src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for density fitting module options.
  38  *
  39  * \author Christian Blau <blau@kth.se>
  40  * \ingroup module_applied_forces
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/applied_forces/densityfitting/densityfittingoptions.h"
  45
  46 #include <string>
  47 #include <vector>
  48
  49 #include <gtest/gtest.h>
  50
  51 #include "gromacs/options/options.h"
  52 #include "gromacs/options/treesupport.h"
  53 #include "gromacs/selection/indexutil.h"
  54 #include "gromacs/utility/keyvaluetreebuilder.h"
  55 #include "gromacs/utility/keyvaluetreemdpwriter.h"
  56 #include "gromacs/utility/keyvaluetreetransform.h"
  57 #include "gromacs/utility/smalloc.h"
  58 #include "gromacs/utility/stringcompare.h"
  59 #include "gromacs/utility/stringstream.h"
  60 #include "gromacs/utility/textwriter.h"
  61
  62 #include "testutils/testasserts.h"
  63 #include "testutils/testmatchers.h"
  64
  65 namespace gmx
  66 {
  67
  68 namespace
  69 {
  70
  71 class DensityFittingOptionsTest : public ::testing::Test
  72 {
  73 public:
  74     DensityFittingOptionsTest() { init_blocka(&defaultGroups_); }
  75     ~DensityFittingOptionsTest() override { done_blocka(&defaultGroups_); }
  76
  77     void setFromMdpValues(const KeyValueTreeObject& densityFittingMdpValues)
  78     {
  79         // set up options
  80         Options densityFittingModuleOptions;
  81         densityFittingOptions_.initMdpOptions(&densityFittingModuleOptions);
  82
  83         // Add rules to transform mdp inputs to densityFittingModule data
  84         KeyValueTreeTransformer transform;
  85         transform.rules()->addRule().keyMatchType("/", StringCompareType::CaseAndDashInsensitive);
  86
  87         densityFittingOptions_.initMdpTransform(transform.rules());
  88
  89         // Execute the transform on the mdpValues
  90         auto transformedMdpValues = transform.transform(densityFittingMdpValues, nullptr);
  91         assignOptionsFromKeyValueTree(&densityFittingModuleOptions, transformedMdpValues.object(), nullptr);
  92     }
  93
  94     static KeyValueTreeObject densityFittingSetActiveAsMdpValues()
  95     {
  96         // Prepare MDP inputs
  97         KeyValueTreeBuilder mdpValueBuilder;
  98         mdpValueBuilder.rootObject().addValue("density-guided-simulation-active", std::string("yes"));
  99         return mdpValueBuilder.build();
 100     }
 101
 102     IndexGroupsAndNames genericIndexGroupsAndNames()
 103     {
 104         done_blocka(&defaultGroups_);
 105         stupid_fill_blocka(&defaultGroups_, 3);
 106         std::vector<std::string> groupNames          = { "A", "protein", "C" };
 107         const char* const        namesAsConstChar[3] = { groupNames[0].c_str(),
 108                                                   groupNames[1].c_str(),
 109                                                   groupNames[2].c_str() };
 110         return { defaultGroups_, namesAsConstChar };
 111     }
 112
 113     IndexGroupsAndNames differingIndexGroupsAndNames()
 114     {
 115         done_blocka(&defaultGroups_);
 116         stupid_fill_blocka(&defaultGroups_, 3);
 117         std::vector<std::string> groupNames          = { "protein", "C", "A" };
 118         const char* const        namesAsConstChar[3] = { groupNames[0].c_str(),
 119                                                   groupNames[1].c_str(),
 120                                                   groupNames[2].c_str() };
 121         return { defaultGroups_, namesAsConstChar };
 122     }
 123
 124     void mangleInternalParameters()
 125     {
 126         densityFittingOptions_.setFitGroupIndices(differingIndexGroupsAndNames());
 127     }
 128
 129 protected:
 130     t_blocka              defaultGroups_;
 131     DensityFittingOptions densityFittingOptions_;
 132 };
 133
 134 TEST_F(DensityFittingOptionsTest, DefaultParameters)
 135 {
 136     const auto defaultParameters = densityFittingOptions_.buildParameters();
 137     EXPECT_FALSE(defaultParameters.active_);
 138     EXPECT_EQ(0, defaultParameters.indices_.size());
 139     EXPECT_EQ(DensitySimilarityMeasureMethod::innerProduct, defaultParameters.similarityMeasureMethod_);
 140     EXPECT_EQ(DensityFittingAmplitudeMethod::Unity, defaultParameters.amplitudeLookupMethod_);
 141     EXPECT_REAL_EQ(1e9, defaultParameters.forceConstant_);
 142     EXPECT_REAL_EQ(0.2, defaultParameters.gaussianTransformSpreadingWidth_);
 143     EXPECT_REAL_EQ(4.0, defaultParameters.gaussianTransformSpreadingRangeInMultiplesOfWidth_);
 144 }
 145
 146 TEST_F(DensityFittingOptionsTest, OptionSetsActive)
 147 {
 148     EXPECT_FALSE(densityFittingOptions_.buildParameters().active_);
 149     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 150     EXPECT_TRUE(densityFittingOptions_.buildParameters().active_);
 151 }
 152
 153 TEST_F(DensityFittingOptionsTest, OutputNoDefaultValuesWhenInactive)
 154 {
 155     // Transform module data into a flat key-value tree for output.
 156
 157     StringOutputStream        stream;
 158     KeyValueTreeBuilder       builder;
 159     KeyValueTreeObjectBuilder builderObject = builder.rootObject();
 160
 161     densityFittingOptions_.buildMdpOutput(&builderObject);
 162     {
 163         TextWriter writer(&stream);
 164         writeKeyValueTreeAsMdp(&writer, builder.build());
 165     }
 166     stream.close();
 167
 168     EXPECT_EQ(stream.toString(),
 169               std::string(
 170                       "\n; Density guided simulation\ndensity-guided-simulation-active = false\n"));
 171 }
 172
 173 TEST_F(DensityFittingOptionsTest, OutputDefaultValuesWhenActive)
 174 {
 175     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 176     // Transform module data into a flat key-value tree for output.
 177
 178     StringOutputStream        stream;
 179     KeyValueTreeBuilder       builder;
 180     KeyValueTreeObjectBuilder builderObject = builder.rootObject();
 181
 182     densityFittingOptions_.buildMdpOutput(&builderObject);
 183     {
 184         TextWriter writer(&stream);
 185         writeKeyValueTreeAsMdp(&writer, builder.build());
 186     }
 187     stream.close();
 188     std::string expectedString = {
 189         "\n"
 190         "; Density guided simulation\n"
 191         "density-guided-simulation-active = true\n"
 192         "density-guided-simulation-group = protein\n"
 193         "; Similarity measure between densities: inner-product, relative-entropy, or "
 194         "cross-correlation\n"
 195         "density-guided-simulation-similarity-measure = inner-product\n"
 196         "; Atom amplitude for spreading onto grid: unity, mass, or charge\n"
 197         "density-guided-simulation-atom-spreading-weight = unity\n"
 198         "density-guided-simulation-force-constant = 1e+09\n"
 199         "density-guided-simulation-gaussian-transform-spreading-width = 0.2\n"
 200         "density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width = 4\n"
 201         "; Reference density file location as absolute path or relative to the gmx mdrun calling "
 202         "location\n"
 203         "density-guided-simulation-reference-density-filename = reference.mrc\n"
 204         "density-guided-simulation-nst = 1\n"
 205         "; Normalize the sum of density voxel values to one\n"
 206         "density-guided-simulation-normalize-densities = true\n"
 207         "; Apply adaptive force scaling\n"
 208         "density-guided-simulation-adaptive-force-scaling = false\n"
 209         "; Time constant for adaptive force scaling in ps\n"
 210         "density-guided-simulation-adaptive-force-scaling-time-constant = 4\n"
 211     };
 212
 213     EXPECT_EQ(expectedString, stream.toString());
 214 }
 215
 216
 217 TEST_F(DensityFittingOptionsTest, CanConvertGroupStringToIndexGroup)
 218 {
 219     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 220
 221     const auto indexGroupAndNames = genericIndexGroupsAndNames();
 222     densityFittingOptions_.setFitGroupIndices(indexGroupAndNames);
 223
 224     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_.size());
 225     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_[0]);
 226 }
 227
 228 TEST_F(DensityFittingOptionsTest, InternalsToKvt)
 229 {
 230     // stores the default internal options
 231     DensityFittingOptions densityFittingOptions;
 232     KeyValueTreeBuilder   builder;
 233     densityFittingOptions.writeInternalParametersToKvt(builder.rootObject());
 234     const auto kvtTree = builder.build();
 235     EXPECT_TRUE(kvtTree.keyExists("density-guided-simulation-group"));
 236     EXPECT_TRUE(kvtTree["density-guided-simulation-group"].isArray());
 237     auto storedIndex = kvtTree["density-guided-simulation-group"].asArray().values();
 238
 239     EXPECT_EQ(0, storedIndex.size());
 240 }
 241
 242 TEST_F(DensityFittingOptionsTest, KvtToInternal)
 243 {
 244     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 245
 246     KeyValueTreeBuilder builder;
 247     auto                addedArray =
 248             builder.rootObject().addUniformArray<std::int64_t>("density-guided-simulation-group");
 249     addedArray.addValue(1);
 250     addedArray.addValue(15);
 251     const auto tree = builder.build();
 252
 253     densityFittingOptions_.readInternalParametersFromKvt(tree);
 254
 255     EXPECT_EQ(2, densityFittingOptions_.buildParameters().indices_.size());
 256     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_[0]);
 257     EXPECT_EQ(15, densityFittingOptions_.buildParameters().indices_[1]);
 258 }
 259
 260 TEST_F(DensityFittingOptionsTest, RoundTripForInternalsIsIdempotent)
 261 {
 262     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 263     {
 264         const IndexGroupsAndNames indexGroupAndNames = genericIndexGroupsAndNames();
 265         densityFittingOptions_.setFitGroupIndices(indexGroupAndNames);
 266     }
 267
 268     DensityFittingParameters parametersBefore = densityFittingOptions_.buildParameters();
 269
 270     KeyValueTreeBuilder builder;
 271     densityFittingOptions_.writeInternalParametersToKvt(builder.rootObject());
 272     const auto inputTree = builder.build();
 273
 274     mangleInternalParameters();
 275
 276     DensityFittingParameters parametersAfter = densityFittingOptions_.buildParameters();
 277     EXPECT_NE(parametersBefore, parametersAfter);
 278
 279     densityFittingOptions_.readInternalParametersFromKvt(inputTree);
 280
 281     parametersAfter = densityFittingOptions_.buildParameters();
 282     EXPECT_EQ(parametersBefore, parametersAfter);
 283 }
 284
 285 } // namespace
 286
 287 } // namespace gmx