XML Input

In this document, you will learn how GEOS classes interact with external information parsed from XML files, and how to add a new XML block that can be interpreted by GEOS. Flow solvers and relative permeability are used as examples.

GEOS data structure overview

Group : the base class of GEOS

All GEOS classes derive from a base class called dataRepository::Group. The Group class provides a way to organize all GEOS objects in a filesystem-like structure. One could think of Group s as file folders that can bear data (stored in Wrapper s), have a parent folder (another Group), and have possibly multiple subfolders (referred to as the subgroups). Below, we briefly review the data members of the Group class that are essential to understand the correspondence between the GEOS data structure and the XML input. For more details, we refer the reader to the extensive documentation of the Data Repository, including the Group class documentation.

In the code listing below, we see that each Group object is at minimum equipped with the following member properties:

• A pointer to the parent Group called m_parent (member classes are prefixed by m_),

• The Group ‘s own data, stored for flexibility in an array of generic data Wrapper s called m_wrappers,

• A map of one or many children (also of type Group) called m_subGroups.

• The m_size and m_capacity members, that are used to set the size and capacity of any objects contained.

• The name of the Group, stored as a string in m_name. This name can be seen as the object unique ID.

  /// The parent Group that contains "this" Group in its "sub-Group" collection.
  Group * m_parent = nullptr;

  /// Specification that this group will have the same m_size as m_parent.
  integer m_sizedFromParent;

  /// The container for the collection of all wrappers continued in "this" Group.
  wrapperMap m_wrappers;

  /// The container for the collection of all sub-groups contained in "this" Group.
  subGroupMap m_subGroups;

  /// The size/length of this Group...and all Wrapper<> that are are specified to have the same size as their
  /// owning group.
  indexType m_size;

  /// The capacity for wrappers in this group...and all Wrapper<> that are specified to have the same size as their
  /// owning group.
  indexType m_capacity;

  /// The name/key of this Group in its parent collection of sub-Groups.
  string m_name;

  /// Verbosity flag for group logs
  integer m_logLevel;


  //END_SPHINX_INCLUDE_02

  /// Restart flag for this group... and subsequently all wrappers in this group.

[Source: src/coreComponents/dataRepository/Group.hpp]

A few words about the ObjectCatalog

What is an ObjectCatalog and why do we need it?

Some classes need external information (physical and/or algorithmic parameters for instance) provided by the user to be instantiated. This is the case when the m_input_flags data member of one of the Group ‘s Wrapper s has an entry set to REQUIRED (we will illustrate this below). In this situation, the required information must be supplied in the XML input file, and if it is absent, an error is raised by GEOS.

To connect the external (XML) and internal (C++) data structures, GEOS uses an ObjectCatalog that maps keys (of type string) to the corresponding classes (one unique key per mapped class). These string keys, referred to as catalogName s, are essential to transfer the information from the XML file to the factory functions in charge of object instantiation (see below).

What is a CatalogName?

The catalogName of an object is a key (of type string) associated with this object’s class. On the one hand, in the XML file, the key is employed by the user as an XML tag to specify the type of object (e.g., the type of solver, constitutive model, etc) to create and use during the simulation. On the other hand, internally, the key provides a way to access the appropriate factory function to instantiate an object of the desired class.

Most of the time, the catalogName and the C++ class name are identical. This helps make the code easier to debug and allows the XML/C++ correspondence to be evident. But strictly speaking, the catalogName can be anything, as long as it refers uniquely to a specific class. The catalogName must not be confused with the object’s name (m_name is a data member of the class that stores the object’s unique ID, not its class key). You can have several objects of the same class and hence the same catalogName, but with different names (i.e. unique ID): several fluid models, several solvers, etc.

How can I add my new externally-accessible class to the ObjectCatalog?

