#ifndef GMX_MDTYPES_AWH_PARAMS_H
#define GMX_MDTYPES_AWH_PARAMS_H
+#include <vector>
+
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/classhelpers.h"
+
+struct t_inpfile;
+struct t_inputrec;
+struct pull_params_t;
+using warninp_t = struct warninp*;
namespace gmx
{
+class ISerializer;
//! Target distribution enum.
enum class AwhTargetType : int
{
//! String for AWH bias reaction coordinate provider.
const char* enumValueToString(AwhCoordinateProviderType enumValue);
-/*! \cond INTERNAL */
-
-//! Parameters for an AWH coordinate dimension.
-struct AwhDimParams
+class AwhDimParams
{
- AwhCoordinateProviderType eCoordProvider; /**< The module providing the reaction coordinate. */
- int coordIndex; /**< Index of reaction coordinate in the provider. */
- double origin; /**< Start value of the interval. */
- double end; /**< End value of the interval. */
- double period; /**< The period of this dimension (= 0 if not periodic). */
- double forceConstant; /**< The force constant in kJ/mol/nm^2, kJ/mol/rad^2 */
- double diffusion; /**< Estimated diffusion constant in units of nm^2/ps, rad^2/ps or ps^-1. */
- double coordValueInit; /**< The initial coordinate value. */
- double coverDiameter; /**< The diameter that needs to be sampled around a point before it is considered covered. */
-};
+public:
+ //! Constructor from input file.
+ AwhDimParams(std::vector<t_inpfile>* inp,
+ const std::string& prefix,
+ const t_inputrec& ir,
+ warninp_t wi,
+ bool bComment);
+ //! Constructor to generate from file reading.
+ explicit AwhDimParams(ISerializer* serializer);
-//! Parameters for an AWH bias.
-struct AwhBiasParams
-{
- // TODO: Turn dimParams into a std::vector when moved into AWH module
- int ndim; /**< Dimension of the coordinate space. */
- AwhDimParams* dimParams; /**< AWH parameters per dimension. */
- AwhTargetType eTarget; /**< Type of target distribution. */
- double targetBetaScaling; /**< Beta scaling value for Boltzmann type target distributions. */
- double targetCutoff; /**< Free energy cutoff value for cutoff type target distribution in kJ/mol.*/
- AwhHistogramGrowthType eGrowth; /**< How the biasing histogram grows. */
- bool bUserData; /**< Is there a user-defined initial PMF estimate and target estimate? */
- double errorInitial; /**< Estimated initial free energy error in kJ/mol. */
- int shareGroup; /**< When >0, the bias is shared with biases of the same group and across multiple simulations when shareBiasMultisim=true */
- gmx_bool equilibrateHistogram; /**< True if the simulation starts out by equilibrating the histogram. */
+ //! Move constructor.
+ AwhDimParams(AwhDimParams&&) = default;
+ //! Move assignment operator.
+ AwhDimParams& operator=(AwhDimParams&&) = default;
+ //! Delete copy constructor.
+ AwhDimParams(const AwhDimParams&) = delete;
+ //! Delete copy assignment.
+ AwhDimParams& operator=(const AwhDimParams&) = delete;
+
+ //! Which module is providing the reaction coordinate.
+ AwhCoordinateProviderType coordinateProvider() const { return eCoordProvider_; }
+ //! Index for reaction coordinate in provider.
+ int coordinateIndex() const { return coordIndex_; }
+ //! Start value for interval.
+ double origin() const { return origin_; }
+ //! End value for interval.
+ double end() const { return end_; }
+ //! Period for the dimension.
+ double period() const { return period_; }
+ //! Set period value dependent on state.
+ void setPeriod(double period) { period_ = period; }
+ //! Force constant for this dimension.
+ double forceConstant() const { return forceConstant_; }
+ //! Estimated diffusion constant.
+ double diffusion() const { return diffusion_; }
+ //! Initial value for coordinate.
+ double initialCoordinate() const { return coordValueInit_; }
+ //! Set initial coordinate value dependent on state.
+ void setInitialCoordinate(double initialCoordinate) { coordValueInit_ = initialCoordinate; }
+ //! Diameter needed to be sampled.
+ double coverDiameter() const { return coverDiameter_; }
+ //! Write datastructure.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! The module providing the reaction coordinate.
+ AwhCoordinateProviderType eCoordProvider_;
+ //! Index of reaction coordinate in the provider.
+ int coordIndex_;
+ //! Start value of the interval.
+ double origin_;
+ //! End value of the interval.
+ double end_;
+ //! The period of this dimension (= 0 if not periodic).
+ double period_;
+ //! The force constant in kJ/mol/nm^2, kJ/mol/rad^2
+ double forceConstant_;
+ //! Estimated diffusion constant in units of nm^2/ps or rad^2/ps or ps^-1.
+ double diffusion_;
+ //! The initial coordinate value.
+ double coordValueInit_;
+ //! The diameter that needs to be sampled around a point before it is considered covered.
+ double coverDiameter_;
};
-//! Parameters for AWH.
-struct AwhParams
+class AwhBiasParams
{
- // TODO: Turn awhBiasParams into a std::vector when moved into AWH module
- int numBias; /**< The number of AWH biases.*/
- AwhBiasParams* awhBiasParams; /**< AWH bias parameters.*/
- int64_t seed; /**< Random seed.*/
- int nstOut; /**< Output step interval.*/
- int nstSampleCoord; /**< Number of samples per coordinate sample (also used for PMF) */
- int numSamplesUpdateFreeEnergy; /**< Number of samples per free energy update. */
- AwhPotentialType ePotential; /**< Type of potential. */
- gmx_bool shareBiasMultisim; /**< When true, share biases with shareGroup>0 between multi-simulations */
+public:
+ //! Constructor from input file.
+ AwhBiasParams(std::vector<t_inpfile>* inp,
+ const std::string& prefix,
+ const t_inputrec& ir,
+ warninp_t wi,
+ bool bComment);
+ //! Constructor to generate from file reading.
+ explicit AwhBiasParams(ISerializer* serializer);
+
+ //! Move constructor.
+ AwhBiasParams(AwhBiasParams&&) = default;
+ //! Move assignment operator.
+ AwhBiasParams& operator=(AwhBiasParams&&) = default;
+ //! Delete copy constructor.
+ AwhBiasParams(const AwhBiasParams&) = delete;
+ //! Delete copy assignment.
+ AwhBiasParams& operator=(const AwhBiasParams&) = delete;
+
+ //! Which target distribution is searched.
+ AwhTargetType targetDistribution() const { return eTarget_; }
+ //! Beta scaling to reach target distribution.
+ double targetBetaScaling() const { return targetBetaScaling_; }
+ //! Cutoff for target.
+ double targetCutoff() const { return targetCutoff_; }
+ //! Which kind of growth to use.
+ AwhHistogramGrowthType growthType() const { return eGrowth_; }
+ //! User provided PMF estimate.
+ bool userPMFEstimate() const { return bUserData_; }
+ //! Estimated initial free energy error in kJ/mol.
+ double initialErrorEstimate() const { return errorInitial_; }
+ //! Dimensions of coordinate space.
+ int ndim() const { return dimParams_.size(); }
+ //! Number of groups to share this bias with.
+ int shareGroup() const { return shareGroup_; }
+ //! If the simulation starts with equilibrating histogram.
+ bool equilibrateHistogram() const { return equilibrateHistogram_; }
+ //! Access to dimension parameters.
+ ArrayRef<AwhDimParams> dimParams() { return dimParams_; }
+ //! Const access to dimension parameters.
+ ArrayRef<const AwhDimParams> dimParams() const { return dimParams_; }
+ //! Write datastructure.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! AWH parameters per dimension.
+ std::vector<AwhDimParams> dimParams_;
+ //! Type of target distribution.
+ AwhTargetType eTarget_;
+ //! Beta scaling value for Boltzmann type target distributions.
+ double targetBetaScaling_;
+ //! Free energy cutoff value for cutoff type target distribution in kJ/mol.
+ double targetCutoff_;
+ //! How the biasing histogram grows.
+ AwhHistogramGrowthType eGrowth_;
+ //! Is there a user-defined initial PMF estimate and target estimate?
+ bool bUserData_;
+ //! Estimated initial free energy error in kJ/mol.
+ double errorInitial_;
+ //! When >0, the bias is shared with biases of the same group and across multiple simulations when shareBiasMultisim=true
+ int shareGroup_;
+ //! True if the simulation starts out by equilibrating the histogram.
+ bool equilibrateHistogram_;
};
+/*! \brief
+ * Structure holding parameter information for AWH.
+ */
+class AwhParams
+{
+public:
+ //! Constructor from input file.
+ AwhParams(std::vector<t_inpfile>* inp, const t_inputrec& ir, warninp_t wi);
+ //! Constructor used to generate awh parameter from file reading.
+ explicit AwhParams(ISerializer* serializer);
-/*! \endcond */
+ //! Move constructor.
+ AwhParams(AwhParams&&) = default;
+ //! Move assignment operator.
+ AwhParams& operator=(AwhParams&&) = default;
+ //! Delete copy constructor.
+ AwhParams(const AwhParams&) = delete;
+ //! Delete copy assignment.
+ AwhParams& operator=(const AwhParams&) = delete;
+
+ //! Get number of biases.
+ int numBias() const { return awhBiasParams_.size(); }
+ //! Get access to bias parameters.
+ ArrayRef<AwhBiasParams> awhBiasParams() { return awhBiasParams_; }
+ //! Const access to bias parameters.
+ ArrayRef<const AwhBiasParams> awhBiasParams() const { return awhBiasParams_; }
+ //! What king of potential is being used. \todo should use actual enum class.
+ AwhPotentialType potential() const { return potentialEnum_; }
+ //! Seed used for starting AWH.
+ int64_t seed() const { return seed_; }
+ //! Output step interval.
+ int nstout() const { return nstOut_; }
+ //! Number of samples per coordinate sample.
+ int nstSampleCoord() const { return nstSampleCoord_; }
+ //! Number of samples per free energy update.
+ int numSamplesUpdateFreeEnergy() const { return numSamplesUpdateFreeEnergy_; }
+ //! If biases are shared in multisim.
+ bool shareBiasMultisim() const { return shareBiasMultisim_; }
+ //! Serialize awh parameters.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! AWH bias parameters.
+ std::vector<AwhBiasParams> awhBiasParams_;
+ //! Random seed.
+ int64_t seed_;
+ //! Output step interval.
+ int nstOut_;
+ //! Number of samples per coordinate sample (also used for PMF)
+ int nstSampleCoord_;
+ //! Number of samples per free energy update.
+ int numSamplesUpdateFreeEnergy_;
+ //! Type of potential.
+ AwhPotentialType potentialEnum_;
+ //! Whether to share biases with shareGroup>0 between multi-simulations.
+ bool shareBiasMultisim_;
+};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff