GeochemicalDatabaseValidator Class Reference

Class for validating MOOSE geochemical database. More...

#include <GeochemicalDatabaseValidator.h>

Public Member Functions
	GeochemicalDatabaseValidator (const FileName filename, const nlohmann::json &db)
void	validate ()
	Validate the thermodynamic database.

Protected Member Functions
bool	isValueReal (const nlohmann::json &value) const
	Check Json::Value can be converted to a Real.
void	checkArrayValues (const nlohmann::json &array, const std::string field) const
	Check Json::Value array is comprised of Reals.
void	checkArrayValues (const std::string type, const std::string species, const std::string field) const
	Check array array values can be converted to Real.
void	checkArraySize (const nlohmann::json &array, const std::string field) const
	Check Json::Value array is the correct size.
void	checkArraySize (const std::string type, const std::string species, const std::string field) const
	Check array is the correct size.
void	checkHeaderField (const std::string field) const
	Check fields are present in the Header section.
void	checkHeaderArray (const std::string field) const
	Check arrays in field can be converted to Reals.
void	checkElements (const std::string element) const
	Check elements in the database Each elemenent should have a real number as their molecular weights.
void	checkBasisSpecies (const std::string species) const
	Check basis species in the database Each basis species should have a real number as their molecular weights, charge, radius and weight for each element.
void	checkSecondarySpecies (const std::string species) const
	Check secondary species in the database Each secondary species should have a real number as their molecular weights, charge, radius, equilibrium constants and weight for each basis species.
void	checkMineralSpecies (const std::string species) const
	Check mineral species in the database Each mineral species should have a real number as their molecular weights, volume, equilibrium constants and weight for each basis species.
void	checkSorbingMineralSpecies (const std::string species) const
	Check sorbing mineral species in the database Each sorbing mineral species should have a real number as their surface area, equilibrium constants and weight for each sorbing site.
void	checkGasSpecies (const std::string species) const
	Check gas species in the database Each gas species should have a real number as their molecular weights, equilibrium constants, weight for each basis species, and fugacity values.
void	checkRedoxSpecies (const std::string species) const
	Check redox couple species in the database Each redox couple species should have a real number as their molecular weights, charge, radius, equilibrium constants and weight for each basis species.
void	checkOxideSpecies (const std::string species) const
	Check oxide species in the database Each oxide species should have a real number as their molecular weights and weight for each basis species.
void	checkSurfaceSpecies (const std::string species) const
	Check surface species in the database Each surface species should have a real number as their molecular weights, charge, and equilibrium constants.
void	checkSpeciesValue (const std::string type, const std::string species, const std::string field) const
	Check given species field value can be converted to a Real.
void	checkSpeciesWeightValue (const std::string type, const std::string species, const std::string field) const
	Check given species stoichiometric weigth values can be converted to a Real.

Protected Attributes
const FileName	_filename
	Database filename.
const nlohmann::json &	_root
	JSON database.
unsigned int	_temperature_size
	Number of temperature points.

Detailed Description

Class for validating MOOSE geochemical database.

Definition at line 18 of file GeochemicalDatabaseValidator.h.

Constructor & Destructor Documentation

GeochemicalDatabaseValidator()

GeochemicalDatabaseValidator::GeochemicalDatabaseValidator	(	const FileName	filename,
		const nlohmann::json &	db
	)

Definition at line 16 of file GeochemicalDatabaseValidator.C.

  : _filename(filename), _root(db)
{
}

Member Function Documentation

checkArraySize() [1/2]

void GeochemicalDatabaseValidator::checkArraySize ( const nlohmann::json &  array, const std::string  field  ) const

protected

Check Json::Value array is the correct size.

Parameters

array	array of values
field	database field name

Definition at line 176 of file GeochemicalDatabaseValidator.C.

{
  if (array.size() != _temperature_size)
    mooseError("The number of values in the ",
               field,
               " field of ",
               _filename,
               " is not equal to the number of temperature values");
}

Referenced by checkGasSpecies(), checkHeaderArray(), checkMineralSpecies(), checkRedoxSpecies(), checkSecondarySpecies(), and validate().

checkArraySize() [2/2]

void GeochemicalDatabaseValidator::checkArraySize ( const std::string  type, const std::string  species, const std::string  field  ) const

protected

Check array is the correct size.

