
+        getScript(node.relpath+varName,function() {
+          node.childrenData = getData(varName);
+          expandNode(o, node, imm, setFocus);
+        });
+      } else {
+        if (!node.childrenVisited) {
+          getNode(o, node);
+        }
+        $(node.getChildrenUL()).slideDown("fast");
+        node.plus_img.innerHTML = ARROW_DOWN;
+        node.expanded = true;
+        if (setFocus) {
+          $(node.expandToggle).focus();
+        }
+      }
+    }
+  }
+
+  const glowEffect = function(n,duration) {
+    n.addClass('glow').delay(duration).queue(function(next) {
+      $(this).removeClass('glow');next();
+    });
+  }
+
+  const highlightAnchor = function() {
+    const aname = hashUrl();
+    const anchor = $(aname);
+    gotoAnchor(anchor,aname);
+  }
+
+  const selectAndHighlight = function(hash,n) {
+    let a;
    if (hash) {
-    var link=stripPath(pathName())+':'+hash.substring(1);
+      const link=stripPath(pathName())+':'+hash.substring(1);
      a=$('.item a[class$="'+link+'"]');
    }
    if (a && a.length) {
@@ -325,58 +288,55 @@ function selectAndHighlight(hash,n)
      $(n.itemDiv).addClass('selected');
      $(n.itemDiv).attr('id','selected');
    }
+    let topOffset=5;
    if ($('#nav-tree-contents .item:first').hasClass('selected')) {
-    $('#nav-sync').css('top','30px');
-  } else {
-    $('#nav-sync').css('top','5px');
+      topOffset+=25;
    }
+    $('#nav-sync').css('top',topOffset+'px');
    showRoot();
  }

-function showNode(o, node, index, hash)
-{
+  const showNode = function(o, node, index, hash) {
    if (node && node.childrenData) {
      if (typeof(node.childrenData)==='string') {
-      var varName    = node.childrenData;
+        const varName = node.childrenData;
        getScript(node.relpath+varName,function() {
          node.childrenData = getData(varName);
          showNode(o,node,index,hash);
-      },true);
+        });
      } else {
        if (!node.childrenVisited) {
          getNode(o, node);
        }
        $(node.getChildrenUL()).css({'display':'block'});
-      node.plus_img.innerHTML = arrowDown;
+        node.plus_img.innerHTML = ARROW_DOWN;
        node.expanded = true;
-      var n = node.children[o.breadcrumbs[index]];
+        const n = node.children[o.breadcrumbs[index]];
        if (index+1<o.breadcrumbs.length) {
          showNode(o,n,index+1,hash);
-      } else {
-        if (typeof(n.childrenData)==='string') {
-          var varName = n.childrenData;
+        } else if (typeof(n.childrenData)==='string') {
+          const varName = n.childrenData;
          getScript(n.relpath+varName,function() {
            n.childrenData = getData(varName);
            node.expanded=false;
            showNode(o,node,index,hash); // retry with child node expanded
-          },true);
+          });
        } else {
-          var rootBase = stripPath(o.toroot.replace(/\..+$/, ''));
+          const rootBase = stripPath(o.toroot.replace(/\..+$/, ''));
          if (rootBase=="index" || rootBase=="pages" || rootBase=="search") {
-            expandNode(o, n, true, true);
+            expandNode(o, n, true, false);
          }
          selectAndHighlight(hash,n);
        }
      }
-    }
    } else {
      selectAndHighlight(hash);
    }
  }

-function removeToInsertLater(element) {
-  var parentNode = element.parentNode;
-  var nextSibling = element.nextSibling;
+  const removeToInsertLater = function(element) {
+    const parentNode = element.parentNode;
+    const nextSibling = element.nextSibling;
    parentNode.removeChild(element);
    return function() {
      if (nextSibling) {
@@ -387,22 +347,19 @@ function removeToInsertLater(element) {
    };
  }

-function getNode(o, po)
-{
-  var insertFunction = removeToInsertLater(po.li);
+  const getNode = function(o, po) {
+    const insertFunction = removeToInsertLater(po.li);
    po.childrenVisited = true;
-  var l = po.childrenData.length-1;
-  for (var i in po.childrenData) {
-    var nodeData = po.childrenData[i];
-    po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2],
-      i==l);
+    const l = po.childrenData.length-1;
+    for (let i in po.childrenData) {
+      const nodeData = po.childrenData[i];
+      po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2], i==l);
    }
    insertFunction();
  }

-function gotoNode(o,subIndex,root,hash,relpath)
-{
-  var nti = navTreeSubIndices[subIndex][root+hash];
+  const gotoNode = function(o,subIndex,root,hash,relpath) {
+    const nti = navTreeSubIndices[subIndex][root+hash];
    o.breadcrumbs = $.extend(true, [], nti ? nti : navTreeSubIndices[subIndex][root]);
    if (!o.breadcrumbs && root!=NAVTREE[0][1]) { // fallback: show index
      navTo(o,NAVTREE[0][1],"",relpath);
@@ -415,22 +372,20 @@ function gotoNode(o,subIndex,root,hash,relpath)
    }
  }

-function navTo(o,root,hash,relpath)
-{
-  var link = cachedLink();
+  const navTo = function(o,root,hash,relpath) {
+    const link = cachedLink();
    if (link) {
-    var parts = link.split('#');
+      const parts = link.split('#');
      root = parts[0];
-    if (parts.length>1) hash = '#'+parts[1].replace(/[^\w\-]/g,'');
-    else hash='';
+      hash = parts.length>1 ? '#'+parts[1].replace(/[^\w-]/g,'') : '';
    }
    if (hash.match(/^#l\d+$/)) {
-    var anchor=$('a[name='+hash.substring(1)+']');
+      const anchor=$('a[name='+hash.substring(1)+']');
      glowEffect(anchor.parent(),1000); // line number
      hash=''; // strip line number anchors
    }
-  var url=root+hash;
-  var i=-1;
+    const url=root+hash;
+    let i=-1;
    while (NAVTREEINDEX[i+1]<=url) i++;
    if (i==-1) { i=0; root=NAVTREE[0][1]; } // fallback: show index
    if (navTreeSubIndices[i]) {
@@ -441,23 +396,47 @@ function navTo(o,root,hash,relpath)
        if (navTreeSubIndices[i]) {
          gotoNode(o,i,root,hash,relpath);
        }
-    },true);
+      });
    }
  }

-function showSyncOff(n,relpath)
-{
+  const showSyncOff = function(n,relpath) {
    n.html('<img src="'+relpath+'sync_off.png" title="'+SYNCOFFMSG+'"/>');
  }

-function showSyncOn(n,relpath)
-{
+  const showSyncOn = function(n,relpath) {
    n.html('<img src="'+relpath+'sync_on.png" title="'+SYNCONMSG+'"/>');
  }

-function toggleSyncButton(relpath)
-{
-  var navSync = $('#nav-sync');
+  const o = {
+    toroot : toroot,
+    node   : {
+      childrenData  : NAVTREE,
+      children      : [],
+      childrenUL    : document.createElement("ul"),
+      getChildrenUL : function() { return this.childrenUL },
+      li            : document.getElementById("nav-tree-contents"),
+      depth         : 0,
+      relpath       : relpath,
+      expanded      : false,
+      isLast        : true,
+      plus_img      : document.createElement("span"),
+    },
+  };
+  o.node.li.appendChild(o.node.childrenUL);
+  o.node.plus_img.className = 'arrow';
+  o.node.plus_img.innerHTML = ARROW_RIGHT;
+
+  const navSync = $('#nav-sync');
+  if (cachedLink()) {
+    showSyncOff(navSync,relpath);
+    navSync.removeClass('sync');
+  } else {
+    showSyncOn(navSync,relpath);
+  }
+
+  navSync.click(() => {
+    const navSync = $('#nav-sync');
    if (navSync.hasClass('sync')) {
      navSync.removeClass('sync');
      showSyncOff(navSync,relpath);
@@ -467,80 +446,38 @@ function toggleSyncButton(relpath)
      showSyncOn(navSync,relpath);
      deleteLink();
    }
-}
-
-var loadTriggered = false;
-var readyTriggered = false;
-var loadObject,loadToRoot,loadUrl,loadRelPath;
-
-$(window).on('load',function(){
-  if (readyTriggered) { // ready first
-    navTo(loadObject,loadToRoot,loadUrl,loadRelPath);
-    showRoot();
-  }
-  loadTriggered=true;
  });

