src/gromacs/applied_forces/densityfittingoptions.cpp

   1 /*
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   4  * Copyright (c) 2019, by the GROMACS development team, led by
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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.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"
  56
  57 #include "densityfittingamplitudelookup.h"
  58
  59 namespace gmx
  60 {
  61
  62 namespace
  63 {
  64
  65 /*! \brief Helper to declare mdp transform rules.
  66  *
  67  * Enforces uniform mdp options that are always prepended with the correct
  68  * string for the densityfitting mdp options.
  69  *
  70  * \tparam ToType type to be transformed to
  71  * \tparam TransformWithFunctionType type of transformation function to be used
  72  *
  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
  77  */
  78 template <class ToType, class TransformWithFunctionType>
  79 void densityfittingMdpTransformFromString(IKeyValueTreeTransformRules * rules,
  80                                           TransformWithFunctionType     transformationFunction,
  81                                           const std::string            &optionTag)
  82 {
  83     rules->addRule()
  84         .from<std::string>("/" + DensityFittingModuleInfo::name_ + "-" + optionTag)
  85         .to<ToType>("/" + DensityFittingModuleInfo::name_ +"/" + optionTag)
  86         .transformWith(transformationFunction);
  87 }
  88 /*! \brief Helper to declare mdp output.
  89  *
  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.
  93  *
  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
  99  */
 100 template <class OptionType>
 101 void addDensityFittingMdpOutputValue(KeyValueTreeObjectBuilder *builder,
 102                                      const OptionType          &option,
 103                                      const std::string         &optionTag)
 104 {
 105     builder->addValue<OptionType>(DensityFittingModuleInfo::name_ + "-" + optionTag,
 106                                   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  */
 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
 128 void DensityFittingOptions::initMdpTransform(IKeyValueTreeTransformRules * rules)
 129 {
 130     const auto &stringIdentityTransform = [](std::string s){
 131             return s;
 132         };
 133     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
 134     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
 135     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_similarityMeasureTag_);
 136     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
 137     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
 138     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_gaussianTransformSpreadingWidthTag_);
 139     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 140     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_referenceDensityFileNameTag_);
 141     densityfittingMdpTransformFromString<std::int64_t>(rules, &fromStdString<std::int64_t>, c_everyNStepsTag_);
 142     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
 143 }
 144
 145 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder *builder) const
 146 {
 147
 148     addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
 149     addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
 150
 151     addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
 152     if (parameters_.active_)
 153     {
 154         addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
 155
 156         addDensityFittingMdpOutputValueComment(builder, "; Similarity measure between densities: inner-product, relative-entropy, or cross-correlation", c_similarityMeasureTag_);
 157         addDensityFittingMdpOutputValue<std::string>(builder,
 158                                                      c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
 159                                                      c_similarityMeasureTag_);
 160
 161         addDensityFittingMdpOutputValueComment(builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge", c_amplitudeMethodTag_);
 162         addDensityFittingMdpOutputValue<std::string>(builder,
 163                                                      c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
 164                                                      c_amplitudeMethodTag_);
 165
 166         addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
 167         addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_, c_gaussianTransformSpreadingWidthTag_);
 168         addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 169         addDensityFittingMdpOutputValueComment(builder, "; Reference density file location as absolute path or relative to the gmx mdrun calling location", c_referenceDensityFileNameTag_);
 170         addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
 171         addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
 172         addDensityFittingMdpOutputValueComment(builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
 173         addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
 174     }
 175 }
 176
 177 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections *options)
 178 {
 179     auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
 180
 181     section.addOption(BooleanOption(c_activeTag_.c_str()).store(&parameters_.active_));
 182     section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
 183
 184     section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
 185                           .enumValue(c_densitySimilarityMeasureMethodNames.m_elements)
 186                           .store(&parameters_.similarityMeasureMethod_));
 187
 188     section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
 189                           .enumValue(c_densityFittingAmplitudeMethodNames.m_elements)
 190                           .store(&parameters_.amplitudeLookupMethod_));
 191
 192     section.addOption(RealOption(c_forceConstantTag_.c_str()).store(&parameters_.forceConstant_));
 193     section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str()).store(&parameters_.gaussianTransformSpreadingWidth_));
 194     section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str()).store(&parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
 195     section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
 196     section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(&parameters_.calculationIntervalInSteps_));
 197     section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(&parameters_.normalizeDensities_));
 198 }
 199
 200 bool DensityFittingOptions::active() const
 201 {
 202     return parameters_.active_;
 203 }
 204
 205 const DensityFittingParameters &DensityFittingOptions::buildParameters()
 206 {
 207     // the options modules does not know unsigned integers so any input of this
 208     // kind is rectified here
 209     if (parameters_.calculationIntervalInSteps_ < 1)
 210     {
 211         parameters_.calculationIntervalInSteps_ = 1;
 212     }
 213     return parameters_;
 214 }
 215
 216 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames &indexGroupsAndNames)
 217 {
 218     if (!parameters_.active_)
 219     {
 220         return;
 221     }
 222     parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
 223 }
 224
 225 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
 226 {
 227     auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_ + "-" + c_groupTag_);
 228     for (const auto &indexValue : parameters_.indices_)
 229     {
 230         groupIndexAdder.addValue(indexValue);
 231     }
 232 }
 233
 234 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject &tree)
 235 {
 236     if (!parameters_.active_)
 237     {
 238         return;
 239     }
 240
 241     if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
 242     {
 243         GMX_THROW(InconsistentInputError(
 244                           "Cannot find atom index vector required for density guided simulation."));
 245     }
 246     auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
 247     parameters_.indices_.resize(kvtIndexArray.size());
 248     std::transform(std::begin(kvtIndexArray), std::end(kvtIndexArray), std::begin(parameters_.indices_),
 249                    [](const KeyValueTreeValue &val) { return val.cast<std::int64_t>(); });
 250 }
 251
 252 void DensityFittingOptions::checkEnergyCaluclationFrequency(EnergyCalculationFrequencyErrors * energyCalculationFrequencyErrors) const
 253 {
 254     if (energyCalculationFrequencyErrors->energyCalculationIntervalInSteps() % parameters_.calculationIntervalInSteps_ != 0)
 255     {
 256         energyCalculationFrequencyErrors->addError("nstcalcenergy (" +
 257                                                    toString(energyCalculationFrequencyErrors->energyCalculationIntervalInSteps())
 258                                                    + ") is not a multiple of " + DensityFittingModuleInfo::name_ + "-" + c_everyNStepsTag_
 259                                                    + " (" + toString(parameters_.calculationIntervalInSteps_) + ") .");
 260     }
 261 }
 262
 263 const std::string &DensityFittingOptions::referenceDensityFileName() const
 264 {
 265     return referenceDensityFileName_;
 266 }
 267 } // namespace gmx