Parameters

type	species type (basis, secondary, etc)
species	species name
field	name of array values to check

Definition at line 188 of file GeochemicalDatabaseValidator.C.

{
  if (_root[type][species][field].size() != _temperature_size)
    mooseError("The number of values in the ",
               field,
               " field of ",
               type,
               " ",
               species,
               " in ",
               _filename,
               " is not equal to the number of temperature values");
}

checkArrayValues() [1/2]

void GeochemicalDatabaseValidator::checkArrayValues ( const nlohmann::json &  array, const std::string  field  ) const

protected

Check Json::Value array is comprised of Reals.

Parameters

array	array of values
field	database field name

Definition at line 139 of file GeochemicalDatabaseValidator.C.

{
  // Check each value in the array can be successfully converted to a Real
  for (auto & item : array.items())
    if (!isValueReal(item.value()))
      mooseError("Array value ",
                 nlohmann::to_string(item.value()),
                 " in the ",
                 field,
                 " field of ",
                 _filename,
                 " cannot be converted to Real");
}

Referenced by checkGasSpecies(), checkHeaderArray(), checkMineralSpecies(), checkRedoxSpecies(), checkSecondarySpecies(), and validate().

checkArrayValues() [2/2]

void GeochemicalDatabaseValidator::checkArrayValues ( const std::string  type, const std::string  species, const std::string  field  ) const

protected

Check array array values can be converted to Real.

Parameters

type	species type (basis, secondary, etc)
species	species name
field	name of array values to check

Definition at line 155 of file GeochemicalDatabaseValidator.C.

{
  // Check each value in the array can be successfully converted to a Real
  for (auto & item : _root[type][species][field].items())
    if (!isValueReal(item.value()))
      mooseError("Array value ",
                 nlohmann::to_string(item.value()),
                 " in the ",
                 field,
                 " field of ",
                 type,
                 " ",
                 species,
                 " in ",
                 _filename,
                 " cannot be converted to Real");
}

checkBasisSpecies()

void GeochemicalDatabaseValidator::checkBasisSpecies ( const std::string  species ) const

protected

Check basis species in the database Each basis species should have a real number as their molecular weights, charge, radius and weight for each element.

Parameters

species

basis species name

Definition at line 274 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("basis species", species, "molecular weight");
 
  // Check charge can be converted to a Real
  checkSpeciesValue("basis species", species, "charge");
 
  // Check ionic radius can be converted to a Real
  checkSpeciesValue("basis species", species, "radius");
 
  // Check element weights can be converted to a Real
  checkSpeciesWeightValue("basis species", species, "elements");
}

Referenced by validate().

checkElements()

void GeochemicalDatabaseValidator::checkElements ( const std::string  element ) const

protected

Check elements in the database Each elemenent should have a real number as their molecular weights.

Parameters

element

element name

Definition at line 267 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("elements", element, "molecular weight");
}

Referenced by validate().

checkGasSpecies()

void GeochemicalDatabaseValidator::checkGasSpecies ( const std::string  species ) const

protected

Check gas species in the database Each gas species should have a real number as their molecular weights, equilibrium constants, weight for each basis species, and fugacity values.

Parameters

species

gas species name

Definition at line 337 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("gas species", species, "molecular weight");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("gas species", species, "species");
 
  // Check the number of logk values and whether they can be converted to a Real
  checkArraySize("gas species", species, "logk");
  checkArrayValues("gas species", species, "logk");
 
  // Check optional fugacity coefficients
  if (_root["gas species"][species].contains("chi"))
    checkArrayValues("gas species", species, "chi");
 
  if (_root["gas species"][species].contains("Pcrit"))
    checkSpeciesValue("gas species", species, "Pcrit");
 
  if (_root["gas species"][species].contains("Tcrit"))
    checkSpeciesValue("gas species", species, "Tcrit");
 
  if (_root["gas species"][species].contains("omega"))
    checkSpeciesValue("gas species", species, "omega");
}

Referenced by validate().

checkHeaderArray()

void GeochemicalDatabaseValidator::checkHeaderArray ( const std::string  field ) const

protected

Check arrays in field can be converted to Reals.

Parameters

field

name of field to check

Definition at line 213 of file GeochemicalDatabaseValidator.C.

{
  // Check that all values are real numbers and of size equal to the temperature
  checkArraySize(_root["Header"][field], "Header:" + field);
  checkArrayValues(_root["Header"][field], "Header:" + field);
}

Referenced by validate().

checkHeaderField()

void GeochemicalDatabaseValidator::checkHeaderField ( const std::string  field ) const

protected

Check fields are present in the Header section.

Parameters

field

name of field to check

Definition at line 205 of file GeochemicalDatabaseValidator.C.

{
  if (!_root["Header"].contains(field))
    mooseError(
        "The MOOSE database ", _filename, " does not have a required \"Header:", field, "\" field");
}

Referenced by validate().

checkMineralSpecies()

void GeochemicalDatabaseValidator::checkMineralSpecies ( const std::string  species ) const

protected

Check mineral species in the database Each mineral species should have a real number as their molecular weights, volume, equilibrium constants and weight for each basis species.

Parameters

species

mineral species name

Definition at line 310 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("mineral species", species, "molecular weight");
 
  // Check molar volume can be converted to a Real
  checkSpeciesValue("mineral species", species, "molar volume");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("mineral species", species, "species");
 
  // Check the number of logk values and whether they can be converted to a Real
  checkArraySize("mineral species", species, "logk");
  checkArrayValues("mineral species", species, "logk");
}

Referenced by validate().

checkOxideSpecies()

void GeochemicalDatabaseValidator::checkOxideSpecies ( const std::string  species ) const

protected

Check oxide species in the database Each oxide species should have a real number as their molecular weights and weight for each basis species.

Parameters

species

oxide species name

Definition at line 384 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("oxides", species, "molecular weight");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("oxides", species, "species");
}

Referenced by validate().

checkRedoxSpecies()

void GeochemicalDatabaseValidator::checkRedoxSpecies ( const std::string  species ) const

protected

Check redox couple species in the database Each redox couple species should have a real number as their molecular weights, charge, radius, equilibrium constants and weight for each basis species.

Parameters

species

redox couple species name

Definition at line 364 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("redox couples", species, "molecular weight");
 
  // Check charge can be converted to a Real
  checkSpeciesValue("redox couples", species, "charge");
 
  // Check ionic radius can be converted to a Real
  checkSpeciesValue("redox couples", species, "radius");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("redox couples", species, "species");
 
  // Check the number of logk values and whether they can be converted to a Real
  checkArraySize("redox couples", species, "logk");
  checkArrayValues("redox couples", species, "logk");
}

Referenced by validate().

checkSecondarySpecies()

void GeochemicalDatabaseValidator::checkSecondarySpecies ( const std::string  species ) const

protected

Check secondary species in the database Each secondary species should have a real number as their molecular weights, charge, radius, equilibrium constants and weight for each basis species.

Parameters

species

secondary species name

Definition at line 290 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("secondary species", species, "molecular weight");
 
  // Check charge can be converted to a Real
  checkSpeciesValue("secondary species", species, "charge");
 
  // Check ionic radius can be converted to a Real
  checkSpeciesValue("secondary species", species, "radius");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("secondary species", species, "species");
 
  // Check the number of logk values and whether they can be converted to a Real
  checkArraySize("secondary species", species, "logk");
  checkArrayValues("secondary species", species, "logk");
}

Referenced by validate().

checkSorbingMineralSpecies()

void GeochemicalDatabaseValidator::checkSorbingMineralSpecies ( const std::string  species ) const

protected

Check sorbing mineral species in the database Each sorbing mineral species should have a real number as their surface area, equilibrium constants and weight for each sorbing site.

Parameters

species

sorbing mineral species name

Definition at line 327 of file GeochemicalDatabaseValidator.C.

{
  // Check surface area can be converted to a Real
  checkSpeciesValue("sorbing minerals", species, "surface area");
 
  // Check sorbing site weights can be converted to a Real
  checkSpeciesWeightValue("sorbing minerals", species, "sorbing sites");
}

Referenced by validate().

checkSpeciesValue()

void GeochemicalDatabaseValidator::checkSpeciesValue ( const std::string  type, const std::string  species, const std::string  field  ) const

protected

Check given species field value can be converted to a Real.

Parameters

type	species type (basis, secondary, etc)
species	species name
field	value to check

Definition at line 221 of file GeochemicalDatabaseValidator.C.

{
  if (!_root[type].contains(species) || !_root[type][species].contains(field))
    mooseError("The ", type, " ", species, " in ", _filename, " does not have a ", field);
 
  // The field value should be a real number
  if (!isValueReal(_root[type][species][field]))
    mooseError(field,
               " value ",
               nlohmann::to_string(_root[type][species][field]),
               " of the ",
               type,
               " ",
               species,
               " in ",
               _filename,
               " cannot be converted to Real");
}

Referenced by checkBasisSpecies(), checkElements(), checkGasSpecies(), checkMineralSpecies(), checkOxideSpecies(), checkRedoxSpecies(), checkSecondarySpecies(), checkSorbingMineralSpecies(), and checkSurfaceSpecies().

checkSpeciesWeightValue()

void GeochemicalDatabaseValidator::checkSpeciesWeightValue ( const std::string  type, const std::string  species, const std::string  field  ) const

protected

Check given species stoichiometric weigth values can be converted to a Real.

Parameters

type	species type (basis, secondary, etc)
species	species name
field	name of values to check

Definition at line 243 of file GeochemicalDatabaseValidator.C.

{
  if (!_root[type].contains(species) || !_root[type][species].contains(field))
    mooseError("The ", type, " ", species, " in ", _filename, " does not have a ", field);
 
  // Each weight value for each constituent should be a real number
  for (auto & item : _root[type][species][field].items())
    if (!isValueReal(item.value()))
      mooseError("Weight value ",
                 nlohmann::to_string(item.value()),
                 " of constituent ",
                 item.key(),
                 " of the ",
                 type,
                 " ",
                 species,
                 " in ",
                 _filename,
                 " cannot be converted to Real");
}

Referenced by checkBasisSpecies(), checkGasSpecies(), checkMineralSpecies(), checkOxideSpecies(), checkRedoxSpecies(), checkSecondarySpecies(), checkSorbingMineralSpecies(), and checkSurfaceSpecies().

checkSurfaceSpecies()

void GeochemicalDatabaseValidator::checkSurfaceSpecies ( const std::string  species ) const

protected

Check surface species in the database Each surface species should have a real number as their molecular weights, charge, and equilibrium constants.

Parameters

species

surface species name

Definition at line 394 of file GeochemicalDatabaseValidator.C.

{
  // Check molecular weight can be converted to a Real
  checkSpeciesValue("surface species", species, "molecular weight");
 
  // Check charge can be converted to a Real
  checkSpeciesValue("surface species", species, "charge");
 
  // Check basis species weights can be converted to a Real
  checkSpeciesWeightValue("surface species", species, "species");
 
  // Check equilibrium constants can be converted to a Real
  checkSpeciesValue("surface species", species, "log K");
  checkSpeciesValue("surface species", species, "dlogK/dT");
}

Referenced by validate().

isValueReal()

bool GeochemicalDatabaseValidator::isValueReal ( const nlohmann::json &  value ) const

protected

Check Json::Value can be converted to a Real.

Parameters

array

array of values

Returns

true/false if the value can/cannot be converted to a Real

Definition at line 122 of file GeochemicalDatabaseValidator.C.

{
  if (value.is_number())
    return true;
  try
  {
    MooseUtils::convert<Real>(value, true);
  }
  catch (const std::invalid_argument & err)
  {
    return false;
  }
 
  return true;
}

Referenced by checkArrayValues(), checkArrayValues(), checkSpeciesValue(), and checkSpeciesWeightValue().

validate()

void GeochemicalDatabaseValidator::validate

(

)

Validate the thermodynamic database.

Definition at line 23 of file GeochemicalDatabaseValidator.C.

