/*
* 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.
//! Enum with the types of metadata to write.
enum class AwhOutputMetaData
{
- NumBlock, //!< The number of blocks.
- TargetError, //!< The target error.
+ NumBlock, //!< The number of blocks.
+ TargetError, //!< The target error.
ScaledSampleWeight, //!< The logarithm of the sample weight relative to a sample weight of 1 at the initial time.
- Count //!< The number of enum values, not including Count.
+ Count //!< The number of enum values, not including Count.
};
//! Enum with different ways of normalizing the output.
enum class Normalization
{
- None, //!< No normalization.
- Coordinate, //!< Scale using the internal/user input coordinate scaling factor.
- FreeEnergy, //!< Normalize free energy values by subtracting the minimum value.
- Distribution //!< Normalize the distribution to 1.
+ None, //!< No normalization.
+ Coordinate, //!< Scale using the internal/user input coordinate scaling factor.
+ FreeEnergy, //!< Normalize free energy values by subtracting the minimum value.
+ Distribution //!< Normalize the distribution to 1.
};
/*! \internal \brief AWH output data block that can be written to an energy file block.
*/
class AwhEnergyBlock
{
- public:
- /*! \brief Constructor
- *
- * \param[in] numPoints Number of points in block.
- * \param[in] normalizationType Type of normalization.
- * \param[in] normalizationValue Value to normalization with.
- */
- AwhEnergyBlock(int numPoints,
- Normalization normalizationType,
- float normalizationValue);
-
- /*! \brief Returns an ArrarRef to the data in the block.
- */
- gmx::ArrayRef<float> data()
- {
- return data_;
- }
-
- const Normalization normalizationType; /**< How to normalize the output data */
- const float normalizationValue; /**< The normalization value */
- private:
- std::vector<float> data_; /**< The data, always float which is enough since this is statistical data */
+public:
+ /*! \brief Constructor
+ *
+ * \param[in] numPoints Number of points in block.
+ * \param[in] normalizationType Type of normalization.
+ * \param[in] normalizationValue Value to normalization with.
+ */
+ AwhEnergyBlock(int numPoints, Normalization normalizationType, float normalizationValue);
+
+ /*! \brief Returns an ArrarRef to the data in the block.
+ */
+ gmx::ArrayRef<float> data() { return data_; }
+
+ const Normalization normalizationType; /**< How to normalize the output data */
+ const float normalizationValue; /**< The normalization value */
+private:
+ std::vector<float> data_; /**< The data, always float which is enough since this is statistical data */
};
/*! \internal \brief Class organizing the output data storing and writing of an AWH bias.
*/
class BiasWriter
{
- public:
- /*! \brief Constructor.
- *
- * \param[in] bias The AWH bias.
- */
- BiasWriter(const Bias &bias);
-
- /*! \brief Returns the number of data blocks.
- *
- * \returns the number of data blocks.
- */
- int numBlocks() const
- {
- return block_.size();
- }
-
- /*! \brief Collect AWH bias data in blocks and write to energy subblocks.
- *
- * \param[in] bias The AWH Bias.
- * \param[in,out] subblock Energy subblocks to write to.
- * \returns the number of blocks written.
- */
- int writeToEnergySubblocks(const Bias &bias, t_enxsubblock *subblock);
-
- private:
- /*! \brief Query if the writer has a block for the given variable.
- *
- * \param[in] outputType Output entry type.
- */
- bool hasVarBlock(AwhOutputEntryType outputType) const
- {
- return outputTypeToBlock_.find(outputType)->second >= 0;
- }
-
- /*! \brief* Find the first block containing the given variable.
- *
- * \param[in] outputType Output entry type.
- * \returns the first block index for the variable, or -1 there is no block.
- */
- int getVarStartBlock(AwhOutputEntryType outputType) const
- {
- return outputTypeToBlock_.find(outputType)->second;
- }
-
- /*! \brief Transfer AWH point data to writer data blocks.
