analyzer.cpp,17 int main(23,516 atom.cpp,262 atom::atom(13,258 atom::~atom(35,653 atom *atom::GetTrueFather(atom::GetTrueFather45,973 bool atom::Output(61,1416 bool atom::OutputXYZLine(78,2040 ostream & operator << operator <<87,2262 bool atom::Compare(97,2547 bool operator < operator <105,2652 bond.cpp,385 bond::bond(14,290 bond::bond(34,691 bond::bond(52,1136 bond::~bond(73,1597 ostream & operator << operator <<84,1788 atom * bond::GetOtherAtom(94,2199 bond * bond::GetFirstBond(107,2583 bond * bond::GetLastBond(116,2865 enum Shading bond::IsUsed(124,3000 bool bond::Contains(133,3217 bool bond::Contains(142,3475 bool bond::MarkUsed(150,3691 void bond::ResetUsed(163,3973 border.cpp,229 void Find_next_suitable_point(5,51 void Tesselation::Find_next_suitable_triangle(63,2078 void Find_second_point_for_Tesselation(141,4691 void Tesselation::Find_starting_triangle(173,5558 void Find_non_convex_border(287,8778 boundary.cpp,1347 BoundaryPointSet::BoundaryPointSet(12,397 BoundaryPointSet::BoundaryPointSet(18,469 BoundaryPointSet::~BoundaryPointSet(25,578 void BoundaryPointSet::AddLine(31,704 ostream & operator << operator <<42,1045 BoundaryLineSet::BoundaryLineSet(50,1273 BoundaryLineSet::BoundaryLineSet(58,1396 BoundaryLineSet::~BoundaryLineSet(72,1836 void BoundaryLineSet::AddTriangle(87,2407 ostream & operator << operator <<94,2656 BoundaryTriangleSet::BoundaryTriangleSet(103,2939 BoundaryTriangleSet::BoundaryTriangleSet(112,3075 BoundaryTriangleSet::~BoundaryTriangleSet(144,4167 void BoundaryTriangleSet::GetNormalVector(159,4691 ostream & operator << operator <<169,5082 class BoundaryPointSet * GetCommonEndpoint(182,5559 Boundaries * GetBoundaryPoints(209,6893 double * GetDiametersOfCluster(384,15165 double VolumeOfConvexEnvelope(470,20313 void PrepareClustersinWater(610,27033 Tesselation::Tesselation(692,31276 Tesselation::~Tesselation(702,31494 void Tesselation::GuessStartingTriangle(714,31995 void Tesselation::TesselateOnBoundary(849,39116 void Tesselation::AddPoint(1003,49558 void Find_next_suitable_point(1024,50156 void Tesselation::Find_next_suitable_triangle(1082,52183 void Find_second_point_for_Tesselation(1160,54796 void Tesselation::Find_starting_triangle(1192,55663 void Find_non_convex_border(1306,58883 builder.cpp,378 static void AddAtoms(62,2281 static void CenterAtoms(259,10538 static void AlignAtoms(314,12598 static void MirrorAtoms(382,15117 static void RemoveAtoms(429,16855 static void MeasureAtoms(487,18852 static void FragmentAtoms(598,23710 static void testroutine(619,24543 static void SaveConfig(692,27108 static int ParseCommandLineOptions(771,29725 int main(1303,56039 config.cpp,445 config::config(13,261 config::~config(89,2039 void config::Edit(102,2590 int config::TestSyntax(367,16198 bool config::GetIsAngstroem(389,16806 char * config::GetDefaultPath(397,16955 void config::SetDefaultPath(406,17101 void config::RetrieveConfigPathAndName(414,17286 void config::Load(444,18309 void config::LoadOld(773,36012 bool config::Save(977,45063 bool config::SaveMPQC(1084,52722 int config::ParseForParameter(1213,58282 datacreator.cpp,954 bool OpenOutputFile(19,468 bool AppendOutputFile(37,1009 bool CreateDataEnergyOrder(56,1690 bool CreateDataDeltaEnergyOrder(89,3244 bool CreateDataForcesOrder(126,5185 bool CreateDataDeltaForcesOrder(158,6656 bool CreateDataDeltaForcesOrderPerAtom(190,8202 bool CreateDataForcesOrderPerAtom(237,10288 bool CreateDataFragment(266,11393 void CreateMaxFragmentOrder(294,12696 void CreateMinFragmentOrder(311,13550 bool CreateDataFragmentOrder(331,14537 void CreateEnergy(358,15708 void CreateMinimumForce(369,16220 void CreateMeanForce(403,17598 void CreateMaximumForce(428,18520 void CreateSameForce(450,19299 void CreateVectorSumForce(460,19630 void CreatePlotHeader(480,20389 bool CreatePlotOrder(517,21999 void AbsEnergyPlotLine(538,23154 void EnergyPlotLine(562,23997 void ForceMagnitudePlotLine(586,24845 void AbsFirstForceValuePlotLine(617,26051 void BoxesForcePlotLine(648,27192 void BoxesFirstForceValuePlotLine(680,28575 element.cpp,112 element::element(13,270 element::~element(23,412 bool element::Output(28,507 bool element::Checkout(43,1115 helpers.cpp,325 double ask_value(15,316 void debug_in(30,757 void debug_in(34,918 void * Malloc(42,1223 void * Calloc(56,1671 void * ReAlloc(71,2182 void Free(88,2787 char* MallocString(103,3192 void bound(121,3685 void flip(134,3996 int pot(147,4205 char *FixedDigitNumber(FixedDigitNumber161,4624 bool IsValidNumber(188,5558 joiner.cpp,17 int main(17,429 moleculelist.cpp,859 MoleculeListClass::MoleculeListClass(13,290 MoleculeListClass::MoleculeListClass(21,496 MoleculeListClass::~MoleculeListClass(33,889 int MolCompare(52,1584 void MoleculeListClass::Output(127,3994 bool MoleculeListClass::AddHydrogenCorrection(142,4664 bool MoleculeListClass::StoreForcesFile(329,12009 bool MoleculeListClass::OutputConfigForListOfFragments(382,14293 MoleculeLeafClass::MoleculeLeafClass(492,18874 MoleculeLeafClass::~MoleculeLeafClass(512,19382 bool MoleculeLeafClass::AddLeaf(550,20693 bool MoleculeLeafClass::FillBondStructureFromReference(564,21475 bool MoleculeLeafClass::FillRootStackForSubgraphs(622,24472 bool MoleculeLeafClass::FillListOfLocalAtoms(662,26126 bool MoleculeLeafClass::AssignKeySetsToFragment(696,27829 void MoleculeLeafClass::TranslateIndicesToGlobalIDs(762,31354 int MoleculeLeafClass::Count(786,32584 molecules.cpp,4521 double LSQ 16,351 molecule::molecule(36,961 molecule::~molecule(69,1815 bool molecule::AddAtom(88,2550 atom * molecule::AddCopyAtom(116,3584 bool molecule::AddHydrogenReplacementAtom(174,7697 bool molecule::AddXYZFile(438,21482 molecule *molecule::CopyMolecule(molecule::CopyMolecule499,23453 bond * molecule::AddBond(563,25434 bool molecule::RemoveBond(582,26231 bool molecule::RemoveBonds(594,26664 void molecule::SetBoxDimension(603,26931 bool molecule::CenterInBox(617,27297 void molecule::CenterEdge(666,28615 void molecule::CenterOrigin(702,29700 Vector * molecule::DetermineCenterOfAll(725,30355 Vector * molecule::DetermineCenterOfGravity(753,31098 void molecule::CenterGravity(782,31922 void molecule::Scale(796,32208 void molecule::Translate(811,32523 void molecule::Mirror(826,32863 void molecule::DetermineCenter(841,33204 void molecule::PrincipalAxisSystem(909,35771 bool molecule::VerletForceIntegration(1020,39893 void molecule::Align(1131,44421 bool molecule::RemoveAtom(1193,46676 bool molecule::CleanupMolecule(1208,47333 atom * molecule::FindAtom(1217,47566 atom * molecule::AskAtom(1231,47958 bool molecule::CheckBounds(1250,48510 double LeastSquareDistance 1267,49011 void molecule::GetAlignvector(1300,50133 bool molecule::Output(1374,52004 bool molecule::OutputTrajectories(1409,53012 void molecule::OutputListOfBonds(1457,55095 bool molecule::Checkout(1480,55797 bool molecule::OutputTrajectoriesXYZ(1488,56002 bool molecule::OutputXYZ(1517,56942 void molecule::CountAtoms(1544,57672 void molecule::CountElements(1579,58991 int molecule::CountCyclicBonds(1601,59545 string molecule::GetColor(1630,60399 void molecule::CalculateOrbitals(1655,60877 void molecule::CreateAdjacencyList(1696,63214 MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(1884,73778 void molecule::CyclicStructureAnalysis(2078,84349 void molecule::SetNextComponentNumber(2284,95178 void molecule::OutputComponentNumber(2305,95927 void molecule::InitComponentNumbers(2313,96194 bond * molecule::FindNextUnused(2330,96839 void molecule::ResetAllBondsToUnused(2341,97177 void molecule::ResetAllAtomNumbers(2352,97396 void