/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
class CoordState
{
- public:
- /*! \brief Constructor.
- *
- * \param[in] awhBiasParams The Bias parameters from inputrec.
- * \param[in] dimParams The dimension Parameters.
- * \param[in] grid The grid.
- */
- CoordState(const AwhBiasParams &awhBiasParams,
- const std::vector<DimParams> &dimParams,
- const Grid &grid);
-
- /*! \brief
- * Sample a new umbrella reference point given the current coordinate value.
- *
- * It is assumed that the probability distribution has been updated.
- *
- * \param[in] grid The grid.
- * \param[in] gridpointIndex The grid point, sets the neighborhood.
- * \param[in] probWeightNeighbor Probability weights of the neighbors.
- * \param[in] step Step number, needed for the random number generator.
- * \param[in] seed Random seed.
- * \param[in] indexSeed Second random seed, should be the bias Index.
- * \returns the index of the sampled point.
- */
- void sampleUmbrellaGridpoint(const Grid &grid,
- int gridpointIndex,
- gmx::ArrayRef<const double> probWeightNeighbor,
- int64_t step,
- int64_t seed,
- int indexSeed);
-
- /*! \brief Update the coordinate value with coordValue.
- *
- * \param[in] grid The grid.
- * \param[in] coordValue The new coordinate value.
- */
- void setCoordValue(const Grid &grid,
- const awh_dvec coordValue);
-
- /*! \brief Restores the coordinate state from history.
- *
- * \param[in] stateHistory The AWH bias state history.
- */
- void restoreFromHistory(const AwhBiasStateHistory &stateHistory);
-
- /*! \brief Returns the current coordinate value.
- */
- const awh_dvec &coordValue() const
- {
- return coordValue_;
- }
-
- /*! \brief Returns the grid point index for the current coordinate value.
- */
- int gridpointIndex() const
- {
- return gridpointIndex_;
- }
-
- /*! \brief Returns the index for the current reference grid point.
- */
- int umbrellaGridpoint() const
- {
- return umbrellaGridpoint_;
- }
-
- private:
- awh_dvec coordValue_; /**< Current coordinate value in (nm or rad) */
- int gridpointIndex_; /**< The grid point index for the current coordinate value */
- int umbrellaGridpoint_; /**< Index for the current reference grid point for the umbrella, only used with umbrella potential type */
+public:
+ /*! \brief Constructor.
+ *
+ * \param[in] awhBiasParams The Bias parameters from inputrec.
+ * \param[in] dimParams The dimension Parameters.
+ * \param[in] grid The grid.
+ */
+ CoordState(const AwhBiasParams& awhBiasParams, const std::vector<DimParams>& dimParams, const Grid& grid);
+
+ /*! \brief
+ * Sample a new umbrella reference point given the current coordinate value.
+ *
+ * It is assumed that the probability distribution has been updated.
+ *
+ * \param[in] grid The grid.
+ * \param[in] gridpointIndex The grid point, sets the neighborhood.
+ * \param[in] probWeightNeighbor Probability weights of the neighbors.
+ * \param[in] step Step number, needed for the random number generator.
+ * \param[in] seed Random seed.
+ * \param[in] indexSeed Second random seed, should be the bias Index.
+ * \returns the index of the sampled point.
+ */
+ void sampleUmbrellaGridpoint(const Grid& grid,
+ int gridpointIndex,
+ gmx::ArrayRef<const double> probWeightNeighbor,
+ int64_t step,
+ int64_t seed,
+ int indexSeed);
+
+ /*! \brief Update the coordinate value with coordValue.
+ *
+ * \param[in] grid The grid.
+ * \param[in] coordValue The new coordinate value.
+ */
+ void setCoordValue(const Grid& grid, const awh_dvec coordValue);
+
+ /*! \brief Restores the coordinate state from history.
+ *
+ * \param[in] stateHistory The AWH bias state history.
+ */
+ void restoreFromHistory(const AwhBiasStateHistory& stateHistory);
+
+ /*! \brief Returns the current coordinate value.
+ */
+ const awh_dvec& coordValue() const { return coordValue_; }
+
+ /*! \brief Returns the grid point index for the current coordinate value.
+ */
+ int gridpointIndex() const { return gridpointIndex_; }
+
+ /*! \brief Returns the index for the current reference grid point.
+ */
+ int umbrellaGridpoint() const { return umbrellaGridpoint_; }
+
+private:
+ awh_dvec coordValue_; /**< Current coordinate value in (nm or rad) */
+ int gridpointIndex_; /**< The grid point index for the current coordinate value */
+ int umbrellaGridpoint_; /**< Index for the current reference grid point for the umbrella, only used with umbrella potential type */
};
-} // namespace gmx
+} // namespace gmx
#endif /* GMX_AWH_COORDSTATE_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff