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39 * Declares the BiasParams class.
41 * This class holds the parameters for the bias. Most are direct copies
42 * of the input that the user provided. Some are a combination of user
43 * input and properties of the simulated system.
45 * \author Viveca Lindahl
46 * \author Berk Hess <hess@kth.se>
50 #ifndef GMX_AWH_BIASPARAMS_H
51 #define GMX_AWH_BIASPARAMS_H
55 #include "gromacs/math/vectypes.h"
56 #include "gromacs/utility/basedefinitions.h"
58 #include "dimparams.h"
68 /*! \internal \brief Constant parameters for the bias.
73 /*! \brief Switch to turn off update skips, useful for testing.
75 enum class DisableUpdateSkips
77 no, /**< Allow update skips (when supported by the method) */
78 yes /**< Disable update skips */
82 * Check if the parameters permit skipping updates.
84 * Generally, we can skip updates of points that are non-local
85 * at the time of the update if we for later times, when the points
86 * with skipped updates have become local, know exactly how to apply
87 * the previous updates. The free energy updates only depend
88 * on local sampling, but the histogram rescaling factors
89 * generally depend on the histogram size (all samples).
90 * If the histogram size is kept constant or the scaling factors
91 * are trivial, this is not a problem. However, if the histogram growth
92 * is scaled down by some factor the size at the time of the update
93 * needs to be known. It would be fairly simple to, for a deterministically
94 * growing histogram, backtrack and calculate this value, but currently
95 * we just disallow this case. This is not a restriction because it
96 * only affects the local Boltzmann target type for which every update
97 * is currently anyway global because the target is always updated globally.
99 * \returns true when we can skip updates.
101 inline bool skipUpdates() const { return (!disableUpdateSkips_ && localWeightScaling == 1); }
104 * Returns the radius that needs to be sampled around a point before it is considered covered.
106 inline const awh_ivec& coverRadius() const { return coverRadius_; }
109 * Returns whether we should sample the coordinate.
111 * \param[in] step The MD step number.
113 inline bool isSampleCoordStep(int64_t step) const
115 return (step > 0 && step % numStepsSampleCoord_ == 0);
119 * Returns whether we should update the free energy.
121 * \param[in] step The MD step number.
123 inline bool isUpdateFreeEnergyStep(int64_t step) const
125 int stepIntervalUpdateFreeEnergy = numSamplesUpdateFreeEnergy_ * numStepsSampleCoord_;
126 return (step > 0 && step % stepIntervalUpdateFreeEnergy == 0);
130 * Returns whether we should update the target distribution.
132 * \param[in] step The MD step number.
134 inline bool isUpdateTargetStep(int64_t step) const { return step % numStepsUpdateTarget_ == 0; }
137 * Returns if to do checks for covering in the initial stage.
139 * To avoid overhead due to expensive checks, we do not check
140 * at every free energy update. However, if checks are
141 * performed too rarely the detection of coverings will be
142 * delayed, ultimately affecting free energy convergence.
144 * \param[in] step Time step.
145 * \returns true at steps where checks should be performed.
146 * \note Only returns true at free energy update steps.
148 bool isCheckCoveringStep(int64_t step) const
150 return step > 0 && (step % numStepsCheckCovering_ == 0);
154 * Returns if to perform checks for anomalies in the histogram.
156 * To avoid overhead due to expensive checks, we do not check
157 * at every free energy update. These checks are only used for
158 * warning the user and can be made as infrequently as
159 * neccessary without affecting the algorithm itself.
161 * \param[in] step Time step.
162 * \returns true at steps where checks should be performed.
163 * \note Only returns true at free energy update steps.
164 * \todo Currently this function just calls isCheckCoveringStep but the checks could be done less frequently.
166 bool isCheckHistogramForAnomaliesStep(int64_t step) const { return isCheckCoveringStep(step); }
168 /*! \brief Constructor.
170 * The local Boltzmann target distibution is defined by
171 * 1) Adding the sampled weights instead of the target weights to the reference weight histogram.
172 * 2) Scaling the weights of these samples by the beta scaling factor.
173 * 3) Setting the target distribution equal the reference weight histogram.
174 * This requires the following special update settings:
175 * localWeightScaling = targetParam
176 * idealWeighthistUpdate = false
177 * Note: these variables could in principle be set to something else also for other target distribution types.
178 * However, localWeightScaling < 1 is in general expected to give lower efficiency and, except for local Boltzmann,
179 * idealWeightHistUpdate = false gives (in my experience) unstable, non-converging results.
181 * \param[in] awhParams AWH parameters.
182 * \param[in] awhBiasParams Bias parameters.
183 * \param[in] dimParams Bias dimension parameters.
184 * \param[in] beta 1/(k_B T) in units of 1/(kJ/mol), should be > 0.
185 * \param[in] mdTimeStep The MD time step.
186 * \param[in] numSharingSimulations The number of simulations to share the bias across.
187 * \param[in] gridAxis The grid axes.
188 * \param[in] disableUpdateSkips If to disable update skips, useful for testing.
189 * \param[in] biasIndex Index of the bias.
191 BiasParams(const AwhParams& awhParams,
192 const AwhBiasParams& awhBiasParams,
193 const std::vector<DimParams>& dimParams,
196 DisableUpdateSkips disableUpdateSkips,
197 int numSharingSimulations,
198 const std::vector<GridAxis>& gridAxis,
202 const double invBeta; /**< 1/beta = kT in kJ/mol */
204 const int64_t numStepsSampleCoord_; /**< Number of steps per coordinate value sample. */
206 const int numSamplesUpdateFreeEnergy_; /**< Number of samples per free energy update. */
208 const int64_t numStepsUpdateTarget_; /**< Number of steps per updating the target distribution. */
209 const int64_t numStepsCheckCovering_; /**< Number of steps per checking for covering. */
211 const int eTarget; /**< Type of target distribution. */
212 const double freeEnergyCutoffInKT; /**< Free energy cut-off in kT for cut-off target distribution. */
213 const double temperatureScaleFactor; /**< Temperature scaling factor for temperature scaled targed distributions. */
214 const bool idealWeighthistUpdate; /**< Update reference weighthistogram using the target distribution? Otherwise use the realized distribution. */
215 const int numSharedUpdate; /**< The number of (multi-)simulations sharing the bias update */
216 const double updateWeight; /**< The probability weight accumulated for each update. */
217 const double localWeightScaling; /**< Scaling factor applied to a sample before adding it to the reference weight histogram (= 1, usually). */
218 const double initialErrorInKT; /**< Estimated initial free energy error in kT. */
219 const double initialHistogramSize; /**< Initial reference weight histogram size. */
221 awh_ivec coverRadius_; /**< The radius (in points) that needs to be sampled around a point before it is considered covered. */
223 const bool convolveForce; /**< True if we convolve the force, false means use MC between umbrellas. */
224 const int biasIndex; /**< Index of the bias, used as a second random seed and for priting. */
226 const bool disableUpdateSkips_; /**< If true, we disallow update skips, even when the method supports it. */
231 #endif /* GMX_AWH_BIASPARAMS_H */