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/strconvert.h"
  55
  56 #include "densityfittingamplitudelookup.h"
  57
  58 namespace gmx
  59 {
  60
  61 namespace
  62 {
  63
  64 /*! \brief Helper to declare mdp transform rules.
  65  *
  66  * Enforces uniform mdp options that are always prepended with the correct
  67  * string for the densityfitting mdp options.
  68  *
  69  * \tparam ToType type to be transformed to
  70  * \tparam TransformWithFunctionType type of transformation function to be used
  71  *
  72  * \param[in] rules KVT transformation rules
  73  * \param[in] transformationFunction the function to transform the flat kvt tree
  74  * \param[in] optionTag string tag that describes the mdp option, appended to the
  75  *                      default string for the density guided simulation
  76  */
  77 template <class ToType, class TransformWithFunctionType>
  78 void densityfittingMdpTransformFromString(IKeyValueTreeTransformRules * rules,
  79                                           TransformWithFunctionType     transformationFunction,
  80                                           const std::string            &optionTag)
  81 {
  82     rules->addRule()
  83         .from<std::string>("/" + DensityFittingModuleInfo::name_ + "-" + optionTag)
  84         .to<ToType>("/" + DensityFittingModuleInfo::name_ +"/" + optionTag)
  85         .transformWith(transformationFunction);
  86 }
  87 /*! \brief Helper to declare mdp output.
  88  *
  89  * Enforces uniform mdp options output strings that are always prepended with the
  90  * correct string for the densityfitting mdp options and are consistent with the
  91  * options name and transformation type.
  92  *
  93  * \tparam OptionType the type of the mdp option
  94  * \param[in] builder the KVT builder to generate the output
  95  * \param[in] option the mdp option
  96  * \param[in] optionTag string tag that describes the mdp option, appended to the
  97  *                      default string for the density guided simulation
  98  */
  99 template <class OptionType>
 100 void addDensityFittingMdpOutputValue(KeyValueTreeObjectBuilder *builder,
 101                                      const OptionType          &option,
 102                                      const std::string         &optionTag)
 103 {
 104     builder->addValue<OptionType>(DensityFittingModuleInfo::name_ + "-" + optionTag,
 105                                   option);
 106 }
 107
 108 /*! \brief Helper to declare mdp output comments.
 109  *
 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.
 113  *
 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
 117  */
 118 void addDensityFittingMdpOutputValueComment(KeyValueTreeObjectBuilder *builder,
 119                                             const std::string         &comment,
 120                                             const std::string         &optionTag)
 121 {
 122     builder->addValue<std::string>("comment-" + DensityFittingModuleInfo::name_ + "-" + optionTag, comment);
 123 }
 124
 125 }   // namespace
 126
 127 void DensityFittingOptions::initMdpTransform(IKeyValueTreeTransformRules * rules)
 128 {
 129     const auto &stringIdentityTransform = [](std::string s){
 130             return s;
 131         };
 132     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
 133     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
 134     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_similarityMeasureTag_);
 135     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
 136     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
 137     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_gaussianTransformSpreadingWidthTag_);
 138     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 139     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_referenceDensityFileNameTag_);
 140     densityfittingMdpTransformFromString<std::int64_t>(rules, &fromStdString<std::int64_t>, c_everyNStepsTag_);
 141     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
 142 }
 143
 144 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder *builder) const
 145 {
 146
 147     addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
 148     addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
 149
 150     addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
 151     if (parameters_.active_)
 152     {
 153         addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
 154
 155         addDensityFittingMdpOutputValueComment(builder, "; Similarity measure between densities: inner-product, relative-entropy, or cross-correlation", c_similarityMeasureTag_);
 156         addDensityFittingMdpOutputValue<std::string>(builder,
 157                                                      c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
 158                                                      c_similarityMeasureTag_);
 159
 160         addDensityFittingMdpOutputValueComment(builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge", c_amplitudeMethodTag_);
 161         addDensityFittingMdpOutputValue<std::string>(builder,
 162                                                      c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
 163                                                      c_amplitudeMethodTag_);
 164
 165         addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
 166         addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_, c_gaussianTransformSpreadingWidthTag_);
 167         addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 168         addDensityFittingMdpOutputValueComment(builder, "; Reference density file location as absolute path or relative to the gmx mdrun calling location", c_referenceDensityFileNameTag_);
 169         addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
 170         addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
 171         addDensityFittingMdpOutputValueComment(builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
 172         addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
 173     }
 174 }
 175
 176 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections *options)
 177 {
 178     auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
 179
 180     section.addOption(BooleanOption(c_activeTag_.c_str()).store(&parameters_.active_));
 181     section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
 182
 183     section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
 184                           .enumValue(c_densitySimilarityMeasureMethodNames.m_elements)
 185                           .store(&parameters_.similarityMeasureMethod_));
 186
 187     section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
 188                           .enumValue(c_densityFittingAmplitudeMethodNames.m_elements)
 189                           .store(&parameters_.amplitudeLookupMethod_));
 190
 191     section.addOption(RealOption(c_forceConstantTag_.c_str()).store(&parameters_.forceConstant_));
 192     section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str()).store(&parameters_.gaussianTransformSpreadingWidth_));
 193     section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str()).store(&parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
 194     section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
 195     section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(&parameters_.calculationIntervalInSteps_));
 196     section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(&parameters_.normalizeDensities_));
 197 }
 198
 199 bool DensityFittingOptions::active() const
 200 {
 201     return parameters_.active_;
 202 }
 203
 204 const DensityFittingParameters &DensityFittingOptions::buildParameters()
 205 {
 206     // the options modules does not know unsigned integers so any input of this
 207     // kind is rectified here
 208     if (parameters_.calculationIntervalInSteps_ < 1)
 209     {
 210         parameters_.calculationIntervalInSteps_ = 1;
 211     }
 212     return parameters_;
 213 }
 214
 215 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames &indexGroupsAndNames)
 216 {
 217     if (!parameters_.active_)
 218     {
 219         return;
 220     }
 221     parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
 222 }
 223
 224 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
 225 {
 226     auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_ + "-" + c_groupTag_);
 227     for (const auto &indexValue : parameters_.indices_)
 228     {
 229         groupIndexAdder.addValue(indexValue);
 230     }
 231 }
 232
 233 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject &tree)
 234 {
 235     if (!parameters_.active_)
 236     {
 237         return;
 238     }
 239
 240     if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
 241     {
 242         GMX_THROW(InconsistentInputError(
 243                           "Cannot find atom index vector required for density guided simulation."));
 244     }
 245     auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
 246     parameters_.indices_.resize(kvtIndexArray.size());
 247     std::transform(std::begin(kvtIndexArray), std::end(kvtIndexArray), std::begin(parameters_.indices_),
 248                    [](const KeyValueTreeValue &val) { return val.cast<std::int64_t>(); });
 249 }
 250
 251 const std::string &DensityFittingOptions::referenceDensityFileName() const
 252 {
 253     return referenceDensityFileName_;
 254 }
 255 } // namespace gmx