Let us consider a flow solver class derived from FlowSolverBase, that itself is derived from PhysicsSolverBase. To instantiate and use this solver, the developer needs to make the derived flow solver class reachable from the XML file, via an XML tag. Internally, this requires adding the derived class information to ObjectCatalog, which is achieved with two main ingredients: 1) a CatalogName() method in the class that lets GEOS know what to search for in the internal ObjectCatalog to instantiate an object of this class, 2) a macro that specifies where to search in the ObjectCatalog.

1. To let GEOS know what to search for in the catalog to instantiate an object of the derived class, the developer must equip the class with a CatalogName() method that returns a string. In this document, we have referred to this returned string as the object’s catalogName, but in fact, the method CatalogName() is what matters since the ObjectCatalog contains all the CatalogName() return values. Below, we illustrate this with the CompositionalMultiphaseFlow solver. The first code listing defines the class name, which in this case is the same as the catalogName shown in the second listing.

/**
 * @class CompositionalMultiphaseBase
 *
 * A compositional multiphase solver
 */
class CompositionalMultiphaseBase : public FlowSolverBase
{

[Source: src/coreComponents/physicsSolvers/fluidFlow/CompositionalMultiphaseBase.hpp]

2. To let GEOS know where to search in the ObjectCatalog, a macro needs to be added at the end of the .cpp file implementing the class. This macro (illustrated below) must contain the type of the base class (in this case, PhysicsSolverBase), and the name of the derived class (continuing with the example used above, this is CompositionalMultiphaseFlow). As a result of this construct, the ObjectCatalog is not a flat list of string s mapping the C++ classes. Instead, the ObjectCatalog forms a tree that reproduces locally the structure of the class diagram, from the base class to the derived classes.

REGISTER_CATALOG_ENTRY( PhysicsSolverBase, CompositionalMultiphaseFVM, string const &, Group * const )

[Source: src/coreComponents/physicsSolvers/fluidFlow/CompositionalMultiphaseFVM.cpp]

Summary: All GEOS objects form a filesystem-like structure. If an object needs to be accessible externally, it must be registered in the ObjectCatalog. This is done by adding CatalogName() method that returns a string key to the object’s class, and by adding the appropriate macro. The catalog has the same tree structure as the class diagram.

Registration: parsing XML input files to instantiate GEOS objects

In this section, we describe with more details the connection between internal GEOS objects and external XML tags parsed from parameter files. We call this process Registration. The registration process works in three steps:

1. The XML document is parsed. Each time a new XML tag is found, the current local scope of the ObjectCatalog is inspected. The goal is to find a catalogName string that matches the XML tag.

2. If it is the case (the current local scope of the ObjectCatalog contains a catalogName identical to the XML tag), then the code creates a new instance of the class that the catalogName refers to. This new object is inserted in the Group tree structure at the appropriate location, as a subgroup.

3. By parsing the XML attributes of the tag, the new object properties are populated. Some checks are performed to ensure that the data supplied is conform, and that all the required information is present.

Let’s look at this process in more details.

Creating a new object and giving it a Catalog name

Consider again that we are registering a flow solver deriving from FlowSolverBase, and assume that this solver is called CppNameOfMySolver. This choice of name is not recommended (we want names that reflect what the solver does!), but for this particular example, we just need to know that this name is the class name inside the C++ code.

To specify parameters of this new solver from an XML file, we need to be sure that the XML tag and the catalogName of the class are identical. Therefore, we equip the CppNameOfMySolver class with a CatalogName() method that returns the solver catalogName (=XML name). Here, this method returns the string “XmlNameOfMySolver”.

