diff --git a/ChemistryLib/CreateChemicalSolverInterface.cpp b/ChemistryLib/CreateChemicalSolverInterface.cpp
index 998581e63582affc2b027484444d60fae45a9c17..83f3afaa1b499129a0e4e94c6865286c3ef820d3 100644
--- a/ChemistryLib/CreateChemicalSolverInterface.cpp
+++ b/ChemistryLib/CreateChemicalSolverInterface.cpp
@@ -104,9 +104,7 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
config.getConfigSubtreeOptional("rates"));
// surface
- auto surface = PhreeqcIOData::createSurface(
- //! \ogs_file_param{prj__chemical_system__surface}
- config.getConfigSubtreeOptional("surface"));
+ auto const& surface = chemical_system->surface;
// exchange
auto const& exchangers = chemical_system->exchangers;
@@ -147,8 +145,8 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
return std::make_unique<PhreeqcIOData::PhreeqcIO>(
*linear_solver, std::move(project_file_name),
std::move(path_to_database), std::move(chemical_system),
- std::move(reaction_rates), std::move(surface), std::move(user_punch),
- std::move(output), std::move(dump), std::move(knobs));
+ std::move(reaction_rates), std::move(user_punch), std::move(output),
+ std::move(dump), std::move(knobs));
}
template <>
diff --git a/ChemistryLib/PhreeqcIO.cpp b/ChemistryLib/PhreeqcIO.cpp
index c2e1e1e138714dd5cd7dde6bfed080203a3dccb9..f754dd71f42c2261a2e04e07b55757f4cea9646d 100644
--- a/ChemistryLib/PhreeqcIO.cpp
+++ b/ChemistryLib/PhreeqcIO.cpp
@@ -42,6 +42,14 @@ namespace PhreeqcIOData
{
namespace
{
+template <class... Ts>
+struct overloaded : Ts...
+{
+ using Ts::operator()...;
+};
+template <class... Ts>
+overloaded(Ts...)->overloaded<Ts...>;
+
template <typename DataBlock>
std::ostream& operator<<(std::ostream& os,
std::vector<DataBlock> const& data_blocks)
@@ -164,20 +172,20 @@ void setReactantMolality(Reactant& reactant,
(*reactant.molality)[chemical_system_id];
}
-template <typename Exchanger>
-void initializeExchangerMolality(Exchanger& exchanger,
- GlobalIndexType const& chemical_system_id,
- MaterialPropertyLib::Phase const& solid_phase,
- ParameterLib::SpatialPosition const& pos,
- double const t)
+template <typename Site>
+void initializeSiteMolality(Site& site,
+ GlobalIndexType const& chemical_system_id,
+ MaterialPropertyLib::Phase const& solid_phase,
+ ParameterLib::SpatialPosition const& pos,
+ double const t)
{
- auto const& solid_constituent = solid_phase.component(exchanger.name);
+ auto const& solid_constituent = solid_phase.component(site.name);
auto const molality =
solid_constituent[MaterialPropertyLib::PropertyType::molality]
.template initialValue<double>(pos, t);
- (*exchanger.molality)[chemical_system_id] = molality;
+ (*site.molality)[chemical_system_id] = molality;
}
template <typename Reactant>
@@ -253,7 +261,6 @@ PhreeqcIO::PhreeqcIO(GlobalLinearSolver& linear_solver,
std::string&& database,
std::unique_ptr<ChemicalSystem>&& chemical_system,
std::vector<ReactionRate>&& reaction_rates,
- std::vector<SurfaceSite>&& surface,
std::unique_ptr<UserPunch>&& user_punch,
std::unique_ptr<Output>&& output,
std::unique_ptr<Dump>&& dump,
@@ -263,7 +270,6 @@ PhreeqcIO::PhreeqcIO(GlobalLinearSolver& linear_solver,
_database(std::move(database)),
_chemical_system(std::move(chemical_system)),
_reaction_rates(std::move(reaction_rates)),
- _surface(std::move(surface)),
_user_punch(std::move(user_punch)),
_output(std::move(output)),
_dump(std::move(dump)),
@@ -341,8 +347,18 @@ void PhreeqcIO::initializeChemicalSystemConcrete(
for (auto& exchanger : _chemical_system->exchangers)
{
- initializeExchangerMolality(exchanger, chemical_system_id, solid_phase,
- pos, t);
+ initializeSiteMolality(exchanger, chemical_system_id, solid_phase, pos,
+ t);
+ }
+
+ for (auto& surface_site : _chemical_system->surface)
+ {
+ if (auto const surface_site_ptr =
+ std::get_if<MoleBasedSurfaceSite>(&surface_site))
+ {
+ initializeSiteMolality(*surface_site_ptr, chemical_system_id,
+ solid_phase, pos, t);
+ }
}
}
@@ -527,7 +543,7 @@ std::ostream& operator<<(std::ostream& os, PhreeqcIO const& phreeqc_io)
<< "\n";
}
- auto const& surface = phreeqc_io._surface;
+ auto const& surface = phreeqc_io._chemical_system->surface;
if (!surface.empty())
{
os << "SURFACE " << chemical_system_id + 1 << "\n";
@@ -536,9 +552,44 @@ std::ostream& operator<<(std::ostream& os, PhreeqcIO const& phreeqc_io)
? chemical_system_id + 1
: phreeqc_io._num_chemical_systems + chemical_system_id + 1;
os << "-equilibrate with solution " << aqueous_solution_id << "\n";
- os << "-sites_units DENSITY"
- << "\n";
- os << surface << "\n";
+
+ // print unit
+ if (std::holds_alternative<DensityBasedSurfaceSite>(
+ surface.front()))
+ {
+ os << "-sites_units density"
+ << "\n";
+ }
+ else
+ {
+ os << "-sites_units absolute"
+ << "\n";
+ }
+
+ for (auto const& surface_site : surface)
+ {
+ std::visit(
+ overloaded{[&os](DensityBasedSurfaceSite const& s) {
+ os << s.name << " " << s.site_density << " "
+ << s.specific_surface_area << " "
+ << s.mass << "\n";
+ },
+ [&os, chemical_system_id](
+ MoleBasedSurfaceSite const& s) {
+ os << s.name << " "
+ << (*s.molality)[chemical_system_id]
+ << "\n";
+ }},
+ surface_site);
+ }
+
+ // overlook the effect of the buildup of charges onto the surface
+ if (std::holds_alternative<MoleBasedSurfaceSite>(surface.front()))
+ {
+ os << "-no_edl"
+ << "\n";
+ }
+
os << "SAVE solution " << chemical_system_id + 1 << "\n";
}
@@ -617,7 +668,7 @@ std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io)
auto const& output = *phreeqc_io._output;
auto const& dropped_item_ids = output.dropped_item_ids;
- auto const& surface = phreeqc_io._surface;
+ auto const& surface = phreeqc_io._chemical_system->surface;
auto const& exchangers = phreeqc_io._chemical_system->exchangers;
if (!surface.empty() && !exchangers.empty())
diff --git a/ChemistryLib/PhreeqcIO.h b/ChemistryLib/PhreeqcIO.h
index bca62ca832b530ebd32401b5eaf6575b45e66f47..5b48e35d61d3f6391ae74b5fc46aaa3838a83a33 100644
--- a/ChemistryLib/PhreeqcIO.h
+++ b/ChemistryLib/PhreeqcIO.h
@@ -27,7 +27,6 @@ namespace PhreeqcIOData
struct ChemicalSystem;
struct ReactionRate;
struct Output;
-struct SurfaceSite;
struct Dump;
struct UserPunch;
@@ -39,7 +38,6 @@ public:
std::string&& database,
std::unique_ptr<ChemicalSystem>&& chemical_system,
std::vector<ReactionRate>&& reaction_rates,
- std::vector<SurfaceSite>&& surface,
std::unique_ptr<UserPunch>&& user_punch,
std::unique_ptr<Output>&& output,
std::unique_ptr<Dump>&& dump,
@@ -111,7 +109,6 @@ private:
std::string const _database;
std::unique_ptr<ChemicalSystem> _chemical_system;
std::vector<ReactionRate> const _reaction_rates;
- std::vector<SurfaceSite> const _surface;
std::unique_ptr<UserPunch> _user_punch;
std::unique_ptr<Output> const _output;
std::unique_ptr<Dump> const _dump;
diff --git a/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp b/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
index c3b704f0ee0439aa9f94147fc282fa1c9badec67..b1c4956410fba618679e4531e8ed4ed8e4075e80 100644
--- a/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
+++ b/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
@@ -56,6 +56,15 @@ void ChemicalSystem::initialize(std::size_t const num_chemical_systems)
{
exchanger.molality->resize(num_chemical_systems);
}
+
+ for (auto& surface_site : surface)
+ {
+ if (auto const surface_site_ptr =
+ std::get_if<MoleBasedSurfaceSite>(&surface_site))
+ {
+ surface_site_ptr->molality->resize(num_chemical_systems);