-function initNavTree(toroot,relpath)
-{
-  var o = new Object();
-  o.toroot = toroot;
-  o.node = new Object();
-  o.node.li = document.getElementById("nav-tree-contents");
-  o.node.childrenData = NAVTREE;
-  o.node.children = new Array();
-  o.node.childrenUL = document.createElement("ul");
-  o.node.getChildrenUL = function() { return o.node.childrenUL; };
-  o.node.li.appendChild(o.node.childrenUL);
-  o.node.depth = 0;
-  o.node.relpath = relpath;
-  o.node.expanded = false;
-  o.node.isLast = true;
-  o.node.plus_img = document.createElement("span");
-  o.node.plus_img.className = 'arrow';
-  o.node.plus_img.innerHTML = arrowRight;
-
-  if (localStorageSupported()) {
-    var navSync = $('#nav-sync');
-    if (cachedLink()) {
-      showSyncOff(navSync,relpath);
-      navSync.removeClass('sync');
-    } else {
-      showSyncOn(navSync,relpath);
-    }
-    navSync.click(function(){ toggleSyncButton(relpath); });
-  }
-
-  if (loadTriggered) { // load before ready
  navTo(o,toroot,hashUrl(),relpath);
  showRoot();
-  } else { // ready before load
-    loadObject  = o;
-    loadToRoot  = toroot;
-    loadUrl     = hashUrl();
-    loadRelPath = relpath;
-    readyTriggered=true;
-  }

-  $(window).bind('hashchange', function(){
+  $(window).bind('hashchange', () => {
+    if (!animationInProgress) {
      if (window.location.hash && window.location.hash.length>1) {
-       var a;
+        let a;
        if ($(location).attr('hash')) {
-         var clslink=stripPath(pathName())+':'+hashValue();
+          const clslink=stripPath(pathName())+':'+hashValue();
          a=$('.item a[class$="'+clslink.replace(/</g,'\\3c ')+'"]');
        }
        if (a==null || !$(a).parent().parent().hasClass('selected')) {
          $('.item').removeClass('selected');
          $('.item').removeAttr('id');
        }
-       var link=stripPath2(pathName());
+        const link=stripPath2(pathName());
        navTo(o,link,hashUrl(),relpath);
-     } else if (!animationInProgress) {
+        } else {
        $('#doc-content').scrollTop(0);
        $('.item').removeClass('selected');
        $('.item').removeAttr('id');
        navTo(o,toroot,hashUrl(),relpath);
      }
-  })
+    }
+  });
+
+  $("div.toc a[href]").click(function(e) {
+    e.preventDefault();
+    const aname = $(this).attr("href");
+    gotoAnchor($(aname),aname);
+  });
 }
 /* @license-end */
--- a/docs/html/navtreedata.js
+++ b/docs/html/navtreedata.js
@@ -24,23 +24,27 @@
 */
 var NAVTREE =
 [
-  [ "New 4DSSE Code", "index.html", [
-    [ "opatIO python module", "md_utils_opatio_readme.html", [
-      [ "Installation", "md_utils_opatio_readme.html#autotoc_md1", null ],
-      [ "General Usage", "md_utils_opatio_readme.html#autotoc_md2", null ],
-      [ "Problems", "md_utils_opatio_readme.html#autotoc_md3", null ]
-    ] ],
+  [ "SERiF", "index.html", [
+    [ "4DSSE: A 4D Stellar Structure and Evolution Code", "index.html", "index" ],
    [ "Test List", "test.html", null ],
+    [ "Namespaces", "namespaces.html", [
+      [ "Namespace List", "namespaces.html", "namespaces_dup" ],
+      [ "Namespace Members", "namespacemembers.html", [
+        [ "All", "namespacemembers.html", null ],
+        [ "Functions", "namespacemembers_func.html", null ],
+        [ "Variables", "namespacemembers_vars.html", null ],
+        [ "Typedefs", "namespacemembers_type.html", null ]
+      ] ]
+    ] ],
    [ "Classes", "annotated.html", [
      [ "Class List", "annotated.html", "annotated_dup" ],
      [ "Class Index", "classes.html", null ],
      [ "Class Hierarchy", "hierarchy.html", "hierarchy" ],
      [ "Class Members", "functions.html", [
-        [ "All", "functions.html", null ],
+        [ "All", "functions.html", "functions_dup" ],
        [ "Functions", "functions_func.html", null ],
-        [ "Variables", "functions_vars.html", null ],
-        [ "Typedefs", "functions_type.html", null ],
-        [ "Related Functions", "functions_rela.html", null ]
+        [ "Variables", "functions_vars.html", "functions_vars" ],
+        [ "Related Symbols", "functions_rela.html", null ]
      ] ]
    ] ],
    [ "Files", "files.html", [
@@ -49,17 +53,22 @@ var NAVTREE =
        [ "All", "globals.html", null ],
        [ "Functions", "globals_func.html", null ],
        [ "Variables", "globals_vars.html", null ],
+        [ "Typedefs", "globals_type.html", null ],
        [ "Macros", "globals_defs.html", null ]
      ] ]
-    ] ]
+    ] ],
+    [ "Examples", "examples.html", "examples" ]
  ] ]
 ];

 var NAVTREEINDEX =
 [
-"DObjectTest_8cpp.html",
-"opatIOTest_8cpp.html#a795aa3821c4c6f206678bc48acf95171"
+"4_d_s_t_a_r_types_8h.html",
+"classserif_1_1polytrope_1_1_poly_solver.html#a3b84b79daceb9eed00d0f353d69f77c1",
+"classserif_1_1resource_1_1_resource_manager.html#a05e35b8fb70f573bca3383f6e3368eb4",
+"namespaceserif_1_1config.html",
+"structserif_1_1eos_1_1helmholtz_1_1_e_o_s.html#a5c59d85e1fe64769c261375834357901"
 ];

-var SYNCONMSG = 'click to disable panel synchronisation';
-var SYNCOFFMSG = 'click to enable panel synchronisation';
+var SYNCONMSG = 'click to disable panel synchronization';
+var SYNCOFFMSG = 'click to enable panel synchronization';
--- a/docs/html/navtreeindex0.js
+++ b/docs/html/navtreeindex0.js
@@ -1,253 +1,253 @@
 var NAVTREEINDEX0 =
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+++ b/docs/html/resize.js
@@ -22,119 +22,126 @@

 @licend  The above is the entire license notice for the JavaScript code in this file
 */
-function initResizable()
-{
-  var cookie_namespace = 'doxygen';
-  var sidenav,navtree,content,header,collapsed,collapsedWidth=0,barWidth=6,desktop_vp=768,titleHeight;

-  function readCookie(cookie)
-  {
-    var myCookie = cookie_namespace+"_"+cookie+"=";
-    if (document.cookie) {
-      var index = document.cookie.indexOf(myCookie);
-      if (index != -1) {
-        var valStart = index + myCookie.length;
-        var valEnd = document.cookie.indexOf(";", valStart);
-        if (valEnd == -1) {
-          valEnd = document.cookie.length;
-        }
-        var val = document.cookie.substring(valStart, valEnd);
-        return val;
-      }
-    }
-    return 0;
-  }
+function initResizable(treeview) {
+  let sidenav,navtree,content,header,footer,barWidth=6;
+  const RESIZE_COOKIE_NAME = ''+'width';

-  function writeCookie(cookie, val, expiration)
-  {
-    if (val==undefined) return;
-    if (expiration == null) {
-      var date = new Date();
-      date.setTime(date.getTime()+(10*365*24*60*60*1000)); // default expiration is one week
-      expiration = date.toGMTString();
-    }
-    document.cookie = cookie_namespace + "_" + cookie + "=" + val + "; expires=" + expiration+"; path=/";
-  }
-
-  function resizeWidth()
-  {
-    var windowWidth = $(window).width() + "px";
-    var sidenavWidth = $(sidenav).outerWidth();
+  function resizeWidth() {
+    const sidenavWidth = $(sidenav).outerWidth();
    content.css({marginLeft:parseInt(sidenavWidth)+"px"});
-    writeCookie('width',sidenavWidth-barWidth, null);
+    if (typeof page_layout!=='undefined' && page_layout==1) {
+      footer.css({marginLeft:parseInt(sidenavWidth)+"px"});
+    }
+    Cookie.writeSetting(RESIZE_COOKIE_NAME,sidenavWidth-barWidth);
  }

-  function restoreWidth(navWidth)
-  {
-    var windowWidth = $(window).width() + "px";
+  function restoreWidth(navWidth) {
    content.css({marginLeft:parseInt(navWidth)+barWidth+"px"});
+    if (typeof page_layout!=='undefined' && page_layout==1) {
+      footer.css({marginLeft:parseInt(navWidth)+barWidth+"px"});
+    }
    sidenav.css({width:navWidth + "px"});
  }

-  function resizeHeight()
+  function resizeHeight(treeview) {
+    const headerHeight = header.outerHeight();
+    const windowHeight = $(window).height();
+    let contentHeight;
+    if (treeview)
    {
-    var headerHeight = header.outerHeight();
-    var footerHeight = footer.outerHeight();
-    var windowHeight = $(window).height() - headerHeight - footerHeight;
-    content.css({height:windowHeight + "px"});
-    navtree.css({height:windowHeight + "px"});
-    sidenav.css({height:windowHeight + "px"});
-    var width=$(window).width();
-    if (width!=collapsedWidth) {
-      if (width<desktop_vp && collapsedWidth>=desktop_vp) {
-        if (!collapsed) {
-          collapseExpand();
+      const footerHeight = footer.outerHeight();
+      let navtreeHeight,sideNavHeight;
+      if (typeof page_layout==='undefined' || page_layout==0) { /* DISABLE_INDEX=NO */
+        contentHeight = windowHeight - headerHeight - footerHeight;
+        navtreeHeight = contentHeight;
+        sideNavHeight = contentHeight;
+      } else if (page_layout==1) { /* DISABLE_INDEX=YES */
+        contentHeight = windowHeight - footerHeight;
+        navtreeHeight = windowHeight - headerHeight;
+        sideNavHeight = windowHeight;
      }
-      } else if (width>desktop_vp && collapsedWidth<desktop_vp) {
-        if (collapsed) {
-          collapseExpand();
+      navtree.css({height:navtreeHeight + "px"});
+      sidenav.css({height:sideNavHeight + "px"});
    }
+    else
+    {
+      contentHeight = windowHeight - headerHeight;
    }
-      collapsedWidth=width;
-    }
+    content.css({height:contentHeight + "px"});
    if (location.hash.slice(1)) {
      (document.getElementById(location.hash.slice(1))||document.body).scrollIntoView();
    }
  }

-  function collapseExpand()
-  {
+  function collapseExpand() {
+    let newWidth;
    if (sidenav.width()>0) {
-      restoreWidth(0);
-      collapsed=true;
-    }
-    else {
-      var width = readCookie('width');
-      if (width>200 && width<$(window).width()) { restoreWidth(width); } else { restoreWidth(200); }
-      collapsed=false;
+      newWidth=0;
+    } else {
+      const width = Cookie.readSetting(RESIZE_COOKIE_NAME,250);
+      newWidth = (width>250 && width<$(window).width()) ? width : 250;
    }
+    restoreWidth(newWidth);
+    const sidenavWidth = $(sidenav).outerWidth();
+    Cookie.writeSetting(RESIZE_COOKIE_NAME,sidenavWidth-barWidth);
  }

  header  = $("#top");
-  sidenav = $("#side-nav");
  content = $("#doc-content");
-  navtree = $("#nav-tree");
  footer  = $("#nav-path");
+  sidenav = $("#side-nav");
+  if (!treeview) {
+//    title   = $("#titlearea");
+//    titleH  = $(title).height();
+//    let animating = false;
+//    content.on("scroll", function() {
+//      slideOpts = { duration: 200,
+//                    step: function() {
+//                        contentHeight = $(window).height() - header.outerHeight();
+//                        content.css({ height : contentHeight + "px" });
+//                      },
+//                    done: function() { animating=false; }
+//                  };
+//      if (content.scrollTop()>titleH && title.css('display')!='none' && !animating) {
+//        title.slideUp(slideOpts);
+//        animating=true;
+//      } else if (content.scrollTop()<=titleH && title.css('display')=='none' && !animating) {
+//        title.slideDown(slideOpts);
+//        animating=true;
+//      }
+//    });
+  } else {
+    navtree = $("#nav-tree");
    $(".side-nav-resizable").resizable({resize: function(e, ui) { resizeWidth(); } });
    $(sidenav).resizable({ minWidth: 0 });
-  $(window).resize(function() { resizeHeight(); });
-  var device = navigator.userAgent.toLowerCase();
-  var touch_device = device.match(/(iphone|ipod|ipad|android)/);
+  }
+  $(window).resize(function() { resizeHeight(treeview); });
+  if (treeview)
+  {
+    const device = navigator.userAgent.toLowerCase();
+    const touch_device = device.match(/(iphone|ipod|ipad|android)/);
    if (touch_device) { /* wider split bar for touch only devices */
      $(sidenav).css({ paddingRight:'20px' });
      $('.ui-resizable-e').css({ width:'20px' });
      $('#nav-sync').css({ right:'34px' });
      barWidth=20;
    }
-  var width = readCookie('width');
+    const width = Cookie.readSetting(RESIZE_COOKIE_NAME,250);
    if (width) { restoreWidth(width); } else { resizeWidth(); }
-  resizeHeight();
-  var url = location.href;
-  var i=url.indexOf("#");
+  }
+  resizeHeight(treeview);
+  const url = location.href;
+  const i=url.indexOf("#");
  if (i>=0) window.location.hash=url.substr(i);
-  var _preventDefault = function(evt) { evt.preventDefault(); };
+  const _preventDefault = function(evt) { evt.preventDefault(); };
+  if (treeview)
+  {
    $("#splitbar").bind("dragstart", _preventDefault).bind("selectstart", _preventDefault);
    $(".ui-resizable-handle").dblclick(collapseExpand);
-  $(window).on('load',resizeHeight);
+    // workaround for firefox
+    $("body").css({overflow: "hidden"});
+  }
+  $(window).on('load',function() { resizeHeight(treeview); });
 }
 /* @license-end */
--- a/docs/html/search/all_0.js
+++ b/docs/html/search/all_0.js
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+  ['4d_20stellar_20structure_20and_20evolution_20code_0',['4DSSE: A 4D Stellar Structure and Evolution Code',['../index.html',1,'']]],
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--- a/docs/html/search/all_1.js
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+  ['accessing_20physical_20constants_4',['Accessing Physical Constants',['../index.html#usage_constants',1,'']]],
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+  ['and_20components_6',['Key Modules and Components',['../index.html#modules_sec',1,'']]],
+  ['and_20contributions_7',['Contact and Contributions',['../index.html#contact_sec',1,'']]],
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+  ['approx8_2eh_10',['approx8.h',['../approx8_8h.html',1,'']]],
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+  ['approx8test_2ecpp_13',['approx8Test.cpp',['../approx8_test_8cpp.html',1,'']]],
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-  ['bytestart_6',['byteStart',['../structTableIndex.html#ad899cf13056eb17b33e1c5e303e10132',1,'TableIndex']]]
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+  ['glvisview_35',['glVisView',['../namespaceserif_1_1probe.html#a80d969f85bc6f4b060158526e8adbe57',1,'serif::probe::glVisView(mfem::GridFunction &amp;u, mfem::Mesh &amp;mesh, const std::string &amp;windowTitle=&quot;grid function&quot;, const std::string &amp;keyset=&quot;&quot;)'],['../namespaceserif_1_1probe.html#a9381305542f12115a9fc9d1273ab851a',1,'serif::probe::glVisView(mfem::Vector &amp;vec, mfem::FiniteElementSpace &amp;fes, const std::string &amp;windowTitle=&quot;vector&quot;, const std::string &amp;keyset=&quot;&quot;)']]],
+  ['gmresinverter_36',['GMRESInverter',['../classserif_1_1polytrope_1_1_g_m_r_e_s_inverter.html#a26e52db2e259ceb0efc74a188a0626df',1,'serif::polytrope::GMRESInverter']]]
 ];
--- a/docs/html/search/functions_7.js
+++ b/docs/html/search/functions_7.js
@@ -1,4 +1,12 @@
 var searchData=
 [
-  ['keys_255',['keys',['../classConstants.html#ab9de36fa145552a3e7964e7e85a67149',1,'Constants']]]
+  ['h3_0',['h3',['../namespaceserif_1_1eos_1_1helmholtz.html#a472cca218e1d9d48c96ab61efe69a62b',1,'serif::eos::helmholtz::h3(std::array&lt; double, 36 &gt; fi, double w0t, double w1t, double w0mt, double w1mt, double w0d, double w1d, double w0md, double w1md)'],['../namespaceserif_1_1eos_1_1helmholtz.html#a2a3eaebe733ba0430616dab3481eecdb',1,'serif::eos::helmholtz::h3(double fi[36], double w0t, double w1t, double w0mt, double w1mt, double w0d, double w1d, double w0md, double w1md)']]],
+  ['h5_1',['h5',['../namespaceserif_1_1eos_1_1helmholtz.html#a8a44afcf150093ff5972a9d0274d06c1',1,'serif::eos::helmholtz::h5(std::array&lt; double, 36 &gt; fi, double w0t, double w1t, double w2t, double w0mt, double w1mt, double w2mt, double w0d, double w1d, double w2d, double w0md, double w1md, double w2md)'],['../namespaceserif_1_1eos_1_1helmholtz.html#a9b3d0f5f705e5a3af5f1d11aac9fa0e3',1,'serif::eos::helmholtz::h5(double fi[36], double w0t, double w1t, double w2t, double w0mt, double w1mt, double w2mt, double w0d, double w1d, double w2d, double w0md, double w1md, double w2md)']]],
+  ['has_2',['has',['../classserif_1_1constant_1_1_constants.html#a71aa21de5e8ee9f5fc23169df28f9a4e',1,'serif::constant::Constants']]],
+  ['hassymbol_3',['hasSymbol',['../classserif_1_1composition_1_1_composition.html#a01e00a40385ebc61c93dba8064733f7f',1,'serif::composition::Composition']]],
+  ['he3he3_5frate_4',['he3he3_rate',['../namespaceserif_1_1network_1_1approx8.html#ad456790029a34224e4435a0a72ada249',1,'serif::network::approx8']]],
+  ['he3he4_5frate_5',['he3he4_rate',['../namespaceserif_1_1network_1_1approx8.html#a9a9fce6f2b20d4793e614bd02ec36c3a',1,'serif::network::approx8']]],
+  ['heap_5fallocate_5fcontiguous_5f2d_5fmemory_6',['heap_allocate_contiguous_2D_memory',['../namespaceserif_1_1eos_1_1helmholtz.html#af20392e2dadcbfc1e09ced18995ca60c',1,'serif::eos::helmholtz']]],
+  ['heap_5fdeallocate_5fcontiguous_5f2d_5fmemory_7',['heap_deallocate_contiguous_2D_memory',['../namespaceserif_1_1eos_1_1helmholtz.html#a99c73f169fb5be7e576102384459f9a5',1,'serif::eos::helmholtz']]],
+  ['helmtable_8',['HELMTable',['../structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html#a884959cf006a38fdad597724891f88b3',1,'serif::eos::helmholtz::HELMTable']]]
 ];
--- a/docs/html/search/functions_8.js
+++ b/docs/html/search/functions_8.js
@@ -1,8 +1,11 @@
 var searchData=
 [
-  ['load_256',['load',['../classOpatIO.html#a3578ac9bad40dd45ada3459f92a93b56',1,'OpatIO']]],
-  ['lock_257',['lock',['../classLockableDObject.html#ade38ca54703913359fc3b4366f6e292a',1,'LockableDObject']]],
-  ['lockabledobject_258',['LockableDObject',['../classLockableDObject.html#ae1a174a2740fa053626fe2820ee0efee',1,'LockableDObject']]],
-  ['lookupclosesttableid_259',['lookupClosestTableID',['../classOpatIO.html#a82715d95a5ddd1e78470b90fbd005c4d',1,'OpatIO']]],
-  ['lookuptableid_260',['lookupTableID',['../classOpatIO.html#a1a4456b7745c0dd559eca72d5d744fc0',1,'OpatIO']]]
+  ['initialize_0',['initialize',['../classserif_1_1constant_1_1_constants.html#a88578dd2dc433c5c862b01a1539862fe',1,'serif::constant::Constants']]],
+  ['isfinalized_1',['isFinalized',['../classserif_1_1polytrope_1_1_polytrope_operator.html#a99b59a8f7cf8ac1f6106ee9cb014c931',1,'serif::polytrope::PolytropeOperator']]],
+  ['isloaded_2',['IsLoaded',['../classserif_1_1mesh_1_1_mesh_i_o.html#aa685c3f323d5189edfa326c866f552d6',1,'serif::mesh::MeshIO']]],
+  ['isloaded_3',['isLoaded',['../classserif_1_1constant_1_1_constants.html#abaebbd4df3f8ce0162b1f6014f2420ac',1,'serif::constant::Constants']]],
+  ['isotope_4',['isotope',['../structserif_1_1composition_1_1_composition_entry.html#a17eb67ef1c07528295db845150c32615',1,'serif::composition::CompositionEntry']]],
+  ['isstiff_5',['isStiff',['../classserif_1_1network_1_1approx8_1_1_approx8_network.html#a2e1f6e00bd622d2186724680dce7184f',1,'serif::network::approx8::Approx8Network']]],
+  ['isvalidcomposition_6',['isValidComposition',['../classserif_1_1composition_1_1_composition.html#a14d19ec7ff396768bfe553522abc44db',1,'serif::composition::Composition']]],
+  ['isvalidsymbol_7',['isValidSymbol',['../classserif_1_1composition_1_1_composition.html#a753bcffca93a4dd8a0f38afc00cf05fb',1,'serif::composition::Composition']]]
 ];
--- a/docs/html/search/mag_sel.svg
+++ b/docs/html/search/mag_sel.svg
@@ -1,59 +1,17 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!-- Created with Inkscape (http://www.inkscape.org/) -->
-
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "https://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
 <svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
   xmlns="http://www.w3.org/2000/svg"
-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
   version="1.1"
   id="svg2"
   width="20"
   height="19"
   viewBox="0 0 20 19"
-   sodipodi:docname="mag_sel.svg"
-   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)">
-  <metadata
-     id="metadata8">
-    <rdf:RDF>
-      <cc:Work
-         rdf:about="">
-        <dc:format>image/svg+xml</dc:format>
-        <dc:type
-           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-        <dc:title></dc:title>
-      </cc:Work>
-    </rdf:RDF>
-  </metadata>
+  >
  <defs
     id="defs6" />
-  <sodipodi:namedview
-     pagecolor="#ffffff"
-     bordercolor="#666666"
-     borderopacity="1"
-     objecttolerance="10"
-     gridtolerance="10"
-     guidetolerance="10"
-     inkscape:pageopacity="0"
-     inkscape:pageshadow="2"
-     inkscape:window-width="1920"
-     inkscape:window-height="2096"
-     id="namedview4"
-     showgrid="false"
-     fit-margin-top="0"
-     fit-margin-left="0"
-     fit-margin-right="0"
-     fit-margin-bottom="0"
-     inkscape:zoom="32"
-     inkscape:cx="5.9792688"
-     inkscape:cy="1.1436277"
-     inkscape:window-x="1920"
-     inkscape:window-y="27"
-     inkscape:window-maximized="0"
-     inkscape:current-layer="svg2" />
  <circle
     style="fill:#000000;fill-opacity:0;stroke:#656565;stroke-width:1.4;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
     id="path4611"
@@ -64,11 +22,10 @@
     style="fill:#656565;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
     d="M 11,7 13.5,10 16,7 Z"
     id="path4609"
-     inkscape:connector-curvature="0"
-     sodipodi:nodetypes="cccc" />
+     />
  <path
     style="fill:none;stroke:#656565;stroke-width:1.4;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
     d="m 8.1085854,11.109059 2.7823556,2.782356"
     id="path4630"
-     inkscape:connector-curvature="0" />
+     />
 </svg>
--- a/docs/html/search/related_0.js
+++ b/docs/html/search/related_0.js
@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['operator_3c_3c_335',['operator&lt;&lt;',['../structConstant.html#ad298f7af7cdfd2e2267fd9e464558e2b',1,'Constant::operator&lt;&lt;()'],['../classDObject.html#a5b2896a287295bf59a0b9e4d0af21161',1,'DObject::operator&lt;&lt;()'],['../classMetadata.html#a9bc49cc23da2d1ff8b3e197630b9dfd2',1,'Metadata::operator&lt;&lt;()']]]
+  ['operator_3c_3c_0',['operator&lt;&lt;',['../structserif_1_1composition_1_1_global_composition.html#a3c072a749c3648607771ac9105181f26',1,'serif::composition::GlobalComposition::operator&lt;&lt;()'],['../structserif_1_1composition_1_1_composition_entry.html#ae7a6a113fc5914248eff5629716d6eb2',1,'serif::composition::CompositionEntry::operator&lt;&lt;()'],['../classserif_1_1composition_1_1_composition.html#a36c2525d21cd932065bb2bb30bc57fb4',1,'serif::composition::Composition::operator&lt;&lt;()'],['../structserif_1_1constant_1_1_constant.html#a387b3e0a55788b0ea04c77ba040c5aaa',1,'serif::constant::Constant::operator&lt;&lt;()'],['../structserif_1_1eos_1_1helmholtz_1_1_h_e_l_m_table.html#a65eea84782fc9b5b69b6f7f2ebf57940',1,'serif::eos::helmholtz::HELMTable::operator&lt;&lt;()'],['../structserif_1_1eos_1_1helmholtz_1_1_e_o_s_input.html#ae6bc0662e64e05608593df6129ab8edb',1,'serif::eos::helmholtz::EOSInput::operator&lt;&lt;()'],['../structserif_1_1eos_1_1helmholtz_1_1_e_o_s.html#a8071bdc90dec68ba933eb59c902a0b7b',1,'serif::eos::helmholtz::EOS::operator&lt;&lt;()']]]
 ];
--- a/docs/html/search/search.css
+++ b/docs/html/search/search.css
@@ -1,100 +1,116 @@
-/*---------------- Search Box */
+/*---------------- Search Box positioning */

