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This is the result of intense work over the last three years. Please let us know how to improve Reaktoro!</div> <div class="header header-item noprint"></div> <div class="container-fluid" id="banner"></div> <div class="container-xl"> <div class="row"> <!-- Sidebar --> <div class="bd-sidebar noprint" id="site-navigation"> <div class="bd-sidebar__content"> <div class="bd-sidebar__top"><div class="navbar-brand-box"> <a class="navbar-brand text-wrap" href="index.html"> <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 --> <img src="_static/reaktoro-for-python-and-cpp.svg" class="logo" alt="logo"> </a> </div><form class="bd-search d-flex align-items-center" action="search.html" method="get"> <i class="icon fas fa-search"></i> <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" > </form><nav class="bd-links" id="bd-docs-nav" aria-label="Main"> <div class="bd-toc-item active"> <ul class="nav bd-sidenav bd-sidenav__home-link"> <li class="toctree-l1"> <a class="reference internal" href="index.html"> Reaktoro </a> </li> </ul> <p aria-level="2" class="caption" role="heading"> <span class="caption-text"> Get Started </span> </p> <ul class="nav bd-sidenav"> <li class="toctree-l1 has-children"> <a class="reference internal" href="installation/index.html"> Installation </a> <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/> <label for="toctree-checkbox-1"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="installation/installation-using-conda.html"> Installation using Conda </a> </li> <li class="toctree-l2"> <a class="reference internal" href="installation/installation-using-cmake.html"> Installation using CMake </a> </li> <li class="toctree-l2"> <a class="reference internal" href="installation/installation-in-google-colab.html"> Installation in Google Colab </a> </li> </ul> </li> <li class="toctree-l1"> <a class="reference external" href="https://reaktoro.org/api"> API Reference </a> </li> <li class="toctree-l1"> <a class="reference external" href="https://reaktoro.org/v1"> Reaktoro v1 </a> </li> </ul> <p aria-level="2" class="caption" role="heading"> <span class="caption-text"> Tutorials </span> </p> <ul class="nav bd-sidenav"> <li class="toctree-l1 has-children"> <a class="reference internal" href="tutorials/basics/index.html"> Basics </a> <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/> <label for="toctree-checkbox-2"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/importing-reaktoro.html"> Importing Reaktoro </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/loading-databases.html"> Loading thermodynamic databases </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/inspecting-databases.html"> Inspecting thermodynamic databases </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/defining-chemical-systems.html"> Defining chemical systems </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/creating-chemical-states.html"> Creating chemical states </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/computing-chemical-properties.html"> Computing chemical properties </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/computing-aqueous-properties.html"> Computing aqueous properties </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/computing-thermo-props-of-species.html"> Computing standard thermodynamic properties of species </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/computing-thermo-props-of-reactions.html"> Computing standard thermodynamic properties of reactions </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/specifying-activity-models.html"> Specifying activity models </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/basics/defining-materials.html"> Defining materials </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="tutorials/equilibrium/index.html"> Chemical Equilibrium </a> <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/> <label for="toctree-checkbox-3"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-basics.html"> Chemical equilibrium: the basics </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-specifying-constraints.html"> Chemical equilibrium with constraints </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-fixed-ph.html"> Chemical equilibrium with fixed pH </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-fixed-ph-charge-balance.html"> Chemical equilibrium with fixed pH and charge balance </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-fixed-phase-amount.html"> Chemical equilibrium with fixed phase amount </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-fixed-fugacity.html"> Chemical equilibrium with fixed fugacity </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-fixed-volume-internal-energy.html"> Chemical equilibrium with fixed volume and internal energy </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-custom-constraints.html"> Chemical equilibrium with custom constraints </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/equilibrium/equilibrium-with-given-component-amounts.html"> Chemical equilibrium with given element and charge amounts </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="tutorials/kinetics/index.html"> Chemical Kinetics </a> <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/> <label for="toctree-checkbox-4"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="tutorials/kinetics/kinetics-basics.html"> Chemical kinetics: the basics </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/kinetics/kinetics-minerals-using-palandri-kharaka-model.html"> Chemical kinetics for mineral reactions using Palandri-Kharaka model </a> </li> <li class="toctree-l2"> <a class="reference internal" href="tutorials/kinetics/kinetics-minerals-custom-surface-area-models.html"> Chemical kinetics for mineral reactions using custom surface area models </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="tutorials/machine-learning/index.html"> Machine Learning </a> <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/> <label for="toctree-checkbox-5"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="tutorials/machine-learning/machine-learning-basics.html"> Machine learning: the basics </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="tutorials/advanced/index.html"> Advanced </a> <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/> <label for="toctree-checkbox-6"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="tutorials/advanced/creating-custom-databases.html"> Creating thermodynamic databases </a> </li> </ul> </li> <li class="toctree-l1"> <a class="reference internal" href="tutorials/bibliography.html"> Bibliography </a> </li> </ul> <p aria-level="2" class="caption" role="heading"> <span class="caption-text"> Applications </span> </p> <ul class="nav bd-sidenav"> <li class="toctree-l1 has-children"> <a class="reference internal" href="applications/solubility/index.html"> Solubility </a> <input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" type="checkbox"/> <label for="toctree-checkbox-7"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="applications/solubility/solubility-calcite-on-acidity-and-temperature.html"> Calcite solubility in water, rainwater, and seawater </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/solubility/solubility-co2-on-salinity-and-temperature.html"> Carbon-dioxide solubility in brines with different salinity and temperature </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="applications/geochemistry/index.html"> Geochemistry </a> <input class="toctree-checkbox" id="toctree-checkbox-8" name="toctree-checkbox-8" type="checkbox"/> <label for="toctree-checkbox-8"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ph-dependence-on-co2-addition-in-seawater.html"> Carbon dioxide (CO₂) dissolution in seawater </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ph-dependence-on-contaminants-in-water.html"> pH-dependence on added contaminants in water </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/evian-water-analysis.html"> Analysis of the Evian water </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/opening-bottle-with-sparkling-water.html"> Opening bottle with sparkling water </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/uraniun-speciation-vs-pH.html"> Uranium (VI) speciation as a function of pH at fixed CO <sub> 2 </sub> partial pressure </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/cement-simulation-with-solid-solutions.html"> The effect of limestone addition on a hydrated cement mix </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ion-exchange-dune-sand.html"> Ion exchange in dune sand and groundwater </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ion-exchange-mix-porewater-extractant.html"> Extraction of exchangeable cations in dune sand </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ion-exchange-cax2-nax-kx-vs-changing-ca-k.html"> Cation exchange competition among Na <sup> + </sup> , K <sup> + </sup> and Ca <sup> 2+ </sup> </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geochemistry/ion-exchange-calcite-cax-vs-ph.html"> Effect of calcite dissolution on exchangeable cations </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="applications/geobiology/index.html"> Geobiology </a> <input class="toctree-checkbox" id="toctree-checkbox-9" name="toctree-checkbox-9" type="checkbox"/> <label for="toctree-checkbox-9"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="applications/geobiology/geobiology-streammodel-fixed-fugacity.html"> Carbonate-rich lakes modeling on the early Earth </a> </li> <li class="toctree-l2"> <a class="reference internal" href="applications/geobiology/geobiology-phreeqc-fixed-fugacity.html"> Phosphate accumulation in carbonate-rich brines </a> </li> </ul> </li> <li class="toctree-l1 has-children"> <a class="reference internal" href="applications/biomass-gasification/index.html"> Biomass Gasification </a> <input class="toctree-checkbox" id="toctree-checkbox-10" name="toctree-checkbox-10" type="checkbox"/> <label for="toctree-checkbox-10"> <i class="fas fa-chevron-down"> </i> </label> <ul> <li class="toctree-l2"> <a class="reference internal" href="applications/biomass-gasification/biomass-gasification.html"> Biomass Gasification </a> </li> </ul> </li> </ul> <p aria-level="2" class="caption" role="heading"> <span class="caption-text"> General </span> </p> <ul class="nav bd-sidenav"> <li class="toctree-l1"> <a class="reference internal" href="general/citing.html"> Citing </a> </li> <li class="toctree-l1"> <a class="reference internal" href="general/faq.html"> FAQ </a> </li> <li class="toctree-l1"> <a class="reference internal" href="general/troubleshooting.html"> Troubleshooting </a> </li> <li class="toctree-l1"> <a class="reference internal" href="general/contributing.html"> Contributing </a> </li> <li class="toctree-l1"> <a class="reference internal" href="general/license.html"> License </a> </li> <li class="toctree-l1"> <a class="reference internal" href="general/development.html"> Development </a> </li> </ul> </div> </nav></div> <div class="bd-sidebar__bottom"> <!-- To handle the deprecated key --> <div class="navbar_extra_footer"> Powered by <a href="https://jupyterbook.org">Jupyter Book</a> </div> </div> </div> <div id="rtd-footer-container"></div> </div> <!-- A tiny helper pixel to detect if we've scrolled --> <div class="sbt-scroll-pixel-helper"></div> <!-- Main content --> <div class="col py-0 content-container"> <div class="header-article row sticky-top noprint"> <div class="col py-1 d-flex 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id="jb-print-toc"> </div> </div> </div> <main id="main-content" role="main"> <div> <section class="tex2jax_ignore mathjax_ignore" id="reaktoro-s-jupyter-book"> <h1>Reaktoro’s Jupyter Book<a class="headerlink" href="#reaktoro-s-jupyter-book" title="Permalink to this headline">#</a></h1> <p>This project documents how Reaktoro’s Python API can be used for several chemical modeling examples.</p> <p>To build this project, follow the steps below, assuming you are in its root directory:</p> <ol class="simple"> <li><p>Create a conda environment with <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">env</span> <span class="pre">create</span> <span class="pre">-f</span> <span class="pre">environment.yml</span></code></p></li> <li><p>Activate the created environment <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">activate</span> <span class="pre">reaktoro-jupyter-book</span></code></p></li> <li><p>Build the project with <code class="docutils literal notranslate"><span class="pre">jupyter-book</span> <span class="pre">build</span> <span class="pre">.</span></code></p></li> </ol> </section> <script type="text/x-thebe-config"> { requestKernel: true, binderOptions: { repo: "binder-examples/jupyter-stacks-datascience", ref: "master", }, codeMirrorConfig: { theme: "abcdef", mode: "python" }, kernelOptions: { name: "python3", path: "./." }, predefinedOutput: true } </script> <script>kernelName = 'python3'</script> </div> </main> <footer class="footer-article noprint"> <!-- Previous / next buttons --> <div class='prev-next-area'> </div> </footer> </div> </div> <div class="footer-content row"> <footer class="col footer"><p> © Copyright 2023.<br/> </p> </footer> </div> </div> </div> </div> <!-- Scripts loaded after <body> so the DOM is not blocked --> <script src="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script> </body> </html>
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