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, 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) { 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>,
 143                                                        c_everyNStepsTag_);
 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_);
 148 }
 149
 150 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const
 151 {
 152
 153     addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
 154     addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
 155
 156     addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
 157     if (parameters_.active_)
 158     {
 159         addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
 160
 161         addDensityFittingMdpOutputValueComment(
 162                 builder,
 163                 "; Similarity measure between densities: inner-product, relative-entropy, or "
 164                 "cross-correlation",
 165                 c_similarityMeasureTag_);
 166         addDensityFittingMdpOutputValue<std::string>(
 167                 builder, c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
 168                 c_similarityMeasureTag_);
 169
 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_);
 176
 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_);
 200     }
 201 }
 202
 203 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections* options)
 204 {
 205     auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
 206
 207     section.addOption(BooleanOption(c_activeTag_.c_str()).store(&parameters_.active_));
 208     section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
 209
 210     section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
 211                               .enumValue(c_densitySimilarityMeasureMethodNames.m_elements)
 212                               .store(&parameters_.similarityMeasureMethod_));
 213
 214     section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
 215                               .enumValue(c_densityFittingAmplitudeMethodNames.m_elements)
 216                               .store(&parameters_.amplitudeLookupMethod_));
 217
 218     section.addOption(RealOption(c_forceConstantTag_.c_str()).store(&parameters_.forceConstant_));
 219     section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str())
 220                               .store(&parameters_.gaussianTransformSpreadingWidth_));
 221     section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str())
 222                               .store(&parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
 223     section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
 224     section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(&parameters_.calculationIntervalInSteps_));
 225     section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(&parameters_.normalizeDensities_));
 226     section.addOption(
 227             BooleanOption(c_adaptiveForceScalingTag_.c_str()).store(&parameters_.adaptiveForceScaling_));
 228     section.addOption(RealOption(c_adaptiveForceScalingTimeConstantTag_.c_str())
 229                               .store(&parameters_.adaptiveForceScalingTimeConstant_));
 230 }
 231
 232 bool DensityFittingOptions::active() const
 233 {
 234     return parameters_.active_;
 235 }
 236
 237 const DensityFittingParameters& DensityFittingOptions::buildParameters()
 238 {
 239     // the options modules does not know unsigned integers so any input of this
 240     // kind is rectified here
 241     if (parameters_.calculationIntervalInSteps_ < 1)
 242     {
 243         parameters_.calculationIntervalInSteps_ = 1;
 244     }
 245     return parameters_;
 246 }
 247
 248 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames)
 249 {
 250     if (!parameters_.active_)
 251     {
 252         return;
 253     }
 254     parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
 255 }
 256
 257 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
 258 {
 259     auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_
 260                                                                      + "-" + c_groupTag_);
 261     for (const auto& indexValue : parameters_.indices_)
 262     {
 263         groupIndexAdder.addValue(indexValue);
 264     }
 265 }
 266
 267 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tree)
 268 {
 269     if (!parameters_.active_)
 270     {
 271         return;
 272     }
 273
 274     if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
 275     {
 276         GMX_THROW(InconsistentInputError(
 277                 "Cannot find atom index vector required for density guided simulation."));
 278     }
 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>(); });
 283 }
 284
 285 void DensityFittingOptions::checkEnergyCaluclationFrequency(
 286         EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const
 287 {
 288     if (energyCalculationFrequencyErrors->energyCalculationIntervalInSteps() % parameters_.calculationIntervalInSteps_
 289         != 0)
 290     {
 291         energyCalculationFrequencyErrors->addError(
 292                 "nstcalcenergy ("
 293                 + toString(energyCalculationFrequencyErrors->energyCalculationIntervalInSteps())
 294                 + ") is not a multiple of " + DensityFittingModuleInfo::name_ + "-" + c_everyNStepsTag_
 295                 + " (" + toString(parameters_.calculationIntervalInSteps_) + ") .");
 296     }
 297 }
 298
 299 const std::string& DensityFittingOptions::referenceDensityFileName() const
 300 {
 301     return referenceDensityFileName_;
 302 }
 303 } // namespace gmx