*/
class PotentialPointData
{
- public:
-
-
- /*!
- * \brief Initialize a new data structure.
- */
- PotentialPointData() :
- PotentialPointData {Vector(0., 0., 0.), real(0.0)}
- {}
-
- /*!
- * \brief Initialize from an argument list
- *
- * \param f Force vector.
- * \param e Energy value.
- *
- * Note that if force was calculated as a scalar, it needs to be multiplied by a unit
- * vector in the direction to which it should be applied.
- */
- PotentialPointData(const Vector &f, const real e) :
- force(f),
- energy(e)
- {}
-
- /*!
- * \brief Force vector calculated for first position.
- */
- Vector force;
-
- /*!
- * \brief Potential energy calculated for this interaction.
- */
- real energy;
+public:
+ /*!
+ * \brief Initialize a new data structure.
+ */
+ PotentialPointData() : PotentialPointData{ Vector(0., 0., 0.), real(0.0) } {}
+
+ /*!
+ * \brief Initialize from an argument list
+ *
+ * \param f Force vector.
+ * \param e Energy value.
+ *
+ * Note that if force was calculated as a scalar, it needs to be multiplied by a unit
+ * vector in the direction to which it should be applied.
+ */
+ PotentialPointData(const Vector& f, const real e) : force(f), energy(e) {}
+
+ /*!
+ * \brief Force vector calculated for first position.
+ */
+ Vector force;
+
+ /*!
+ * \brief Potential energy calculated for this interaction.
+ */
+ real energy;
};
/*!
* are specified by the user and then, during integration, GROMACS provides
* the current positions of each pair for the restraint potential to be evaluated.
* In such a case, the potential can be implemented by overriding evaluate().
- * \todo Template headers can help to build compatible calculation methods with different input requirements.
- * For reference, see https://github.com/kassonlab/sample_restraint
+ * \todo Template headers can help to build compatible calculation methods with different input
+ * requirements. For reference, see https://github.com/kassonlab/sample_restraint
*
* \ingroup module_restraint
*/
class IRestraintPotential
{
- public:
- virtual ~IRestraintPotential() = default;
-
- /*!
- * \brief Calculate a force vector according to two input positions at a given time.
- *
- * If not overridden by derived class, returns a zero vector.
- * \param r1 position of first site
- * \param r2 position of second site
- * \param t simulation time in picoseconds
- * \return force vector and potential energy to be applied by calling code.
- *
- * \todo The virtual function call should be replaced by a (table of) function objects retrieved before the run.
- */
- virtual PotentialPointData evaluate(Vector r1,
- Vector r2,
- double t) = 0;
-
-
- /*!
- * \brief Call-back hook for restraint implementations.
- *
- * An update function to be called on the simulation master rank/thread periodically
- * by the Restraint framework.
- * Receives the same input as the evaluate() method, but is only called on the master
- * rank of a simulation to allow implementation code to be thread-safe without knowing
- * anything about the domain decomposition.
- *
- * \param v position of the first site
- * \param v0 position of the second site
- * \param t simulation time
- *
- * \internal
- * We give the definition here because we don't want plugins to have to link against
- * libgromacs right now (complicated header maintenance and no API stability guarantees).
- * But once we've had plugin restraints wrap themselves in a Restraint template,
- * we can set update = 0
- *
- * \todo: Provide gmxapi facility for plugin restraints to wrap themselves
- * with a default implementation to let this class be pure virtual.
- */
- virtual void update(gmx::Vector v,
- gmx::Vector v0,
- double t)
- {
- (void)v;
- (void)v0;
- (void)t;
- }
-
-
- /*!
- * \brief Find out what sites this restraint is configured to act on.
- * \return
- */
- virtual std::vector<int> sites() const = 0;
-
- /*!
- * \brief Allow Session-mediated interaction with other resources or workflow elements.
- *
- * \param resources temporary access to the resources provided by the session for additional configuration.
- *
- * A module implements this method to receive a handle to resources configured for this particular workflow
- * element.
- *
- * \internal
- * \todo This should be more general than the RestraintPotential interface.
- */
- virtual void bindSession(gmxapi::SessionResources* resources) { (void)resources; }
+public:
+ virtual ~IRestraintPotential() = default;
+
+ /*!
+ * \brief Calculate a force vector according to two input positions at a given time.
+ *
+ * If not overridden by derived class, returns a zero vector.
+ * \param r1 position of first site
+ * \param r2 position of second site
+ * \param t simulation time in picoseconds
+ * \return force vector and potential energy to be applied by calling code.
+ *
+ * \todo The virtual function call should be replaced by a (table of) function objects retrieved before the run.
+ */
+ virtual PotentialPointData evaluate(Vector r1, Vector r2, double t) = 0;
+
+
+ /*!
+ * \brief Call-back hook for restraint implementations.
+ *
+ * An update function to be called on the simulation master rank/thread periodically
+ * by the Restraint framework.
+ * Receives the same input as the evaluate() method, but is only called on the master
+ * rank of a simulation to allow implementation code to be thread-safe without knowing
+ * anything about the domain decomposition.
+ *
+ * \param v position of the first site
+ * \param v0 position of the second site
+ * \param t simulation time
+ *
+ * \internal
+ * We give the definition here because we don't want plugins to have to link against
+ * libgromacs right now (complicated header maintenance and no API stability guarantees).
+ * But once we've had plugin restraints wrap themselves in a Restraint template,
+ * we can set update = 0
+ *
+ * \todo: Provide gmxapi facility for plugin restraints to wrap themselves
+ * with a default implementation to let this class be pure virtual.
+ */
+ virtual void update(gmx::Vector v, gmx::Vector v0, double t)
+ {
+ (void)v;
+ (void)v0;
+ (void)t;
+ }
+
+
+ /*!
+ * \brief Find out what sites this restraint is configured to act on.
+ * \return
+ */
+ virtual std::vector<int> sites() const = 0;
+
+ /*!
+ * \brief Allow Session-mediated interaction with other resources or workflow elements.
+ *
+ * \param resources temporary access to the resources provided by the session for additional configuration.
+ *
+ * A module implements this method to receive a handle to resources configured for this particular workflow
+ * element.
+ *
+ * \internal
+ * \todo This should be more general than the RestraintPotential interface.
+ */
+ virtual void bindSession(gmxapi::SessionResources* resources) { (void)resources; }
};
-} // end namespace gmx
+} // end namespace gmx
-#endif //GMX_PULLING_PULLPOTENTIAL_H
+#endif // GMX_PULLING_PULLPOTENTIAL_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff