src/gromacs/applied_forces/tests/densityfittingoptions.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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/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",
  99                                               std::string("yes"));
 100         return mdpValueBuilder.build();
 101     }
 102
 103     IndexGroupsAndNames genericIndexGroupsAndNames()
 104     {
 105         done_blocka(&defaultGroups_);
 106         stupid_fill_blocka(&defaultGroups_, 3);
 107         std::vector<std::string> groupNames   = { "A", "protein", "C" };
 108         const char* const namesAsConstChar[3] = { groupNames[0].c_str(), 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(), groupNames[1].c_str(),
 119                                                   groupNames[2].c_str() };
 120         return { defaultGroups_, namesAsConstChar };
 121     }
 122
 123     void mangleInternalParameters()
 124     {
 125         densityFittingOptions_.setFitGroupIndices(differingIndexGroupsAndNames());
 126     }
 127
 128 protected:
 129     t_blocka              defaultGroups_;
 130     DensityFittingOptions densityFittingOptions_;
 131 };
 132
 133 TEST_F(DensityFittingOptionsTest, DefaultParameters)
 134 {
 135     const auto defaultParameters = densityFittingOptions_.buildParameters();
 136     EXPECT_FALSE(defaultParameters.active_);
 137     EXPECT_EQ(0, defaultParameters.indices_.size());
 138     EXPECT_EQ(DensitySimilarityMeasureMethod::innerProduct, defaultParameters.similarityMeasureMethod_);
 139     EXPECT_EQ(DensityFittingAmplitudeMethod::Unity, defaultParameters.amplitudeLookupMethod_);
 140     EXPECT_REAL_EQ(1e9, defaultParameters.forceConstant_);
 141     EXPECT_REAL_EQ(0.2, defaultParameters.gaussianTransformSpreadingWidth_);
 142     EXPECT_REAL_EQ(4.0, defaultParameters.gaussianTransformSpreadingRangeInMultiplesOfWidth_);
 143 }
 144
 145 TEST_F(DensityFittingOptionsTest, OptionSetsActive)
 146 {
 147     EXPECT_FALSE(densityFittingOptions_.buildParameters().active_);
 148     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 149     EXPECT_TRUE(densityFittingOptions_.buildParameters().active_);
 150 }
 151
 152 TEST_F(DensityFittingOptionsTest, OutputNoDefaultValuesWhenInactive)
 153 {
 154     // Transform module data into a flat key-value tree for output.
 155
 156     StringOutputStream        stream;
 157     KeyValueTreeBuilder       builder;
 158     KeyValueTreeObjectBuilder builderObject = builder.rootObject();
 159
 160     densityFittingOptions_.buildMdpOutput(&builderObject);
 161     {
 162         TextWriter writer(&stream);
 163         writeKeyValueTreeAsMdp(&writer, builder.build());
 164     }
 165     stream.close();
 166
 167     EXPECT_EQ(stream.toString(),
 168               std::string(
 169                       "\n; Density guided simulation\ndensity-guided-simulation-active = false\n"));
 170 }
 171
 172 TEST_F(DensityFittingOptionsTest, OutputDefaultValuesWhenActive)
 173 {
 174     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 175     // Transform module data into a flat key-value tree for output.
 176
 177     StringOutputStream        stream;
 178     KeyValueTreeBuilder       builder;
 179     KeyValueTreeObjectBuilder builderObject = builder.rootObject();
 180
 181     densityFittingOptions_.buildMdpOutput(&builderObject);
 182     {
 183         TextWriter writer(&stream);
 184         writeKeyValueTreeAsMdp(&writer, builder.build());
 185     }
 186     stream.close();
 187     std::string expectedString = {
 188         "\n"
 189         "; Density guided simulation\n"
 190         "density-guided-simulation-active = true\n"
 191         "density-guided-simulation-group = protein\n"
 192         "; Similarity measure between densities: inner-product, relative-entropy, or "
 193         "cross-correlation\n"
 194         "density-guided-simulation-similarity-measure = inner-product\n"
 195         "; Atom amplitude for spreading onto grid: unity, mass, or charge\n"
 196         "density-guided-simulation-atom-spreading-weight = unity\n"
 197         "density-guided-simulation-force-constant = 1e+09\n"
 198         "density-guided-simulation-gaussian-transform-spreading-width = 0.2\n"
 199         "density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width = 4\n"
 200         "; Reference density file location as absolute path or relative to the gmx mdrun calling "
 201         "location\n"
 202         "density-guided-simulation-reference-density-filename = reference.mrc\n"
 203         "density-guided-simulation-nst = 1\n"
 204         "; Normalize the sum of density voxel values to one\n"
 205         "density-guided-simulation-normalize-densities = true\n"
 206         "; Apply adaptive force scaling\n"
 207         "density-guided-simulation-adaptive-force-scaling = false\n"
 208         "; Time constant for adaptive force scaling in ps\n"
 209         "density-guided-simulation-adaptive-force-scaling-time-constant = 4\n"
 210     };
 211
 212     EXPECT_EQ(expectedString, stream.toString());
 213 }
 214
 215
 216 TEST_F(DensityFittingOptionsTest, CanConvertGroupStringToIndexGroup)
 217 {
 218     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 219
 220     const auto indexGroupAndNames = genericIndexGroupsAndNames();
 221     densityFittingOptions_.setFitGroupIndices(indexGroupAndNames);
 222
 223     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_.size());
 224     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_[0]);
 225 }
 226
 227 TEST_F(DensityFittingOptionsTest, InternalsToKvt)
 228 {
 229     // stores the default internal options
 230     DensityFittingOptions densityFittingOptions;
 231     KeyValueTreeBuilder   builder;
 232     densityFittingOptions.writeInternalParametersToKvt(builder.rootObject());
 233     const auto kvtTree = builder.build();
 234     EXPECT_TRUE(kvtTree.keyExists("density-guided-simulation-group"));
 235     EXPECT_TRUE(kvtTree["density-guided-simulation-group"].isArray());
 236     auto storedIndex = kvtTree["density-guided-simulation-group"].asArray().values();
 237
 238     EXPECT_EQ(0, storedIndex.size());
 239 }
 240
 241 TEST_F(DensityFittingOptionsTest, KvtToInternal)
 242 {
 243     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 244
 245     KeyValueTreeBuilder builder;
 246     auto                addedArray =
 247             builder.rootObject().addUniformArray<std::int64_t>("density-guided-simulation-group");
 248     addedArray.addValue(1);
 249     addedArray.addValue(15);
 250     const auto tree = builder.build();
 251
 252     densityFittingOptions_.readInternalParametersFromKvt(tree);
 253
 254     EXPECT_EQ(2, densityFittingOptions_.buildParameters().indices_.size());
 255     EXPECT_EQ(1, densityFittingOptions_.buildParameters().indices_[0]);
 256     EXPECT_EQ(15, densityFittingOptions_.buildParameters().indices_[1]);
 257 }
 258
 259 TEST_F(DensityFittingOptionsTest, RoundTripForInternalsIsIdempotent)
 260 {
 261     setFromMdpValues(densityFittingSetActiveAsMdpValues());
 262     {
 263         const IndexGroupsAndNames indexGroupAndNames = genericIndexGroupsAndNames();
 264         densityFittingOptions_.setFitGroupIndices(indexGroupAndNames);
 265     }
 266
 267     DensityFittingParameters parametersBefore = densityFittingOptions_.buildParameters();
 268
 269     KeyValueTreeBuilder builder;
 270     densityFittingOptions_.writeInternalParametersToKvt(builder.rootObject());
 271     const auto inputTree = builder.build();
 272
 273     mangleInternalParameters();
 274
 275     DensityFittingParameters parametersAfter = densityFittingOptions_.buildParameters();
 276     EXPECT_NE(parametersBefore, parametersAfter);
 277
 278     densityFittingOptions_.readInternalParametersFromKvt(inputTree);
 279
 280     parametersAfter = densityFittingOptions_.buildParameters();
 281     EXPECT_EQ(parametersBefore, parametersAfter);
 282 }
 283
 284 } // namespace
 285
 286 } // namespace gmx