struct ensemble_input_param_type
{
/// distance histogram parameters
- size_t nBins{0};
- double binWidth{0.};
+ size_t nBins{ 0 };
+ double binWidth{ 0. };
/// Flat-bottom potential boundaries.
- double minDist{0};
- double maxDist{0};
+ double minDist{ 0 };
+ double maxDist{ 0 };
/// Experimental reference distribution.
PairHist experimental{};
/// Number of samples to store during each window.
- unsigned int nSamples{0};
- double samplePeriod{0};
+ unsigned int nSamples{ 0 };
+ double samplePeriod{ 0 };
/// Number of windows to use for smoothing histogram updates.
- unsigned int nWindows{0};
+ unsigned int nWindows{ 0 };
/// Harmonic force coefficient
- double k{0};
+ double k{ 0 };
/// Smoothing factor: width of Gaussian interpolation for histogram
- double sigma{0};
-
+ double sigma{ 0 };
};
// \todo We should be able to automate a lot of the parameter setting stuff
// The statically compiled fast parameter structure would be generated with a recursive variadic template
// the way a tuple is. ref https://eli.thegreenplace.net/2014/variadic-templates-in-c/
-std::unique_ptr<ensemble_input_param_type>
-makeEnsembleParams(size_t nbins,
- double binWidth,
- double minDist,
- double maxDist,
- const std::vector<double>& experimental,
- unsigned int nSamples,
- double samplePeriod,
- unsigned int nWindows,
- double k,
- double sigma);
+std::unique_ptr<ensemble_input_param_type> makeEnsembleParams(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ const std::vector<double>& experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma);
/*!
* \brief a residue-pair bias calculator for use in restrained-ensemble simulations.
* Applies a force between two sites according to the difference between an experimentally observed
* site pair distance distribution and the distance distribution observed earlier in the simulation
* trajectory. The sampled distribution is averaged from the previous `nwindows` histograms from all
- * ensemble members. Each window contains a histogram populated with `nsamples` distances recorded at
- * `sample_period` step intervals.
+ * ensemble members. Each window contains a histogram populated with `nsamples` distances recorded
+ * at `sample_period` step intervals.
*
* \internal
- * During a the window_update_period steps of a window, the potential applied is a harmonic function of
- * the difference between the sampled and experimental histograms. At the beginning of the window, this
- * difference is found and a Gaussian blur is applied.
+ * During a the window_update_period steps of a window, the potential applied is a harmonic function
+ * of the difference between the sampled and experimental histograms. At the beginning of the
+ * window, this difference is found and a Gaussian blur is applied.
*/
class EnsemblePotential
{
- public:
- using input_param_type = ensemble_input_param_type;
-
- /* No default constructor. Parameters must be provided. */
- EnsemblePotential() = delete;
-
- /*!
- * \brief Constructor called by the wrapper code to produce a new instance.
- *
- * This constructor is called once per simulation per GROMACS process. Note that until
- * gmxapi 0.0.8 there is only one instance per simulation in a thread-MPI simulation.
- *
- * \param params
- */
- explicit EnsemblePotential(const input_param_type& params);
-
- /*!
- * \brief Deprecated constructor taking a parameter list.
- *
- * \param nbins
- * \param binWidth
- * \param minDist
- * \param maxDist
- * \param experimental
- * \param nSamples
- * \param samplePeriod
- * \param nWindows
- * \param k
- * \param sigma
- */
- EnsemblePotential(size_t nbins,
- double binWidth,
- double minDist,
- double maxDist,
- PairHist experimental,
- unsigned int nSamples,
- double samplePeriod,
- unsigned int nWindows,
- double k,
- double sigma);
-
- /*!
- * \brief Evaluates the pair restraint potential.
- *
- * In parallel simulations, the gmxapi framework does not make guarantees about where or
- * how many times this function is called. It should be simple and stateless; it should not
- * update class member data (see ``ensemblepotential.cpp``. For a more controlled API hook
- * and to manage state in the object, use ``callback()``.
- *
- * \param v position of the site for which force is being calculated.
- * \param v0 reference site (other member of the pair).
- * \param t current simulation time (ps).
- * \return container for force and potential energy data.
- */
- // Implementation note for the future: If dispatching this virtual function is not fast
- // enough, the compiler may be able to better optimize a free
- // function that receives the current restraint as an argument.
- gmx::PotentialPointData calculate(gmx::Vector v,
- gmx::Vector v0,
- gmx_unused double t);
-
- /*!
- * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
- *
- * Defining this function in a plugin potential is optional. If the function is defined,
- * the restraint framework calls this function (on the first rank only in a parallel simulation) before calling calculate().
- *
- * The callback may use resources provided by the Session in the callback to perform updates
- * to the local or global state of an ensemble of simulations. Future gmxapi releases will
- * include additional optimizations, allowing call-back frequency to be expressed, and more
- * general Session resources, as well as more flexible call signatures.
- */
- void callback(gmx::Vector v,
- gmx::Vector v0,
- double t,
- const Resources& resources);
-
- private:
- /// Width of bins (distance) in histogram
- size_t nBins_;
- double binWidth_;
-
- /// Flat-bottom potential boundaries.
- double minDist_;
- double maxDist_;
- /// Smoothed historic distribution for this restraint. An element of the array of restraints in this simulation.
- // Was `hij` in earlier code.
- PairHist histogram_;
- PairHist experimental_;
-
- /// Number of samples to store during each window.
- unsigned int nSamples_;
- unsigned int currentSample_;
- double samplePeriod_;
- double nextSampleTime_;
- /// Accumulated list of samples during a new window.
- std::vector<double> distanceSamples_;
-
- /// Number of windows to use for smoothing histogram updates.
- size_t nWindows_;
- size_t currentWindow_;
- double windowStartTime_;
- double nextWindowUpdateTime_;
- /// The history of nwindows histograms for this restraint.
- std::vector<std::unique_ptr<plugin::Matrix<double>>> windows_;
-
- /// Harmonic force coefficient
- double k_;
- /// Smoothing factor: width of Gaussian interpolation for histogram
- double sigma_;
+public:
+ using input_param_type = ensemble_input_param_type;
+
+ /* No default constructor. Parameters must be provided. */
+ EnsemblePotential() = delete;
+
+ /*!
+ * \brief Constructor called by the wrapper code to produce a new instance.
+ *
+ * This constructor is called once per simulation per GROMACS process. Note that until
+ * gmxapi 0.0.8 there is only one instance per simulation in a thread-MPI simulation.
+ *
+ * \param params
+ */
+ explicit EnsemblePotential(const input_param_type& params);
+
+ /*!
+ * \brief Deprecated constructor taking a parameter list.
+ *
+ * \param nbins
+ * \param binWidth
+ * \param minDist
+ * \param maxDist
+ * \param experimental
+ * \param nSamples
+ * \param samplePeriod
+ * \param nWindows
+ * \param k
+ * \param sigma
+ */
+ EnsemblePotential(size_t nbins,
+ double binWidth,
+ double minDist,
+ double maxDist,
+ PairHist experimental,
+ unsigned int nSamples,
+ double samplePeriod,
+ unsigned int nWindows,
+ double k,
+ double sigma);
+
+ /*!
+ * \brief Evaluates the pair restraint potential.
+ *
+ * In parallel simulations, the gmxapi framework does not make guarantees about where or
+ * how many times this function is called. It should be simple and stateless; it should not
+ * update class member data (see ``ensemblepotential.cpp``. For a more controlled API hook
+ * and to manage state in the object, use ``callback()``.
+ *
+ * \param v position of the site for which force is being calculated.
+ * \param v0 reference site (other member of the pair).
+ * \param t current simulation time (ps).
+ * \return container for force and potential energy data.
+ */
+ // Implementation note for the future: If dispatching this virtual function is not fast
+ // enough, the compiler may be able to better optimize a free
+ // function that receives the current restraint as an argument.
+ gmx::PotentialPointData calculate(gmx::Vector v, gmx::Vector v0, gmx_unused double t);
+
+ /*!
+ * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
+ *
+ * Defining this function in a plugin potential is optional. If the function is defined,
+ * the restraint framework calls this function (on the first rank only in a parallel simulation) before calling calculate().
+ *
+ * The callback may use resources provided by the Session in the callback to perform updates
+ * to the local or global state of an ensemble of simulations. Future gmxapi releases will
+ * include additional optimizations, allowing call-back frequency to be expressed, and more
+ * general Session resources, as well as more flexible call signatures.
+ */
+ void callback(gmx::Vector v, gmx::Vector v0, double t, const Resources& resources);
+
+private:
+ /// Width of bins (distance) in histogram
+ size_t nBins_;
+ double binWidth_;
+
+ /// Flat-bottom potential boundaries.
+ double minDist_;
+ double maxDist_;
+ /// Smoothed historic distribution for this restraint. An element of the array of restraints in this simulation.
+ // Was `hij` in earlier code.
+ PairHist histogram_;
+ PairHist experimental_;
+
+ /// Number of samples to store during each window.
+ unsigned int nSamples_;
+ unsigned int currentSample_;
+ double samplePeriod_;
+ double nextSampleTime_;
+ /// Accumulated list of samples during a new window.
+ std::vector<double> distanceSamples_;
+
+ /// Number of windows to use for smoothing histogram updates.
+ size_t nWindows_;
+ size_t currentWindow_;
+ double windowStartTime_;
+ double nextWindowUpdateTime_;
+ /// The history of nwindows histograms for this restraint.
+ std::vector<std::unique_ptr<plugin::Matrix<double>>> windows_;
+
+ /// Harmonic force coefficient
+ double k_;
+ /// Smoothing factor: width of Gaussian interpolation for histogram
+ double sigma_;
};
/*!
*/
class EnsembleRestraint : public ::gmx::IRestraintPotential, private EnsemblePotential
{
- public:
- using EnsemblePotential::input_param_type;
-
- EnsembleRestraint(std::vector<int> sites,
- const input_param_type& params,
- std::shared_ptr<Resources> resources
- ) :
- EnsemblePotential(params),
- sites_{std::move(sites)},
- resources_{std::move(resources)}
- {}
-
- ~EnsembleRestraint() override = default;
-
- /*!
- * \brief Implement required interface of gmx::IRestraintPotential
- *
- * \return list of configured site indices.
- *
- * \todo remove to template header
- * \todo abstraction of site references
- */
- std::vector<int> sites() const override
- {
- return sites_;
- }
-
- /*!
- * \brief Implement the interface gmx::IRestraintPotential
- *
- * Dispatch to calculate() method.
- *
- * \param r1 coordinate of first site
- * \param r2 reference coordinate (second site)
- * \param t simulation time
- * \return calculated force and energy
- *
- * \todo remove to template header.
- */
- gmx::PotentialPointData evaluate(gmx::Vector r1,
- gmx::Vector r2,
- double t) override
- {
- return calculate(r1,
- r2,
- t);
- };
-
- /*!
- * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
- *
- * Implements optional override of gmx::IRestraintPotential::update
- *
- * This boilerplate will disappear into the Restraint template in an upcoming gmxapi release.
- */
- void update(gmx::Vector v,
- gmx::Vector v0,
- double t) override
- {
- // Todo: use a callback period to mostly bypass this and avoid excessive mutex locking.
- callback(v,
- v0,
- t,
- *resources_);
- };
-
- /*!
- * \brief Implement the binding protocol that allows access to Session resources.
- *
- * The client receives a non-owning pointer to the session and cannot extent the life of the session. In
- * the future we can use a more formal handle mechanism.
- *
- * \param session pointer to the current session
- */
- void bindSession(gmxapi::SessionResources* session) override
- {
- resources_->setSession(session);
- }
-
- void setResources(std::unique_ptr<Resources>&& resources)
- {
- resources_ = std::move(resources);
- }
-
- private:
- std::vector<int> sites_;
-// double callbackPeriod_;
-// double nextCallback_;
- std::shared_ptr<Resources> resources_;
+public:
+ using EnsemblePotential::input_param_type;
+
+ EnsembleRestraint(std::vector<int> sites,
+ const input_param_type& params,
+ std::shared_ptr<Resources> resources) :
+ EnsemblePotential(params), sites_{ std::move(sites) }, resources_{ std::move(resources) }
+ {
+ }
+
+ ~EnsembleRestraint() override = default;
+
+ /*!
+ * \brief Implement required interface of gmx::IRestraintPotential
+ *
+ * \return list of configured site indices.
+ *
+ * \todo remove to template header
+ * \todo abstraction of site references
+ */
+ std::vector<int> sites() const override { return sites_; }
+
+ /*!
+ * \brief Implement the interface gmx::IRestraintPotential
+ *
+ * Dispatch to calculate() method.
+ *
+ * \param r1 coordinate of first site
+ * \param r2 reference coordinate (second site)
+ * \param t simulation time
+ * \return calculated force and energy
+ *
+ * \todo remove to template header.
+ */
+ gmx::PotentialPointData evaluate(gmx::Vector r1, gmx::Vector r2, double t) override
+ {
+ return calculate(r1, r2, t);
+ };
+
+ /*!
+ * \brief An update function to be called on the simulation master rank/thread periodically by the Restraint framework.
+ *
+ * Implements optional override of gmx::IRestraintPotential::update
+ *
+ * This boilerplate will disappear into the Restraint template in an upcoming gmxapi release.
+ */
+ void update(gmx::Vector v, gmx::Vector v0, double t) override
+ {
+ // Todo: use a callback period to mostly bypass this and avoid excessive mutex locking.
+ callback(v, v0, t, *resources_);
+ };
+
+ /*!
+ * \brief Implement the binding protocol that allows access to Session resources.
+ *
+ * The client receives a non-owning pointer to the session and cannot extent the life of the
+ * session. In the future we can use a more formal handle mechanism.
+ *
+ * \param session pointer to the current session
+ */
+ void bindSession(gmxapi::SessionResources* session) override
+ {
+ resources_->setSession(session);
+ }
+
+ void setResources(std::unique_ptr<Resources>&& resources) { resources_ = std::move(resources); }
+
+private:
+ std::vector<int> sites_;
+ // double callbackPeriod_;
+ // double nextCallback_;
+ std::shared_ptr<Resources> resources_;
};
// Important: Just declare the template instantiation here for client code.
// We will explicitly instantiate a definition in the .cpp file where the input_param_type is defined.
-extern template
-class RestraintModule<EnsembleRestraint>;
+extern template class RestraintModule<EnsembleRestraint>;
} // end namespace plugin
-#endif //HARMONICRESTRAINT_ENSEMBLEPOTENTIAL_H
+#endif // HARMONICRESTRAINT_ENSEMBLEPOTENTIAL_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff