* \param[in] dimParams The bias dimensions parameters.
* \param[in] grid The grid.
* \param[in] point Point for umbrella center.
+ * \param[in] neighborLambdaDhdl An array containing the dHdL at the neighboring lambda
+ * points. The array is of length numLambdas+1, where numLambdas is the number of free
+ * energy lambda states. Element 0 in the array is the dHdL
+ * of the current state and elements 1..numLambdas contain the dHdL of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
* \param[in,out] force Force vector to set.
* Returns the umbrella potential.
*/
double calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
const BiasGrid& grid,
int point,
+ ArrayRef<const double> neighborLambdaDhdl,
gmx::ArrayRef<double> force) const;
/*! \brief
* \param[in] dimParams The bias dimensions parameters.
* \param[in] grid The grid.
* \param[in] probWeightNeighbor Probability weights of the neighbors.
+ * \param[in] neighborLambdaDhdl An array containing the dHdL at the neighboring lambda
+ * points. The array is of length numLambdas+1, where numLambdas is the number of free
+ * energy lambda states. Element 0 in the array is the dHdL
+ * of the current state and elements 1..numLambdas contain the dHdL of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
* \param[in] forceWorkBuffer Force work buffer, values only used internally.
* \param[in,out] force Bias force vector to set.
*/
void calcConvolvedForce(const std::vector<DimParams>& dimParams,
const BiasGrid& grid,
gmx::ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
gmx::ArrayRef<double> forceWorkBuffer,
gmx::ArrayRef<double> force) const;
* This function should only be called when the bias force is not being convolved.
* It is assumed that the probability distribution has been updated.
*
- * \param[in] dimParams Bias dimension parameters.
- * \param[in] grid The grid.
- * \param[in] probWeightNeighbor Probability weights of the neighbors.
- * \param[in,out] biasForce The AWH bias force.
- * \param[in] step Step number, needed for the random number generator.
- * \param[in] seed Random seed.
- * \param[in] indexSeed Second random seed, should be the bias Index.
+ * \param[in] dimParams Bias dimension parameters.
+ * \param[in] grid The grid.
+ * \param[in] probWeightNeighbor Probability weights of the neighbors.
+ * \param[in] neighborLambdaDhdl An array containing the dHdL at the neighboring lambda
+ * points. The array is of length numLambdas+1, where numLambdas is the number of free
+ * energy lambda states. Element 0 in the array is the dHdL
+ * of the current state and elements 1..numLambdas contain the dHdL of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
+ * \param[in,out] biasForce The AWH bias force.
+ * \param[in] step Step number, needed for the random number generator.
+ * \param[in] seed Random seed.
+ * \param[in] indexSeed Second random seed, should be the bias Index.
+ * \param[in] onlySampleUmbrellaGridpoint Only sample the umbrella gridpoint without calculating
+ * force and potential.
* \returns the new potential value.
*/
double moveUmbrella(const std::vector<DimParams>& dimParams,
const BiasGrid& grid,
gmx::ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
gmx::ArrayRef<double> biasForce,
int64_t step,
int64_t seed,
- int indexSeed);
+ int indexSeed,
+ bool onlySampleUmbrellaGridpoint);
private:
/*! \brief
* it here since this saves us from doing extra exponential function evaluations
* later on.
*
- * \param[in] dimParams The bias dimensions parameters
- * \param[in] grid The grid.
- * \param[out] weight Probability weights of the neighbors, SIMD aligned.
+ * \param[in] dimParams The bias dimensions parameters
+ * \param[in] grid The grid.
+ * \param[in] neighborLambdaEnergies An array containing the energy of the system
+ * in neighboring lambdas. The array is of length numLambdas+1, where numLambdas is
+ * the number of free energy lambda states. Element 0 in the array is the energy
+ * of the current state and elements 1..numLambdas contain the energy of the system in the
+ * neighboring lambda states (also including the current state). When there are no free
+ * energy lambda state dimensions this can be empty.
+ * \param[out] weight Probability weights of the neighbors, SIMD aligned.
* \returns the convolved bias.
*/
double updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
const BiasGrid& grid,
+ ArrayRef<const double> neighborLambdaEnergies,
std::vector<double, AlignedAllocator<double>>* weight) const;
/*! \brief
* These samples do not affect the (future) sampling and are thus
* pure observables. Statisics of these are stored in the energy file.
*
+ * \param[in] dimParams The bias dimensions parameters
* \param[in] grid The grid.
* \param[in] probWeightNeighbor Probability weights of the neighbors.
* \param[in] convolvedBias The convolved bias.
*/
- void sampleCoordAndPmf(const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
- double convolvedBias);
+ void sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
+ const BiasGrid& grid,
+ gmx::ArrayRef<const double> probWeightNeighbor,
+ double convolvedBias);
/*! \brief
* Calculates the convolved bias for a given coordinate value.
*
*/
inline HistogramSize histogramSize() const { return histogramSize_; }
+ /*! \brief Sets the umbrella grid point to the current grid point
+ */
+ void setUmbrellaGridpointToGridpoint() { coordState_.setUmbrellaGridpointToGridpoint(); }
+
/* Data members */
private:
CoordState coordState_; /**< The Current coordinate state */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff