src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp

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   4  * Copyright (c) 2019,2020, 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/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>
  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>
 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  */
 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) { return s; };
 131     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
 132     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
 133     densityfittingMdpTransformFromString<std::string>(
 134             rules, stringIdentityTransform, c_similarityMeasureTag_);
 135     densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
 136     densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
 137     densityfittingMdpTransformFromString<real>(
 138             rules, &fromStdString<real>, c_gaussianTransformSpreadingWidthTag_);
 139     densityfittingMdpTransformFromString<real>(
 140             rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 141     densityfittingMdpTransformFromString<std::string>(
 142             rules, stringIdentityTransform, c_referenceDensityFileNameTag_);
 143     densityfittingMdpTransformFromString<std::int64_t>(
 144             rules, &fromStdString<std::int64_t>, c_everyNStepsTag_);
 145     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
 146     densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_adaptiveForceScalingTag_);
 147     densityfittingMdpTransformFromString<real>(
 148             rules, &fromStdString<real>, c_adaptiveForceScalingTimeConstantTag_);
 149     const auto& stringRVecToStringRVecWithCheck = [](const std::string& str) {
 150         return stringIdentityTransformWithArrayCheck<real, 3>(
 151                 str,
 152                 "Reading three real values as vector while parsing the .mdp input failed in "
 153                         + DensityFittingModuleInfo::name_ + ".");
 154     };
 155     densityfittingMdpTransformFromString<std::string>(
 156             rules, stringRVecToStringRVecWithCheck, c_translationTag_);
 157
 158     const auto& stringMatrixToStringMatrixWithCheck = [](const std::string& str) {
 159         return stringIdentityTransformWithArrayCheck<real, 9>(
 160                 str,
 161                 "Reading nine real values as vector while parsing the .mdp input failed in "
 162                         + DensityFittingModuleInfo::name_ + ".");
 163     };
 164     densityfittingMdpTransformFromString<std::string>(
 165             rules, stringMatrixToStringMatrixWithCheck, c_transformationMatrixTag_);
 166 }
 167
 168 //! Name the methods that may be used to evaluate similarity between densities
 169 static const EnumerationArray<DensitySimilarityMeasureMethod, const char*> c_densitySimilarityMeasureMethodNames = {
 170     { "inner-product", "relative-entropy", "cross-correlation" }
 171 };
 172 //! The names of the methods to determine the amplitude of the atoms to be spread on a grid
 173 static const EnumerationArray<DensityFittingAmplitudeMethod, const char*> c_densityFittingAmplitudeMethodNames = {
 174     { "unity", "mass", "charge" }
 175 };
 176
 177 void DensityFittingOptions::buildMdpOutput(KeyValueTreeObjectBuilder* builder) const
 178 {
 179
 180     addDensityFittingMdpOutputValueComment(builder, "", "empty-line");
 181     addDensityFittingMdpOutputValueComment(builder, "; Density guided simulation", "module");
 182
 183     addDensityFittingMdpOutputValue(builder, parameters_.active_, c_activeTag_);
 184     if (parameters_.active_)
 185     {
 186         addDensityFittingMdpOutputValue(builder, groupString_, c_groupTag_);
 187
 188         addDensityFittingMdpOutputValueComment(
 189                 builder,
 190                 "; Similarity measure between densities: inner-product, relative-entropy, or "
 191                 "cross-correlation",
 192                 c_similarityMeasureTag_);
 193         addDensityFittingMdpOutputValue<std::string>(
 194                 builder,
 195                 c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
 196                 c_similarityMeasureTag_);
 197
 198         addDensityFittingMdpOutputValueComment(
 199                 builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge", c_amplitudeMethodTag_);
 200         addDensityFittingMdpOutputValue<std::string>(
 201                 builder,
 202                 c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
 203                 c_amplitudeMethodTag_);
 204
 205         addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
 206         addDensityFittingMdpOutputValue(builder,
 207                                         parameters_.gaussianTransformSpreadingWidth_,
 208                                         c_gaussianTransformSpreadingWidthTag_);
 209         addDensityFittingMdpOutputValue(builder,
 210                                         parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
 211                                         c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
 212         addDensityFittingMdpOutputValueComment(builder,
 213                                                "; Reference density file location as absolute path "
 214                                                "or relative to the gmx mdrun calling location",
 215                                                c_referenceDensityFileNameTag_);
 216         addDensityFittingMdpOutputValue(builder, referenceDensityFileName_, c_referenceDensityFileNameTag_);
 217         addDensityFittingMdpOutputValue(builder, parameters_.calculationIntervalInSteps_, c_everyNStepsTag_);
 218         addDensityFittingMdpOutputValueComment(
 219                 builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
 220         addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
 221         addDensityFittingMdpOutputValueComment(
