docs(docs): built docs

Note for now much of the docs is LLM written. This was done to save time and focus on code development. The docs have been LOOSLEY reviewed. However, the code itself has been either fully written by hand or fully reviewed. Therefore, the docs should at the moment be seen as a loose resource rather than authoratiative (and this is on top of the general ability for docs to drift)

docs/filters/custom_sections.c

@@ -0,0 +1,348 @@
+
+/*
+ * Doxygen documentation filter.
+ *
+ * Supports:
+ *   @requires
+ *   @contribution
+ *   @true_if
+ *
+ * We have this as a C not a python file to avoid spinning up the python interpreter separately for every file.
+ * We have this as a C and not a C++ file to avoid large binaries for something as simple as documentation generation and so we can more easily generate portable binaries.
+ */
+
+#include <ctype.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define MAX_LINE_LENGTH 240
+
+typedef struct {
+    const char *name;
+    const char *title;
+    const char *cssClass;
+} Command;
+
+// To add additional custom sections to the documentation edit this, you may also want to edit
+// the doxygen-extra.css file to customize the class styling
+static const Command commands[] = {
+    {"@requires", "Requirements", "serif-requires"},
+    {"@contribution", "Equation Contributions", "serif-contribution"},
+    {"@true_if", "Compile Time True Type If", "serif-true-if"}
+};
+
+#define COMMAND_COUNT (sizeof(commands) / sizeof(commands[0]))
+
+typedef struct {
+    char *text;
+    size_t length;
+    size_t prefixLength;
+    size_t contentStart;
+    size_t contentLength;
+    size_t newlineStart;
+    int commandIndex;
+} Line;
+
+typedef struct {
+    Line *data;
+    size_t count;
+    size_t capacity;
+} LineArray;
+
+static void *checked_realloc(void *ptr, size_t size) {
+    void *result = realloc(ptr, size);
+    if (!result) {
+        fprintf(stderr, "ERROR: Out of memory.\n");
+        exit(EXIT_FAILURE);
+    }
+    return result;
+}
+
+/* Read a complete line, including its newline. */
+static int read_line(FILE *file, Line *line) {
+    size_t capacity = 256;
+    size_t length = 0;
+    char *buffer = checked_realloc(NULL, capacity);
+
+    int character;
+    while ((character = fgetc(file)) != EOF) {
+        if (length + 1 >= capacity) {
+            capacity *= 2;
+            buffer = checked_realloc(buffer, capacity);
+        }
+
+        buffer[length++] = (char)character;
+
+        if (character == '\n')
+            break;
+    }
+
+    if (length == 0) {
+        free(buffer);
+        return 0;
+    }
+
+    buffer[length] = '\0';
+
+    line->text = buffer;
+    line->length = length;
+    line->commandIndex = -1;
+    line->prefixLength = 0;
+    line->contentStart = 0;
+    line->contentLength = 0;
+
+    line->newlineStart = length;
+
+    while (line->newlineStart > 0 &&
+           (buffer[line->newlineStart - 1] == '\n' ||
+            buffer[line->newlineStart - 1] == '\r')) {
+        --line->newlineStart;
+    }
+
+    return 1;
+}
+
+/* Recognize the supported Doxygen commands. */
+static void parse_line(Line *line) {
+    const char *text = line->text;
+    const size_t end = line->newlineStart;
+    size_t pos = 0;
+
+    while (pos < end && (text[pos] == ' ' || text[pos] == '\t'))
+        ++pos;
+
+    if (pos == end || text[pos] != '*')
+        return;
+
+    ++pos;
+
+    /* Require whitespace after the comment marker. */
+    if (pos == end || (text[pos] != ' ' && text[pos] != '\t'))
+        return;
+
+    while (pos < end && (text[pos] == ' ' || text[pos] == '\t'))
+        ++pos;
+
+    for (size_t index = 0; index < COMMAND_COUNT; ++index) {
+        const Command *command = &commands[index];
+        size_t nameLength = strlen(command->name);
+
+        if (nameLength > end - pos)
+            continue;
+
+        if (strncmp(text + pos, command->name, nameLength) != 0)
+            continue;
+
+        size_t start = pos + nameLength;
+
+        if (start == end || !isspace((unsigned char)text[start]))
+            continue;
+
+        while (start < end && isspace((unsigned char)text[start]))
+            ++start;
+
+        size_t contentEnd = end;
+
+        while (contentEnd > start &&
+               isspace((unsigned char)text[contentEnd - 1])) {
+            --contentEnd;
+        }
+
+        if (start == contentEnd)
+            continue;
+
+        line->commandIndex = (int)index;
+        line->prefixLength = pos;
+        line->contentStart = start;
+        line->contentLength = contentEnd - start;
+        return;
+    }
+}
+
+static void append_line(LineArray *lines, Line line) {
+    if (lines->count == lines->capacity) {
+        size_t capacity = lines->capacity ? lines->capacity * 2 : 128;
+        lines->data = checked_realloc(
+            lines->data,
+            capacity * sizeof(Line)
+        );
+        lines->capacity = capacity;
+    }
+
+    lines->data[lines->count++] = line;
+}
+
+static size_t generated_length(
+    const Line *line,
+    const Command *command,
+    int first,
+    int last
+) {
+    size_t length = line->prefixLength +
+                    strlen("<li></li>") +
+                    line->contentLength;
+
+    if (first) {
+        length += strlen("<table class=\"\"><tr><th></th></tr><tr><td><ul>");
+        length += strlen(command->cssClass);
+        length += strlen(command->title);
+    }
+
+    if (last)
+        length += strlen("</ul></td></tr></table>");
+
+    return length;
+}
+
+static void write_original(const Line *line) {
+    fwrite(line->text, 1, line->length, stdout);
+}
+
+static void write_transformed(
+    const Line *line,
+    const Command *command,
+    int first,
+    int last
+) {
+    fwrite(line->text, 1, line->prefixLength, stdout);
+
+    if (first) {
+        printf(
+            "<table class=\"%s\"><tr><th>%s</th></tr><tr><td><ul>",
+            command->cssClass,
+            command->title
+        );
+    }
+
+    fputs("<li>", stdout);
+
+    fwrite(
+        line->text + line->contentStart,
+        1,
+        line->contentLength,
+        stdout
+    );
+
+    fputs("</li>", stdout);
+
+    if (last)
+        fputs("</ul></td></tr></table>", stdout);
+
+    fwrite(
+        line->text + line->newlineStart,
+        1,
+        line->length - line->newlineStart,
+        stdout
+    );
+}
+
+static void transform(const LineArray *lines) {
+    size_t index = 0;
+
+    while (index < lines->count) {
+        const Line *line = &lines->data[index];
+
+        if (line->commandIndex < 0) {
+            write_original(line);
+            ++index;
+            continue;
+        }
+
+        size_t start = index;
+        int commandIndex = line->commandIndex;
+
+        while (index < lines->count &&
+               lines->data[index].commandIndex == commandIndex) {
+            ++index;
+        }
+
+        size_t end = index;
+        const Command *command = &commands[commandIndex];
+
+        int overflow = 0;
+
+        for (size_t item = start; item < end; ++item) {
+            size_t length = generated_length(
+                &lines->data[item],
+                command,
+                item == start,
+                item == end - 1
+            );
+
+            if (length > MAX_LINE_LENGTH) {
+                overflow = 1;
+                break;
+            }
+        }
+
+        if (overflow) {
+            fprintf(
+                stderr,
+                "WARNING: %s group at input line %zu exceeds "
+                "%d characters after transformation; "
+                "original text retained.\n",
+                command->name,
+                start + 1,
+                MAX_LINE_LENGTH
+            );
+        }
+
+        for (size_t item = start; item < end; ++item) {
+            if (overflow) {
+                write_original(&lines->data[item]);
+            } else {
+                write_transformed(
+                    &lines->data[item],
+                    command,
+                    item == start,
+                    item == end - 1
+                );
+            }
+        }
+    }
+}
+
+int main(int argc, char **argv) {
+    // Validation
+    if (argc != 2) {
+        fprintf(stderr, "Usage: %s <source-file>\n", argv[0]);
+        return EXIT_FAILURE;
+    }
+
+    FILE *file = fopen(argv[1], "rb");
+
+    if (!file) {
+        fprintf(stderr, "ERROR: Cannot open '%s'.\n", argv[1]);
+        return EXIT_FAILURE;
+    }
+
+    // Parsing
+    LineArray lines = {0};
+    Line line;
+
+    while (read_line(file, &line)) {
+        parse_line(&line);
+        append_line(&lines, line);
+    }
+
+    // Clean up file handles
+    if (ferror(file)) {
+        fprintf(stderr, "ERROR: Failed reading '%s'.\n", argv[1]);
+        fclose(file);
+        return EXIT_FAILURE;
+    }
+
+    fclose(file);
+
+    // Transformation and output
+    transform(&lines);
+
+    // Cleanup memory
+    for (size_t index = 0; index < lines.count; ++index)
+        free(lines.data[index].text);
+
+    free(lines.data);
+
+    return ferror(stdout) ? EXIT_FAILURE : EXIT_SUCCESS;
+}

docs/filters/meson.build

@@ -0,0 +1,2 @@
+project('doxygen-custom-sections-serif', 'c', version : '1.0.0')
+executable('serif-custom-sections', 'custom_sections.c')

docs/html/_c_o_m_p_o_n_e_n_t_s_8md.html

@@ -0,0 +1,123 @@
+<!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" lang="en-US">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<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>SERiF: src/include/serif/utils/serialize/COMPONENTS.md 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>
+<script type="text/javascript" src="clipboard.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<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/x-mathjax-config">
+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></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"/>
+<link href="doxygen-extra.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 id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">SERiF<span id="projectnumber">&#160;v0.0.1a</span>
+   </div>
+   <div id="projectbrief">Stellar Evolution and Rotation in Four Dimensions</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.13.2 -->
+<script type="text/javascript">
+/* @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);
+  $(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function(){initNavTree('_c_o_m_p_o_n_e_n_t_s_8md.html',''); initResizable(true); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<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">src/include/serif/utils/serialize/COMPONENTS.md File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="_c_o_m_p_o_n_e_n_t_s_8md.html">COMPONENTS.md</a></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>
+</div>
+</body>
+</html>

docs/html/_formulas.aux

@@ -0,0 +1,2 @@
+\relax 
+\gdef \@abspage@last{15}

docs/html/_formulas.log

@@ -0,0 +1,161 @@
+This is pdfTeX, Version 3.141592653-2.6-1.40.27 (TeX Live 2025) (preloaded format=latex 2025.3.8)  30 SEP 2026 15:48
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**_formulas
+(./_formulas.tex
+LaTeX2e <2024-11-01> patch level 2
+L3 programming layer <2025-01-18>
+(/usr/local/texlive/2025/texmf-dist/tex/latex/base/article.cls
+Document Class: article 2024/06/29 v1.4n Standard LaTeX document class
+(/usr/local/texlive/2025/texmf-dist/tex/latex/base/size10.clo
+File: size10.clo 2024/06/29 v1.4n Standard LaTeX file (size option)
+)
+\c@part=\count196
+\c@section=\count197
+\c@subsection=\count198
+\c@subsubsection=\count199
+\c@paragraph=\count266
+\c@subparagraph=\count267
+\c@figure=\count268
+\c@table=\count269
+\abovecaptionskip=\skip49
+\belowcaptionskip=\skip50
+\bibindent=\dimen141
+) (/usr/local/texlive/2025/texmf-dist/tex/generic/iftex/iftex.sty
+Package: iftex 2024/12/12 v1.0g TeX engine tests
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/base/ifthen.sty
+Package: ifthen 2024/03/16 v1.1e Standard LaTeX ifthen package (DPC)
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/epsfig.sty
+Package: epsfig 2024/01/14 v1.7b (e)psfig emulation (SPQR)
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/graphicx.sty
+Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR)
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/keyval.sty
+Package: keyval 2022/05/29 v1.15 key=value parser (DPC)
+\KV@toks@=\toks17
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/graphics.sty
+Package: graphics 2024/08/06 v1.4g Standard LaTeX Graphics (DPC,SPQR)
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/trig.sty
+Package: trig 2023/12/02 v1.11 sin cos tan (DPC)
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/graphics-cfg/graphics.cfg
+File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
+)
+Package graphics Info: Driver file: dvips.def on input line 106.
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics-def/dvips.def
+File: dvips.def 2022/09/22 v3.1e Graphics/color driver for dvips
+))
+\Gin@req@height=\dimen142
+\Gin@req@width=\dimen143
+)
+\epsfxsize=\dimen144
+\epsfysize=\dimen145
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/base/inputenc.sty
+Package: inputenc 2024/02/08 v1.3d Input encoding file
+\inpenc@prehook=\toks18
+\inpenc@posthook=\toks19
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/xcolor/xcolor.sty
+Package: xcolor 2024/09/29 v3.02 LaTeX color extensions (UK)
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics-cfg/color.cfg
+File: color.cfg 2016/01/02 v1.6 sample color configuration
+)
+Package xcolor Info: Driver file: dvips.def on input line 274.
+(/usr/local/texlive/2025/texmf-dist/tex/latex/graphics/mathcolor.ltx)
+Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1349.
+Package xcolor Info: Model `RGB' extended on input line 1365.
+Package xcolor Info: Model `HTML' substituted by `rgb' on input line 1367.
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+Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1370.
+Package xcolor Info: Model `Gray' substituted by `gray' on input line 1371.
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+)
+(/usr/local/texlive/2025/texmf-dist/tex/latex/newunicodechar/newunicodechar.sty
+Package: newunicodechar 2018/04/08 v1.2 Defining Unicode characters
+) (/usr/local/texlive/2025/texmf-dist/tex/latex/l3backend/l3backend-dvips.def
+File: l3backend-dvips.def 2024-05-08 L3 backend support: dvips
+\l__pdf_internal_box=\box52
+\l__pdf_backend_content_box=\box53
+\l__pdf_backend_model_box=\box54
+\g__pdf_backend_annotation_int=\count270
+\g__pdf_backend_link_int=\count271
+\g__pdf_backend_link_sf_int=\count272
+)
+No file _formulas.aux.
+\openout1 = `_formulas.aux'.
+
+LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
+LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
+LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
+LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
+LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
+LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 30.
+LaTeX Font Info:    ... okay on input line 30.
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+LaTeX Font Info:    External font `cmex10' loaded for size
+(Font)              <7> on input line 31.
+LaTeX Font Info:    External font `cmex10' loaded for size
+(Font)              <5> on input line 31.
+
+
+[1
+
+]
+
+[2]
+
+[3]
+
+[4]
+
+[5]
+
+[6]
+
+[7]
+
+[8]
+
+[9]
+
+[10]
+
+[11]
+
+[12]
+
+[13]
+
+[14]
+! Undefined control sequence.
+l.79 \[\boldsymbol
+                  {\rho}_h = E\mathbf{c}.
+The control sequence at the end of the top line
+of your error message was never \def'ed. If you have
+misspelled it (e.g., `\hobx'), type `I' and the correct
+spelling (e.g., `I\hbox'). Otherwise just continue,
+and I'll forget about whatever was undefined.
+
+
+
+[15] (./_formulas.aux)
+ ***********
+LaTeX2e <2024-11-01> patch level 2
+L3 programming layer <2025-01-18>
+ ***********
+ ) 
+Here is how much of TeX's memory you used:
+ 1581 strings out of 473191
+ 25843 string characters out of 5715827
+ 420202 words of memory out of 5000000
+ 24868 multiletter control sequences out of 15000+600000
+ 559764 words of font info for 39 fonts, out of 8000000 for 9000
+ 1141 hyphenation exceptions out of 8191
+ 72i,5n,79p,224b,103s stack positions out of 10000i,1000n,20000p,200000b,200000s
+
+Output written on _formulas.dvi (15 pages, 3568 bytes).

docs/html/_formulas.tex

@@ -0,0 +1,83 @@
+\documentclass{article}
+\usepackage{iftex}
+\usepackage{ifthen}
+\usepackage{epsfig}
+\usepackage[utf8]{inputenc}
+\usepackage{xcolor}
+\ifPDFTeX
+\usepackage{newunicodechar}
+  \makeatletter
+    \def\doxynewunicodechar#1#2{%
+    \@tempswafalse
+    \edef\nuc@tempa{\detokenize{#1}}%
+    \if\relax\nuc@tempa\relax
+      \nuc@emptyargerr
+    \else
+      \edef\@tempb{\expandafter\@car\nuc@tempa\@nil}%
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+<div class="textblock"><code>#include &lt;algorithm&gt;</code><br />
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+  <div class="headertitle"><div class="title">actions.hpp File Reference</div></div>
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+<div class="textblock"><code>#include &lt;algorithm&gt;</code><br />
+<code>#include &lt;concepts&gt;</code><br />
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+<code>#include &quot;<a class="el" href="action__storage_8hpp.html">serif/geometry/deformation/detail/action_storage.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="spaces_8hpp.html">serif/geometry/deformation/spaces.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="geometry_2deformation_2workspace_8hpp.html">serif/geometry/deformation/workspace.hpp</a>&quot;</code><br />
+</div><div class="textblock"><div class="dynheader">
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+</div>
+</div><div class="textblock"><div class="dynheader">
+This graph shows which files directly or indirectly include this file:</div>
+<div class="dyncontent">
+<div class="center"><div class="zoom"><iframe scrolling="no" frameborder="0" src="actions_8hpp__dep__incl.svg" width="100%" height="600"><p><b>This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead.</b></p></iframe></div></div>
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+</div><table class="memberdecls">
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif.html">serif</a></td></tr>
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+<tr class="memitem:a28c839bb898ee76ac62ceaddadcba6b1"><td class="memTemplItemLeft" align="right" valign="top"><a class="el" href="namespaceserif_1_1geometry_1_1deformation.html#a08306ee593c172f4877facc061e98f97">DeformationStatus</a>&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1geometry_1_1deformation.html#a28c839bb898ee76ac62ceaddadcba6b1">serif::geometry::deformation::apply_jacobian_transpose</a> (const Map &amp;map, std::span&lt; const double &gt; parameters, std::span&lt; const double &gt; displacement_dual, std::span&lt; double &gt; parameter_dual, <a class="el" href="namespaceserif_1_1geometry_1_1deformation.html#ae1f99a74025eac52e6ff4a4b77fb41c6">DeformationWorkspace</a>&lt; Map &gt; &amp;workspace)</td></tr>
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+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle"><div class="title">all.hpp File Reference</div></div>
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+<p>File containing validate_schema, which selects the topology validators required by the schema type.  
+<a href="#details">More...</a></p>
+<div class="textblock"><code>#include &quot;<a class="el" href="discretization_2domain_2mesh_2topology_8hpp.html">serif/discretization/domain/mesh/topology.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="discretization_2domain_2schema_2concepts_8hpp.html">serif/discretization/domain/schema/concepts.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="results_8hpp.html">serif/discretization/domain/schema/validation/results.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="validator_8hpp.html">serif/discretization/domain/schema/validation/validator.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="schema_2validation_2boundary_8hpp.html">serif/discretization/domain/schema/validation/boundary.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="connected_8hpp.html">serif/discretization/domain/schema/validation/connected.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="inscribed_8hpp.html">serif/discretization/domain/schema/validation/inscribed.hpp</a>&quot;</code><br />
+</div><div class="textblock"><div class="dynheader">
+Include dependency graph for all.hpp:</div>
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+</div><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="namespaces" name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif.html">serif</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1discretization.html">serif::discretization</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1discretization_1_1domain.html">serif::discretization::domain</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1discretization_1_1domain_1_1schema.html">serif::discretization::domain::schema</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1discretization_1_1domain_1_1schema_1_1validation.html">serif::discretization::domain::schema::validation</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><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:ac7b1768feeba6a687afd25651fd43022" id="r_ac7b1768feeba6a687afd25651fd43022"><td class="memTemplParams" colspan="2">template&lt;IsSchema SchemaT&gt; </td></tr>
+<tr class="memitem:ac7b1768feeba6a687afd25651fd43022"><td class="memTemplItemLeft" align="right" valign="top"><a class="el" href="structserif_1_1discretization_1_1domain_1_1schema_1_1validation_1_1_schema_validation_result.html">SchemaValidationResult</a>&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1discretization_1_1domain_1_1schema_1_1validation.html#ac7b1768feeba6a687afd25651fd43022">serif::discretization::domain::schema::validation::validate_schema</a> (const <a class="el" href="classserif_1_1discretization_1_1domain_1_1mesh_1_1_mesh_topology.html">mesh::MeshTopology</a> &amp;topology)</td></tr>
+<tr class="memdesc:ac7b1768feeba6a687afd25651fd43022"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validate a mesh against a schema.  <br /></td></tr>
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+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>File containing validate_schema, which selects the topology validators required by the schema type. </p>
+<dl class="section author"><dt>Author</dt><dd>Emily M. Boudreaux </dd></dl>
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+<div class="textblock"><code>#include &quot;<a class="el" href="amg_8hpp.html">serif/backend/mfem/solver/preconditioner/inverse/amg.hpp</a>&quot;</code><br />
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner.html">serif::solver::preconditioner</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner_1_1backend.html">serif::solver::preconditioner::backend</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner_1_1backend_1_1mfem.html">serif::solver::preconditioner::backend::mfem</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
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+<tr class="memdesc:a93b06736f1aa8006a04b04059080bd34"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prepare fixed-cycle BoomerAMG on this process; MPI must already be initialized and remains caller-owned.  <br /></td></tr>
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+<div class="textblock"><code>#include &lt;expected&gt;</code><br />
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+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner.html">serif::solver::preconditioner</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner_1_1backend.html">serif::solver::preconditioner::backend</a></td></tr>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1solver_1_1preconditioner_1_1backend_1_1mfem.html">serif::solver::preconditioner::backend::mfem</a></td></tr>
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+<tr class="memdesc:a93b06736f1aa8006a04b04059080bd34"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prepare fixed-cycle BoomerAMG on this process; MPI must already be initialized and remains caller-owned.  <br /></td></tr>
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+  <div class="headertitle"><div class="title">angular_momentum.hpp File Reference</div></div>
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+<p>File containing the angular momentum constraint equation, which enforces a global constraint on the total angular momentum of a system.  
+<a href="#details">More...</a></p>
+<div class="textblock"><code>#include &lt;cmath&gt;</code><br />
+<code>#include &lt;string_view&gt;</code><br />
+<code>#include &quot;<a class="el" href="equations_2contributions_8hpp.html">serif/equations/contributions.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="point_8hpp.html">serif/equations/point.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="rigid__rotation_8hpp.html">serif/equations/rigid_rotation.hpp</a>&quot;</code><br />
+</div><div class="textblock"><div class="dynheader">
+Include dependency graph for angular_momentum.hpp:</div>
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+<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Angular momentum constraint equation, which enforces a global constraint on the total angular momentum of a system.  <a href="classserif_1_1equations_1_1_angular_momentum_constraint.html#details">More...</a><br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+Namespaces</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif.html">serif</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1equations.html">serif::equations</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>File containing the angular momentum constraint equation, which enforces a global constraint on the total angular momentum of a system. </p>
+<dl class="section author"><dt>Author</dt><dd>Emily M. Boudreaux</dd></dl>
+<dl class="section note"><dt>Note</dt><dd>The angular momentum constraint is a global constraint that is enforced by integrating the point-wise contributions of the angular momentum density over the entire domain. The integrand is given by \( j_\parallel = \rho \Omega s^2\), where \(s^2 = |\hat{n} × (r − r_{c})|^2\) is the cylindrical radius squared, and \(\hat{n}\) is the unit rotation axis. The solver will integrate this over the domain and compare it to the target angular momentum to enforce the constraint.</dd></dl>
+<p>A few important notes about the implementation</p>
+<ul>
+<li>The way the equation system plugs into the mfem backend is such that equations should only ever return point wise contributions to the residual, not a global integrated residual. This is why we return \( j_\parallel = \rho \Omega s^2\) as the residual, rather than \( j_\parallel - J_{\text{target}}\). However we still need to subtract the target angular momentum from the integrated residual to enforce the constraint. This is done by implementing the method ::residual_offset() which returns \( -J_{\text{target}}\). The backend will automatically detect and, if present, subtract this from the integrated residual to enforce the constraint.</li>
+<li>The solver can choose to validate the angular momentum constraint by integrating the ::validation_integrand() over the domain and then passing this result to ::validate_integral(double result). Note that this is not specific to this equation but a feature of the overall system </li>
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+Include dependency graph for archive.cpp:</div>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif.html">serif</a></td></tr>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1utils.html">serif::utils</a></td></tr>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceserif_1_1utils_1_1serialize.html">serif::utils::serialize</a></td></tr>
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