- *
- * \param[in] metaDataIndex Meta data block index.
- * \param[in] metaDataType The type of meta data to write.
- * \param[in] bias The AWH Bias.
- */
- void transferMetaDataToWriter(gmx::index metaDataIndex,
- AwhOutputMetaData metaDataType,
- const Bias &bias);
-
- /*! \brief Transfer AWH point data to writer data blocks.
- *
- * \param[in] outputType Output entry type.
- * \param[in] pointIndex The point index.
- * \param[in] bias The AWH Bias.
- * \param[in] pmf PMF values.
- */
- void transferPointDataToWriter(AwhOutputEntryType outputType,
- int pointIndex,
- const Bias &bias,
- gmx::ArrayRef<const float> pmf);
-
- /*! \brief
- * Prepare the bias output data.
- *
- * \param[in] bias The AWH Bias.
- */
- void prepareBiasOutput(const Bias &bias);
-
- private:
- std::vector<AwhEnergyBlock> block_; /**< The data blocks */
- std::map<AwhOutputEntryType, int> outputTypeToBlock_; /**< Start block index for each variable, -1 when variable should not be written */
+public:
+ /*! \brief Constructor.
+ *
+ * \param[in] bias The AWH bias.
+ */
+ BiasWriter(const Bias& bias);
+
+ /*! \brief Returns the number of data blocks.
+ *
+ * \returns the number of data blocks.
+ */
+ int numBlocks() const { return block_.size(); }
+
+ /*! \brief Collect AWH bias data in blocks and write to energy subblocks.
+ *
+ * \param[in] bias The AWH Bias.
+ * \param[in,out] subblock Energy subblocks to write to.
+ * \returns the number of blocks written.
+ */
+ int writeToEnergySubblocks(const Bias& bias, t_enxsubblock* subblock);
+
+private:
+ /*! \brief Query if the writer has a block for the given variable.
+ *
+ * \param[in] outputType Output entry type.
+ */
+ bool hasVarBlock(AwhOutputEntryType outputType) const
+ {
+ return outputTypeToBlock_.find(outputType)->second >= 0;
+ }
+
+ /*! \brief* Find the first block containing the given variable.
+ *
+ * \param[in] outputType Output entry type.
+ * \returns the first block index for the variable, or -1 there is no block.
+ */
+ int getVarStartBlock(AwhOutputEntryType outputType) const
+ {
+ return outputTypeToBlock_.find(outputType)->second;
+ }
+
+ /*! \brief Transfer AWH point data to writer data blocks.
+ *
+ * \param[in] metaDataIndex Meta data block index.
+ * \param[in] metaDataType The type of meta data to write.
+ * \param[in] bias The AWH Bias.
+ */
+ void transferMetaDataToWriter(gmx::index metaDataIndex, AwhOutputMetaData metaDataType, const Bias& bias);
+
+ /*! \brief Transfer AWH point data to writer data blocks.
+ *
+ * \param[in] outputType Output entry type.
+ * \param[in] pointIndex The point index.
+ * \param[in] bias The AWH Bias.
+ * \param[in] pmf PMF values.
+ */
+ void transferPointDataToWriter(AwhOutputEntryType outputType,
+ int pointIndex,
+ const Bias& bias,
+ gmx::ArrayRef<const float> pmf);
+
+ /*! \brief
+ * Prepare the bias output data.
+ *
+ * \param[in] bias The AWH Bias.
+ */
+ void prepareBiasOutput(const Bias& bias);
+
+private:
+ std::vector<AwhEnergyBlock> block_; /**< The data blocks */
+ std::map<AwhOutputEntryType, int> outputTypeToBlock_; /**< Start block index for each variable, -1 when variable should not be written */
};
-} // namespace gmx
+} // namespace gmx
-#endif /* GMX_AWH_BIASWRITER_H */
+#endif /* GMX_AWH_BIASWRITER_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff