home.md

-# open-source SHEMAT-Suite
\ No newline at end of file
+# SHEMAT-Suite Wiki #
+
+**SHEMAT-Suite (Simulator for HEat and MAss Transport)** is a
+numerical code for computing flow, heat and species transport
+equations in porous media. The governing equations of the code are the
+groundwater flow equation, the heat transport equation and the species
+transport equation.
+
+SHEMAT-Suite includes parameter estimation and data assimilation
+approaches, both stochastic (Monte Carlo, ensemble Kalman filter) and
+deterministic (Bayesian inversion using automatic differentiation for
+calculating derivatives).
+
+SHEMAT-Suite is written in Fortran-95.
+
+SHEMAT-Suite uses finite-difference discretization on a Cartesian grid
+with x, y, z coordinates and block centered nodes.  The system of
+equations can be solved explicitly, implicitly or semi-implicitly.
+
+[More detailed information on the equations](./equations)
+
+
+## Table of Contents ##
+
+[[_TOC_]]
+
+## Installation ##
+
+Guide to installing SHEMAT-Suite:
+[Installation](./howtos/installation_requirements)
+
+## Tutorial ##
+
+If you want to run SHEMAT-Suite for the first time you should check
+the [SHEMAT-Suite Tutorial](./tutorial).
+
+## For Developers ##
+
+[Fortran-95 styleguide](./howtos/styleguide) for SHEMAT-Suite.
+
+[Doxygen documentation](./howtos/doxygen).
+
+## Most visited pages ##
+
+[Input File](./tutorial/input_file)
+
+[Compilation](./tutorial/compilation)
+
+[Equations and Discretization](./equations)
+
+## Howtos ##
+[howtos](./howtos)
+
+## Property Modules ##
+[props](./props)
+
+## User Directories ##
+[user](./user)
+
+## Branches ##
+[branches](./branches)
+
+![shemat_suite_branches](uploads/1d66b69ef413debec99f1d86e7aa09a2/shemat_suite_branches.png)
+
+## Outline of the directories in branch master ##
+
+![shemat_suite_forward](uploads/6c0aef0549d4ffbd608dd7a077507c17/shemat_suite_forward.png)
+
+  **Table:** Important code developments of
+  SHEMAT-Suite.
+  * ($`^{\mathrm{x}}`$) Functionalities not available in
+	the open-source package.
+  * (\*) Simplified functionality available in
+	the open-source package.
+  * (\*\*) SHEMAT-Suite functionality available
+	open-source, additional software required.\
+
+| **Newly implemented functionality**                                                                              | **Key Reference**                               |
+| ---------------------------------------------------------------------------------------------------------------- | ----------------------------------------------- |
+| Inverse parameter estimation based on automatic differentiation                                                  | Rath et al., 2006                               |
+| Latent heat effects due to freezing and melting                                                                  | Mottaghy and Rath, 2006                         |
+| Monte Carlo techniques for uncertainty quantification and reduction                                              | Vogt et al., 2010                               |
+| Borehole heat exchanger module(\*)                                                                               | Mottaghy and Dijkshoorn, 2012                   |
+| Shared-memory parallelization                                                                                    | Wolf, 2011                                      |
+| Data assimilation based on the ensemble Kalman Filter                                                            | Vogt et al., 2012                               |
+| Multi-phase flow module using automatic differentiation ($`^{\mathrm{x}}`$)                                      | Büsing et al., 2014                             |
+| Distributed-memory parallelization ($`^{\mathrm{x}}`$)                                                           | Rostami and Bücker, 2014                        |
+| Anisotropic flow module using the full permeability tensor ($`^{\mathrm{x}}`$)                                   | Chen et al., 2016                               |
+| Supercritical water/steam module using automatic differentiation ($`^{\mathrm{x}}`$)                             | Büsing et al., 2017                             |
+| Optimal borehole positioning with respect to reservoir characterization via optimal experimental design (\*\*)   | Seidler et al., 2016                            |
+| Efficient two-phase flow in heterogeneous porous media using exact Jacobians ($`^{\mathrm{x}}`$)                 | Büsing, 2020                                    |
+
+1. Rath, V., Wolf, A., & Bücker, H. M., Joint three-dimensional
+   inversion of coupled groundwater flow and heat transfer based on
+   automatic differentiation: sensitivity calculation, verification,
+   and synthetic examples, Geophysical Journal International, 167(1),
+   453–466 (2006).  http://dx.doi.org/10.1111/j.1365-246x.2006.03074.x
+2. Mottaghy, D., & Rath, V., Latent heat effects in subsurface heat
+   transport modelling and their impact on palaeotemperature
+   reconstructions, Geophysical Journal International, 164(1), 236–245
+   (2006).  http://dx.doi.org/10.1111/j.1365-246x.2005.02843.x
+3. Vogt, C., Mottaghy, D., Wolf, A., Rath, V., Pechnig, R., & Clauser,
+   C., Reducing temperature uncertainties by stochastic geothermal
+   reservoir modelling, Geophysical Journal International, 181(1),
+   321–333 (2010).  http://dx.doi.org/10.1111/j.1365-246x.2009.04498.x
+4. Mottaghy, D., & Dijkshoorn, L., Implementing an effective finite
+   difference formulation for borehole heat exchangers into a heat and
+   mass transport code, Renewable Energy, 45(), 59–71 (2012).
+   http://dx.doi.org/10.1016/j.renene.2012.02.013
+5. Wolf, A., Ein softwarekonzept zur hierarchischen parallelisierung
+   von stochastischen und deterministischen inversionsproblemen auf
+   modernen ccnuma-plattformen unter nutzung automatischer
+   programmtransformation. (Doctoral dissertation) (2011). RWTH Aachen
+   University.
+6. Vogt, C., Marquart, G., Kosack, C., Wolf, A., & Clauser, C.,
+   Estimating the permeability distribution and its uncertainty at the
+   egs demonstration reservoir soultz-sous-forêts using the ensemble
+   Kalman filter, Water Resources Research, 48(8), (2012).
+   http://dx.doi.org/10.1029/2011wr011673
+7. Büsing, H., Willkomm, J., Bischof, C. H., & Clauser, C., Using
+   exact jacobians in an implicit newton method for solving multiphase
+   flow in porous media, International Journal of Computational
+   Science and Engineering, 9(5/6), 499 (2014).
+   http://dx.doi.org/10.1504/ijcse.2014.064535
+8. Rostami, M. A., & H. M. B\"ucker, Preservation of non-uniform
+   memory architecture characteristics when going from a nested OpenMP
+   to a hybrid MPI/OpenMP approach, In M. S. Obaidat, J. Kacprzyk, &
+   T. {\"O}ren, SIMULTECH 2014, Proceedings of the 4th International
+   Conference on Simulation and Modeling Methodologies, Technologies
+   and Applications, Vienna, Austria, August~28--30, 2014
+   (pp. 286–291) (2014). : SciTePress.
+9. Chen, T., Clauser, C., Marquart, G., Willbrand, K., & Büsing, H.,
+   Modeling anisotropic flow and heat transport by using mimetic
+   finite differences, Advances in Water Resources, 94(), 441–456
+   (2016).  http://dx.doi.org/10.1016/j.advwatres.2016.06.006
+10. Büsing, H., Vogt, C., Ebigbo, A., & Klitzsch, N., Numerical study
+    on co2leakage detection using electrical streaming potential data,
+    Water Resources Research, 53(1), 455–469 (2017).
+    http://dx.doi.org/10.1002/2016wr019803
+11. Seidler, R., Padalkina, K., Bücker, H. M., Ebigbo, A., Herty, M.,
+    Marquart, G., & Niederau, J., Optimal experimental design for
+    reservoir property estimates in geothermal exploration,
+    Computational Geosciences, 20(2), 375–383 (2016).
+    http://dx.doi.org/10.1007/s10596-016-9565-4
+12. H. Büsing, Efficient solution techniques for two-phase flow in
+    heterogeneous porous media using exact Jacobians, Computational
+    Geosciences, In Review (2020).