docs: update wrappers & doc description

src/coreComponents/constitutive/capillaryPressure/VanGenuchtenCapillaryPressure.cpp

@@ -36,7 +36,7 @@ VanGenuchtenCapillaryPressure::VanGenuchtenCapillaryPressure( string const & nam
   registerWrapper( viewKeyStruct::phaseMinVolumeFractionString(), &m_phaseMinVolumeFraction ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Minimum volume fraction value for each phase" );
+    setDescription( "Minimum volume fraction value for each phase (between 0 and 1) used to compute the capillary pressure" );
 
   registerWrapper( viewKeyStruct::phaseCapPressureExponentInvString(), &m_phaseCapPressureExponentInv ).
     setApplyDefaultValue( 0.5 ).

src/coreComponents/constitutive/docs/CO2BrineFluid.rst

@@ -40,7 +40,16 @@ The user can parameterize the construction of the table by specifying the salini
 | FlashModel | CO2Solubility | :math:`p_{min}` | :math:`p_{max}` | :math:`\Delta p` | :math:`T_{min}` | :math:`T_{max}` | :math:`\Delta T` | Salinity | 
 +------------+---------------+-----------------+-----------------+------------------+-----------------+-----------------+------------------+----------+
 
-Note that the pressures are in Pascal, temperatures are in Kelvin, and the salinity is a molality (moles of NaCl per kg of brine). 
+**Parameter Descriptions**:
+
+- **p_min**: The minimum pressure value [Pa] for which the density table is defined. It sets the lower boundary of the pressure range.
+- **p_max**: The maximum pressure value [Pa] for the density table. It sets the upper boundary of the pressure range.
+- **Δp (Delta p)**: The increment in pressure [Pa] between successive values in the pressure axis of the table. It defines the resolution of the pressure dimension.
+- **T_min**: The minimum temperature value [K] for the density table. This sets the lower boundary of the temperature range.
+- **T_max**: The maximum temperature value [K] for the density table. It sets the upper boundary of the temperature range.
+- **ΔT (Delta T)**: The increment in temperature [K] between successive values in the temperature axis of the table. It defines the resolution of the temperature dimension.
+- **Salinity**: Salinity is expressed in molality (moles of NaCl per kg of brine).
+
 The temperature must be between 283.15 and 623.15 Kelvin.
 The table is populated using the model of Duan and Sun (2003).
 Specifically, we solve the following nonlinear CO2 equation of state (equation (A1) in Duan and Sun, 2003) for each pair :math:`(p,T)` to obtain the reduced volume, :math:`V_r`.
@@ -92,6 +101,15 @@ The user defines the pressure (in Pascal) and temperature (in Kelvin) axis of th
 | DensityFun | SpanWagnerCO2Density | :math:`p_{min}` | :math:`p_{max}` | :math:`\Delta p` | :math:`T_{min}` | :math:`T_{max}` | :math:`\Delta T` |
 +------------+----------------------+-----------------+-----------------+------------------+-----------------+-----------------+------------------+
 
+**Parameter Descriptions**:
+
+- **p_min**: The minimum pressure value [Pa] for which the density table is defined. It sets the lower boundary of the pressure range.
+- **p_max**: The maximum pressure value [Pa] for the density table. It sets the upper boundary of the pressure range.
+- **Δp (Delta p)**: The increment in pressure [Pa] between successive values in the pressure axis of the table. It defines the resolution of the pressure dimension.
+- **T_min**: The minimum temperature value [K] for the density table. This sets the lower boundary of the temperature range.
+- **T_max**: The maximum temperature value [K] for the density table. It sets the upper boundary of the temperature range.
+- **ΔT (Delta T)**: The increment in temperature [K] between successive values in the temperature axis of the table. It defines the resolution of the temperature dimension.
+
 This correlation is valid for pressures less than :math:`8 \times 10^8` Pascal and temperatures less than 1073.15 Kelvin.  
 Using these parameters, GEOS internally constructs a two-dimensional table storing the values of density as a function of pressure and temperature.
 This table is populated as explained in the work of Span and Wagner (1996) by solving the following nonlinear Helmholtz energy equation for each pair :math:`(p,T)` to obtain the value of density, :math:`\rho_{g}`:
@@ -110,6 +128,15 @@ The pressure and temperature axis of the viscosity table can be parameterized in
 | ViscosityFun | FenghourCO2Viscosity | :math:`p_{min}` | :math:`p_{max}` | :math:`\Delta p` | :math:`T_{min}` | :math:`T_{max}` | :math:`\Delta T` |
 +--------------+----------------------+-----------------+-----------------+------------------+-----------------+-----------------+------------------+
 
+**Parameter Descriptions**:
+
+- **p_min**: The minimum pressure value [Pa] for which the density table is defined. It sets the lower boundary of the pressure range.
+- **p_max**: The maximum pressure value [Pa] for the density table. It sets the upper boundary of the pressure range.
+- **Δp (Delta p)**: The increment in pressure [Pa] between successive values in the pressure axis of the table. It defines the resolution of the pressure dimension.
+- **T_min**: The minimum temperature value [K] for the density table. This sets the lower boundary of the temperature range.
+- **T_max**: The maximum temperature value [K] for the density table. It sets the upper boundary of the temperature range.
+- **ΔT (Delta T)**: The increment in temperature [K] between successive values in the temperature axis of the table. It defines the resolution of the temperature dimension.
+
 This correlation is valid for pressures less than :math:`3 \times 10^8` Pascal and temperatures less than 1493.15 Kelvin.  
 This table is populated as explained in the work of Fenghour and Wakeham (1998) by computing the CO2 phase viscosity, :math:`\mu_g`, as follows:
 
@@ -133,9 +160,18 @@ The user specifies the (constant) salinity and defines the pressure and temperat
 | DensityFun | PhillipsBrineDensity | :math:`p_{min}` | :math:`p_{max}` | :math:`\Delta p` | :math:`T_{min}` | :math:`T_{max}` | :math:`\Delta T` | Salinity | 
 +------------+----------------------+-----------------+-----------------+------------------+-----------------+-----------------+------------------+----------+
 
+**Parameter Descriptions**:
+
+- **p_min**: The minimum pressure value [Pa] for which the density table is defined. It sets the lower boundary of the pressure range.
+- **p_max**: The maximum pressure value [Pa] for the density table. It sets the upper boundary of the pressure range.
+- **Δp (Delta p)**: The increment in pressure [Pa] between successive values in the pressure axis of the table. It defines the resolution of the pressure dimension.
+- **T_min**: The minimum temperature value [K] for the density table. This sets the lower boundary of the temperature range.
+- **T_max**: The maximum temperature value [K] for the density table. It sets the upper boundary of the temperature range.
+- **ΔT (Delta T)**: The increment in temperature [K] between successive values in the temperature axis of the table. It defines the resolution of the temperature dimension.
+- **Salinity**: Salinity is expressed in molality (moles of NaCl per kg of brine).
+
 The pressure must be in Pascal and must be less than :math:`5 \times 10^7` Pascal.
 The temperature must be in Kelvin and must be between 283.15 and 623.15 Kelvin.
-The salinity is a molality (moles of NaCl per kg of brine).
 Using these parameters, GEOS performs a preprocessing step to construct a two-dimensional table storing the brine density, :math:`\rho_{\ell,table}` for the specified salinity as a function of pressure and temperature using the expression:
 
 .. math::

src/coreComponents/constitutive/fluid/multifluid/CO2Brine/CO2BrineFluid.cpp

@@ -105,7 +105,7 @@ CO2BrineFluid( string const & name, Group * const parent ):
   registerWrapper( viewKeyStruct::writeCSVFlagString(), &m_writeCSV ).
     setInputFlag( InputFlags::OPTIONAL ).
     setRestartFlags( RestartFlags::NO_WRITE ).
-    setDescription( "When set to 1, write PVT tables into a CSV file.\n "
+    setDescription( "When set to 1, write PVT tables into a CSV file.\n"
                     "if the table is requested to be output in the log, and it is too large, a CSV file will be generated even if `writeCSV` is set to 0." ).
     setDefaultValue( 0 );
 

src/coreComponents/constitutive/fluid/multifluid/MultiFluidBase.cpp

@@ -41,7 +41,7 @@ MultiFluidBase::MultiFluidBase( string const & name, Group * const parent )
 
   registerWrapper( viewKeyStruct::componentMolarWeightString(), &m_componentMolarWeight ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Component molar weights" );
+    setDescription( "Component molar weights [kg/mol]" );
 
   registerWrapper( viewKeyStruct::phaseNamesString(), &m_phaseNames ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).

src/coreComponents/constitutive/fluid/multifluid/constant/InvariantImmiscibleFluid.cpp

@@ -22,7 +22,7 @@ InvariantImmiscibleFluid::InvariantImmiscibleFluid( string const & name, Group *
 
   registerWrapper( viewKeyStruct::componentMolarWeightString(), &m_componentMolarWeight )
     .setInputFlag( dataRepository::InputFlags::REQUIRED )
-    .setDescription( "Molar weights of components" );
+    .setDescription( "Component molar weights [kg/mol]" );
 
   // Densities: constant phase densities
   registerWrapper( "densities", &m_densities )

src/coreComponents/constitutive/fluid/multifluid/reactive/ReactiveBrineFluid.cpp

@@ -76,7 +76,8 @@ ReactiveBrineFluid( string const & name, Group * const parent ):
     setInputFlag( InputFlags::OPTIONAL ).
     setRestartFlags( RestartFlags::NO_WRITE ).
     setDescription( "When set to 1, write PVT tables into a CSV file.\n"
-                    "If the table is requested to be output in the log, and it is too large, a CSV file will be generated even if `writeCSV` is set to 0." );
+                    "If the table is requested to be output in the log, and it is too large,"
+                    "a CSV file will be generated even if `writeCSV` is set to 0." );
 
   // if this is a thermal model, we need to make sure that the arrays will be properly displayed and saved to restart
   if( isThermal() )

src/coreComponents/constitutive/fluid/singlefluid/CompressibleSinglePhaseFluid.cpp

@@ -43,7 +43,7 @@ CompressibleSinglePhaseFluid::CompressibleSinglePhaseFluid( string const & name,
   registerWrapper( viewKeyStruct::compressibilityString(), &m_compressibility ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Fluid compressibility" );
+    setDescription( "Fluid compressibility [Pa^-1]" );
 
   registerWrapper( viewKeyStruct::viscosibilityString(), &m_viscosibility ).
     setApplyDefaultValue( 0.0 ).
@@ -53,7 +53,7 @@ CompressibleSinglePhaseFluid::CompressibleSinglePhaseFluid( string const & name,
   registerWrapper( viewKeyStruct::referencePressureString(), &m_referencePressure ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Reference pressure" );
+    setDescription( "Reference pressure [Pa]" );
 
   registerWrapper( viewKeyStruct::referenceDensityString(), &m_referenceDensity ).
     setApplyDefaultValue( 1000.0 ).

src/coreComponents/constitutive/fluid/singlefluid/ProppantSlurryFluid.cpp

@@ -33,7 +33,7 @@ ProppantSlurryFluid::ProppantSlurryFluid( string const & name, Group * const par
   registerWrapper( viewKeyStruct::compressibilityString(), &m_compressibility ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Fluid compressibility" );
+    setDescription( "Fluid compressibility [Pa^-1]" );
 
   registerWrapper( viewKeyStruct::referenceProppantDensityString(), &m_referenceProppantDensity ).
     setApplyDefaultValue( 1400.0 ).
@@ -43,7 +43,7 @@ ProppantSlurryFluid::ProppantSlurryFluid( string const & name, Group * const par
   registerWrapper( viewKeyStruct::referencePressureString(), &m_referencePressure ).
     setApplyDefaultValue( 1e5 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Reference pressure" );
+    setDescription( "Reference pressure [Pa]" );
 
   registerWrapper( viewKeyStruct::referenceDensityString(), &m_referenceDensity ).
     setApplyDefaultValue( 1000.0 ).

src/coreComponents/constitutive/permeability/PressurePermeability.cpp

@@ -42,7 +42,7 @@ PressurePermeability::PressurePermeability( string const & name, Group * const p
 
   registerWrapper( viewKeyStruct::referencePressureString(), &m_referencePressure ).
     setInputFlag( InputFlags::REQUIRED ).
-    setDescription( "Reference pressure for the pressure permeability model" );
+    setDescription( "Reference pressure for the pressure permeability model [Pa]" );
 
   registerWrapper( viewKeyStruct::referencePermeabilityString(), &m_referencePermeability ).
     setApplyDefaultValue( 0.0 ).

src/coreComponents/constitutive/relativePermeability/BrooksCoreyBakerRelativePermeability.cpp

@@ -34,7 +34,7 @@ BrooksCoreyBakerRelativePermeability::BrooksCoreyBakerRelativePermeability( stri
   registerWrapper( viewKeyStruct::phaseMinVolumeFractionString(), &m_phaseMinVolumeFraction ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Minimum volume fraction value for each phase" );
+    setDescription( "Minimum volume fraction value for each phase (between 0 and 1) used to compute the relative permeability " );
 
   registerWrapper( viewKeyStruct::waterOilRelPermExponentString(), &m_waterOilRelPermExponent ).
     setApplyDefaultValue( 1.0 ).

src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.cpp

@@ -38,7 +38,7 @@ BrooksCoreyRelativePermeability::BrooksCoreyRelativePermeability( string const &
   registerWrapper( viewKeyStruct::phaseMinVolumeFractionString(), &m_phaseMinVolumeFraction ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Minimum volume fraction value for each phase" );
+    setDescription( "Minimum volume fraction value for each phase (between 0 and 1) used to compute the relative permeability " );
 
   registerWrapper( viewKeyStruct::phaseRelPermExponentString(), &m_phaseRelPermExponent ).
     setApplyDefaultValue( 1.0 ).

src/coreComponents/constitutive/solid/porosity/PorosityBase.cpp

@@ -34,7 +34,7 @@ PorosityBase::PorosityBase( string const & name, Group * const parent ):
 {
   registerWrapper( viewKeyStruct::defaultReferencePorosityString(), &m_defaultReferencePorosity ).
     setInputFlag( InputFlags::REQUIRED ).
-    setDescription( "Default value of the reference porosity" );
+    setDescription( "The default porosity value of the rock at the reference pressure" );
 
   registerField< fields::porosity::porosity >( &m_newPorosity );
 

src/coreComponents/constitutive/solid/porosity/PressurePorosity.cpp

@@ -32,11 +32,11 @@ PressurePorosity::PressurePorosity( string const & name, Group * const parent ):
 {
   registerWrapper( viewKeyStruct::referencePressureString(), &m_referencePressure ).
     setInputFlag( InputFlags::REQUIRED ).
-    setDescription( "Reference pressure for solid compressibility" );
+    setDescription( "Reference pressure for solid compressibility [Pa]" );
 
   registerWrapper( viewKeyStruct::compressibilityString(), &m_compressibility ).
     setInputFlag( InputFlags::REQUIRED ).
-    setDescription( "Solid compressibility" );
+    setDescription( "Solid compressibility [Pa^-1]" );
 }
 
 REGISTER_CATALOG_ENTRY( ConstitutiveBase, PressurePorosity, string const &, Group * const )

src/coreComponents/fieldSpecification/FieldSpecificationBase.cpp

@@ -30,7 +30,9 @@ FieldSpecificationBase::FieldSpecificationBase( string const & name, Group * par
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
     setInputFlag( InputFlags::REQUIRED ).
     setSizedFromParent( 0 ).
-    setDescription( "Name of sets that boundary condition is applied to." );
+    setDescription( "Names of sets that the boundary condition is applied to.\n"
+                    "A set can contain heterogeneous elements in the mesh (volumes, nodes, faces, edges).\n"
+                    "A set can be be defined by a 'Geometry' component, or correspond to imported sets in case of an external mesh" );
 
   registerWrapper( viewKeyStruct::objectPathString(), &m_objectPath ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRef ).
@@ -40,12 +42,14 @@ FieldSpecificationBase::FieldSpecificationBase( string const & name, Group * par
   registerWrapper( viewKeyStruct::fieldNameString(), &m_fieldName ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRef ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Name of field that boundary condition is applied to." );
+    setDescription( "Name of field that boundary condition is applied to.\n"
+                    "A field can represent a physical variable. (pressure, temperature, global composition fraction of the fluid, ...)" );
 
   registerWrapper( viewKeyStruct::componentString(), &m_component ).
     setApplyDefaultValue( -1 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Component of field (if tensor) to apply boundary condition to." );
+    setDescription( "Component of field (if tensor) to apply boundary condition to.\n"
+                    "The component must use the order in which the phaseNames have been defined in the Constitutive Element." );
 
   registerWrapper( viewKeyStruct::directionString(), &m_direction ).
     setApplyDefaultValue( {0, 0, 0} ).
@@ -65,7 +69,7 @@ FieldSpecificationBase::FieldSpecificationBase( string const & name, Group * par
   registerWrapper( viewKeyStruct::scaleString(), &m_scale ).
     setApplyDefaultValue( 0.0 ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Scale factor for value of the boundary condition." );
+    setDescription( "Apply a scaling factor for the value of the boundary condition." );
 
   registerWrapper( viewKeyStruct::initialConditionString(), &m_initialCondition ).
     setApplyDefaultValue( 0 ).

src/coreComponents/fileIO/Outputs/MemoryStatsOutput.cpp

@@ -42,7 +42,7 @@ MemoryStatsOutput::MemoryStatsOutput( string const & name,
   this->registerWrapper( viewKeysStruct::writeCSV, &m_writeCSV ).
     setApplyDefaultValue( csvOutputDefault ? 1 : 0 ).
     setInputFlag( dataRepository::InputFlags::OPTIONAL ).
-    setDescription( "When set to 1, write the same statistics as the 'logLevel' allows to output in a CSV file" );
+    setDescription( "When set to 1, write the statistics into a CSV file.\nWhen set to 0, no output" );
 }
 
 void MemoryStatsOutput::postInputInitialization()

src/coreComponents/mesh/docs/Mesh.rst

@@ -13,6 +13,10 @@ or by importing meshes from various common mesh file formats.
 This latter options allows one to work with more complex geometries,
 such as unstructured meshes comprised of a variety of element types (polyhedral elements).
 
+.. note::
+  GEOS uses a right-handed Cartesian coordinate system (X: right, Y: forward, Z: upward) that is consistently applied throughout the mesh definition and discretization processes. 
+  This convention affects mesh topology, and finite element / volume computations. 
+
 ************************
 Internal Mesh Generation
 ************************

src/coreComponents/physicsSolvers/fluidFlow/CompositionalMultiphaseBase.cpp

@@ -115,7 +115,7 @@ CompositionalMultiphaseBase::CompositionalMultiphaseBase( const string & name,
     setSizedFromParent( 0 ).
     setInputFlag( InputFlags::OPTIONAL ).
     setApplyDefaultValue( 0.2 ).
-    setDescription( "Target (absolute) change in phase volume fraction in a time step" );
+    setDescription( "Target (absolute) change in the phase volume fraction within a single time step." );
   this->registerWrapper( viewKeyStruct::targetRelativeCompDensChangeString(), &m_targetRelativeCompDensChange ).
     setSizedFromParent( 0 ).
     setInputFlag( InputFlags::OPTIONAL ).
@@ -131,7 +131,7 @@ CompositionalMultiphaseBase::CompositionalMultiphaseBase( const string & name,
     setSizedFromParent( 0 ).
     setInputFlag( InputFlags::OPTIONAL ).
     setApplyDefaultValue( 0.5 ).
-    setDescription( "Maximum (absolute) change in a component fraction in a Newton iteration" );
+    setDescription( "Maximum (absolute) allowed change in the composition fraction of any component within a single time step, in a Newton iteration" );
   this->registerWrapper( viewKeyStruct::maxRelativePresChangeString(), &m_maxRelativePresChange ).
     setSizedFromParent( 0 ).
     setInputFlag( InputFlags::OPTIONAL ).

src/coreComponents/physicsSolvers/fluidFlow/ImmiscibleMultiphaseFlow.cpp

@@ -90,7 +90,7 @@ ImmiscibleMultiphaseFlow::ImmiscibleMultiphaseFlow( const string & name,
     setSizedFromParent( 0 ).
     setInputFlag( InputFlags::OPTIONAL ).
     setApplyDefaultValue( 0.2 ).
-    setDescription( "Target (absolute) change in phase volume fraction in a time step" );
+    setDescription( "Target (absolute) change in the phase volume fraction within a single time step." );
 }
 
 void ImmiscibleMultiphaseFlow::postInputInitialization()