{
  // Check that the database has a Header key (required)
  if (!_root.contains("Header"))
    mooseError("The MOOSE database ", _filename, " does not have a required \"Header\" field");
 
  // Check that temperatures are present
  checkHeaderField("temperatures");
 
  // The size of the temperature array is used to check all other arrays, which must
  // have the same number of elements
  _temperature_size = _root["Header"]["temperatures"].size();
 
  // Now check that the values are all Real
  checkHeaderArray("temperatures");
 
  // Check the pressure values are present and are Reals
  checkHeaderField("pressures");
  checkHeaderArray("pressures");
 
  // Check activity model coefficients
  checkHeaderField("activity model");
 
  // If the activity model is Debye-Huckel, test the coefficients are also present
  // and are Reals
  if (_root["Header"]["activity model"] == "debye-huckel")
  {
    checkHeaderField("adh");
    checkHeaderArray("adh");
 
    checkHeaderField("bdh");
    checkHeaderArray("bdh");
 
    checkHeaderField("bdot");
    checkHeaderArray("bdot");
  }
 
  // Check fugacity model is specified
  checkHeaderField("fugacity model");
 
  // If there are neutral species, check their arrays of coefficients
  if (_root["Header"].contains("neutral species"))
    for (auto & ns : _root["Header"]["neutral species"].items())
      for (auto & coeffs : ns.value().items())
      {
        if (coeffs.key() == "note")
          continue;
 
        // Check that there are a correct number of values and that they are real numbers
        auto values = coeffs.value();
        checkArraySize(values, "Header:neutral species:" + ns.key() + ":" + coeffs.key());
        checkArrayValues(values, "Header:neutral species:" + ns.key() + ":" + coeffs.key());
      }
 
  // Check the element data
  for (auto & el : _root["elements"].items())
    checkElements(el.key());
 
  // Check the basis species data
  for (auto & species : _root["basis species"].items())
    checkBasisSpecies(species.key());
 
  // Check the secondary species data
  if (_root.contains("secondary species"))
    for (auto & species : _root["secondary species"].items())
      checkSecondarySpecies(species.key());
 
  // Check the mineral species data
  if (_root.contains("mineral species"))
    for (auto & species : _root["mineral species"].items())
      checkMineralSpecies(species.key());
 
  // Check the sorbing mineral species data
  if (_root.contains("sorbing minerals"))
    for (auto & species : _root["sorbing minerals"].items())
      checkSorbingMineralSpecies(species.key());
 
  // Check the gas species data
  if (_root.contains("gas species"))
    for (auto & species : _root["gas species"].items())
      checkGasSpecies(species.key());
 
  // Check the redox couple data
  if (_root.contains("redox couples"))
    for (auto & species : _root["redox couples"].items())
      checkRedoxSpecies(species.key());
 
  // Check the oxide species data
  if (_root.contains("oxides"))
    for (auto & species : _root["oxides"].items())
      checkOxideSpecies(species.key());
 
  // Check the surface species data
  if (_root.contains("surface species"))
    for (auto & species : _root["surface species"].items())
      checkSurfaceSpecies(species.key());
}

Referenced by GeochemicalDatabaseReader::validate().

Member Data Documentation

_filename

const FileName GeochemicalDatabaseValidator::_filename

protected

Database filename.

Definition at line 173 of file GeochemicalDatabaseValidator.h.

Referenced by checkArraySize(), checkArraySize(), checkArrayValues(), checkArrayValues(), checkHeaderField(), checkSpeciesValue(), checkSpeciesWeightValue(), and validate().

_root

const nlohmann::json& GeochemicalDatabaseValidator::_root

protected

JSON database.

Definition at line 175 of file GeochemicalDatabaseValidator.h.

Referenced by checkArraySize(), checkArrayValues(), checkGasSpecies(), checkHeaderArray(), checkHeaderField(), checkSpeciesValue(), checkSpeciesWeightValue(), and validate().

_temperature_size

unsigned int GeochemicalDatabaseValidator::_temperature_size

protected

Number of temperature points.

Definition at line 177 of file GeochemicalDatabaseValidator.h.

Referenced by checkArraySize(), checkArraySize(), and validate().

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The documentation for this class was generated from the following files:

• geochemistry/include/utils/GeochemicalDatabaseValidator.h
• geochemistry/src/utils/GeochemicalDatabaseValidator.C