The interface Comsol PhreeqC, or iCP, couples two standalone simulation softwares.

<a href="https://www.comsol.com">Comsol Multiphysics®</a> is powerful general-purpose simulation software for modelling coupled physics systems. It has a very intuitive graphical user interface with flexible configuration options for the whole modelling workflow, from geometry generation to result visualization.

<a href="https://www.usgs.gov/software/phreeqc-version-3">PhreeqC </a>is perhaps the most widely used geochemical code in the scientific community and is distributed free of charge. The program is based on equilibrium chemistry of aqueous solutions interacting with minerals, gases, solid solutions, exchangers, and sorption surfaces, but it also includes the capability to model kinetic reactions with user-defined rate equations. The use of extensible chemical databases allows application of the reaction, transport, and inverse-modelling capabilities to almost any chemical reaction that is recognized to influence rain-, soil-, ground and surface water quality.

iCP maximizes the synergies between Comsol and PhreeqC, providing a numerical platform that can efficiently simulate a wide number of multiphysics problems coupled with geochemistry. It is written in Java and uses the IPhreeqc C++ dynamic library and the Comsol Java API. It also takes advantage of the multicore computer architecture by balancing the computational load over different threads.

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About

iCP is a powerful tool for those consultants or researchers who need to tackle coupled geochemical problems. The flexibility and wide applicability of iCP make it suitable for a large number of modelling challenges, which cover most of the needs of both industry and academia. iCP inherits all the modelling capabilities of Comsol and couples them with geochemical systems provided by PhreeqC and the extensive geochemical databases developed for this code.

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iCP also considers couplings between chemical and physical processes, such as chemically-induced porosity changes and their impact on fluid flow and solute transport, or the effect of liquid saturation and temperature on geochemistry.

Capabilities

If you are interested in iCP please fill out the <a href="/form/icp-license-request">licence request form</a> to get your license.

If you are interested in the iCP technology please contact techlabs@amphos21.com

3 months

Basic Support

Trial

Perpetual

Advanced Support

R&D allowed

Commercial Allowed

Commercial

Licensing

Amphos 21 Consulting offers iCP training courses in two different formats both in Barcelona and at your site:

 - **iCP Basics**: This training course is held for three days, with about six hours per day reserved for PHREEQC, COMSOL and iCP fundamentals along with hands-on instructions and two hours planned for one-on-one support and review.
- **iCP Customized**: If you are already an advanced user of any of the COMSOL or PHREEQC softwares and prefer to focus more on iCP and its applications, we can customize the course under our iCP Customized format. In iCP Customized, course materials can be adapted to your specific requirements and problems of interest. Our experienced consultants can assist you in developing COMSOL, PHREEQC or iCP models of your real-world problems.

Please contact us through our contact page to submit your request for iCP training courses. The detailed layouts of the courses are as below:

**iCP Basics:**
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  <thead>
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      <th className="w-1/4 ..."></th>
      <th className="w-1/4 ...">DAY 1</th>
      <th className="w-1/4 ...">DAY 2</th>
      <th className="w-1/4 ...">DAY 3</th>
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      <td >Morning</td>
      <td >COMSOL Basics</td>
      <td >iCP Basics</td>
      <td >iCP: Training Examples</td>
    </tr>
    <tr>
      <td >Afternoon</td>
      <td>COMSOL Basics</td>
      <td>iCP: First Steps</td>
      <td>iCP: Training Examples</td>
    </tr>
  </tbody>
</table>
</div>

<br>

**iCP Customized:**

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    </tr>
  </thead>
  <tbody>
    <tr className="bg-gray-200">
      <td>Morning  	</td>
      <td>iCP Basics</td>
      <td>Client’s Models</td>
      <td>Client’s Models</td>
    </tr>
    <tr >
      <td>Afternoon	</td>
      <td>iCP: Training Examples</td>
      <td>Client’s Models</td>
      <td>Client’s Models</td>
    </tr>
  </tbody>
</table>
</div>

Check out the <a href="/icp-workshops/">previous iCP</a> workshops:


Training

How to cite iCP:

*Nardi, A., Idiart, A., Trinchero, P., de Vries, L. M., and J. Molinero*. **Interface COMSOL-PHREEQC (iCP), an efficient numerical framework for the solution of coupled multiphysics and geochemistry.** Computers & Geosciences 69 (2014): 10-21.


Cite

iCP is a project of the iMaGe initiative and is supported by a partnership formed by:

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Posiva

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Andra

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Jülich

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Amphos 21

Partners

If you have questions check the <a href="/software-faqs/icp">iCP Faqs</a> page.

FAQS

Find the <a href="https://www.researchgate.net/project/iCP-interface-Comsol-Phreeqc">full list of publications</a> on the iCP project on Researchgate.

