src/gromacs/awh/biaswriter.h

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  35
  36 /*! \internal \file
  37  *
  38  * \brief
  39  * This file contains the BiasWriter class that prepares and writes data of a Bias to an energy file.
  40  *
  41  * \author Viveca Lindahl
  42  * \author Berk Hess <hess@kth.se>
  43  * \ingroup module_awh
  44  */
  45
  46 #ifndef GMX_AWH_BIASWRITER_H
  47 #define GMX_AWH_BIASWRITER_H
  48
  49 #include <map>
  50 #include <vector>
  51
  52 #include "gromacs/fileio/enxio.h"
  53 #include "gromacs/utility/arrayref.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55
  56 struct gmx_multisim_t;
  57 struct t_enxsubblock;
  58
  59 namespace gmx
  60 {
  61 class Bias;
  62
  63 /* TODO: the post-simulations AWH reader and this AWH writer are totally
  64  * disconnected although they read/write the same data. I'm not sure how
  65  * to handle that or if it should be left as it is until the writing is done
  66  * in a differen format (i.e. TNG) than the current energy file.
  67  */
  68
  69 //! Enum with the AWH variables to write.
  70 enum class AwhOutputEntryType
  71 {
  72     MetaData,           //!< Meta data.
  73     CoordValue,         //!< Coordinate value.
  74     Pmf,                //!< The pmf.
  75     Bias,               //!< The bias.
  76     Visits,             //!< The number of visits.
  77     Weights,            //!< The weights.
  78     Target              //!< The target distribition.
  79 };
  80
  81 //! Enum with the types of metadata to write.
  82 enum class AwhOutputMetaData
  83 {
  84     NumBlock,           //!< The number of blocks.
  85     TargetError,        //!< The target error.
  86     ScaledSampleWeight, //!< The logarithm of the sample weight relative to a sample weight of 1 at the initial time.
  87     Count               //!< The number of enum values, not including Count.
  88 };
  89
  90 //! Enum with different ways of normalizing the output.
  91 enum class Normalization
  92 {
  93     None,         //!< No normalization.
  94     Coordinate,   //!< Scale using the internal/user input coordinate scaling factor.
  95     FreeEnergy,   //!< Normalize free energy values by subtracting the minimum value.
  96     Distribution  //!< Normalize the distribution to 1.
  97 };
  98
  99 /*! \internal \brief AWH output data block that can be written to an energy file block.
 100  */
 101 class AwhEnergyBlock
 102 {
 103     public:
 104         /*! \brief Constructor
 105          *
 106          * \param[in] numPoints           Number of points in block.
 107          * \param[in] normalizationType   Value for normalization type enum.
 108          * \param[in] normalizationValue  Normalization value.
 109          */
 110         AwhEnergyBlock(int            numPoints,
 111                        Normalization  normalizationType,
 112                        float          normalizationValue);
 113
 114         /*! \brief Returns an ArrarRef to the data in the block.
 115          */
 116         gmx::ArrayRef<float> data()
 117         {
 118             return data_;
 119         }
 120
 121         const Normalization normalizationType;  /**< How to normalize the output data */
 122         const float         normalizationValue; /**< The normalization value */
 123     private:
 124         std::vector<float>  data_;              /**< The data, always float which is enough since this is statistical data */
 125 };
 126
 127 /*! \internal \brief Class organizing the output data storing and writing of an AWH bias.
 128  */
 129 class BiasWriter
 130 {
 131     private:
 132         /*! \brief Query if the writer has a block for the given variable.
 133          *
 134          * \param[in] outputType  Output entry type.
 135          */
 136         bool hasVarBlock(AwhOutputEntryType outputType) const
 137         {
 138             return outputTypeToBlock_.find(outputType)->second >= 0;
 139         }
 140
 141         /*! \brief* Find the first block containing the given variable.
 142          *
 143          * \param[in] outputType  Output entry type.
 144          * \returns the first block index for the variable, or -1 there is no block.
 145          */
 146         int getVarStartBlock(AwhOutputEntryType outputType) const
 147         {
 148             return outputTypeToBlock_.find(outputType)->second;
 149         }
 150
 151         /*! \brief Transfer AWH point data to writer data blocks.
 152          *
 153          * \param[in] metaDataIndex  Meta data block index.
 154          * \param[in] metaDataType   The type of meta data to write.
 155          * \param[in] bias           The AWH Bias.
 156          */
 157         void transferMetaDataToWriter(size_t             metaDataIndex,
 158                                       AwhOutputMetaData  metaDataType,
 159                                       const Bias        &bias);
 160
 161         /*! \brief Transfer AWH point data to writer data blocks.
 162          *
 163          * \param[in] outputType  Output entry type.
 164          * \param[in] pointIndex  The point index.
 165          * \param[in] bias        The AWH Bias.
 166          * \param[in] pmf         PMF values.
 167          */
 168         void transferPointDataToWriter(AwhOutputEntryType          outputType,
 169                                        int                         pointIndex,
 170                                        const Bias                 &bias,
 171                                        gmx::ArrayRef<const float>  pmf);
 172
 173     public:
 174         /*! \brief Constructor.
 175          *
 176          * \param[in] bias  The AWH bias.
 177          */
 178         BiasWriter(const Bias &bias);
 179
 180         /*! \brief Returns the number of data blocks.
 181          *
 182          * \returns the number of data blocks.
 183          */
 184         int numBlocks() const
 185         {
 186             return block_.size();
 187         }
 188
 189     private:
 190         /*! \brief
 191          * Prepare the bias output data.
 192          *
 193          * \param[in] bias  The AWH Bias.
 194          */
 195         void prepareBiasOutput(const Bias &bias);
 196
 197     public:
 198         /*! \brief Collect AWH bias data in blocks and write to energy subblocks.
 199          *
 200          * \param[in]     bias      The AWH Bias.
 201          * \param[in,out] subblock  Energy subblocks to write to.
 202          * \returns the number of blocks written.
 203          */
 204         int writeToEnergySubblocks(const Bias &bias, t_enxsubblock *subblock);
 205
 206     private:
 207         std::vector<AwhEnergyBlock>       block_;             /**< The data blocks */
 208         std::map<AwhOutputEntryType, int> outputTypeToBlock_; /**< Start block index for each variable, -1 when variable should not be written */
 209 };
 210
 211 }       // namespace gmx
 212
 213 #endif  /* GMX_AWH_BIASWRITER_H */