+ }
+ }
}
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/ChemicalSystem.h b/ChemistryLib/PhreeqcIOData/ChemicalSystem.h
index 9e50e9cb5ff2ba2160f78cb412f2a564f5a1fb57..22b209ca175badf3ddde1d84126dbb055b6eb19c 100644
--- a/ChemistryLib/PhreeqcIOData/ChemicalSystem.h
+++ b/ChemistryLib/PhreeqcIOData/ChemicalSystem.h
@@ -11,12 +11,14 @@
#pragma once
#include <memory>
+#include <variant>
#include <vector>
#include "AqueousSolution.h"
#include "EquilibriumReactant.h"
#include "Exchange.h"
#include "KineticReactant.h"
+#include "Surface.h"
namespace ChemistryLib
{
@@ -27,11 +29,14 @@ struct ChemicalSystem
ChemicalSystem(std::unique_ptr<AqueousSolution>&& aqueous_solution_,
std::vector<KineticReactant>&& kinetic_reactants_,
std::vector<EquilibriumReactant>&& equilibrium_reactants_,
- std::vector<ExchangeSite>&& exchangers_)
+ std::vector<ExchangeSite>&& exchangers_,
+ std::vector<std::variant<DensityBasedSurfaceSite,
+ MoleBasedSurfaceSite>>&& surface_)
: aqueous_solution(std::move(aqueous_solution_)),
kinetic_reactants(std::move(kinetic_reactants_)),
equilibrium_reactants(std::move(equilibrium_reactants_)),
- exchangers(std::move(exchangers_))
+ exchangers(std::move(exchangers_)),
+ surface(std::move(surface_))
{
}
@@ -41,6 +46,8 @@ struct ChemicalSystem
std::vector<KineticReactant> kinetic_reactants;
std::vector<EquilibriumReactant> equilibrium_reactants;
std::vector<ExchangeSite> exchangers;
+ std::vector<std::variant<DensityBasedSurfaceSite, MoleBasedSurfaceSite>>
+ surface;
};
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp
index 6319c899a41d0e290c14e2449a75f34e91618911..1aef5665d1ea563ab0d045d99539690318fdc29e 100644
--- a/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp
@@ -16,9 +16,11 @@
#include "CreateEquilibriumReactants.h"
#include "CreateExchange.h"
#include "CreateKineticReactant.h"
+#include "CreateSurface.h"
#include "EquilibriumReactant.h"
#include "Exchange.h"
#include "KineticReactant.h"
+#include "Surface.h"
namespace ChemistryLib
{
@@ -47,10 +49,16 @@ std::unique_ptr<ChemicalSystem> createChemicalSystem(
//! \ogs_file_param{prj__chemical_system__exchangers}
config.getConfigSubtreeOptional("exchangers"), mesh);
+ // surface
+ auto surface = createSurface(
+ //! \ogs_file_param{prj__chemical_system__surface}
+ config.getConfigSubtreeOptional("surface"), mesh);
+
return std::make_unique<ChemicalSystem>(std::move(aqueous_solution),
std::move(kinetic_reactants),
std::move(equilibrium_reactants),
- std::move(exchangers));
+ std::move(exchangers),
+ std::move(surface));
}
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateSurface.cpp b/ChemistryLib/PhreeqcIOData/CreateSurface.cpp
index 9c526bac265bb23074c753cebed6d7b59505e4fa..161767afb0b0261333c0fc31cf288d5cc7d74cfe 100644
--- a/ChemistryLib/PhreeqcIOData/CreateSurface.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateSurface.cpp
@@ -8,48 +8,79 @@
*
*/
-#include <optional>
+#include "CreateSurface.h"
#include "BaseLib/ConfigTree.h"
+#include "MeshLib/Mesh.h"
#include "Surface.h"
namespace ChemistryLib
{
namespace PhreeqcIOData
{
-std::vector<SurfaceSite> createSurface(
- std::optional<BaseLib::ConfigTree> const& config)
+std::vector<std::variant<DensityBasedSurfaceSite, MoleBasedSurfaceSite>>
+createSurface(std::optional<BaseLib::ConfigTree> const& config,
+ MeshLib::Mesh& mesh)
{
if (!config)
{
return {};
}
- std::vector<SurfaceSite> surface;
- for (auto const& site_config :
- //! \ogs_file_param{prj__chemical_system__surface__site}
- config->getConfigSubtreeList("site"))
+ std::vector<std::variant<DensityBasedSurfaceSite, MoleBasedSurfaceSite>>
+ surface;
+
+ auto const surface_site_unit =
+ //! \ogs_file_attr{prj__chemical_system__surface__site_unit}
