*/
class BiasParams
{
- public:
- /*! \brief Switch to turn off update skips, useful for testing.
- */
- enum class DisableUpdateSkips
- {
- no, /**< Allow update skips (when supported by the method) */
- yes /**< Disable update skips */
- };
-
- /*! \brief
- * Check if the parameters permit skipping updates.
- *
- * Generally, we can skip updates of points that are non-local
- * at the time of the update if we for later times, when the points
- * with skipped updates have become local, know exactly how to apply
- * the previous updates. The free energy updates only depend
- * on local sampling, but the histogram rescaling factors
- * generally depend on the histogram size (all samples).
- * If the histogram size is kept constant or the scaling factors
- * are trivial, this is not a problem. However, if the histogram growth
- * is scaled down by some factor the size at the time of the update
- * needs to be known. It would be fairly simple to, for a deterministically
- * growing histogram, backtrack and calculate this value, but currently
- * we just disallow this case. This is not a restriction because it
- * only affects the local Boltzmann target type for which every update
- * is currently anyway global because the target is always updated globally.
- *
- * \returns true when we can skip updates.
- */
- inline bool skipUpdates() const
- {
- return (!disableUpdateSkips_ && localWeightScaling == 1);
- }
-
- /*! \brief
- * Returns the the radius that needs to be sampled around a point before it is considered covered.
- */
- inline const awh_ivec &coverRadius() const
- {
- return coverRadius_;
- }
-
- /*! \brief
- * Returns whether we should sample the coordinate.
- *
- * \param[in] step The MD step number.
- */
- inline bool isSampleCoordStep(int64_t step) const
- {
- return (step > 0 && step % numStepsSampleCoord_ == 0);
- }
-
- /*! \brief
- * Returns whether we should update the free energy.
- *
- * \param[in] step The MD step number.
- */
- inline bool isUpdateFreeEnergyStep(int64_t step) const
- {
- int stepIntervalUpdateFreeEnergy = numSamplesUpdateFreeEnergy_*numStepsSampleCoord_;
- return (step > 0 && step % stepIntervalUpdateFreeEnergy == 0);
- }
-
- /*! \brief
- * Returns whether we should update the target distribution.
- *
- * \param[in] step The MD step number.
- */
- inline bool isUpdateTargetStep(int64_t step) const
- {
- return step % numStepsUpdateTarget_ == 0;
- }
-
- /*! \brief
- * Returns if to do checks for covering in the initial stage.
- *
- * To avoid overhead due to expensive checks, we do not check
- * at every free energy update. However, if checks are
- * performed too rarely the detection of coverings will be
- * delayed, ultimately affecting free energy convergence.
- *
- * \param[in] step Time step.
- * \returns true at steps where checks should be performed.
- * \note Only returns true at free energy update steps.
- */
- bool isCheckCoveringStep(int64_t step) const
- {
- return step > 0 && (step % numStepsCheckCovering_ == 0);
- }
-
- /*! \brief
- * Returns if to perform checks for anomalies in the histogram.
- *
- * To avoid overhead due to expensive checks, we do not check
- * at every free energy update. These checks are only used for
- * warning the user and can be made as infrequently as
- * neccessary without affecting the algorithm itself.
- *
- * \param[in] step Time step.
- * \returns true at steps where checks should be performed.
- * \note Only returns true at free energy update steps.
- * \todo Currently this function just calls isCheckCoveringStep but the checks could be done less frequently.
- */
- bool isCheckHistogramForAnomaliesStep(int64_t step) const
- {
- return isCheckCoveringStep(step);
- }
-
- /*! \brief Constructor.
- *
- * The local Boltzmann target distibution is defined by
- * 1) Adding the sampled weights instead of the target weights to the reference weight histogram.
- * 2) Scaling the weights of these samples by the beta scaling factor.
- * 3) Setting the target distribution equal the reference weight histogram.
- * This requires the following special update settings:
- * localWeightScaling = targetParam
- * idealWeighthistUpdate = false
- * Note: these variables could in principle be set to something else also for other target distribution types.
- * However, localWeightScaling < 1 is in general expected to give lower efficiency and, except for local Boltzmann,
- * idealWeightHistUpdate = false gives (in my experience) unstable, non-converging results.
- *
- * \param[in] awhParams AWH parameters.
- * \param[in] awhBiasParams Bias parameters.
- * \param[in] dimParams Bias dimension parameters.
- * \param[in] beta 1/(k_B T) in units of 1/(kJ/mol), should be > 0.
- * \param[in] mdTimeStep The MD time step.
- * \param[in] numSharingSimulations The number of simulations to share the bias across.
- * \param[in] gridAxis The grid axes.
- * \param[in] disableUpdateSkips If to disable update skips, useful for testing.
- * \param[in] biasIndex Index of the bias.
- */
- BiasParams(const AwhParams &awhParams,
- const AwhBiasParams &awhBiasParams,
- const std::vector<DimParams> &dimParams,
- double beta,
- double mdTimeStep,
- DisableUpdateSkips disableUpdateSkips,
- int numSharingSimulations,
- const std::vector<GridAxis> &gridAxis,
- int biasIndex);
-
- /* Data members */
- const double invBeta; /**< 1/beta = kT in kJ/mol */
- private:
- const int64_t numStepsSampleCoord_; /**< Number of steps per coordinate value sample. */
- public:
- const int numSamplesUpdateFreeEnergy_; /**< Number of samples per free energy update. */
- private:
- const int64_t numStepsUpdateTarget_; /**< Number of steps per updating the target distribution. */
- const int64_t numStepsCheckCovering_; /**< Number of steps per checking for covering. */
- public:
- const int eTarget; /**< Type of target distribution. */
- const double freeEnergyCutoffInKT; /**< Free energy cut-off in kT for cut-off target distribution. */
- const double temperatureScaleFactor; /**< Temperature scaling factor for temperature scaled targed distributions. */
- const bool idealWeighthistUpdate; /**< Update reference weighthistogram using the target distribution? Otherwise use the realized distribution. */
- const int numSharedUpdate; /**< The number of (multi-)simulations sharing the bias update */
- const double updateWeight; /**< The probability weight accumulated for each update. */
- const double localWeightScaling; /**< Scaling factor applied to a sample before adding it to the reference weight histogram (= 1, usually). */
- const double initialErrorInKT; /**< Estimated initial free energy error in kT. */
- const double initialHistogramSize; /**< Initial reference weight histogram size. */
- private:
- awh_ivec coverRadius_; /**< The radius (in points) that needs to be sampled around a point before it is considered covered. */
- public:
- const bool convolveForce; /**< True if we convolve the force, false means use MC between umbrellas. */
- const int biasIndex; /**< Index of the bias, used as a second random seed and for priting. */
- private:
- const bool disableUpdateSkips_; /**< If true, we disallow update skips, even when the method supports it. */
+public:
+ /*! \brief Switch to turn off update skips, useful for testing.
+ */
+ enum class DisableUpdateSkips
+ {
+ no, /**< Allow update skips (when supported by the method) */
+ yes /**< Disable update skips */
+ };
+
+ /*! \brief
+ * Check if the parameters permit skipping updates.
+ *
+ * Generally, we can skip updates of points that are non-local
+ * at the time of the update if we for later times, when the points
+ * with skipped updates have become local, know exactly how to apply
+ * the previous updates. The free energy updates only depend
+ * on local sampling, but the histogram rescaling factors
+ * generally depend on the histogram size (all samples).
+ * If the histogram size is kept constant or the scaling factors
+ * are trivial, this is not a problem. However, if the histogram growth
+ * is scaled down by some factor the size at the time of the update
+ * needs to be known. It would be fairly simple to, for a deterministically
+ * growing histogram, backtrack and calculate this value, but currently
+ * we just disallow this case. This is not a restriction because it
+ * only affects the local Boltzmann target type for which every update
+ * is currently anyway global because the target is always updated globally.
+ *
+ * \returns true when we can skip updates.
+ */
+ inline bool skipUpdates() const { return (!disableUpdateSkips_ && localWeightScaling == 1); }
+
+ /*! \brief
+ * Returns the radius that needs to be sampled around a point before it is considered covered.
+ */
+ inline const awh_ivec& coverRadius() const { return coverRadius_; }
+
+ /*! \brief
+ * Returns whether we should sample the coordinate.
+ *
+ * \param[in] step The MD step number.
+ */
+ inline bool isSampleCoordStep(int64_t step) const
+ {
+ return (step > 0 && step % numStepsSampleCoord_ == 0);
+ }
+
+ /*! \brief
+ * Returns whether we should update the free energy.
+ *
+ * \param[in] step The MD step number.
+ */
+ inline bool isUpdateFreeEnergyStep(int64_t step) const
+ {
+ int stepIntervalUpdateFreeEnergy = numSamplesUpdateFreeEnergy_ * numStepsSampleCoord_;
+ return (step > 0 && step % stepIntervalUpdateFreeEnergy == 0);
+ }
+
+ /*! \brief
+ * Returns whether we should update the target distribution.
+ *
+ * \param[in] step The MD step number.
+ */
+ inline bool isUpdateTargetStep(int64_t step) const { return step % numStepsUpdateTarget_ == 0; }
+
+ /*! \brief
+ * Returns if to do checks for covering in the initial stage.
+ *
+ * To avoid overhead due to expensive checks, we do not check
+ * at every free energy update. However, if checks are
+ * performed too rarely the detection of coverings will be
+ * delayed, ultimately affecting free energy convergence.
+ *
+ * \param[in] step Time step.
+ * \returns true at steps where checks should be performed.
+ * \note Only returns true at free energy update steps.
+ */
+ bool isCheckCoveringStep(int64_t step) const
+ {
+ return step > 0 && (step % numStepsCheckCovering_ == 0);
+ }
+
+ /*! \brief
+ * Returns if to perform checks for anomalies in the histogram.
+ *
+ * To avoid overhead due to expensive checks, we do not check
+ * at every free energy update. These checks are only used for
+ * warning the user and can be made as infrequently as
+ * neccessary without affecting the algorithm itself.
+ *
+ * \param[in] step Time step.
+ * \returns true at steps where checks should be performed.
+ * \note Only returns true at free energy update steps.
+ * \todo Currently this function just calls isCheckCoveringStep but the checks could be done less frequently.
+ */
+ bool isCheckHistogramForAnomaliesStep(int64_t step) const { return isCheckCoveringStep(step); }
+
+ /*! \brief Constructor.
+ *
+ * The local Boltzmann target distibution is defined by
+ * 1) Adding the sampled weights instead of the target weights to the reference weight histogram.
+ * 2) Scaling the weights of these samples by the beta scaling factor.
+ * 3) Setting the target distribution equal the reference weight histogram.
+ * This requires the following special update settings:
+ * localWeightScaling = targetParam
+ * idealWeighthistUpdate = false
+ * Note: these variables could in principle be set to something else also for other target distribution types.
+ * However, localWeightScaling < 1 is in general expected to give lower efficiency and, except for local Boltzmann,
+ * idealWeightHistUpdate = false gives (in my experience) unstable, non-converging results.
+ *
+ * \param[in] awhParams AWH parameters.
+ * \param[in] awhBiasParams Bias parameters.
+ * \param[in] dimParams Bias dimension parameters.
+ * \param[in] beta 1/(k_B T) in units of 1/(kJ/mol), should be > 0.
+ * \param[in] mdTimeStep The MD time step.
+ * \param[in] numSharingSimulations The number of simulations to share the bias across.
+ * \param[in] gridAxis The grid axes.
+ * \param[in] disableUpdateSkips If to disable update skips, useful for testing.
+ * \param[in] biasIndex Index of the bias.
+ */
+ BiasParams(const AwhParams& awhParams,
+ const AwhBiasParams& awhBiasParams,
+ const std::vector<DimParams>& dimParams,
+ double beta,
+ double mdTimeStep,
+ DisableUpdateSkips disableUpdateSkips,
+ int numSharingSimulations,
+ const std::vector<GridAxis>& gridAxis,
+ int biasIndex);
+
+ /* Data members */
+ const double invBeta; /**< 1/beta = kT in kJ/mol */
+private:
+ const int64_t numStepsSampleCoord_; /**< Number of steps per coordinate value sample. */
+public:
+ const int numSamplesUpdateFreeEnergy_; /**< Number of samples per free energy update. */
+private:
+ const int64_t numStepsUpdateTarget_; /**< Number of steps per updating the target distribution. */
+ const int64_t numStepsCheckCovering_; /**< Number of steps per checking for covering. */
+public:
+ const int eTarget; /**< Type of target distribution. */
+ const double freeEnergyCutoffInKT; /**< Free energy cut-off in kT for cut-off target distribution. */
+ const double temperatureScaleFactor; /**< Temperature scaling factor for temperature scaled targed distributions. */
+ const bool idealWeighthistUpdate; /**< Update reference weighthistogram using the target distribution? Otherwise use the realized distribution. */
+ const int numSharedUpdate; /**< The number of (multi-)simulations sharing the bias update */
+ const double updateWeight; /**< The probability weight accumulated for each update. */
+ const double localWeightScaling; /**< Scaling factor applied to a sample before adding it to the reference weight histogram (= 1, usually). */
+ const double initialErrorInKT; /**< Estimated initial free energy error in kT. */
+ const double initialHistogramSize; /**< Initial reference weight histogram size. */
+private:
+ awh_ivec coverRadius_; /**< The radius (in points) that needs to be sampled around a point before it is considered covered. */
+public:
+ const bool convolveForce; /**< True if we convolve the force, false means use MC between umbrellas. */
+ const int biasIndex; /**< Index of the bias, used as a second random seed and for priting. */
+private:
+ const bool disableUpdateSkips_; /**< If true, we disallow update skips, even when the method supports it. */
};
-} // namespace gmx
+} // namespace gmx
#endif /* GMX_AWH_BIASPARAMS_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff