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35 /*! \internal \file
36 * \brief
37 * Implements force provider for density fitting
38 *
39 * \author Christian Blau <blau@kth.se>
40 * \ingroup module_applied_forces
41 */
42 #include "gmxpre.h"
43
44 #include "densityfittingoptions.h"
45
46 #include "gromacs/applied_forces/densityfitting/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/enumerationhelpers.h"
52 #include "gromacs/utility/exceptions.h"
53 #include "gromacs/utility/keyvaluetreebuilder.h"
54 #include "gromacs/utility/keyvaluetreetransform.h"
55 #include "gromacs/utility/mdmodulenotification.h"
56 #include "gromacs/utility/strconvert.h"
57
58 #include "densityfittingamplitudelookup.h"
59
60 namespace gmx
61 {
62
63 namespace
64 {
65
66 /*! \brief Helper to declare mdp transform rules.
67 *
68 * Enforces uniform mdp options that are always prepended with the correct
69 * string for the densityfitting mdp options.
70 *
71 * \tparam ToType type to be transformed to
72 * \tparam TransformWithFunctionType type of transformation function to be used
73 *
74 * \param[in] rules KVT transformation rules
75 * \param[in] transformationFunction the function to transform the flat kvt tree
76 * \param[in] optionTag string tag that describes the mdp option, appended to the
77 * default string for the density guided simulation
78 */
79 template<class ToType, class TransformWithFunctionType>
densityfittingMdpTransformFromString(IKeyValueTreeTransformRules * rules,TransformWithFunctionType transformationFunction,const std::string & optionTag)80 void densityfittingMdpTransformFromString(IKeyValueTreeTransformRules* rules,
81 TransformWithFunctionType transformationFunction,
82 const std::string& optionTag)
83 {
84 rules->addRule()
85 .from<std::string>("/" + DensityFittingModuleInfo::name_ + "-" + optionTag)
86 .to<ToType>("/" + DensityFittingModuleInfo::name_ + "/" + optionTag)
87 .transformWith(transformationFunction);
88 }
89 /*! \brief Helper to declare mdp output.
90 *
91 * Enforces uniform mdp options output strings that are always prepended with the
92 * correct string for the densityfitting mdp options and are consistent with the
93 * options name and transformation type.
94 *
95 * \tparam OptionType the type of the mdp option
96 * \param[in] builder the KVT builder to generate the output
97 * \param[in] option the mdp option
98 * \param[in] optionTag string tag that describes the mdp option, appended to the
99 * default string for the density guided simulation
100 */
101 template<class OptionType>
addDensityFittingMdpOutputValue(KeyValueTreeObjectBuilder * builder,const OptionType & option,const std::string & optionTag)102 void addDensityFittingMdpOutputValue(KeyValueTreeObjectBuilder* builder,
103 const OptionType& option,
104 const std::string& optionTag)
105 {
106 builder->addValue<OptionType>(DensityFittingModuleInfo::name_ + "-" + optionTag, option);
107 }
108
109 /*! \brief Helper to declare mdp output comments.
110 *
111 * Enforces uniform mdp options comment output strings that are always prepended
112 * with the correct string for the densityfitting mdp options and are consistent
113 * with the options name and transformation type.
