src/gromacs/applied_forces/densityfittingoptions.cpp

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