We have deliberately distinguished the class name from the catalog/XML name for the sake of clarity in this example. It is nevertheless a best practice to use the same name for the class and for the catalogName. This is the case below for the existing CompositionalMultiphaseFVM class.

class CompositionalMultiphaseFVM : public CompositionalMultiphaseBase
{

  /**
   * @brief name of the solver in the object catalog
   * @return string that contains the catalog name to generate a new object through the object catalog.
   */
  static string catalogName() { return "CompositionalMultiphaseFVM"; }
  /**
   * @copydoc PhysicsSolverBase::getCatalogName()
   */
  string getCatalogName() const override { return catalogName(); }

[Source: src/coreComponents/physicsSolvers/fluidFlow/CompositionalMultiphaseFVM.hpp]

Parsing XML and searching the ObjectCatalog in scope

Now that we have implemented a CatalogName() method returning a specific key (of type string), we can have a block in our XML input file with a tag that corresponds to the catalogName “XmlNameOfMySolver”. This is how the XML block would look like.

<Problem>
  <Solvers
    gravityVector="{ 0.0, 0.0, -9.81 }">
    <XmlNameOfMySolver name="nameOfThisSolverInstance"
                             verboseLevel="1"
                             gravityFlag="1"
                             temperature="297.15" />
      <LinearSolverParameters newtonTol="1.0e-6"
                              maxIterNewton="15"
                              useDirectSolver="1"/>
    </XmlNameOfMySolver>
  </Solvers>
</Problem>

Here, we see that the XML structure defines a parent node “Problem”, that has (among many others) a child node “Solvers”. In the “Solvers” block, we have placed the new solver block as a child node of the “Solvers” block with the XML tag corresponding to the catalogName of the new class. We will see in details next how the GEOS internal structure constructed from this block mirrors the XML file structure.

Instantiating the new solver

Above, we have specified an XML block with the tag “XmlNameOfMySolver”. Now, when reading the XML file and encountering an “XmlNameOfMySolver” solver block, we add a new instance of the class CppNameOfMySolver in the filesystem structure as explained below.

We saw that in the XML file, the new solver block appeared as child node of the XML block “Solvers”. The internal construction mirrors this XML structure. Specifically, the new object of class CppNameOfMySolver is registered as a subgroup (to continue the analogy used so far, as a subfolder) of its parent Group, the class PhysicsSolverManager (that has a catalogName “Solvers”). To do this, the method CreateChild of the PhysicsSolverManager class is used.

// Variable values in this example:
// --------------------------------
// childKey = "XmlNameOfMySolver" (string)
// childName = "nameOfThisSolverInstance" (string)
// PhysicsSolverBase::CatalogInterface = the Catalog attached to the base Solver class
// hasKeyName = bool method to test if the childKey string is present in the Catalog
// registerGroup = method to create a new instance of the solver and add it to the group tree

Group * PhysicsSolverManager::createChild( string const & childKey, string const & childName )
{
  Group * rval = nullptr;
  if( PhysicsSolverBase::CatalogInterface::hasKeyName( childKey ) )
  {
    GEOS_LOG_RANK_0( "Adding Solver of type " << childKey << ", named " << childName );
    rval = &registerGroup( childName,
                           PhysicsSolverBase::CatalogInterface::factory( childKey, childName, this ) );
  }
  return rval;
}

[Source: src/coreComponents/physicsSolvers/PhysicsSolverManager.cpp]

In the code listing above, we see that in the PhysicsSolverManager class, the ObjectCatalog is searched to find the catalogName “CompositionalMultiphaseFlow” in the scope of the PhysicsSolverBase class. Then, the factory function of the base class PhysicsSolverBase is called. The catalogName (stored in childKey) is passed as an argument of the factory function to ensure that it instantiates an object of the desired derived class.

As explained above, this is working because 1) the XML tag matches the catalogName of the CompositionalMultiphaseFlow class and 2) a macro is placed at the end of the .cpp file implementing the CompositionalMultiphaseFlow class to let the ObjectCatalog know that CompositionalMultiphaseFlow is a derived class of PhysicsSolverBase.

Note that several instances of the same type of solver can be created, as long as they each have a different name.

Filling the objects with data (wrappers)

After finding and placing the new solver Group in the filesystem hierarchy, properties are read and stored. This is done by registering data wrappers. We refer to the documentation of the Data Repository for additional details about the Wrapper s. The method used to do that is called registerWrapper and is placed in the class constructor when the data is required in the XML file. Note that some properties are registered at the current (derived) class level, and other properties can also be registered at a base class level.

