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<divclass="textblock"><p>Unified header for the scratchpad memory management system. </p>
<p>This is the main include file for the scratchpad subsystem. It provides a single include point for all scratchpad-related functionality, including the abstract base class, concrete implementations, type definitions, the StateBlob container, utility functions, and formatters for debugging.</p>
<dlclass="section user"><dt>What are Scratchpads?</dt><dd>Scratchpads are temporary working memory containers used by computational engines during ODE integration and reaction network calculations. They serve several critical purposes:</dd></dl>
<ul>
<li><b>Performance</b>: Pre-allocate memory once and reuse across iterations, avoiding repeated heap allocations during time-critical computations.</li>
<li><b>Caching</b>: Store intermediate results (Jacobians, derivatives, etc.) that can be reused across solver steps.</li>
<li><b>Thread Safety</b>: Provide thread-local storage for parallel execution, where each thread operates on its own independent scratchpad instance.</li>
<li><b>State Management</b>: Encapsulate engine-specific working state separate from the engine's persistent configuration.</li>
</ul>
<dlclass="section user"><dt>Architecture Overview</dt><dd>The scratchpad system consists of:</dd></dl>
<ul>
<li><b>AbstractScratchPad</b>: Base interface defining <code>is_initialized()</code> and <code>clone()</code></li>
<li><code>GraphEngineScratchPad</code>: CppAD ADFun and Jacobian caches</li>
<li><code>AdaptiveEngineViewScratchPad</code>: Active species/reactions for adaptive networks</li>
<li><code>DefinedEngineViewScratchPad</code>: Species/reactions for static networks</li>
<li><code>MultiscalePartitioningEngineViewScratchPad</code>: QSE groups and SUNDIALS context</li>
</ul>
</li>
<li><b>StateBlob</b>: Container managing multiple scratchpads with type-safe access</li>
<li><b>Utilities</b>: Helper functions for exception-based retrieval</li>
<li><b>Formatters</b>: std::format specializations for debugging output</li>
</ul>
<dlclass="section user"><dt>Why Use Scratchpads?</dt><dd>During numerical integration of stiff reaction networks, engines must:<oltype="1">
<li>Evaluate right-hand side functions (species derivatives)</li>
<li>Compute sparse Jacobian matrices</li>
<li>Solve linear systems within Newton iterations</li>
</ol>
</dd></dl>
<p>These operations require substantial temporary memory. Without scratchpads, each evaluation would allocate and deallocate working buffers, causing:</p><ul>
<li>Memory fragmentation</li>
<li>Cache thrashing</li>
<li>Unnecessary allocation overhead</li>
</ul>
<p>Scratchpads solve this by providing persistent, reusable working memory that lives for the duration of an integration step (or longer).</p>
<dlclass="section user"><dt>Thread Safety Model</dt><dd>The scratchpad system is designed for thread-local usage:</dd></dl>
<ul>
<li>Scratchpads are <b>not thread-safe</b> by design</li>
<li>Each thread must have its own scratchpad instances</li>
<li>Use <code>StateBlob::clone_structure()</code> to create independent copies for workers</li>
<li>The original scratchpad/blob remains usable by the main thread</li>
<divclass="line"><spanclass="comment">// Need to initialize before use</span></div>
<divclass="line">}</div>
<divclass="ttc"id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html"><divclass="ttname"><ahref="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html">gridfire::engine::scratch::StateBlob</a></div><divclass="ttdoc">Container for managing a collection of typed scratchpad instances.</div><divclass="ttdef"><b>Definition</b> blob.h:114</div></div>
<divclass="ttc"id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_a1633fec8fc3592bdf954ee1603f5e2a8"><divclass="ttname"><ahref="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#a1633fec8fc3592bdf954ee1603f5e2a8">gridfire::engine::scratch::StateBlob::get_status</a></div><divclass="ttdeci">ScratchPadStatus get_status() const</div><divclass="ttdoc">Get the status of a specific scratchpad type.</div><divclass="ttdef"><b>Definition</b> blob.h:445</div></div>
<divclass="ttc"id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_a8c998621c476665e812be930664286e6ad6d348ab4faddf5de5ec5aa302695ab5"><divclass="ttname"><ahref="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#a8c998621c476665e812be930664286e6ad6d348ab4faddf5de5ec5aa302695ab5">gridfire::engine::scratch::StateBlob::ScratchPadStatus::ENROLLED_NOT_INITIALIZED</a></div><divclass="ttdeci">@ ENROLLED_NOT_INITIALIZED</div><divclass="ttdoc">Scratchpad enrolled but not yet initialized.</div><divclass="ttdef"><b>Definition</b> blob.h:164</div></div>
<divclass="ttc"id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_aa06d7bb89e67c4b6fd584d8f32a251bf"><divclass="ttname"><ahref="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa06d7bb89e67c4b6fd584d8f32a251bf">gridfire::engine::scratch::StateBlob::enroll</a></div><divclass="ttdeci">void enroll()</div><divclass="ttdoc">Enroll a new scratchpad type into the blob.</div><divclass="ttdef"><b>Definition</b> blob.h:196</div></div>
<divclass="ttc"id="aclassgridfire_1_1engine_1_1scratch_1_1_state_blob_html_aa45357f0c368d7403306452c5ea56af0"><divclass="ttname"><ahref="classgridfire_1_1engine_1_1scratch_1_1_state_blob.html#aa45357f0c368d7403306452c5ea56af0">gridfire::engine::scratch::StateBlob::clone_structure</a></div><divclass="ttdeci">std::unique_ptr< StateBlob > clone_structure() const</div><divclass="ttdoc">Create a deep copy of this blob with all enrolled scratchpads.</div><divclass="ttdef"><b>Definition</b> blob.h:361</div></div>
<divclass="ttc"id="anamespacegridfire_1_1engine_1_1scratch_html"><divclass="ttname"><ahref="namespacegridfire_1_1engine_1_1scratch.html">gridfire::engine::scratch</a></div><divclass="ttdoc">Scratchpad memory management for computational engines.</div><divclass="ttdef"><b>Definition</b> blob.h:69</div></div>
<divclass="ttc"id="anamespacegridfire_1_1engine_1_1scratch_html_ab8f89f710094bfc93b84e26c818249b9"><divclass="ttname"><ahref="namespacegridfire_1_1engine_1_1scratch.html#ab8f89f710094bfc93b84e26c818249b9">gridfire::engine::scratch::get_state</a></div><divclass="ttdeci">CTX * get_state(StateBlob &ctx)</div><divclass="ttdoc">Retrieve a scratchpad from a StateBlob, throwing on error.</div><divclass="ttdef"><b>Definition</b> utils.h:87</div></div>
<divclass="ttc"id="ascratchpads_8h_html"><divclass="ttname"><ahref="scratchpads_8h.html">scratchpads.h</a></div><divclass="ttdoc">Unified header for the scratchpad memory management system.</div></div>
<divclass="ttc"id="astructgridfire_1_1engine_1_1scratch_1_1_adaptive_engine_view_scratch_pad_html"><divclass="ttname"><ahref="structgridfire_1_1engine_1_1scratch_1_1_adaptive_engine_view_scratch_pad.html">gridfire::engine::scratch::AdaptiveEngineViewScratchPad</a></div><divclass="ttdoc">Scratchpad for storing working memory used by AdaptiveEngineView computations.</div><divclass="ttdef"><b>Definition</b> engine_adaptive_scratchpad.h:66</div></div>
<divclass="ttc"id="astructgridfire_1_1engine_1_1scratch_1_1_adaptive_engine_view_scratch_pad_html_a8fc25bac8529777504a206fc9fa2a5d6"><divclass="ttname"><ahref="structgridfire_1_1engine_1_1scratch_1_1_adaptive_engine_view_scratch_pad.html#a8fc25bac8529777504a206fc9fa2a5d6">gridfire::engine::scratch::AdaptiveEngineViewScratchPad::initialize</a></div><divclass="ttdeci">void initialize(const AdaptiveEngineView &engine)</div><divclass="ttdoc">Initialize the scratchpad from an AdaptiveEngineView.</div><divclass="ttdef"><b>Definition</b> engine_adaptive_scratchpad.h:102</div></div>
<divclass="ttc"id="astructgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad_html"><divclass="ttname"><ahref="structgridfire_1_1engine_1_1scratch_1_1_graph_engine_scratch_pad.html">gridfire::engine::scratch::GraphEngineScratchPad</a></div><divclass="ttdoc">Scratchpad for storing CppAD automatic differentiation state for GraphEngine.</div><divclass="ttdef"><b>Definition</b> engine_graph_scratchpad.h:83</div></div>
<li><aclass="el"href="scratchpad__abstract_8h.html"title="Abstract base class for scratchpad memory used during engine computations.">scratchpad_abstract.h</a> - AbstractScratchPad base class</li>
<li><aclass="el"href="engine__graph__scratchpad_8h.html"title="Scratchpad implementation for the GraphEngine using CppAD automatic differentiation.">engine_graph_scratchpad.h</a> - GraphEngineScratchPad</li>
<li><aclass="el"href="engine__adaptive__scratchpad_8h.html"title="Scratchpad implementation for the AdaptiveEngineView.">engine_adaptive_scratchpad.h</a> - AdaptiveEngineViewScratchPad</li>
<li><aclass="el"href="engine__multiscale__scratchpad_8h.html"title="Scratchpad implementation for the MultiscalePartitioningEngineView.">engine_multiscale_scratchpad.h</a> - MultiscalePartitioningEngineViewScratchPad</li>
<li><aclass="el"href="engine__defined__scratchpad_8h.html"title="Scratchpad implementation for the DefinedEngineView.">engine_defined_scratchpad.h</a> - DefinedEngineViewScratchPad</li>
<li>types.h - ScratchPadType enumeration</li>
<li><aclass="el"href="blob_8h.html"title="Container class for managing multiple scratchpad instances.">blob.h</a> - StateBlob container</li>
<liclass="footer">Generated by <ahref="https://www.doxygen.org/index.html"><imgclass="footer"src="doxygen.svg"width="104"height="31"alt="doxygen"/></a> 1.13.2 </li>