+ config->getConfigAttribute<std::string>("site_unit", "mole");
+
+ if (surface_site_unit == "density")
{
- //! \ogs_file_param{prj__chemical_system__surface__site__name}
- auto name = site_config.getConfigParameter<std::string>("name");
+ for (auto const& site_config :
+ //! \ogs_file_param{prj__chemical_system__surface__site}
+ config->getConfigSubtreeList("site"))
+ {
+ //! \ogs_file_param{prj__chemical_system__surface__site__name}
+ auto name = site_config.getConfigParameter<std::string>("name");
+
+ auto const site_density =
+ //! \ogs_file_param{prj__chemical_system__surface__site__site_density}
+ site_config.getConfigParameter<double>("site_density");
+
+ auto const specific_surface_area =
+ //! \ogs_file_param{prj__chemical_system__surface__site__specific_surface_area}
+ site_config.getConfigParameter<double>("specific_surface_area");
+
+ auto const mass =
+ //! \ogs_file_param{prj__chemical_system__surface__site__mass}
+ site_config.getConfigParameter<double>("mass");
- auto const site_density =
- //! \ogs_file_param{prj__chemical_system__surface__site__site_density}
- site_config.getConfigParameter<double>("site_density");
+ surface.push_back(DensityBasedSurfaceSite(
+ std::move(name), site_density, specific_surface_area, mass));
+ }
+
+ return surface;
+ }
+
+ if (surface_site_unit == "mole")
+ {
+ for (auto const& site_config :
+ //! \ogs_file_param{prj__chemical_system__surface__site}
+ config->getConfigSubtreeList("site"))
+ {
+ //! \ogs_file_param{prj__chemical_system__surface__site__name}
+ auto name = site_config.getConfigParameter<std::string>("name");
- auto const specific_surface_area =
- //! \ogs_file_param{prj__chemical_system__surface__site__specific_surface_area}
- site_config.getConfigParameter<double>("specific_surface_area");
+ auto const molality = MeshLib::getOrCreateMeshProperty<double>(
+ mesh, name, MeshLib::MeshItemType::IntegrationPoint, 1);
- auto const mass =
- //! \ogs_file_param{prj__chemical_system__surface__site__mass}
- site_config.getConfigParameter<double>("mass");
+ surface.push_back(MoleBasedSurfaceSite(std::move(name), molality));
+ }
- surface.emplace_back(
- std::move(name), site_density, specific_surface_area, mass);
+ return surface;
}
- return surface;
+ OGS_FATAL("Surface site unit should be either of 'density' or 'mole'.");
}
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateSurface.h b/ChemistryLib/PhreeqcIOData/CreateSurface.h
index 849dd6fe72ffa2fcd1a2c1e6c1fed7184220f931..392b435cc5d409f77f45cc49808b2544597e0250 100644
--- a/ChemistryLib/PhreeqcIOData/CreateSurface.h
+++ b/ChemistryLib/PhreeqcIOData/CreateSurface.h
@@ -11,6 +11,7 @@
#pragma once
#include <optional>
+#include <variant>
#include <vector>
namespace BaseLib
@@ -18,13 +19,20 @@ namespace BaseLib
class ConfigTree;
}
+namespace MeshLib
+{
+class Mesh;
+}
+
namespace ChemistryLib
{
namespace PhreeqcIOData
{
-struct SurfaceSite;
+struct DensityBasedSurfaceSite;
+struct MoleBasedSurfaceSite;
-std::vector<SurfaceSite> createSurface(
- std::optional<BaseLib::ConfigTree> const& config);
+std::vector<std::variant<DensityBasedSurfaceSite, MoleBasedSurfaceSite>>
+createSurface(std::optional<BaseLib::ConfigTree> const& config,
+ MeshLib::Mesh& mesh);
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/Surface.cpp b/ChemistryLib/PhreeqcIOData/Surface.cpp
deleted file mode 100644
index 53fbafc54beebdd4be65db7bfc49b74eecd8da74..0000000000000000000000000000000000000000
--- a/ChemistryLib/PhreeqcIOData/Surface.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-/**
- * \file
- * \copyright
- * Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
- * Distributed under a Modified BSD License.
- * See accompanying file LICENSE.txt or
- * http://www.opengeosys.org/project/license
- *
- */
-
-#include "Surface.h"
-
-#include <ostream>
-
-namespace ChemistryLib
-{
-namespace PhreeqcIOData
-{
-std::ostream& operator<<(std::ostream& os, SurfaceSite const& surface_site)
-{
- os << surface_site.name << " " << surface_site.site_density << " "
- << surface_site.specific_surface_area << " " << surface_site.mass
- << "\n";
-
- return os;
-}
-} // namespace PhreeqcIOData
-} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/Surface.h b/ChemistryLib/PhreeqcIOData/Surface.h
index 4edb777a0c562f8ee0a7f630b3d67dc4977b5e3b..aae9ae54ed800bfc2aff569c3b7e8ebb4fd9d079 100644
--- a/ChemistryLib/PhreeqcIOData/Surface.h
+++ b/ChemistryLib/PhreeqcIOData/Surface.h
@@ -10,24 +10,20 @@
#pragma once
-#include <iosfwd>
#include <string>
-namespace BaseLib
-{
-class ConfigTree;
-}
+#include "MeshLib/PropertyVector.h"
namespace ChemistryLib
{
namespace PhreeqcIOData
{
-struct SurfaceSite
+struct DensityBasedSurfaceSite
{
- SurfaceSite(std::string name_,
- double const site_density_,
- double const specific_surface_area_,
- double const mass_)
+ DensityBasedSurfaceSite(std::string name_,
+ double const site_density_,
+ double const specific_surface_area_,
+ double const mass_)
: name(std::move(name_)),
site_density(site_density_),
specific_surface_area(specific_surface_area_),
@@ -35,13 +31,22 @@ struct SurfaceSite
{
}
- friend std::ostream& operator<<(std::ostream& os,
- SurfaceSite const& surface_site);
-
std::string const name;
double const site_density;
double const specific_surface_area;
double const mass;
};
+
+struct MoleBasedSurfaceSite
+{
+ MoleBasedSurfaceSite(std::string name_,
+ MeshLib::PropertyVector<double>* const molality_)
+ : name(std::move(name_)), molality(molality_)
+ {
+ }
+
+ std::string const name;
+ MeshLib::PropertyVector<double>* molality;
+};
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/Documentation/ProjectFile/prj/chemical_system/surface/a_site_unit.md b/Documentation/ProjectFile/prj/chemical_system/surface/a_site_unit.md
new file mode 100644
index 0000000000000000000000000000000000000000..5bcba7ad2acff716d2a3c72cec56c589e53eb3c4
--- /dev/null
+++ b/Documentation/ProjectFile/prj/chemical_system/surface/a_site_unit.md
@@ -0,0 +1 @@
+Define site unit for surface complexation model. Either `density` to use sites per square nanometre or `mole` to use moles per kilogram of water are allowed.
diff --git a/ProcessLib/ComponentTransport/Tests.cmake b/ProcessLib/ComponentTransport/Tests.cmake
index 9317c623a967b94fc14352ef8517a374feb02310..281e5468f586258926d0b1cc49d785ccf0670067 100644
--- a/ProcessLib/ComponentTransport/Tests.cmake
+++ b/ProcessLib/ComponentTransport/Tests.cmake
@@ -816,6 +816,7 @@ if (NOT OGS_USE_MPI)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/KineticReactant/1d_isofrac_flag_formula.prj RUNTIME 20)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/KineticReactant_AllAsComponents/KineticReactant2.prj RUNTIME 60)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption.prj RUNTIME 60)
+ OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_SitesMoles.prj RUNTIME 33)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/LookupTable/RadionuclideSorption.prj RUNTIME 10)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/EquilibriumPhase/calciteDissolvePrecipitateOnly.prj RUNTIME 25)
OgsTest(PROJECTFILE Parabolic/ComponentTransport/ReactiveTransport/EquilibriumPhase/calcitePorosityChange.prj RUNTIME 25)
diff --git a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption.prj b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption.prj
index 82988e7ddba4a5e40c385663ff8859ab74d8c516..b7a295da4cd7ae3f9c39f4a55c5a2b9f0b854bbf 100644
--- a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption.prj
+++ b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption.prj
@@ -464,7 +464,7 @@
<saturation_index>0.0</saturation_index>
</phase_component>
</equilibrium_reactants>
- <surface>
+ <surface site_unit="density">
<site>
<!--Qz = Mineral phase: Quartz, amorphous Silica-->
<name>QzOH</name>
diff --git a/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_SitesMoles.prj b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_SitesMoles.prj
new file mode 100644
index 0000000000000000000000000000000000000000..349c89c911634c142aa1bea93fa368b44fdf58c2
--- /dev/null
+++ b/Tests/Data/Parabolic/ComponentTransport/ReactiveTransport/SurfaceComplexation/RadionuclideSorption_SitesMoles.prj
@@ -0,0 +1,859 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<OpenGeoSysProject>
+ <meshes>
+ <mesh>RadionuclideSorption.vtu</mesh>
+ <mesh>RadionuclideSorption_ReactiveDomain.vtu</mesh>
+ <mesh>RadionuclideSorption_left.vtu</mesh>
+ <mesh>RadionuclideSorption_right.vtu</mesh>
+ </meshes>
+ <processes>
+ <process>
+ <name>hc</name>
+ <type>ComponentTransport</type>
+ <integration_order>2</integration_order>
+ <coupling_scheme>staggered</coupling_scheme>
+ <process_variables>
+ <concentration>Na</concentration>
+ <concentration>Cl</concentration>
+ <concentration>Ca</concentration>
+ <concentration>C(4)</concentration>
+ <concentration>H</concentration>
+ <!--Radionuclide-->
+ <concentration>U(6)</concentration>
+ <pressure>pressure</pressure>
+ </process_variables>
+ <specific_body_force>0 0</specific_body_force>
+ <secondary_variables>
+ <secondary_variable internal_name="darcy_velocity" output_name="darcy_velocity"/>
+ </secondary_variables>
+ </process>
+ </processes>
+ <media>
+ <medium id="0">
+ <phases>
+ <phase>
+ <type>AqueousLiquid</type>
+ <components>
+ <component>
+ <name>Na</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>Cl</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>Ca</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>C(4)</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>H</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>U(6)</name>
+ <properties>
+ <property>
+ <name>pore_diffusion</name>
+ <type>Constant</type>
+ <value>1e-9</value>
+ </property>
+ <property>
+ <name>retardation_factor</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>decay_rate</name>
+ <type>Parameter</type>
+ <parameter_name>decay</parameter_name>
+ </property>
+ </properties>
+ </component>
+ </components>
+ <properties>
+ <property>
+ <name>density</name>
+ <type>Constant</type>
+ <value>1e3</value>
+ </property>
+ <property>
+ <name>viscosity</name>
+ <type>Constant</type>
+ <value>1e-3</value>
+ </property>
+ </properties>
+ </phase>
+ <phase>
+ <type>Solid</type>
+ <components>
+ <component>
+ <name>Calcite</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>10</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>AlbOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>8.538e-04</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>GibbOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>2.236e-05</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>HemOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>5.285e-05</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>KaoOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>4.269e-05</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>MusOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>3.497e-04</value>
+ </property>
+ </properties>
+ </component>
+ <component>
+ <name>QzOH</name>
+ <properties>
+ <property>
+ <name>molality</name>
+ <type>Constant</type>
+ <value>2.419e-04</value>
+ </property>
+ </properties>
+ </component>
+ </components>
+ </phase>
+ </phases>
+ <properties>
+ <property>
+ <name>permeability</name>
+ <type>Parameter</type>
+ <parameter_name>kappa</parameter_name>
+ </property>
+ <property>
+ <name>porosity</name>
+ <type>Parameter</type>
+ <parameter_name>porosity</parameter_name>
+ </property>
+ <property>
+ <name>longitudinal_dispersivity</name>
+ <type>Constant</type>
+ <value>0.2</value>
+ </property>
+ <property>
+ <name>transversal_dispersivity</name>
+ <type>Constant</type>
+ <value>0.2</value>
+ </property>
+ </properties>
+ </medium>
+ </media>
+ <time_loop>
+ <global_process_coupling>
+ <max_iter>6</max_iter>
+ <convergence_criteria>
+ <!-- convergence criterion for the first process (p) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (Na) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (Cl) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (Ca) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (C(4)) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (H) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <!-- convergence criterion for the second process (U(6)) -->
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ </convergence_criteria>
+ </global_process_coupling>
+ <processes>
+ <!-- convergence criterion for hydraulic equation -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (Na) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (Cl) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (Ca) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (C(4)) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (H) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ <!-- convergence criterion for component transport equation (U(6)) -->
+ <process ref="hc">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <reltol>1e-14</reltol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>115000</t_end>
+ <timesteps>
+ <pair>
+ <repeat>115</repeat>
+ <delta_t>1000</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ </processes>
+ <output>
+ <type>VTK</type>
+ <prefix>RadionuclideSorption</prefix>
+ <suffix>_ts_{:timestep}_t_{:time}</suffix>
+ <timesteps>
+ <pair>
+ <repeat>5</repeat>
+ <each_steps>23</each_steps>
+ </pair>
+ </timesteps>
+ <variables>
+ <variable>Na</variable>
+ <variable>Cl</variable>
+ <variable>Ca</variable>
+ <variable>C(4)</variable>
+ <variable>H</variable>
+ <variable>U(6)</variable>
+ <variable>pressure</variable>
+ <variable>darcy_velocity</variable>
+ </variables>
+ </output>
+ </time_loop>
+ <chemical_system chemical_solver="Phreeqc">
+ <mesh>RadionuclideSorption_ReactiveDomain</mesh>
+ <linear_solver>general_linear_solver</linear_solver>
+ <database>PSINA_12_07_110615_DAV_s_hzdr.dat</database>
+ <solution>
+ <temperature>14</temperature>
+ <pressure>1</pressure>
+ <pe>4</pe>
+ <components>
+ <component>Na</component>
+ <component>Cl</component>
+ <component>Ca</component>
+ <component>C(4)</component>
+ <!--Radionuclides-->
+ <component>U(6)</component>
+ </components>
+ </solution>
+ <equilibrium_reactants>
+ <phase_component>
+ <name>Calcite</name>
+ <saturation_index>0.0</saturation_index>
+ </phase_component>
+ </equilibrium_reactants>
+ <surface site_unit="mole">
+ <site>
+ <!--Qz = Mineral phase: Quartz, amorphous Silica-->
+ <name>QzOH</name>
+ </site>
+ <site>
+ <!--Alb = Mineral group: Feldspar (albite)-->
+ <name>AlbOH</name>
+ </site>
+ <site>
+ <!--Mus = Mineral group: Mica (muscovite)-->
+ <name>MusOH</name>
+ </site>
+ <site>
+ <!--Hem = Mineral group: Fe(III)-oxids/-hydroxids (hematite)-->
+ <name>HemOH</name>
+ </site>
+ <site>
+ <!--Gibb = Mineral group: Al-hydroxids (gibbsite)-->
+ <name>GibbOH</name>
+ </site>
+ <site>
+ <!--Kao = Mineral group: 2-layer-clay minerals (kaolinite)-->
+ <name>KaoOH</name>
+ </site>
+ </surface>
+ <user_punch>
+ <headline>Kd_U(6)</headline>
+ <statement>k1=(mol("QzOUO2CO3-") + mol("QzOUO2+")+ mol("QzOUO2(OH)"))</statement>
+ <statement>k2=(mol("AlbOUO2+"))</statement>
+ <statement>k3=(mol("MusOUO2+") + mol("MusOUO2CO3-"))</statement>
+ <statement>k4=(mol("HemOUO2CO3-") + mol("HemOUO2+"))</statement>
+ <statement>k5=(mol("(GibbO)2UO2") + mol("GibbOUO2(OH)")+ mol("GibbO(UO2)3(OH)5") + mol("GibbOUO2+"))</statement>
+ <statement>k6=(mol("KaoOUO2+") + mol("KaoOUO2(OH)") + mol("KaoOUO2CO3-"))</statement>
+ <!-- -->
+ <statement>g_Tot=10388 # Kd = (mol_sorb/g_tot)/(mol_aq) --> Kd in l/g = m³/kg</statement>
+ <statement>if TOT("U(6)") > 0 then kd_U(6) = ((k1+k2+k3+k4+k5+k6)/TOT("U(6)")/g_tot) else kd_U(6) = 0 </statement>
+ <statement>PUNCH kd_U(6)</statement>
+ </user_punch>
+ <knobs>
+ <max_iter>250</max_iter>
+ <relative_convergence_tolerance>1e-6</relative_convergence_tolerance>
+ <tolerance>1e-20</tolerance>
+ <step_size>5</step_size>
+ <scaling>1</scaling>
+ </knobs>
+ </chemical_system>
+ <parameters>
+ <parameter>
+ <name>kappa</name>
+ <type>Constant</type>
+ <values>1.019368e-11</values>
+ </parameter>
+ <parameter>
+ <name>porosity</name>
+ <type>Constant</type>
+ <value>0.2</value>
+ </parameter>
+ <parameter>
+ <name>retardation</name>
+ <type>Constant</type>
+ <value>1</value>
+ </parameter>
+ <parameter>
+ <name>decay</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>p0</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>p_Neumann_left</name>
+ <type>Constant</type>
+ <value>3e-2</value>
+ </parameter>
+ <parameter>
+ <name>p_Dirichlet_right</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>c0_Na</name>
+ <type>Constant</type>
+ <value>1e-3</value>
+ </parameter>
+ <parameter>
+ <name>c0_Cl</name>
+ <type>Constant</type>
+ <value>6e-2</value>
+ </parameter>
+ <parameter>
+ <name>c0_Ca</name>
+ <type>Constant</type>
+ <value>2.502e-2</value>
+ </parameter>
+ <parameter>
+ <name>c0_C(4)</name>
+ <type>Constant</type>
+ <value>1e-3</value>
+ </parameter>
+ <parameter>
+ <name>c0_H</name>
+ <type>Constant</type>
+ <!--pH=7-->
+ <value>1e-7</value>
+ </parameter>
+ <parameter>
+ <name>c0</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>c_left_Na</name>
+ <type>Constant</type>
+ <value>1e-3</value>
+ </parameter>
+ <parameter>
+ <name>c_left_Cl</name>
+ <type>Constant</type>
+ <value>6e-2</value>
+ </parameter>
+ <parameter>
+ <name>c_left_Ca</name>
+ <type>Constant</type>
+ <value>2.502e-2</value>
+ </parameter>
+ <parameter>
+ <name>c_left_C(4)</name>
+ <type>Constant</type>
+ <value>1e-3</value>
+ </parameter>
+ <parameter>
+ <name>c_left_H</name>
+ <type>Constant</type>
+ <!--pH=7-->
+ <value>1e-7</value>
+ </parameter>
+ <parameter>
+ <name>c_spatial</name>
+ <type>Constant</type>
+ <value>1</value>
+ </parameter>
+ <parameter>
+ <name>c_left_default</name>
+ <type>CurveScaled</type>
+ <curve>c_temporal_default</curve>
+ <parameter>c_spatial</parameter>
+ </parameter>
+ </parameters>
+ <curves>
+ <curve>
+ <name>c_temporal_default</name>
+ <coords>0 10000 10000.001 115000</coords>
+ <values>1e-8 1e-8 0 0</values>
+ </curve>
+ </curves>
+ <process_variables>
+ <process_variable>
+ <name>pressure</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>p0</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Neumann</type>
+ <parameter>p_Neumann_left</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_right</mesh>
+ <type>Dirichlet</type>
+ <parameter>p_Dirichlet_right</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>Na</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0_Na</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_Na</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>Cl</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0_Cl</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_Cl</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>Ca</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0_Ca</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_Ca</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>C(4)</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0_C(4)</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_C(4)</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>H</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0_H</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_H</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <!--Radionuclides-->
+ <process_variable>
+ <name>U(6)</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>c0</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>RadionuclideSorption_left</mesh>
+ <type>Dirichlet</type>
+ <parameter>c_left_default</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ </process_variables>
+ <nonlinear_solvers>
+ <nonlinear_solver>
+ <name>basic_picard</name>
+ <type>Picard</type>
+ <max_iter>10</max_iter>
+ <linear_solver>general_linear_solver</linear_solver>
+ </nonlinear_solver>
+ </nonlinear_solvers>
+ <linear_solvers>
+ <linear_solver>
+ <name>general_linear_solver</name>
+ <lis>-i bicgstab -p ilut -tol 1e-8 -maxiter 20000</lis>
+ <eigen>
+ <solver_type>BiCGSTAB</solver_type>
+ <precon_type>ILUT</precon_type>
+ <max_iteration_step>10000</max_iteration_step>
+ <error_tolerance>1e-12</error_tolerance>
+ </eigen>
+ <petsc>
+ <prefix>hc</prefix>
+ <parameters>-hc_ksp_type bcgs -hc_pc_type bjacobi -hc_ksp_rtol 1e-8 -hc_ksp_max_it 20000</parameters>
+ </petsc>
+ </linear_solver>
+ </linear_solvers>
+ <test_definition>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>pressure</field>
+ <absolute_tolerance>1e-6</absolute_tolerance>
+ <relative_tolerance>1e-10</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>darcy_velocity</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-6</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>Na</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>Cl</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>Ca</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>C(4)</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>H</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>RadionuclideSorption_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
+ <field>U(6)</field>
+ <absolute_tolerance>1e-10</absolute_tolerance>
+ <relative_tolerance>1e-16</relative_tolerance>
+ </vtkdiff>
+ </test_definition>
+</OpenGeoSysProject>