Discover all the <a href="/tags/icp">blog</a> posts related with iCP 

Conference **Posters**:

- <a href="/static/posters/Poster_Clay00108_HCM.pdf"> Hydro-chemo-mechanical modelling of bentonite sealing components</a>
- <a href="/static/posters/Abarca_et_al_2018.pdf"> Reactive transport model of uranium mobility in the riparian zone</a>
- <a href="/static/posters/Abarca_et_al_EGU.jpg">Feedback between reactive transport and convective mixing during CO<sub>2</sub> migration in a saline aquifer </a>
- <a href="/static/posters/Abarca_et_al_Migration_2017.pdf">Impact of transport pathways in Radium accumulation under groundwater discharge areas</a>
- <a href="/static/posters/Idiart et al_CebamaPoster_NUWCEM.pdf">Reactive transport processes at a low-pH concrete / clay
interface: a benchmark modelling study</a>
- <a href="/static/posters/Idiartetal_PosterNUWCEM2018.pdf">A systematic modelling study of concrete-bentonite interaction in radioactive waste disposal</a>
- <a href="/static/posters/Idiartetal-Poster-EURADWASTE2019.pdf">Benchmark of reactive transport models within Cebama: Application to a concrete/clay interface</a>
- <a href="/static/posters/Molinero_et_al_COMSOL_Conference_2013.jpg">An innovative Reactive Transport Modelling Apporach for the Chemical Evolution of a HLW Cell in the Callovo-Oxfordian Formation</a>
- <a href="/static/posters/Nardi_et_al_COMSOL_Conference_2012.jpg">Coupling Multiphysics with geochemistry</a>
- <a href="/static/posters/Silva_et_al_Migration2017.pdf">Modeling of Geochemical Evolution and Reactive Transport of Radionuclides in the Near Field of a Disposal Cell for High Level Vitrified Waste in the Callovo Oxfordian Claystone</a>
- <a href="/static/posters/Tincopa_et_al_COMSOL_Conference_2013.jpg">Relevance of Hydro-Mechanical-Chemical Processes Involved in the construction and Operation of Copper Heap Leach Pads</a>
- <a href="/static/posters/Trinchero_et_al_COMSOL_Conference_2013.jpg">Coupled Palaehydrological Microbial and Geochemical Reactive Transport Model of the Olkiluoto Site (Finland)</a>




Publications

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iCP  is an interface to couple Comsol and Phreeqc.

interface Comsol Phreeqc

iDP stands for interface DarcyTools-PFLOTRAN. The main objective of this interface is to develop a powerful reactive transport platform that integrates DarcyTools flow simulation capabilities with the reactive transport possibilities of PFLOTRAN. DarcyTools can create and run complex flow simulations, while PFLOTRAN is known for its strong scalability in High Performance Computing (HPC). This is achieved with the help of libraries such as PETSc. The iDP interface is written in a modular, cross-platform and extensible way using Fortran and Python.

Until 2018, only a single iDP code was being developed, now called *iDP classic*. This code only allows converting models that use cartesian structured grids. However, DarcyTools is able to generate and use cartesian unstructured grids, and PFLOTRAN can also handle them. Being able to convert this type of grids would increase the versatility of the framework.

For that reason, a new modification, iDP-UG was created. iDP-UG is used specifically for the conversion of DarcyTools models that use cartesian unstructured grids. Almost all the code has been written from scratch, with very few pieces adapted from iDP classic. As a consequence, iDP-UG needs to be considered a completely separate tool.


iDP classic provides a graphical user interface to generate the configuration required for the simulation. A DarcyTools subdomain can be selected from a steady state flow solution for use in a transient reactive transport simulation running in PFLOTRAN. This can be extended to a quasi-transient reactive-transport simulation by using several steady state flow solutions.

In iDP-UG, a basic graphical user interface is used only for specifying the input and output paths. Most of the configuration, on the other hand, is defined in a configuration file. As opposed to iDP classic, in iDP-UG both flow and transport are solved in PFLOTRAN. DarcyTools is used to generate the properties of the model, such as the permeability and porosity fields, and the cartesian unstructured grid.


One of the best codes available to simulate groundwater flow in crystalline, fractured rock is DarcyTools. DarcyTools, property of SKB (The Swedish Nuclear Fuel and Waste Management Company), has been developed by CFE AB (Computer-aided Fluid Engineering AB) and MFRDC (Michel Ferry R& D Consulting). The code has been through more than 10 years of continuous development. The main Developers are Urban Svensson & Michel Ferry. The DarcyTools code is based on the finite volume method and uses MPI for its parallelization.

DarcyTools

PFLOTRAN is a next-generation, open source , reactive flow and transport simulator for modelling subsurface processes that has been developed with high performance computing and efficiency in mind. To this end it has been built on top of well-known frameworks like MPI, PETSc and HDF. It implements the finite volume method and has been written in Fortran 90, in a modular way,. It has demonstrated peta-scale performance in simulations of uranium migration in the superfund Hanford 300 Area as part of the SciDAC-2 programme. The entire code is release under the GNU Lesser General Public License. For more information you may visit  [PFLOTRAN website](https://www.pflotran.org/)

PFlotran

If you would like to reference iDP in your publications, please use the following reference: 

*de Vries LM, Molinero J, Ebrahimi H, Svensson U & Lichtner P* (2013). **High Performance Reactive Transport Simulation of Hyperalkaline Plume Migration in Fractured Rock.** Mineralogical Magazine, 77(5) 982.

If you are interested in the iDP technology please contact at techlabs@amphos21.com

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Screenshots

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iDP is an interface to couple DarcyTools and FLOTRAN

interface DarcyTools PFlotran

iGP is the interface between GiD and PFLOTRAN and is developed by Amphos 21. iGP provides a powerful and user-friendly pre and post-processing environment to PFLOTRAN. In iGP, the user can define different regions, set different materials, apply different boundary and initial conditions, mesh complex geometries (using structured, semi-structured or fully unstructured grids), run PFLOTRAN and post-process the results.

- Work with all the 3D element types available on GiD (e.g. tetrahedrons, triangular and rectangular prisms, etc.)
- Fully compatible with structured, semi-structured and unstructured meshes.
- Apply boundary conditions directly into the geometry.
- Create and customize materials with different properties and apply them to geometrical entities.
- Automatically generate PFLOTRAN input files and run them on the user’s machine.
- Post-process the results with contour plots, scatter plots, animations, etc.

GiD is a powerful universal, adaptive and user-friendly pre and postprocessor for numerical simulations in science and engineering and is developed by the International Center for Numerical Methods in Engineering (CIMNE), a research and development organization based in Barcelona (Spain).

![GiD](/uploads/whatsgid_848f7f4fed.png "GiD")

For more information check the [GiD web page ](https://www.gidhome.com).



PFLOTRAN is a next-generation, open source , reactive flow and transport simulator for modelling subsurface processes that has been developed with high performance computing and efficiency in mind. To this end it has been built on top of well-known frameworks like MPI, PETSc and HDF. It implements the finite volume method and has been written, in a modular way, in Fortran 90. It has demonstrated peta-scale performance in simulations of uranium migration in the superfund Hanford 300 Area as part of the SciDAC-2 programme. All the code is release under the GNU Lesser General Public License license.


![GiD](/uploads/pfrlotran01_molinero_et_al_b8435c9c13.png "GiD")

For more information visit the [PFLOTRAN web page](https://www.pflotran.org/).



If you would like to reference iDP in your publications, please use the following reference: 

*Amphos 21 *(2016).** iGP: interface between GiD and PFLOTRAN.**

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Cimne

Amphos21

To get iGP, fill in the <a href="/form/software-download-request">software request form </a>.


Download

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iGP is the interface between GiD and PFLOTRAN.

interface GiD PFlotran

The computer code MARFA (Migration Analysis for Radionuclides in the FAr field) uses an extremely efficient particle-based Monte Carlo method to simulate the transport of radionuclides in fractured rock systems. The algorithm uses non-interacting particles to represent packets of radionuclide mass. These particles are moved through the system according to rules that mimic the underlying physical transport and retention processes. In contrast to the conventional random walk particle tracking algorithm, which use a specified time step and random spatial displacement, the MARFA algorithms use a fixed spatial displacement and a random transit time for the displacement. The use of a fixed spatial displacement makes the code extremely robust and computationally efficient.

The physical processes represented in MARFA include advection, longitudinal dispersion, Fickian diffusion into an infinite or finite rock matrix, equilibrium sorption, decay, and in-growth. Because the algorithm uses non-interacting particles, the transport and retention processes are limited to those that depend linearly on radionuclide concentration. Multiple non-branching decay chains of arbitrary length are supported, as is full heterogeneity in the transport and retention properties.

Two variants of the code are provided. These two versions differ in how particles are routed through the computational domain.

In MARFA Static Path (SP) transport is assumed to occur along a set of trajectories or pathways that originate at radionuclide source locations. The trajectories are intended to represent the movement of hypothetical, advectively transported groundwater tracers and are typically calculated by streamline tracing using a numerically computed flow field. The groundwater velocity and retention properties along each pathway may change in time, but the pathway trajectories are fixed.


MARFA Node Routing (NR) allows the transport effects of changing flow directions to be represented by abandoning the fixed pathways and performing node routing within MARFA. MARFA NR has been frozen to version 4.2 and will no longer be updated. An on-going project is focused on the development of a new version of MARFA (MARFA DFN) tightly integrated to a Discrete Fracture Network (DFN) code.

