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Reaktoro
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Get Started
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Installation
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<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>
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Tutorials
</span>
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Basics
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<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>
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<a class="reference internal" href="tutorials/equilibrium/index.html">
Chemical Equilibrium
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<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>
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<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>
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<a class="reference internal" href="tutorials/machine-learning/machine-learning-basics.html">
Machine learning: the basics
</a>
</li>
</ul>
</li>
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Advanced
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<a class="reference internal" href="tutorials/advanced/creating-custom-databases.html">
Creating thermodynamic databases
</a>
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</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>
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<a class="reference internal" href="applications/solubility/index.html">
Solubility
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<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
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Carbon dioxide (CO₂) dissolution in seawater
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pH-dependence on added contaminants in water
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Analysis of the Evian water
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Opening bottle with sparkling water
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Uranium (VI) speciation as a function of pH at fixed CO
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The effect of limestone addition on a hydrated cement mix
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<a class="reference internal" href="applications/geochemistry/ion-exchange-dune-sand.html">
Ion exchange in dune sand and groundwater
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<a class="reference internal" href="applications/geochemistry/ion-exchange-mix-porewater-extractant.html">
Extraction of exchangeable cations in dune sand
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<a class="reference internal" href="applications/geochemistry/ion-exchange-cax2-nax-kx-vs-changing-ca-k.html">
Cation exchange competition among Na
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and Ca
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<a class="reference internal" href="applications/geochemistry/ion-exchange-calcite-cax-vs-ph.html">
Effect of calcite dissolution on exchangeable cations
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Carbonate-rich lakes modeling on the early Earth
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<a class="reference internal" href="applications/geobiology/geobiology-phreeqc-fixed-fugacity.html">
Phosphate accumulation in carbonate-rich brines
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Biomass Gasification
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Biomass Gasification
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<h1>Reaktoro</h1>
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<p><img alt="" src="_images/reaktoro-for-python-and-cpp.svg" /></p>
<section class="tex2jax_ignore mathjax_ignore" id="reaktoro">
<h1>Reaktoro<a class="headerlink" href="#reaktoro" title="Permalink to this headline">#</a></h1>
<p>Welcome to the documentation for Reaktoro, an open source computational framework developed in C++ and Python to simulate chemically reactive processes.</p>
<p>Reaktoro has been designed from the ground up to be a flexible and extensible computational modeling framework for simulating chemical reactions. Reaktoro’s algorithms for chemical equilibrium and chemical kinetics calculations can be applied in a wide variety of modeling applications, from geochemical modeling of water-gas-rock systems to modeling the combustion of energetic materials.</p>
<p>Examples of specific and broad applications that Reaktoro can be useful for include, but are not limited to:</p>
<ul class="simple">
<li><p>speciation calculations in aqueous electrolyte solutions, seawater, groundwater</p></li>
<li><p>dissolution of gas in aqueous solutions</p></li>
<li><p>mineral dissolution and precipitation in aqueous solutions</p></li>
<li><p>mixing of aqueous and/or gaseous solutions</p></li>
<li><p>evaporation processes</p></li>
<li><p>ion exchange processes</p></li>
<li><p>kinetically controlled reactions (e.g., mineral, aqueous, gaseous reactions)</p></li>
<li><p>adiabatic flame temperatures at constant pressure or volume</p></li>
<li><p>thermodynamic modeling of cement hydration and corrosion in concrete</p></li>
<li><p>ore formation processes</p></li>
<li><p>hydrometallurgical process</p></li>
<li><p>fluid-rock chemical reactions in geothermal energy systems</p></li>
<li><p>scaling in wells due to mineral precipitation</p></li>
<li><p>carbon storage in geological media via solubility and mineral trapping mechanisms</p></li>
<li><p>geological disposal of radioactive waste</p></li>
</ul>
<p>Reaktoro can also be coupled with other software (e.g. reservoir simulators) to model even more complex processes such as:</p>
<ul class="simple">
<li><p>reactive transport in porous media at pore or reservoir scale</p></li>
<li><p>reactive fluid flow for combustion modeling</p></li>
</ul>
<p>For large-scale modeling applications where millions to billions of chemical equilibrium and/or chemical kinetics calculations are required, Reaktoro offers accelerated <em><strong>on-demand machine learning</strong></em> (ODML) solvers that can speed up chemical reaction calculations by one to three orders of magnitude as demonstrated in <span id="id1">Leal <em>et al.</em> [<a class="reference internal" href="tutorials/bibliography.html#id136" title="Allan M. M. Leal, Dmitrii A. Kulik, and Martin O. Saar. Ultra-Fast Reactive Transport Simulations When Chemical Reactions Meet Machine Learning: Chemical Equilibrium. arXiv, pages 1–25, aug 2017. URL: http://arxiv.org/abs/1708.04825, arXiv:1708.04825, doi:http://arxiv.org/abs/1708.04825.">2017</a>]</span>, <span id="id2">Leal <em>et al.</em> [<a class="reference internal" href="tutorials/bibliography.html#id213" title="Allan M M Leal, Svetlana Kyas, Dmitrii A. Kulik, and Martin O. Saar. Accelerating Reactive Transport Modeling: On-Demand Machine Learning Algorithm for Chemical Equilibrium Calculations. Transport in Porous Media, 133(2):161–204, jun 2020. URL: http://link.springer.com/10.1007/s11242-020-01412-1, doi:10.1007/s11242-020-01412-1.">2020</a>]</span> and <span id="id3">Kyas <em>et al.</em> [<a class="reference internal" href="tutorials/bibliography.html#id4" title="Svetlana Kyas, Diego Volpatto, Martin O. Saar, and Allan M. M. Leal. Accelerated reactive transport simulations in heterogeneous porous media using Reaktoro and Firedrake. Computational Geosciences, 26(2):295–327, apr 2022. URL: http://arxiv.org/abs/2009.01194 https://link.springer.com/10.1007/s10596-021-10126-2, arXiv:2009.01194, doi:10.1007/s10596-021-10126-2.">2022</a>]</span>.</p>
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Get Started</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="installation/index.html">Installation</a></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>
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<li class="toctree-l1"><a class="reference internal" href="tutorials/basics/index.html">Basics</a><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"><a class="reference internal" href="tutorials/equilibrium/index.html">Chemical Equilibrium</a><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>
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</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/kinetics/index.html">Chemical Kinetics</a><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"><a class="reference internal" href="tutorials/machine-learning/index.html">Machine Learning</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorials/machine-learning/machine-learning-basics.html">Machine learning: the basics</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials/advanced/index.html">Advanced</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorials/advanced/creating-custom-databases.html">Creating thermodynamic databases</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials/bibliography.html">Bibliography</a></li>
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<li class="toctree-l1"><a class="reference internal" href="applications/solubility/index.html">Solubility</a><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"><a class="reference internal" href="applications/geochemistry/index.html">Geochemistry</a><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"><a class="reference internal" href="applications/geobiology/index.html">Geobiology</a><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"><a class="reference internal" href="applications/biomass-gasification/index.html">Biomass Gasification</a><ul>
<li class="toctree-l2"><a class="reference internal" href="applications/biomass-gasification/biomass-gasification.html">Biomass Gasification</a></li>
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