114 *
115 * \param[in] builder the KVT builder to generate the output
116 * \param[in] comment on the mdp option
117 * \param[in] optionTag string tag that describes the mdp option
118 */
addDensityFittingMdpOutputValueComment(KeyValueTreeObjectBuilder * builder,const std::string & comment,const std::string & optionTag)119 void addDensityFittingMdpOutputValueComment(KeyValueTreeObjectBuilder* builder,
120 const std::string& comment,
121 const std::string& optionTag)
122 {
123 builder->addValue<std::string>("comment-" + DensityFittingModuleInfo::name_ + "-" + optionTag, comment);
124 }
125
126 } // namespace
127
initMdpTransform(IKeyValueTreeTransformRules * rules)128 void DensityFittingOptions::initMdpTransform(IKeyValueTreeTransformRules* rules)
129 {
130 const auto& stringIdentityTransform = [](std::string s) { return s; };
131 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
132 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
133 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
134 c_similarityMeasureTag_);
135 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
136 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
137 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
138 c_gaussianTransformSpreadingWidthTag_);
139 densityfittingMdpTransformFromString<real>(
140 rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
141 densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
142 c_referenceDensityFileNameTag_);
143 densityfittingMdpTransformFromString<std::int64_t>(rules, &fromStdString<std::int64_t>,
144 c_everyNStepsTag_);
145 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
146 densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_adaptiveForceScalingTag_);
147 densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
148 c_adaptiveForceScalingTimeConstantTag_);
149 const auto& stringRVecToStringRVecWithCheck = [](const std::string& str) {
150 return stringIdentityTransformWithArrayCheck<real, 3>(
151 str, "Reading three real values as vector while parsing the .mdp input failed in "
152 + DensityFittingModuleInfo::name_ + ".");
153 };
154 densityfittingMdpTransformFromString<std::string>(rules, stringRVecToStringRVecWithCheck,
155 c_translationTag_);
156
157 const auto& stringMatrixToStringMatrixWithCheck = [](const std::string& str) {
158 return stringIdentityTransformWithArrayCheck<real, 9>(
159 str, "Reading nine real values as vector while parsing the .mdp input failed in "
160 + DensityFittingModuleInfo::name_ + ".");
161 };
162 densityfittingMdpTransformFromString<std::string>(rules, stringMatrixToStringMatrixWithCheck,
163 c_transformationMatrixTag_);
164 }
165
166 //! Name the methods that may be used to evaluate similarity between densities
167 static const EnumerationArray<DensitySimilarityMeasureMethod, const char*> c_densitySimilarityMeasureMethodNames = {
168 { "inner-product", "relative-entropy", "cross-correlation" }
169 };
170 //! The names of the methods to determine the amplitude of the atoms to be spread on a grid
171 static const EnumerationArray<DensityFittingAmplitudeMethod, const char*> c_densityFittingAmplitudeMethodNames = {
172 { "unity", "mass", "charge" }
173 };
174
buildMdpOutput(KeyValueTreeObjectBuilder * builder) const175 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const
176 {
177
178 addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
179 addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
180
181 addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
182 if (parameters_.active_)
183 {
184 addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
185
186 addDensityFittingMdpOutputValueComment(
187 builder,
188 "; Similarity measure between densities: inner-product, relative-entropy, or "
189 "cross-correlation",
190 c_similarityMeasureTag_);
191 addDensityFittingMdpOutputValue<std::string>(
192 builder, c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
193 c_similarityMeasureTag_);
194
195 addDensityFittingMdpOutputValueComment(
196 builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge",
197 c_amplitudeMethodTag_);
198 addDensityFittingMdpOutputValue<std::string>(
199 builder, c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
200 c_amplitudeMethodTag_);
201
202 addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
203 addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_,
204 c_gaussianTransformSpreadingWidthTag_);
205 addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
206 c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
207 addDensityFittingMdpOutputValueComment(builder,
208 "; Reference density file location as absolute path "
209 "or relative to the gmx mdrun calling location",
210 c_referenceDensityFileNameTag_);
211 addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
212 addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
213 addDensityFittingMdpOutputValueComment(
214 builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
215 addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
216 addDensityFittingMdpOutputValueComment(builder, "; Apply adaptive force scaling",
217 c_adaptiveForceScalingTag_);
218 addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScaling_,
219 c_adaptiveForceScalingTag_);
220 addDensityFittingMdpOutputValueComment(builder,
221 "; Time constant for adaptive force scaling in ps",
222 c_adaptiveForceScalingTimeConstantTag_);
223 addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScalingTimeConstant_,
224 c_adaptiveForceScalingTimeConstantTag_);
225 }
226 }
227
initMdpOptions(IOptionsContainerWithSections * options)228 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections* options)
229 {
230 auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
231
232 section.addOption(BooleanOption(c_activeTag_.c_str()).store(¶meters_.active_));
233 section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
234
235 section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
236 .enumValue(c_densitySimilarityMeasureMethodNames)
237 .store(¶meters_.similarityMeasureMethod_));
238
239 section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
240 .enumValue(c_densityFittingAmplitudeMethodNames)
241 .store(¶meters_.amplitudeLookupMethod_));
242
243 section.addOption(RealOption(c_forceConstantTag_.c_str()).store(¶meters_.forceConstant_));
244 section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str())
245 .store(¶meters_.gaussianTransformSpreadingWidth_));
246 section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str())
247 .store(¶meters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
248 section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
249 section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(¶meters_.calculationIntervalInSteps_));
250 section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(¶meters_.normalizeDensities_));
251 section.addOption(
252 BooleanOption(c_adaptiveForceScalingTag_.c_str()).store(¶meters_.adaptiveForceScaling_));
253 section.addOption(RealOption(c_adaptiveForceScalingTimeConstantTag_.c_str())
254 .store(¶meters_.adaptiveForceScalingTimeConstant_));
255 section.addOption(StringOption(c_translationTag_.c_str()).store(¶meters_.translationString_));
256 section.addOption(
257 StringOption(c_transformationMatrixTag_.c_str()).store(¶meters_.transformationMatrixString_));
258 }
259
active() const260 bool DensityFittingOptions::active() const
261 {
262 return parameters_.active_;
263 }
264
buildParameters()265 const DensityFittingParameters& DensityFittingOptions::buildParameters()
266 {
267 // the options modules does not know unsigned integers so any input of this
268 // kind is rectified here
269 if (parameters_.calculationIntervalInSteps_ < 1)
270 {
271 parameters_.calculationIntervalInSteps_ = 1;
272 }
273 return parameters_;
274 }
275
setFitGroupIndices(const IndexGroupsAndNames & indexGroupsAndNames)276 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames)
277 {
278 if (!parameters_.active_)
279 {
280 return;
281 }
282 parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
283 }
284
writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)285 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
286 {
287 auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_
288 + "-" + c_groupTag_);
289 for (const auto& indexValue : parameters_.indices_)
290 {
291 groupIndexAdder.addValue(indexValue);
292 }
293 }
294
readInternalParametersFromKvt(const KeyValueTreeObject & tree)295 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tree)
296 {
297 if (!parameters_.active_)
298 {
299 return;
300 }
301
302 if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
303 {
304 GMX_THROW(InconsistentInputError(
305 "Cannot find atom index vector required for density guided simulation."));
306 }
307 auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
308 parameters_.indices_.resize(kvtIndexArray.size());
309 std::transform(std::begin(kvtIndexArray), std::end(kvtIndexArray), std::begin(parameters_.indices_),
310 [](const KeyValueTreeValue& val) { return val.cast<std::int64_t>(); });
311 }
312
checkEnergyCaluclationFrequency(EnergyCalculationFrequencyErrors * energyCalculationFrequencyErrors) const313 void DensityFittingOptions::checkEnergyCaluclationFrequency(
314 EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const
315 {
316 if (energyCalculationFrequencyErrors->energyCalculationIntervalInSteps() % parameters_.calculationIntervalInSteps_
317 != 0)
318 {
319 energyCalculationFrequencyErrors->addError(
320 "nstcalcenergy ("
321 + toString(energyCalculationFrequencyErrors->energyCalculationIntervalInSteps())
322 + ") is not a multiple of " + DensityFittingModuleInfo::name_ + "-" + c_everyNStepsTag_
323 + " (" + toString(parameters_.calculationIntervalInSteps_) + ") .");
324 }
325 }
326
referenceDensityFileName() const327 const std::string& DensityFittingOptions::referenceDensityFileName() const
328 {
329 return referenceDensityFileName_;
330 }
331 } // namespace gmx
332