src/gromacs/applied_forces/densityfitting/densityfittingoptions.h

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  35 /*! \internal \file
  36  * \brief
  37  * Declares options for density fitting
  38  *
  39  * \author Christian Blau <blau@kth.se>
  40  * \ingroup module_applied_forces
  41  */
  42 #ifndef GMX_APPLIED_FORCES_DENSITYFITTINGOPTIONS_H
  43 #define GMX_APPLIED_FORCES_DENSITYFITTINGOPTIONS_H
  44
  45 #include <string>
  46
  47 #include "gromacs/mdtypes/imdpoptionprovider.h"
  48
  49 #include "densityfittingparameters.h"
  50
  51 namespace gmx
  52 {
  53
  54 class EnergyCalculationFrequencyErrors;
  55 class IndexGroupsAndNames;
  56 class KeyValueTreeObject;
  57 class KeyValueTreeBuilder;
  58
  59 /*! \internal
  60  * \brief Input data storage for density fitting
  61  */
  62 class DensityFittingOptions final : public IMdpOptionProvider
  63 {
  64 public:
  65     //! From IMdpOptionProvider
  66     void initMdpTransform(IKeyValueTreeTransformRules* rules) override;
  67
  68     /*! \brief
  69      * Build mdp parameters for density fitting to be output after pre-processing.
  70      * \param[in, out] builder the builder for the mdp options output KV-tree.
  71      * \note This should be symmetrical to option initialization without
  72      *       employing manual prefixing with the section name string once
  73      *       the legacy code blocking this design is removed.
  74      */
  75     void buildMdpOutput(KeyValueTreeObjectBuilder* builder) const override;
  76
  77     /*! \brief
  78      * Connect option name and data.
  79      */
  80     void initMdpOptions(IOptionsContainerWithSections* options) override;
  81
  82     //! Report if this set of options is active
  83     bool active() const;
  84
  85     //! Process input options to parameters, including input file reading.
  86     const DensityFittingParameters& buildParameters();
  87
  88     /*! \brief Evaluate and store atom indices.
  89      *
  90      * During pre-processing, use the group string from the options to
  91      * evaluate the indices of the atoms to be subject to forces from this
  92      * module.
  93      */
  94     void setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames);
  95
  96     //! Store the paramers that are not mdp options in the tpr file
  97     void writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder);
  98
  99     //! Set the internal parameters that are stored in the tpr file
 100     void readInternalParametersFromKvt(const KeyValueTreeObject& tree);
 101
 102     //! Return the file name of the reference density
 103     const std::string& referenceDensityFileName() const;
 104
 105     //! Check if input parameters are consistent with other simulation parameters
 106     void checkEnergyCaluclationFrequency(EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const;
 107
 108 private:
 109     const std::string c_activeTag_ = "active";
 110
 111     /*! \brief Denote the .mdp option that defines the group of fit atoms.
 112      * \note Changing this string will break .tpr backwards compability
 113      */
 114     const std::string c_groupTag_  = "group";
 115     std::string       groupString_ = "protein";
 116
 117     const std::string c_similarityMeasureTag_ = "similarity-measure";
 118
 119     const std::string c_amplitudeMethodTag_ = "atom-spreading-weight";
 120
 121     const std::string c_forceConstantTag_ = "force-constant";
 122
 123     const std::string c_gaussianTransformSpreadingWidthTag_ = "gaussian-transform-spreading-width";
 124     const std::string c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_ =
 125             "gaussian-transform-spreading-range-in-multiples-of-width";
 126
 127     const std::string c_referenceDensityFileNameTag_ = "reference-density-filename";
 128     std::string       referenceDensityFileName_      = "reference.mrc";
 129
 130     const std::string c_everyNStepsTag_ = "nst";
 131
 132     const std::string c_normalizeDensitiesTag_ = "normalize-densities";
 133
 134     const std::string c_adaptiveForceScalingTag_ = "adaptive-force-scaling";
 135
 136     const std::string c_adaptiveForceScalingTimeConstantTag_ =
 137             "adaptive-force-scaling-time-constant";
 138
 139     const std::string c_translationTag_ = "shift-vector";
 140
 141     const std::string c_transformationMatrixTag_ = "transformation-matrix";
 142
 143     DensityFittingParameters parameters_;
 144 };
 145
 146 } // namespace gmx
 147
 148 #endif