-#FSearchBox {
-    float: left;
+#main-menu > li:last-child {
+    /* This <li> object is the parent of the search bar */
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    height: 36px;
+    margin-right: 1em;
+}
+
+/*---------------- Search box styling */
+
+.SRPage * {
+    font-weight: normal;
+    line-height: normal;
+}
+
+dark-mode-toggle {
+    margin-left: 5px;
+    display: flex;
+    float: right;
 }

 #MSearchBox {
+    display: inline-block;
    white-space : nowrap;
-    float: none;
-    margin-top: 0px;
-    right: 0px;
-    width: 170px;
-    height: 24px;
+    background: white;
+    border-radius: 0.65em;
+    box-shadow: inset 0.5px 0.5px 3px 0px #555;
    z-index: 102;
-    display: inline;
-    position: absolute;
 }

-#MSearchBox .left
-{
-    display:block;
-    position:absolute;
-    left:10px;
-    width:20px;
-    height:19px;
-    background:url('search_l.png') no-repeat;
-    background-position:right;
+#MSearchBox .left {
+    display: inline-block;
+    vertical-align: middle;
+    height: 1.4em;
 }

 #MSearchSelect {
-    display:block;
-    position:absolute;
+    display: inline-block;
+    vertical-align: middle;
    width: 20px;
    height: 19px;
+    background-image: url('mag_sel.svg');
+    margin: 0 0 0 0.3em;
+    padding: 0;
 }

-.left #MSearchSelect {
-    left:4px;
+#MSearchSelectExt {
+    display: inline-block;
+    vertical-align: middle;
+    width: 10px;
+    height: 19px;
+    background-image: url('mag.svg');
+    margin: 0 0 0 0.5em;
+    padding: 0;
 }

-.right #MSearchSelect {
-    right:5px;
-}

 #MSearchField {
-    display:block;
-    position:absolute;
+    display: inline-block;
+    vertical-align: middle;
+    width: 7.5em;
    height: 19px;
-    background:url('search_m.png') repeat-x;
+    margin: 0 0.15em;
+    padding: 0;
+    line-height: 1em;
    border:none;
-    width:111px;
-    margin-left:20px;
-    padding-left:4px;
    color: #909090;
    outline: none;
-    font: 9pt Arial, Verdana, sans-serif;
+    font-family: Arial,Verdana,sans-serif;
    -webkit-border-radius: 0px;
+    border-radius: 0px;
+    background: none;
 }

-#FSearchBox #MSearchField {
-    margin-left:15px;
+@media(hover: none) {
+    /* to avoid zooming on iOS */
+    #MSearchField {
+        font-size: 16px;
+    }
 }

 #MSearchBox .right {
-    display:block;
-    position:absolute;
-    right:10px;
-    top:0px;
-    width:20px;
-    height:19px;
-    background:url('search_r.png') no-repeat;
-    background-position:left;
+    display: inline-block;
+    vertical-align: middle;
+    width: 1.4em;
+    height: 1.4em;
 }

 #MSearchClose {
    display: none;
-    position: absolute;
-    top: 4px;
+    font-size: inherit;
    background : none;
    border: none;
-    margin: 0px 4px 0px 0px;
-    padding: 0px 0px;
+    margin: 0;
+    padding: 0;
    outline: none;
+
 }

-.left #MSearchClose {
-    left: 6px;
-}
-
-.right #MSearchClose {
-    right: 2px;
+#MSearchCloseImg {
+    padding: 0.3em;
+    margin: 0;
 }

 .MSearchBoxActive #MSearchField {
-    color: #000000;
+    color: black;
 }

+
+
 /*---------------- Search filter selection */

 #MSearchSelectWindow {
@@ -123,7 +139,7 @@

 span.SelectionMark {
    margin-right: 4px;
-    font-family: monospace;
+    font-family: 'JetBrains Mono',Consolas,Monaco,'Andale Mono','Ubuntu Mono',monospace,fixed;
    outline-style: none;
    text-decoration: none;
 }
@@ -131,7 +147,7 @@ span.SelectionMark {
 a.SelectItem {
    display: block;
    outline-style: none;
-    color: #000000; 
+    color: black;
    text-decoration: none;
    padding-left:   6px;
    padding-right: 12px;
@@ -139,13 +155,13 @@ a.SelectItem {

 a.SelectItem:focus,
 a.SelectItem:active {
-    color: #000000; 
+    color: black;
    outline-style: none;
    text-decoration: none;
 }

 a.SelectItem:hover {
-    color: #FFFFFF;
+    color: white;
    background-color: #3D578C;
    outline-style: none;
    text-decoration: none;
@@ -156,7 +172,7 @@ a.SelectItem:hover {
 /*---------------- Search results window */

 iframe#MSearchResults {
-    width: 60ex;
+    /*width: 60ex;*/
    height: 15em;
 }

@@ -164,9 +180,12 @@ iframe#MSearchResults {
    display: none;
    position: absolute;
    left: 0; top: 0;
-    border: 1px solid #000;
+    border: 1px solid black;
    background-color: #EEF1F7;
    z-index:10000;
+    width: 300px;
+    height: 400px;
+    overflow: auto;
 }

 /* ----------------------------------- */
@@ -174,7 +193,6 @@ iframe#MSearchResults {

 #SRIndex {
    clear:both; 
-    padding-bottom: 15px;
 }

 .SREntry {
@@ -187,8 +205,9 @@ iframe#MSearchResults {
    padding: 1px 5px;
 }

-body.SRPage {
+div.SRPage {
    margin: 5px 2px;
+    background-color: #EEF1F7;
 }

 .SRChildren {
@@ -211,6 +230,7 @@ a.SRScope {
    display: block;
    color: #425E97;
    font-family: Arial,Verdana,sans-serif;
+    font-size: 8pt;
    text-decoration: none;
    outline: none;
 }
@@ -222,29 +242,27 @@ a.SRScope:focus, a.SRScope:active {

 span.SRScope {
    padding-left: 4px;
+    font-family: Arial,Verdana,sans-serif;
 }

 .SRPage .SRStatus {
    padding: 2px 5px;
    font-size: 8pt;
    font-style: italic;
+    font-family: Arial,Verdana,sans-serif;
 }

 .SRResult {
    display: none;
 }

-DIV.searchresults {
+div.searchresults {
    margin-left: 10px;
    margin-right: 10px;
 }

 /*---------------- External search page results */

-.searchresult {
-    background-color: #F0F3F8;
-}
-
 .pages b {
   color: white;
   padding: 5px 5px 3px 5px;
--- a/docs/html/search/search.js
+++ b/docs/html/search/search.js
--- a/docs/html/search/searchdata.js
+++ b/docs/html/search/searchdata.js
@@ -1,39 +1,42 @@
 var indexSectionsWithContent =
 {
-  0: "_abcdeghiklmnoprstuvwx~",
-  1: "bcdhlmnot",
-  2: "_cdlmoprt",
-  3: "abcdghiklmnoprstuvwx~",
-  4: "bcdehilmnorsuv",
-  5: "dp",
-  6: "o",
-  7: "e",
-  8: "ot"
+  0: "4abcdefghijklmnopqrstuvwxyz~",
+  1: "acdefghjlmnoprsx",
+  2: "ps",
+  3: "4acdehimnpruw",
+  4: "abcdefghiklmnoprstuvwx~",
+  5: "acdefgijlmnpqrstuvxyz",
+  6: "aemrv",
+  7: "o",
+  8: "bdst",
+  9: "4acelst"
 };

 var indexSectionNames =
 {
  0: "all",
  1: "classes",
-  2: "files",
-  3: "functions",
-  4: "variables",
-  5: "typedefs",
-  6: "related",
-  7: "defines",
-  8: "pages"
+  2: "namespaces",
+  3: "files",
+  4: "functions",
+  5: "variables",
+  6: "typedefs",
+  7: "related",
+  8: "defines",
+  9: "pages"
 };

 var indexSectionLabels =
 {
  0: "All",
  1: "Classes",
-  2: "Files",
-  3: "Functions",
-  4: "Variables",
-  5: "Typedefs",
-  6: "Friends",
-  7: "Macros",
-  8: "Pages"
+  2: "Namespaces",
+  3: "Files",
+  4: "Functions",
+  5: "Variables",
+  6: "Typedefs",
+  7: "Friends",
+  8: "Macros",
+  9: "Pages"
 };

--- a/docs/html/search/typedefs_0.js
+++ b/docs/html/search/typedefs_0.js
@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['datatype_333',['DataType',['../classDObject.html#a79a2ecac4130ef3df272bdfeed26a620',1,'DObject']]]
+  ['array2d_0',['array2D',['../namespaceserif_1_1eos_1_1helmholtz.html#ac00f6833cce78bfca46f3c96e94dcdaa',1,'serif::eos::helmholtz']]]
 ];
--- a/docs/html/search/typedefs_1.js
+++ b/docs/html/search/typedefs_1.js
@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['plugin_334',['Plugin',['../classDObject.html#af11334d08ef85c68b3aae7554548e5a7',1,'DObject']]]
+  ['eostable_0',['EOSTable',['../namespaceserif_1_1eos.html#abf1dc5cb6b18a585e8c1872de53651f8',1,'serif::eos']]]
 ];
--- a/docs/html/tabs.css
+++ b/docs/html/tabs.css
--- a/docs/latex/Makefile
+++ b/docs/latex/Makefile
@@ -1,23 +1,42 @@
-LATEX_CMD=pdflatex
+LATEX_CMD?=pdflatex
+MKIDX_CMD?=makeindex
+BIBTEX_CMD?=bibtex
+LATEX_COUNT?=8
+MANUAL_FILE?=refman

-all: refman.pdf
+all: $(MANUAL_FILE).pdf

-pdf: refman.pdf
+pdf: $(MANUAL_FILE).pdf

-refman.pdf: clean refman.tex
-	$(LATEX_CMD) refman
-	makeindex refman.idx
-	$(LATEX_CMD) refman
-	latex_count=8 ; \
-	while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $$latex_count -gt 0 ] ;\
+$(MANUAL_FILE).pdf: clean $(MANUAL_FILE).tex
+	$(LATEX_CMD) $(MANUAL_FILE) || \
+	if [ $$? != 0 ] ; then \
+	        \echo "Please consult $(MANUAL_FILE).log to see the error messages" ; \
+	        false; \
+	fi
+	$(MKIDX_CMD) $(MANUAL_FILE).idx
+	$(LATEX_CMD) $(MANUAL_FILE) || \
+	if [ $$? != 0 ] ; then \
+	        \echo "Please consult $(MANUAL_FILE).log to see the error messages" ; \
+	        false; \
+	fi
+	latex_count=$(LATEX_COUNT) ; \
+	while grep -E -s 'Rerun (LaTeX|to get cross-references right|to get bibliographical references right)' $(MANUAL_FILE).log && [ $$latex_count -gt 0 ] ;\
 	    do \
 	      echo "Rerunning latex...." ;\
-	      $(LATEX_CMD) refman ;\
+	      $(LATEX_CMD) $(MANUAL_FILE) || \
+	      if [ $$? != 0 ] ; then \
+	              \echo "Please consult $(MANUAL_FILE).log to see the error messages" ; \
+	              false; \
+	      fi; \
 	      latex_count=`expr $$latex_count - 1` ;\
 	    done
-	makeindex refman.idx
-	$(LATEX_CMD) refman
-
+	$(MKIDX_CMD) $(MANUAL_FILE).idx
+	$(LATEX_CMD) $(MANUAL_FILE) || \
+	if [ $$? != 0 ] ; then \
+	        \echo "Please consult $(MANUAL_FILE).log to see the error messages" ; \
+	        false; \
+	fi

 clean:
-	rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf
+	rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl $(MANUAL_FILE).pdf
--- a/docs/latex/_d_object_8cpp.tex
+++ b/docs/latex/_d_object_8cpp.tex
@@ -8,9 +8,46 @@ Implementation of the \doxylink{class_d_object}{DObject} class.
 {\ttfamily \#include "{}DObject.\+h"{}}\newline
 {\ttfamily \#include $<$iostream$>$}\newline
 {\ttfamily \#include $<$stdexcept$>$}\newline
+\doxysubsubsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+std\+::ostream \& \mbox{\hyperlink{_d_object_8cpp_aa54e75574f0302a2ca7252f9f0f0b3f1}{operator$<$$<$}} (std\+::ostream \&os, const \mbox{\hyperlink{class_d_object}{DObject}} \&obj)
+\begin{DoxyCompactList}\small\item\em Provides a human-\/readable summary of the \doxylink{class_d_object}{DObject}. \end{DoxyCompactList}\end{DoxyCompactItemize}


 \doxysubsection{Detailed Description}
 Implementation of the \doxylink{class_d_object}{DObject} class. 

 Provides the implementation for a universal data container with plugin support. 
+
+Definition in file \mbox{\hyperlink{_d_object_8cpp_source}{DObject.\+cpp}}.
+
+
+
+\doxysubsection{Function Documentation}
+\Hypertarget{_d_object_8cpp_aa54e75574f0302a2ca7252f9f0f0b3f1}\index{DObject.cpp@{DObject.cpp}!operator$<$$<$@{operator$<$$<$}}
+\index{operator$<$$<$@{operator$<$$<$}!DObject.cpp@{DObject.cpp}}
+\doxysubsubsection{\texorpdfstring{operator$<$$<$()}{operator<<()}}
+{\footnotesize\ttfamily \label{_d_object_8cpp_aa54e75574f0302a2ca7252f9f0f0b3f1} 
+std\+::ostream \& operator$<$$<$ (\begin{DoxyParamCaption}\item[{std\+::ostream \&}]{os}{, }\item[{const \mbox{\hyperlink{class_d_object}{DObject}} \&}]{obj}{}\end{DoxyParamCaption})}
+
+
+
+Provides a human-\/readable summary of the \doxylink{class_d_object}{DObject}. 
+
+Useful for quick inspection or logging during debugging sessions.
+
+
+\begin{DoxyParams}{Parameters}
+{\em os} & The output stream to write to. \\
+\hline
+{\em obj} & The \doxylink{class_d_object}{DObject} to summarize. \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A reference to the output stream. 
+\end{DoxyReturn}
+
+
+Definition at line \mbox{\hyperlink{_d_object_8cpp_source_l00126}{126}} of file \mbox{\hyperlink{_d_object_8cpp_source}{DObject.\+cpp}}.
+
--- a/docs/latex/_d_object_8h.tex
+++ b/docs/latex/_d_object_8h.tex
@@ -5,7 +5,6 @@
 Defines the \doxylink{class_d_object}{DObject} class, a universal data container for the project.  


-{\ttfamily \#include "{}Metadata.\+h"{}}\newline
 {\ttfamily \#include $<$variant$>$}\newline
 {\ttfamily \#include $<$memory$>$}\newline
 {\ttfamily \#include $<$vector$>$}\newline
@@ -24,3 +23,6 @@ class \mbox{\hyperlink{class_d_object}{DObject}}
 Defines the \doxylink{class_d_object}{DObject} class, a universal data container for the project. 

 The \doxylink{class_d_object}{DObject} class encapsulates arbitrary data and its associated metadata, providing a consistent interface for public-\/facing functions. It includes support for dynamically registered plugins. 
+
+Definition in file \mbox{\hyperlink{_d_object_8h_source}{DObject.\+h}}.
+
--- a/docs/latex/_d_object_8h_source.tex
+++ b/docs/latex/_d_object_8h_source.tex
@@ -2,61 +2,108 @@
 \hypertarget{_d_object_8h_source}{}\label{_d_object_8h_source}\index{src/dobj/public/DObject.h@{src/dobj/public/DObject.h}}
 \mbox{\hyperlink{_d_object_8h}{Go to the documentation of this file.}}
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+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00161}00161\ \ \ \ \ \ \ \ \ \}}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00162}00162\ \ \ \ \ \}}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00163}00163\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00171}00171\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_ab1718571434e84e90f1ec463e4786a8a}{setData}}(\textcolor{keyword}{const}\ \mbox{\hyperlink{class_d_object_a55b7cdac36a3a518ba6e1ecef0e25dcd}{DataType}}\&\ data);}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00172}00172\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00180}00180\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_a6f0023aee463e71d92442dcf61b6ed47}{setDebugging}}(\textcolor{keywordtype}{bool}\ enableDebug);}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00181}00181\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00187}00187\ \ \ \ \ \textcolor{keywordtype}{bool}\ \mbox{\hyperlink{class_d_object_ae47bf220fbe2173cf6933c2380035dbd}{isDebuggingEnabled}}()\ const\ noexcept;}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00188}00188\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00194}00194\ \ \ \ \ \textcolor{keywordtype}{int}\ \mbox{\hyperlink{class_d_object_a3dce47a519f9da5085c0c5ac1eea4f38}{setErrorCode}}(\textcolor{keywordtype}{int}\ code)\ noexcept;}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00195}00195\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00201}00201\ \ \ \ \ \textcolor{keywordtype}{int}\ \mbox{\hyperlink{class_d_object_afa8926d916081de72478cb8813c25e98}{getErrorCode}}()\ const\ noexcept;}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00202}00202\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00203}00203\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00212}00212\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_a15afffdf339150fc872bf63bdd08d581}{registerPlugin}}(const\ std::\textcolor{keywordtype}{string}\&\ \textcolor{keywordtype}{id},\ \mbox{\hyperlink{class_d_object_af11334d08ef85c68b3aae7554548e5a7}{Plugin}}\ plugin);}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00213}00213\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00221}00221\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_a99b8688849e11501033a25f61efb8356}{unregisterPlugin}}(const\ std::\textcolor{keywordtype}{string}\&\ \textcolor{keywordtype}{id});}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00222}00222\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00230}00230\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_a99072eb52bb22745f0248f273fbf28fb}{runPlugin}}(const\ std::\textcolor{keywordtype}{string}\&\ \textcolor{keywordtype}{id});}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00231}00231\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00237}00237\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_d_object_a1223275dcbbf20334ea11707346acb93}{runAllPlugins}}();}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00238}00238\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00248}00248\ \ \ \ \ friend\ std::ostream\&\ operator<<(std::ostream\&\ os,\ const\ \mbox{\hyperlink{class_d_object}{DObject}}\&\ obj);}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00249}00249\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00250}00250\ private:}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00251}\mbox{\hyperlink{class_d_object_ad7ba02f6d87ce64792149096f3310b21}{00251}}\ \ \ \ \ \mbox{\hyperlink{class_d_object_a55b7cdac36a3a518ba6e1ecef0e25dcd}{DataType}}\ \mbox{\hyperlink{class_d_object_ad7ba02f6d87ce64792149096f3310b21}{data\_}};\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00252}\mbox{\hyperlink{class_d_object_accf5c10d4afc3969607e11b0055312d5}{00252}}\ \ \ \ \ \textcolor{keywordtype}{bool}\ \mbox{\hyperlink{class_d_object_accf5c10d4afc3969607e11b0055312d5}{debugEnabled\_}}\ =\ false;\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00253}\mbox{\hyperlink{class_d_object_ad8de5890e8dae5fc7e72fabca2520fc3}{00253}}\ \ \ \ \ \textcolor{keywordtype}{int}\ \mbox{\hyperlink{class_d_object_ad8de5890e8dae5fc7e72fabca2520fc3}{errorCode\_}}\ =\ 0;\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00254}\mbox{\hyperlink{class_d_object_ae9f7e4d2fbabc076961a40185676e208}{00254}}\ \ \ \ \ std::map<std::\textcolor{keywordtype}{string},\ \mbox{\hyperlink{class_d_object_af11334d08ef85c68b3aae7554548e5a7}{Plugin}}>\ \mbox{\hyperlink{class_d_object_ae9f7e4d2fbabc076961a40185676e208}{plugins\_}};\ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00255}00255\ \};}
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00256}00256\ }
+\DoxyCodeLine{\Hypertarget{_d_object_8h_source_l00257}00257\ \textcolor{preprocessor}{\#endif\ }\textcolor{comment}{//\ DOBJECT\_H}}

 \end{DoxyCode}
--- a/docs/latex/_lockable_d_object_8h.tex
+++ b/docs/latex/_lockable_d_object_8h.tex
@@ -18,3 +18,6 @@ class \mbox{\hyperlink{class_lockable_d_object}{Lockable\+DObject}}
 A lightweight wrapper for \doxylink{class_d_object}{DObject} that adds locking capabilities. 

 This class allows safe concurrent access to a \doxylink{class_d_object}{DObject} by providing locking and unlocking methods. 
+
+Definition in file \mbox{\hyperlink{_lockable_d_object_8h_source}{Lockable\+DObject.\+h}}.
+
--- a/docs/latex/_lockable_d_object_8h_source.tex
+++ b/docs/latex/_lockable_d_object_8h_source.tex
@@ -2,28 +2,48 @@
 \hypertarget{_lockable_d_object_8h_source}{}\label{_lockable_d_object_8h_source}\index{src/dobj/public/LockableDObject.h@{src/dobj/public/LockableDObject.h}}
 \mbox{\hyperlink{_lockable_d_object_8h}{Go to the documentation of this file.}}
 \begin{DoxyCode}{0}
-\DoxyCodeLine{00001\ \textcolor{preprocessor}{\#ifndef\ LOCKABLE\_DOBJECT\_H}}
-\DoxyCodeLine{00002\ \textcolor{preprocessor}{\#define\ LOCKABLE\_DOBJECT\_H}}
-\DoxyCodeLine{00003\ }
-\DoxyCodeLine{00004\ \textcolor{preprocessor}{\#include\ "{}\mbox{\hyperlink{_d_object_8h}{DObject.h}}"{}}}
-\DoxyCodeLine{00005\ \textcolor{preprocessor}{\#include\ <mutex>}}
-\DoxyCodeLine{00006\ }
-\DoxyCodeLine{00014\ }
-\DoxyCodeLine{00019\ \textcolor{keyword}{class\ }\mbox{\hyperlink{class_lockable_d_object_ae1a174a2740fa053626fe2820ee0efee}{LockableDObject}}\ \{}
-\DoxyCodeLine{00020\ \textcolor{keyword}{public}:}
-\DoxyCodeLine{00024\ \ \ \ \ \mbox{\hyperlink{class_lockable_d_object_ae1a174a2740fa053626fe2820ee0efee}{LockableDObject}}()\ =\ \textcolor{keywordflow}{default};}
-\DoxyCodeLine{00025\ }
-\DoxyCodeLine{00030\ \ \ \ \ \mbox{\hyperlink{class_d_object}{DObject}}\&\ \mbox{\hyperlink{class_lockable_d_object_adcfe201fc728cc1c6fcf638a566ba9a1}{get}}();}
-\DoxyCodeLine{00031\ }
-\DoxyCodeLine{00035\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_lockable_d_object_ade38ca54703913359fc3b4366f6e292a}{lock}}();}
-\DoxyCodeLine{00036\ }
-\DoxyCodeLine{00040\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_lockable_d_object_a1481ed99dcd837490bf28309aadaedfb}{unlock}}();}
-\DoxyCodeLine{00041\ }
-\DoxyCodeLine{00042\ \textcolor{keyword}{private}:}
-\DoxyCodeLine{00043\ \ \ \ \ \mbox{\hyperlink{class_d_object}{DObject}}\ object\_;\ \ \ \ \ \ \ \ }
-\DoxyCodeLine{00044\ \ \ \ \ std::mutex\ mutex\_;\ \ \ \ \ \ }
-\DoxyCodeLine{00045\ \};}
-\DoxyCodeLine{00046\ }
-\DoxyCodeLine{00047\ \textcolor{preprocessor}{\#endif\ }\textcolor{comment}{//\ LOCKABLE\_DOBJECT\_H}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00001}00001\ \textcolor{comment}{/*\ ***********************************************************************}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00002}00002\ \textcolor{comment}{//}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00003}00003\ \textcolor{comment}{//\ \ \ Copyright\ (C)\ 2025\ -\/-\/\ The\ 4D-\/STAR\ Collaboration}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00004}00004\ \textcolor{comment}{//\ \ \ File\ Author:\ Emily\ Boudreaux}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00005}00005\ \textcolor{comment}{//\ \ \ Last\ Modified:\ March\ 17,\ 2025}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00006}00006\ \textcolor{comment}{//}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00007}00007\ \textcolor{comment}{//\ \ \ 4DSSE\ is\ free\ software;\ you\ can\ use\ it\ and/or\ modify}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00008}00008\ \textcolor{comment}{//\ \ \ it\ under\ the\ terms\ and\ restrictions\ the\ GNU\ General\ Library\ Public}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00009}00009\ \textcolor{comment}{//\ \ \ License\ version\ 3\ (GPLv3)\ as\ published\ by\ the\ Free\ Software\ Foundation.}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00010}00010\ \textcolor{comment}{//}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00011}00011\ \textcolor{comment}{//\ \ \ 4DSSE\ is\ distributed\ in\ the\ hope\ that\ it\ will\ be\ useful,}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00012}00012\ \textcolor{comment}{//\ \ \ but\ WITHOUT\ ANY\ WARRANTY;\ without\ even\ the\ implied\ warranty\ of}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00013}00013\ \textcolor{comment}{//\ \ \ MERCHANTABILITY\ or\ FITNESS\ FOR\ A\ PARTICULAR\ PURPOSE.}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00014}00014\ \textcolor{comment}{//\ \ \ See\ the\ GNU\ Library\ General\ Public\ License\ for\ more\ details.}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00015}00015\ \textcolor{comment}{//}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00016}00016\ \textcolor{comment}{//\ \ \ You\ should\ have\ received\ a\ copy\ of\ the\ GNU\ Library\ General\ Public\ License}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00017}00017\ \textcolor{comment}{//\ \ \ along\ with\ this\ software;\ if\ not,\ write\ to\ the\ Free\ Software}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00018}00018\ \textcolor{comment}{//\ \ \ Foundation,\ Inc.,\ 59\ Temple\ Place,\ Suite\ 330,\ Boston,\ MA\ 02111-\/1307\ USA}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00019}00019\ \textcolor{comment}{//}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00020}00020\ \textcolor{comment}{//\ ***********************************************************************\ */}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00021}00021\ \textcolor{preprocessor}{\#ifndef\ LOCKABLE\_DOBJECT\_H}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00022}00022\ \textcolor{preprocessor}{\#define\ LOCKABLE\_DOBJECT\_H}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00023}00023\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00024}00024\ \textcolor{preprocessor}{\#include\ "{}\mbox{\hyperlink{_d_object_8h}{DObject.h}}"{}}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00025}00025\ \textcolor{preprocessor}{\#include\ <mutex>}}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00026}00026\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00034}00034\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00039}\mbox{\hyperlink{class_lockable_d_object}{00039}}\ \textcolor{keyword}{class\ }\mbox{\hyperlink{class_lockable_d_object_ae1a174a2740fa053626fe2820ee0efee}{LockableDObject}}\ \{}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00040}00040\ \textcolor{keyword}{public}:}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00044}\mbox{\hyperlink{class_lockable_d_object_ae1a174a2740fa053626fe2820ee0efee}{00044}}\ \ \ \ \ \mbox{\hyperlink{class_lockable_d_object_ae1a174a2740fa053626fe2820ee0efee}{LockableDObject}}()\ =\ \textcolor{keywordflow}{default};}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00045}00045\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00050}00050\ \ \ \ \ \mbox{\hyperlink{class_d_object}{DObject}}\&\ \mbox{\hyperlink{class_lockable_d_object_adcfe201fc728cc1c6fcf638a566ba9a1}{get}}();}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00051}00051\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00055}00055\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_lockable_d_object_ade38ca54703913359fc3b4366f6e292a}{lock}}();}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00056}00056\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00060}00060\ \ \ \ \ \textcolor{keywordtype}{void}\ \mbox{\hyperlink{class_lockable_d_object_a1481ed99dcd837490bf28309aadaedfb}{unlock}}();}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00061}00061\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00062}00062\ \textcolor{keyword}{private}:}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00063}\mbox{\hyperlink{class_lockable_d_object_a1eb1ca1d9cf979dcb9eead96054b89bb}{00063}}\ \ \ \ \ \mbox{\hyperlink{class_d_object}{DObject}}\ \mbox{\hyperlink{class_lockable_d_object_a1eb1ca1d9cf979dcb9eead96054b89bb}{object\_}};\ \ \ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00064}\mbox{\hyperlink{class_lockable_d_object_a712cd3ea0c565f7e9089a651ef79b7bd}{00064}}\ \ \ \ \ std::mutex\ \mbox{\hyperlink{class_lockable_d_object_a712cd3ea0c565f7e9089a651ef79b7bd}{mutex\_}};\ \ \ \ \ \ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00065}00065\ \};}
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00066}00066\ }
+\DoxyCodeLine{\Hypertarget{_lockable_d_object_8h_source_l00067}00067\ \textcolor{preprocessor}{\#endif\ }\textcolor{comment}{//\ LOCKABLE\_DOBJECT\_H}}

 \end{DoxyCode}
--- a/Show More
+++ b/Show More