src/gromacs/topology/tests/mtop.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements test of mtop routines
  38  *
  39  * \author Roland Schulz <roland.schulz@intel.com>
  40  * \ingroup module_topology
  41  */
  42 #include "gmxpre.h"
  43
  44 #include <gtest/gtest.h>
  45
  46 #include "gromacs/topology/mtop_util.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48
  49 namespace gmx
  50 {
  51 namespace
  52 {
  53
  54 /*! \brief Initializes a basic topology with 9 atoms with settle*/
  55 void createBasicTop(gmx_mtop_t* mtop)
  56 {
  57     gmx_moltype_t moltype;
  58     moltype.atoms.nr             = NRAL(F_SETTLE);
  59     std::vector<int>& iatoms     = moltype.ilist[F_SETTLE].iatoms;
  60     const int         settleType = 0;
  61     iatoms.push_back(settleType);
  62     iatoms.push_back(0);
  63     iatoms.push_back(1);
  64     iatoms.push_back(2);
  65     mtop->moltype.push_back(moltype);
  66
  67     mtop->molblock.resize(1);
  68     mtop->molblock[0].type = 0;
  69     mtop->molblock[0].nmol = 3;
  70     mtop->natoms           = moltype.atoms.nr * mtop->molblock[0].nmol;
  71     gmx_mtop_finalize(mtop);
  72 }
  73
  74 /*! \brief
  75  * Creates dummy topology with two differently sized residues.
  76  *
  77  * Residue begin and end are set to allow checking routines
  78  * that make use of the boundaries.
  79  *
  80  * \returns The residue ranges.
  81  */
  82 std::vector<gmx::Range<int>> createTwoResidueTopology(gmx_mtop_t* mtop)
  83 {
  84     auto& moltype        = mtop->moltype.emplace_back();
  85     int   residueOneSize = 5;
  86     int   residueTwoSize = 4;
  87     moltype.atoms.nr     = residueOneSize + residueTwoSize;
  88     snew(moltype.atoms.atom, residueOneSize + residueTwoSize);
  89     for (int i = 0; i < residueOneSize; i++)
  90     {
  91         moltype.atoms.atom[i].resind = 0;
  92     }
  93     for (int i = residueOneSize; i < residueOneSize + residueTwoSize; i++)
  94     {
  95         moltype.atoms.atom[i].resind = 1;
  96     }
  97
  98     mtop->molblock.resize(1);
  99     mtop->molblock[0].type = 0;
 100     mtop->molblock[0].nmol = 1;
 101     mtop->natoms           = moltype.atoms.nr * mtop->molblock[0].nmol;
 102     gmx_mtop_finalize(mtop);
 103     std::vector<gmx::Range<int>> residueRange;
 104     residueRange.emplace_back(0, residueOneSize);
 105     residueRange.emplace_back(residueOneSize, residueOneSize + residueTwoSize);
 106     return residueRange;
 107 }
 108
 109 TEST(MtopTest, RangeBasedLoop)
 110 {
 111     gmx_mtop_t mtop;
 112     createBasicTop(&mtop);
 113     int count = 0;
 114     for (const AtomProxy atomP : AtomRange(mtop))
 115     {
 116         EXPECT_EQ(atomP.globalAtomNumber(), count);
 117         ++count;
 118     }
 119     EXPECT_EQ(count, 9);
 120 }
 121
 122 TEST(MtopTest, Operators)
 123 {
 124     gmx_mtop_t mtop;
 125     createBasicTop(&mtop);
 126     AtomIterator it(mtop);
 127     AtomIterator otherIt(mtop);
 128     EXPECT_EQ((*it).globalAtomNumber(), 0);
 129     EXPECT_EQ(it->globalAtomNumber(), 0);
 130     EXPECT_TRUE(it == otherIt);
 131     EXPECT_FALSE(it != otherIt);
 132     ++it;
 133     EXPECT_EQ(it->globalAtomNumber(), 1);
 134     it++;
 135     EXPECT_EQ(it->globalAtomNumber(), 2);
 136     EXPECT_TRUE(it != otherIt);
 137     EXPECT_FALSE(it == otherIt);
 138 }
 139
 140 TEST(MtopTest, CanFindResidueStartAndEndAtoms)
 141 {
 142     gmx_mtop_t mtop;
 143     auto       expectedResidueRange = createTwoResidueTopology(&mtop);
 144
 145     auto atomRanges = atomRangeOfEachResidue(mtop.molblock[0], mtop);
 146     ASSERT_EQ(atomRanges.size(), expectedResidueRange.size());
 147     for (gmx::index i = 0; i < gmx::ssize(atomRanges); i++)
 148     {
 149         EXPECT_EQ(atomRanges[i].begin(), expectedResidueRange[i].begin());
 150         EXPECT_EQ(atomRanges[i].end(), expectedResidueRange[i].end());
 151         ASSERT_EQ(atomRanges[i].size(), expectedResidueRange[i].size());
 152     }
 153     int rangeIndex = 0;
 154     for (const auto& range : atomRanges)
 155     {
 156         auto referenceRangeIt = expectedResidueRange[rangeIndex].begin();
 157         for (int i : range)
 158         {
 159             EXPECT_EQ(i, *referenceRangeIt);
 160             referenceRangeIt++;
 161         }
 162         rangeIndex++;
 163     }
 164 }
 165
 166 } // namespace
 167
 168 } // namespace gmx