Avogadro::Calc::EnergyCalculator#
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class EnergyCalculator#
Subclassed by LennardJones, UFF
Public Functions
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EnergyCalculator() = default#
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virtual ~EnergyCalculator() = default#
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virtual EnergyCalculator *newInstance() const = 0#
Create a new instance of the model. Ownership passes to the caller.
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virtual std::string identifier() const = 0#
- Returns:
a unique identifier for this calculator.
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virtual std::string name() const = 0#
- Returns:
A short translatable name for this method (e.g., MMFF94, UFF, etc.)
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virtual std::string description() const = 0#
- Returns:
a description of the method
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inline virtual std::string userOptions() const#
Return a JSON object string describing optional user-editable settings for this model. Empty string means no user options.
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inline virtual bool setUserOptions(const std::string &optionsJson)#
Set user-selected options serialized as a JSON object string.
- Returns:
True on success.
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virtual Core::Molecule::ElementMask elements() const = 0#
Indicate if your method only treats a subset of elements.
- Returns:
an element mask corresponding to the defined subset
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inline virtual bool acceptsUnitCell() const#
Indicate if your method can handle unit cells.
- Returns:
true if unit cells are supported
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inline virtual bool acceptsIons() const#
Indicate if your method can handle ions Many methods only treat neutral systems, either a neutral molecule or a neutral unit cell.
- Returns:
true if ions are supported
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inline virtual bool acceptsRadicals() const#
Indicate if your method can handle radicals Most methods only treat closed-shell molecules.
- Returns:
true if radicals are supported
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virtual Real value(const Eigen::VectorXd &x) = 0#
Calculate the energy for this method.
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virtual void gradient(const Eigen::VectorXd &x, Eigen::VectorXd &grad)#
Calculate the gradients for this method, defaulting to numerical finite-difference methods
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void finiteGradient(const Eigen::VectorXd &x, Eigen::VectorXd &grad, int accuracy = 0)#
Calculate numerical gradients for this method.
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virtual Real evaluate(const Eigen::VectorXd &x, Eigen::VectorXd *grad = nullptr)#
Evaluate the energy and optionally gradients in one call.
Derived classes with efficient fused implementations should override this.
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virtual void hessian(const Eigen::VectorXd &x, Eigen::MatrixXd &hess)#
Calculate the Hessian matrix for this method, defaulting to numerical finite-difference methods.
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void finiteHessian(const Eigen::VectorXd &x, Eigen::MatrixXd &hess, int accuracy = 0)#
Calculate numerical Hessian for this method.
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void cleanGradients(Eigen::VectorXd &grad)#
Called to ‘clean’ gradients
- Parameters:
grad – (e.g., for constraints)
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Real constraintEnergies(const Eigen::VectorXd &x)#
Called to get the energies for the current set of constraints. which should be added to the value() method for real energies in derived classes
- Returns:
the sum of the constraint energies
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void constraintGradients(const Eigen::VectorXd &x, Eigen::VectorXd &grad)#
Called to get the gradients for the current set of constraints. which should be added to the gradient() method in derived classes.
- Parameters:
x – the current coordinates
grad – the gradient vector to be updated with constraint gradients
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std::vector<Core::Constraint> constraints() const#
Called to get the constraints for this method.
- Returns:
the constraints for this method
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void setConstraints(const std::vector<Core::Constraint> &constraints)#
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inline void setMask(Eigen::VectorXd mask)#
Called to update the “frozen” mask (e.g., during editing)
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inline Eigen::VectorXd mask() const#
- Returns:
the frozen atoms mask
Protected Functions
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void appendError(const std::string &errorString, bool newLine = true) const#
Append an error to the error string for the model.
- Parameters:
errorString – The error to be added.
newLine – Add a new line after the error string?
Protected Attributes
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Eigen::VectorXd m_mask#
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std::vector<Core::Constraint> m_distanceConstraints#
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std::vector<Core::Constraint> m_angleConstraints#
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std::vector<Core::Constraint> m_torsionConstraints#
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std::vector<Core::Constraint> m_outOfPlaneConstraints#
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EnergyCalculator() = default#