 222                 builder, "; Apply adaptive force scaling", c_adaptiveForceScalingTag_);
 223         addDensityFittingMdpOutputValue(
 224                 builder, parameters_.adaptiveForceScaling_, c_adaptiveForceScalingTag_);
 225         addDensityFittingMdpOutputValueComment(builder,
 226                                                "; Time constant for adaptive force scaling in ps",
 227                                                c_adaptiveForceScalingTimeConstantTag_);
 228         addDensityFittingMdpOutputValue(builder,
 229                                         parameters_.adaptiveForceScalingTimeConstant_,
 230                                         c_adaptiveForceScalingTimeConstantTag_);
 231     }
 232 }
 233
 234 void DensityFittingOptions::initMdpOptions(IOptionsContainerWithSections* options)
 235 {
 236     auto section = options->addSection(OptionSection(DensityFittingModuleInfo::name_.c_str()));
 237
 238     section.addOption(BooleanOption(c_activeTag_.c_str()).store(&parameters_.active_));
 239     section.addOption(StringOption(c_groupTag_.c_str()).store(&groupString_));
 240
 241     section.addOption(EnumOption<DensitySimilarityMeasureMethod>(c_similarityMeasureTag_.c_str())
 242                               .enumValue(c_densitySimilarityMeasureMethodNames)
 243                               .store(&parameters_.similarityMeasureMethod_));
 244
 245     section.addOption(EnumOption<DensityFittingAmplitudeMethod>(c_amplitudeMethodTag_.c_str())
 246                               .enumValue(c_densityFittingAmplitudeMethodNames)
 247                               .store(&parameters_.amplitudeLookupMethod_));
 248
 249     section.addOption(RealOption(c_forceConstantTag_.c_str()).store(&parameters_.forceConstant_));
 250     section.addOption(RealOption(c_gaussianTransformSpreadingWidthTag_.c_str())
 251                               .store(&parameters_.gaussianTransformSpreadingWidth_));
 252     section.addOption(RealOption(c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_.c_str())
 253                               .store(&parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_));
 254     section.addOption(StringOption(c_referenceDensityFileNameTag_.c_str()).store(&referenceDensityFileName_));
 255     section.addOption(Int64Option(c_everyNStepsTag_.c_str()).store(&parameters_.calculationIntervalInSteps_));
 256     section.addOption(BooleanOption(c_normalizeDensitiesTag_.c_str()).store(&parameters_.normalizeDensities_));
 257     section.addOption(
 258             BooleanOption(c_adaptiveForceScalingTag_.c_str()).store(&parameters_.adaptiveForceScaling_));
 259     section.addOption(RealOption(c_adaptiveForceScalingTimeConstantTag_.c_str())
 260                               .store(&parameters_.adaptiveForceScalingTimeConstant_));
 261     section.addOption(StringOption(c_translationTag_.c_str()).store(&parameters_.translationString_));
 262     section.addOption(
 263             StringOption(c_transformationMatrixTag_.c_str()).store(&parameters_.transformationMatrixString_));
 264 }
 265
 266 bool DensityFittingOptions::active() const
 267 {
 268     return parameters_.active_;
 269 }
 270
 271 const DensityFittingParameters& DensityFittingOptions::buildParameters()
 272 {
 273     // the options modules does not know unsigned integers so any input of this
 274     // kind is rectified here
 275     if (parameters_.calculationIntervalInSteps_ < 1)
 276     {
 277         parameters_.calculationIntervalInSteps_ = 1;
 278     }
 279     return parameters_;
 280 }
 281
 282 void DensityFittingOptions::setFitGroupIndices(const IndexGroupsAndNames& indexGroupsAndNames)
 283 {
 284     if (!parameters_.active_)
 285     {
 286         return;
 287     }
 288     parameters_.indices_ = indexGroupsAndNames.indices(groupString_);
 289 }
 290
 291 void DensityFittingOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
 292 {
 293     auto groupIndexAdder = treeBuilder.addUniformArray<std::int64_t>(DensityFittingModuleInfo::name_
 294                                                                      + "-" + c_groupTag_);
 295     for (const auto& indexValue : parameters_.indices_)
 296     {
 297         groupIndexAdder.addValue(indexValue);
 298     }
 299 }
 300
 301 void DensityFittingOptions::readInternalParametersFromKvt(const KeyValueTreeObject& tree)
 302 {
 303     if (!parameters_.active_)
 304     {
 305         return;
 306     }
 307
 308     if (!tree.keyExists(DensityFittingModuleInfo::name_ + "-" + c_groupTag_))
 309     {
 310         GMX_THROW(InconsistentInputError(
 311                 "Cannot find atom index vector required for density guided simulation."));
 312     }
 313     auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
 314     parameters_.indices_.resize(kvtIndexArray.size());
 315     std::transform(std::begin(kvtIndexArray),
 316                    std::end(kvtIndexArray),
 317                    std::begin(parameters_.indices_),
 318                    [](const KeyValueTreeValue& val) { return val.cast<std::int64_t>(); });
 319 }
 320
 321 void DensityFittingOptions::checkEnergyCaluclationFrequency(
 322         EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) const
 323 {
 324     if (energyCalculationFrequencyErrors->energyCalculationIntervalInSteps() % parameters_.calculationIntervalInSteps_
 325         != 0)
 326     {
 327         energyCalculationFrequencyErrors->addError(
 328                 "nstcalcenergy ("
 329                 + toString(energyCalculationFrequencyErrors->energyCalculationIntervalInSteps())
 330                 + ") is not a multiple of " + DensityFittingModuleInfo::name_ + "-" + c_everyNStepsTag_
 331                 + " (" + toString(parameters_.calculationIntervalInSteps_) + ") .");
 332     }
 333 }
 334
 335 const std::string& DensityFittingOptions::referenceDensityFileName() const
 336 {
 337     return referenceDensityFileName_;
 338 }
 339 } // namespace gmx