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     ForceCorrelationVolume, //!< The volume of the force correlation tensor.
  80     FrictionTensor          //!< The full friction tensor.
  81 };
  82
  83 //! Enum with the types of metadata to write.
  84 enum class AwhOutputMetaData
  85 {
  86     NumBlock,           //!< The number of blocks.
  87     TargetError,        //!< The target error.
  88     ScaledSampleWeight, //!< The logarithm of the sample weight relative to a sample weight of 1 at the initial time.
  89     Count               //!< The number of enum values, not including Count.
  90 };
  91
  92 //! Enum with different ways of normalizing the output.
  93 enum class Normalization
  94 {
  95     None,         //!< No normalization.
  96     Coordinate,   //!< Scale using the internal/user input coordinate scaling factor.
  97     FreeEnergy,   //!< Normalize free energy values by subtracting the minimum value.
  98     Distribution  //!< Normalize the distribution to 1.
  99 };
 100
 101 /*! \internal \brief AWH output data block that can be written to an energy file block.
 102  */
 103 class AwhEnergyBlock
 104 {
 105     public:
 106         /*! \brief Constructor
 107          *
 108          * \param[in] numPoints           Number of points in block.
 109          * \param[in] normalizationType   Type of normalization.
 110          * \param[in] normalizationValue  Value to normalization with.
 111          */
 112         AwhEnergyBlock(int            numPoints,
 113                        Normalization  normalizationType,
 114                        float          normalizationValue);
 115
 116         /*! \brief Returns an ArrarRef to the data in the block.
 117          */
 118         gmx::ArrayRef<float> data()
 119         {
 120             return data_;
 121         }
 122
 123         const Normalization normalizationType;  /**< How to normalize the output data */
 124         const float         normalizationValue; /**< The normalization value */
 125     private:
 126         std::vector<float>  data_;              /**< The data, always float which is enough since this is statistical data */
 127 };
 128
 129 /*! \internal \brief Class organizing the output data storing and writing of an AWH bias.
 130  */
 131 class BiasWriter
 132 {
 133     public:
 134         /*! \brief Constructor.
 135          *
 136          * \param[in] bias  The AWH bias.
 137          */
 138         BiasWriter(const Bias &bias);
 139
 140         /*! \brief Returns the number of data blocks.
 141          *
 142          * \returns the number of data blocks.
 143          */
 144         int numBlocks() const
 145         {
 146             return block_.size();
 147         }
 148
 149         /*! \brief Collect AWH bias data in blocks and write to energy subblocks.
 150          *
 151          * \param[in]     bias      The AWH Bias.
 152          * \param[in,out] subblock  Energy subblocks to write to.
 153          * \returns the number of blocks written.
 154          */
 155         int writeToEnergySubblocks(const Bias &bias, t_enxsubblock *subblock);
 156
 157     private:
 158         /*! \brief Query if the writer has a block for the given variable.
 159          *
 160          * \param[in] outputType  Output entry type.
 161          */
 162         bool hasVarBlock(AwhOutputEntryType outputType) const
 163         {
 164             return outputTypeToBlock_.find(outputType)->second >= 0;
 165         }
 166
 167         /*! \brief* Find the first block containing the given variable.
 168          *
 169          * \param[in] outputType  Output entry type.
 170          * \returns the first block index for the variable, or -1 there is no block.
 171          */
 172         int getVarStartBlock(AwhOutputEntryType outputType) const
 173         {
 174             return outputTypeToBlock_.find(outputType)->second;
 175         }
 176
 177         /*! \brief Transfer AWH point data to writer data blocks.
 178          *
 179          * \param[in] metaDataIndex  Meta data block index.
 180          * \param[in] metaDataType   The type of meta data to write.
 181          * \param[in] bias           The AWH Bias.
 182          */
 183         void transferMetaDataToWriter(gmx::index             metaDataIndex,
 184                                       AwhOutputMetaData      metaDataType,
 185                                       const Bias            &bias);
 186
 187         /*! \brief Transfer AWH point data to writer data blocks.
 188          *
 189          * \param[in] outputType  Output entry type.
 190          * \param[in] pointIndex  The point index.
 191          * \param[in] bias        The AWH Bias.
 192          * \param[in] pmf         PMF values.
 193          */
 194         void transferPointDataToWriter(AwhOutputEntryType          outputType,
 195                                        int                         pointIndex,
 196                                        const Bias                 &bias,
 197                                        gmx::ArrayRef<const float>  pmf);
 198
 199         /*! \brief
 200          * Prepare the bias output data.
 201          *
 202          * \param[in] bias  The AWH Bias.
 203          */
 204         void prepareBiasOutput(const Bias &bias);
 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 */