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37 * Implements force provider for density fitting
39 * \author Christian Blau <blau@kth.se>
40 * \ingroup module_applied_forces
44 #include "densityfittingoptions.h"
46 #include "gromacs/applied_forces/densityfitting.h"
47 #include "gromacs/math/densityfit.h"
48 #include "gromacs/options/basicoptions.h"
49 #include "gromacs/options/optionsection.h"
50 #include "gromacs/selection/indexutil.h"
51 #include "gromacs/utility/exceptions.h"
52 #include "gromacs/utility/keyvaluetreebuilder.h"
53 #include "gromacs/utility/keyvaluetreetransform.h"
54 #include "gromacs/utility/mdmodulenotification.h"
55 #include "gromacs/utility/strconvert.h"
57 #include "densityfittingamplitudelookup.h"
65 /*! \brief Helper to declare mdp transform rules.
67 * Enforces uniform mdp options that are always prepended with the correct
68 * string for the densityfitting mdp options.
70 * \tparam ToType type to be transformed to
71 * \tparam TransformWithFunctionType type of transformation function to be used
73 * \param[in] rules KVT transformation rules
74 * \param[in] transformationFunction the function to transform the flat kvt tree
75 * \param[in] optionTag string tag that describes the mdp option, appended to the
76 * default string for the density guided simulation
78 template<class ToType, class TransformWithFunctionType>
79 void densityfittingMdpTransformFromString(IKeyValueTreeTransformRules* rules,
80 TransformWithFunctionType transformationFunction,
81 const std::string& optionTag)
84 .from<std::string>("/" + DensityFittingModuleInfo::name_ + "-" + optionTag)
85 .to<ToType>("/" + DensityFittingModuleInfo::name_ + "/" + optionTag)
86 .transformWith(transformationFunction);
88 /*! \brief Helper to declare mdp output.
90 * Enforces uniform mdp options output strings that are always prepended with the
91 * correct string for the densityfitting mdp options and are consistent with the
92 * options name and transformation type.
94 * \tparam OptionType the type of the mdp option
95 * \param[in] builder the KVT builder to generate the output
96 * \param[in] option the mdp option
97 * \param[in] optionTag string tag that describes the mdp option, appended to the
98 * default string for the density guided simulation
100 template<class OptionType>
101 void addDensityFittingMdpOutputValue(KeyValueTreeObjectBuilder* builder,
102 const OptionType& option,
103 const std::string& optionTag)
105 builder->addValue<OptionType>(DensityFittingModuleInfo::name_ + "-" + optionTag, option);
108 /*! \brief Helper to declare mdp output comments.
110 * Enforces uniform mdp options comment output strings that are always prepended
111 * with the correct string for the densityfitting mdp options and are consistent
112 * with the options name and transformation type.
114 * \param[in] builder the KVT builder to generate the output
115 * \param[in] comment on the mdp option
116 * \param[in] optionTag string tag that describes the mdp option
118 void addDensityFittingMdpOutputValueComment(KeyValueTreeObjectBuilder* builder,
119 const std::string& comment,
120 const std::string& optionTag)
122 builder->addValue<std::string>("comment-" + DensityFittingModuleInfo::name_ + "-" + optionTag, comment);
127 void DensityFittingOptions::initMdpTransform(IKeyValueTreeTransformRules* rules)
129 const auto& stringIdentityTransform = [](std::string s) { return s; };
130 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
131 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
132 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
133 c_similarityMeasureTag_);
134 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
135 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
136 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
137 c_gaussianTransformSpreadingWidthTag_);
138 densityfittingMdpTransformFromString<real>(
139 rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
140 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
141 c_referenceDensityFileNameTag_);
142 densityfittingMdpTransformFromString<std::int64_t>(rules, &fromStdString<std::int64_t>,
144 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
145 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_adaptiveForceScalingTag_);
146 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
147 c_adaptiveForceScalingTimeConstantTag_);
150 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const
153 addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
154 addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
156 addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
157 if (parameters_.active_)
159 addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
161 addDensityFittingMdpOutputValueComment(
163 "; Similarity measure between densities: inner-product, relative-entropy, or "
165 c_similarityMeasureTag_);
166 addDensityFittingMdpOutputValue<std::string>(
167 builder, c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
168 c_similarityMeasureTag_);
170 addDensityFittingMdpOutputValueComment(
171 builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge",
172 c_amplitudeMethodTag_);
173 addDensityFittingMdpOutputValue<std::string>(
174 builder, c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
175 c_amplitudeMethodTag_);
177 addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
178 addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_,
179 c_gaussianTransformSpreadingWidthTag_);
180 addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
181 c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
182 addDensityFittingMdpOutputValueComment(builder,
183 "; Reference density file location as absolute path "
184 "or relative to the gmx mdrun calling location",
185 c_referenceDensityFileNameTag_);
186 addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
187 addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
188 addDensityFittingMdpOutputValueComment(
189 builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
190 addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
191 addDensityFittingMdpOutputValueComment(builder, "; Apply adaptive force scaling",
192 c_adaptiveForceScalingTag_);
193 addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScaling_,
194 c_adaptiveForceScalingTag_);
195 addDensityFittingMdpOutputValueComment(builder,
196 "; Time constant for adaptive force scaling in ps",
197 c_adaptiveForceScalingTimeConstantTag_);
198 addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScalingTimeConstant_,
199 c_adaptiveForceScalingTimeConstantTag_);
203 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections* options)
205 auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
207 section.addOption(BooleanOption(c_activeTag_.c_str()).store(¶meters_.active_));
208 section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
210 section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
211 .enumValue(c_densitySimilarityMeasureMethodNames.m_elements)
212 .store(¶meters_.similarityMeasureMethod_));
214 section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
215 .enumValue(c_densityFittingAmplitudeMethodNames.m_elements)
216 .store(¶meters_.amplitudeLookupMethod_));
218 section.addOption(RealOption(c_forceConstantTag_.c_str()).store(¶meters_.forceConstant_));
219 section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str())
220 .store(¶meters_.gaussianTransformSpreadingWidth_));
221 section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str())
222 .store(¶meters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
223 section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
224 section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(¶meters_.calculationIntervalInSteps_));
225 section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(¶meters_.normalizeDensities_));
227 BooleanOption(c_adaptiveForceScalingTag_.c_str()).store(¶meters_.adaptiveForceScaling_));
228 section.addOption(RealOption(c_adaptiveForceScalingTimeConstantTag_.c_str())
229 .store(¶meters_.adaptiveForceScalingTimeConstant_));
232 bool DensityFittingOptions::active() const
234 return parameters_.active_;
237 const DensityFittingParameters& DensityFittingOptions::buildParameters()
239 // the options modules does not know unsigned integers so any input of this
240 // kind is rectified here
241 if (parameters_.calculationIntervalInSteps_ < 1)
243 parameters_.calculationIntervalInSteps_ = 1;
248 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames)
250 if (!parameters_.active_)
254 parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
257 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
259 auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_
260 + "-" + c_groupTag_);
261 for (const auto& indexValue : parameters_.indices_)
263 groupIndexAdder.addValue(indexValue);
267 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tree)
269 if (!parameters_.active_)
274 if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
276 GMX_THROW(InconsistentInputError(
277 "Cannot find atom index vector required for density guided simulation."));
279 auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
280 parameters_.indices_.resize(kvtIndexArray.size());
281 std::transform(std::begin(kvtIndexArray), std::end(kvtIndexArray), std::begin(parameters_.indices_),
282 [](const KeyValueTreeValue& val) { return val.cast<std::int64_t>(); });
285 void DensityFittingOptions::checkEnergyCaluclationFrequency(
286 EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const
288 if (energyCalculationFrequencyErrors->energyCalculationIntervalInSteps() % parameters_.calculationIntervalInSteps_
291 energyCalculationFrequencyErrors->addError(
293 + toString(energyCalculationFrequencyErrors->energyCalculationIntervalInSteps())
294 + ") is not a multiple of " + DensityFittingModuleInfo::name_ + "-" + c_everyNStepsTag_
295 + " (" + toString(parameters_.calculationIntervalInSteps_) + ") .");
299 const std::string& DensityFittingOptions::referenceDensityFileName() const
301 return referenceDensityFileName_;