Here, the only data (=wrapper) that is defined at the level of our CppNameOfMySolver class is temperature, and everything else is registered at the base class level. We register a property of temperature, corresponding to the member class m_temperature of CppNameOfMySolver. The registration also checks if a property is required or optional (here, it is required), and provides a brief description that will be used in the auto-generated code documentation.

  this->registerWrapper( viewKeyStruct::inputTemperatureString(), &m_inputTemperature ).
    setInputFlag( InputFlags::REQUIRED ).
    setDescription( "Temperature" );
//END_SPHINX_INCLUDE_00

[Source: src/coreComponents/physicsSolvers/fluidFlow/CompositionalMultiphaseBase.cpp]

This operation is done recursively if XML tags are nested.

To summarize:

• Every class in GEOS derive from a Group in a filesystem-like structure. A Group must have a parent Group, can have data (in Wrapper s), and can have one or many children (the subgroups). There is an ObjectCatalog in which the classes derived from Group are identified by a key called the catalogName.

• When parsing XML input files, GEOS inspects each object’s scope in the ObjectCatalog to find classes with the same catalogName as the XML tag. Once it finds an XML tag in the ObjectCatalog, it registers it inside the filesystem structure.

• In the registration process, properties from the XML file are parsed and used to allocate member data Wrapper s and fully instantiate the Group class.

• If XML tags are nested, subgroups are allocated and processed in a nested manner.

The correspondence between XML and class hierarchy is thus respected, and the internal object hierarchy mirrors the XML structure.

Example: adding a new relative permeability model

This example is taken from the class BrooksCoreyRelativePermeability, derived from RelativePermeabilityBase.

Implement a CatalogName function (.hpp):

As explained above we add the class to the ObjectCatalog in two steps. First we implement the CatalogName function:

  static string catalogName() { return "BrooksCoreyRelativePermeability"; }

[source: src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.hpp]

Then in the .cpp file we add the macro to register the catalog entry:

REGISTER_CATALOG_ENTRY( ConstitutiveBase, BrooksCoreyRelativePermeability, string const &, Group * const )

[source: src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.cpp]

Now every time a “BrooksCoreyRelativePermeability” string is encountered inside a Relative Permeability catalog, we will instantiate a class BrooksCoreyRelativePermeability.

Declare the Wrapper s keys (.hpp):

When attaching properties (i.e. data Wrapper s) to a class, a similar registration process must be done. Every property is accessed through its ViewKey namespace. In this namespace, we define string s that correspond to the tags of XML attributes of the “BrooksCoreyRelativePermeability” block.

  struct viewKeyStruct : RelativePermeabilityBase::viewKeyStruct
  {
    static constexpr char const * phaseMinVolumeFractionString() { return "phaseMinVolumeFraction"; }
    static constexpr char const * phaseRelPermExponentString() { return "phaseRelPermExponent"; }
    static constexpr char const * phaseRelPermMaxValueString() { return "phaseRelPermMaxValue"; }
    static constexpr char const * volFracScaleString() { return "volFracScale"; }
  } vieKeysBrooksCoreyRelativePermeability;

[source: src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.hpp]

Declare data members (.hpp):

The data members are defined in the class. They will ultimately contain the data read from the XML file (other data members not read from the XML file can also exist).

  array1d< real64 > m_phaseMinVolumeFraction;
  array1d< real64 > m_phaseRelPermExponent;
  array1d< real64 > m_phaseRelPermMaxValue;

  real64 m_volFracScale;

[source: src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.hpp]

Implement the data registration process (registerWrapper):

The registration process done in the class constructor puts everything together. It connects the attributes values in the XML file to class member data. For instance, in the listing below, the first registerWrapper call means that we want to read in the XML file the attribute value corresponding to the attribute tag ‘’phaseMinVolumeFraction’’ defined in the .hpp file, and that we want to store the read values into the m_phaseMinVolumeFraction data members. We see that this input is not required. If it is absent from the XML file, the default value is used instead. The short description that completes the registration will be added to the auto-generated documentation.