MARFA is designed to accept flow fields computed by both DFN and Equivalent Continuous Porous Media (ECPM) based software. MARFA has been used this way to evaluate the performance of a potential geologic repository for spent nuclear fuel.

Please refer to MARFA <a href="https://bitbucket.org/marfa_account/marfa-docs_git/downloads/marfa_user_manual_v5.0_rn1.pdf">User’s Manual</a> for more information.


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Description

- Robust and efficient algorithm using fixed spatial displacement
- Advection and longitudinal dispersion
- Wide range of matrix retention processes including single, multiple, and infinite matrix layers
- Full heterogeneity in transport and retention properties
- Decay chains of arbitrary length
- Piecewise steady flow fields
- Colloid-facilitated transport
- Optional downscaling algorithm to recover transport effects of unrepresented subgrid velocity - variability
- Temporal changes in radionuclide retention properties (smart Kd)

MARFA development was funded by the Swedish Nuclear Fuel and Waste Management Company (SKB) and Posiva (Finland).

MARFA is open source with a BSD-3 license and available on bitbucket at this repository.

Contact Amphos 21 (techlabs@amphos21.com) if you have any requests.

THIS SOFTWARE IS PROVIDED BY AMPHOS 21 “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL AMPHOS 21 OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

License

*Trinchero, P., Painter, S. L., Poteri, A., Sanglas, J., Cvetkovic, V., & Selroos, J.‐O.* (2020). **A particle‐based conditional sampling scheme for the simulation of transport in fractured rock with diffusion into stagnant water and rock matrix.** Water Resources Research, 56, e2019WR026958. https://doi.org/10.1029/2019WR026958

*Painter, S., J. Mancillas, V. Cvetkovic, and O. Pensado,* **“Time-Domain Particle Tracking Method for Simulating Transport with Retention and First-Order Transformation”** Water Resources Research, 44, doi:10.1029/2007WR005944, 2008.

*Painter, S. and V. Cvetkovic,* **“Upscaling Discrete Fracture Network Simulations: An Alternative to Continuum Transport Models”** Water Resources Research 41, doi:10.1029/2004WR003682, 2005.

*Painter S., and Mancillas, J.,* **“Marfa user’s manual: Migration analysis of radionuclides in the far field”** POSIVA Working Report 2013-01, Posiva Oy, Helsinki, Finland., 2013

*Selroos, J.-O. and S. L. Painter,* **“Effect of transport-pathway simplifications on projected releases of radionuclides from a nuclear waste repository” **(Sweden), Hydrogeology Journal, 8, 2012

*Trinchero, P., Painter, S., Ebrahimi, H., Koskinen, L., Molinero, J. and Selroos, J.O.,* **“Modelling radionuclide transport in fractured media with a dynamic update of Kd values”**. Computers & geosciences, 86, pp.55-63, 2016.

References

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MARFA uses an extremely efficient particle-based Monte Carlo method to simulate the transport of radionuclides in fractured rock systems.

MARFA

SPANA (formerly MEDUSA) is a graphic user interface to the chemical equilibrium diagrams software SED-PREDOM. The chemical equilibrium constants needed for SPANA diagrams are contained in DATABASE (formerly HYDRA). The [SPANA](https://sites.google.com/site/chemdiagr/) software is developed by I. Puigdomènech .

The new software Chimera extracts the information contained in databases written in a format compatible with the geochemical code [PhreeqC](https://www.usgs.gov/software/phreeqc-version-3) (Parkhurst and Appelo, 2013) and automatically converts this information into a format compatible with the SPANA/DATABASE code.

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Chimera has been developed by I. Puigdomènech (SKB) and Amphos 21 (https://www.amphos21.com). The development has received funding from SKB, the Swedish company for nuclear waste management.

Following the philosophy of the creator of SPANA, we open the CHIMERA software to all public. Chimera is released under GNU Lesser General Public License (LGPL). In short, this means that you can copy and install it on as many computers as you like. You can obtain the source code freely and you can even modify the source code. Any changes made to the source code need to be made public, if they are redistributed. All use of the software is at your own risk. Any questions concerning the installation or use of this software can be directed to database@amphos21.com.

In order to reference Chimera in your publications:

**Chimera (2019). A tool for extracting PhreeqC databases into SPANA format.** Amphos 21.  https://www.amphos21.com

Chimera is written in Java and is provided in an executable file, no installation is needed. Fill in <a href="/form/software-download-request/"> the form </a>and you will receive the <b>download</b> link.

<a href="https://www.java.com/download/">Java Runtime Environment (JRE)</a> must be also installed to run Java software.



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Chimera extracts the information contained in PhreeqC databases and converts them to the SPANA/DATABASE format.

Technologies

interface Comsol Phreeqc

interface DarcyTools PFlotran

interface GiD PFlotran

MARFA

Chimera