src/gromacs/applied_forces/densityfitting/densityfittingparameters.h

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  35 /*! \internal \file
  36  * \brief
  37  * Declares parameters needed to evaluate forces and energies for density fitting
  38  *
  39  * \author Christian Blau <blau@kth.se>
  40  * \ingroup module_applied_forces
  41  */
  42 #ifndef GMX_APPLIED_FORCES_DENSITYFITTINGPARAMETERS_H
  43 #define GMX_APPLIED_FORCES_DENSITYFITTINGPARAMETERS_H
  44
  45 #include <string>
  46 #include <vector>
  47
  48 #include "gromacs/math/densityfit.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50
  51 #include "densityfittingamplitudelookup.h"
  52
  53 namespace gmx
  54 {
  55
  56 /*! \internal
  57  * \brief Holding all directly user-provided parameters for density fitting.
  58  *
  59  * Also used for setting all default parameters.
  60  */
  61 struct DensityFittingParameters
  62 {
  63     //! Indicate if density fitting is active
  64     bool active_ = false;
  65     //! Indices of the atoms that shall be fit to the density
  66     std::vector<index> indices_;
  67     //! Determines how to measure similarity between simulated and reference density
  68     DensitySimilarityMeasureMethod similarityMeasureMethod_ = DensitySimilarityMeasureMethod::innerProduct;
  69     //! Determines with what weight atoms are spread
  70     DensityFittingAmplitudeMethod amplitudeLookupMethod_ = DensityFittingAmplitudeMethod::Unity;
  71     //! The force constant to be used for the density fitting
  72     real forceConstant_ = 1e9;
  73     //! The spreading width used for the gauss transform of atoms onto the density grid
  74     real gaussianTransformSpreadingWidth_ = 0.2;
  75     //! The spreading range for spreading atoms onto the grid in multiples of the spreading width
  76     real gaussianTransformSpreadingRangeInMultiplesOfWidth_ = 4.0;
  77     //! Apply density fitting forces only every n-steps
  78     std::int64_t calculationIntervalInSteps_ = 1;
  79     //! Normalize reference and simulated densities
  80     bool normalizeDensities_ = true;
  81     //! Perform adaptive force scaling during the simulation
  82     bool adaptiveForceScaling_ = false;
  83     //! The time constant for the adaptive force scaling in ps
  84     real adaptiveForceScalingTimeConstant_ = 4;
  85     //! Translation of the structure, so that the coordinates that are fitted are x+translation
  86     std::string translationString_ = "";
  87     //! Linear transformation of the structure, so that the coordinates that are fitted are Matrix * x
  88     std::string transformationMatrixString_ = "";
  89 };
  90
  91 /*!\brief Check if two structs holding density fitting parameters are equal.
  92  *
  93  * \param[in] lhs left hand side to be compared
  94  * \param[in] rhs right hand side to be compared
  95  * \returns true if all elements in DensityFittingParameters are equal, else false
  96  */
  97 bool operator==(const DensityFittingParameters& lhs, const DensityFittingParameters& rhs);
  98
  99 /*!\brief Check if two structs holding density fitting parameters are not equal.
 100  *
 101  * \param[in] lhs left hand side to be compared
 102  * \param[in] rhs right hand side to be compared
 103  * \returns true if lhs is not equal rhs
 104  */
 105 bool operator!=(const DensityFittingParameters& lhs, const DensityFittingParameters& rhs);
 106
 107 } // namespace gmx
 108
 109 #endif // GMX_APPLIED_FORCES_DENSITYFITTINGPARAMETERS_H