BrooksCoreyRelativePermeability::BrooksCoreyRelativePermeability( string const & name,
                                                                  Group * const parent )
  : RelativePermeabilityBase( name, parent )
{
  registerWrapper( viewKeyStruct::phaseMinVolumeFractionString(), &m_phaseMinVolumeFraction ).
    setApplyDefaultValue( 0.0 ).
    setInputFlag( InputFlags::OPTIONAL ).
    setDescription( "Minimum volume fraction value for each phase" );

  registerWrapper( viewKeyStruct::phaseRelPermExponentString(), &m_phaseRelPermExponent ).
    setApplyDefaultValue( 1.0 ).
    setInputFlag( InputFlags::OPTIONAL ).
    setDescription( "Minimum relative permeability power law exponent for each phase" );


  registerWrapper( viewKeyStruct::phaseRelPermMaxValueString(), &m_phaseRelPermMaxValue ).
    setApplyDefaultValue( 0.0 ).
    setInputFlag( InputFlags::OPTIONAL ).
    setDescription( "Maximum relative permeability value for each phase" );

  registerWrapper( viewKeyStruct::volFracScaleString(), &m_volFracScale ).
    setApplyDefaultValue( 1.0 ).
    setDescription( "Factor used to scale the phase relative permeability, defined as: one minus the sum of the phase minimum volume fractions." );

[source: src/coreComponents/constitutive/relativePermeability/BrooksCoreyRelativePermeability.cpp]

The XML block

We are ready to use the relative permeability model in GEOS. The corresponding XML block (child node of the “Constitutive” block) reads:

<Constitutive>
  <BrooksCoreyBakerRelativePermeability name="relperm"
                                        phaseNames="{oil, gas, water}"
                                        phaseMinVolumeFraction="{0.05, 0.05, 0.05}"
                                        waterOilRelPermExponent="{2.5, 1.5}"
                                        waterOilRelPermMaxValue="{0.8, 0.9}"
                                        gasOilRelPermExponent="{3, 3}"
                                        gasOilRelPermMaxValue="{0.4, 0.9}"/>
<Constitutive>

With this construct, we instruct the ConstitutiveManager class (whose catalogName is “Constitutive”) to instantiate a subgroup of type BrooksCoreyRelativePermeability. We also fill the data members of the values that we want to use for the simulation. For a simulation with multiple regions, we could define multiple relative permeability models in the “Constitutive” XML block (yielding multiple relperm subgroups in GEOS), with a unique name attribute for each model.

For more examples on how to contribute to GEOS, please read Adding a new Physics Solver

Input Schema Generation

A schema file is a useful tool for validating input .xml files and constructing user-interfaces. Rather than manually maintaining the schema during development, GEOS is designed to automatically generate one by traversing the documentation structure.

To generate the schema, run GEOS with the input, schema, and the (optional) schema_level arguments, i.e.: geosx -i input.xml -s schema.xsd. There are two ways to limit the scope of the schema:

1. Setting the verbosity flag for an object in the documentation structure. If the schema-level argument is used, then only objects (and their children) and attributes with (verbosity < schema-level) will be output.

2. By supplying a limited input xml file. When GEOS builds its data structure, it will only include objects that are listed within the xml (or those that are explicitly appended when those objects are initialized). The code will add all available attributes for these objects to the schema.

To take advantage of this design it is necessary to use the automatic xml parsing approach that relies upon the documentation node. If values are read in manually, then the schema can not be used to validate xml those inputs.

Note: the lightweight xml parser that is used in GEOS cannot be used to validate inputs with the schema directly. As such, it is necessary to use an external tool for validation, such as the geosx_tools python module.