OutputAlreadyVisited(2365,97689 int molecule::GuesstimateFragmentCount(2382,98216 bool molecule::ScanBufferIntoKeySet(2403,99047 bool molecule::ParseKeySetFile(2435,100271 bool molecule::StoreKeySetFile(2515,103341 bool molecule::StoreAdjacencyToFile(2571,105077 bool molecule::CheckAdjacencyFileAgainstMolecule(2606,106282 bool molecule::CheckOrderAtSite(2684,109955 bool molecule::CreateMappingLabelsToConfigSequence(2847,118616 int molecule::FragmentMolecule(2892,120867 bool molecule::PickLocalBackEdges(3084,130811 bool molecule::StoreOrderAtSiteFile(3121,132491 bool molecule::ParseOrderAtSiteFromFile(3152,133743 void molecule::CreateListOfBondsPerAtom(3209,136178 void molecule::BreadthFirstSearchAdd(3280,139568 bool molecule::BuildInducedSubgraph(3404,147541 int molecule::LookForRemovalCandidate(3459,149968 molecule * molecule::StoreFragmentFromKeySet(3487,151103 struct UniqueFragments 3782,166770 config *configuration;UniqueFragments::configuration3783,166795 atom *Root;UniqueFragments::Root3784,166820 Graph *Leaflet;UniqueFragments::Leaflet3785,166834 KeySet *FragmentSet;UniqueFragments::FragmentSet3786,166852 int ANOVAOrder;UniqueFragments::ANOVAOrder3787,166875 int FragmentCounter;UniqueFragments::FragmentCounter3788,166893 int CurrentIndex;UniqueFragments::CurrentIndex3789,166916 double TEFactor;UniqueFragments::TEFactor3790,166936 int *ShortestPathList;UniqueFragments::ShortestPathList3791,166955 bool **UsedList;UniqueFragments::UsedList3792,166980 bond **BondsPerSPList;UniqueFragments::BondsPerSPList3793,166999 int *BondsPerSPCount;UniqueFragments::BondsPerSPCount3794,167024 void molecule::SPFragmentGenerator(3811,168011 bool molecule::CheckForConnectedSubgraph(3945,176059 int molecule::PowerSetGenerator(4004,178457 void molecule::ScanForPeriodicCorrection(4156,186870 double * molecule::ReturnFullMatrixforSymmetric(4242,190359 bool KeyCompare::operator() KeyCompare::operator()4257,190766 inline void InsertFragmentIntoGraph(4294,192008 inline void InsertGraphIntoGraph(4323,193480 void molecule::FragmentBOSSANOVA(4357,195580 inline int CompareDoubles 4547,207047 int * molecule::IsEqualToWithinThreshold(4563,207650 int * molecule::GetFatherSonAtomicMap(4688,213580 bool molecule::OutputTemperatureFromTrajectories(4734,215516 parser.cpp,1173 bool FilePresent(24,588 bool TestParams(43,1017 MatrixContainer::MatrixContainer(56,1344 MatrixContainer::~MatrixContainer(69,1863 bool MatrixContainer::ParseMatrix(109,3580 bool MatrixContainer::ParseFragmentMatrix(210,7695 bool MatrixContainer::AllocateMatrix(260,9629 bool MatrixContainer::ResetMatrix(284,10737 double MatrixContainer::FindMaxValue(296,11067 double MatrixContainer::FindMinValue(312,11530 bool MatrixContainer::SetLastMatrix(330,12035 bool MatrixContainer::SetLastMatrix(343,12489 bool MatrixContainer::SumSubManyBodyTerms(358,13130 bool MatrixContainer::WriteTotalFragments(412,16895 bool MatrixContainer::WriteLastMatrix(445,17902 bool EnergyMatrix::ParseIndices(473,18785 bool EnergyMatrix::SumSubEnergy(494,19731 bool EnergyMatrix::ParseFragmentMatrix(518,20903 bool ForceMatrix::ParseIndices(550,22485 bool ForceMatrix::SumSubForces(597,24393 bool ForceMatrix::ParseFragmentMatrix(628,25589 KeySetsContainer::KeySetsContainer(679,27595 KeySetsContainer::~KeySetsContainer(690,27804 bool KeySetsContainer::ParseKeySets(707,28606 bool KeySetsContainer::ParseManyBodyTerms(751,30268 bool KeySetsContainer::Contains(814,32310 periodentafel.cpp,516 periodentafel::periodentafel(16,396 periodentafel::~periodentafel(29,703 bool periodentafel::AddElement(40,947 bool periodentafel::RemoveElement(52,1308 bool periodentafel::CleanupPeriodtable(60,1520 element * periodentafel::FindElement(70,1786 element * periodentafel::FindElement(94,2687 element * periodentafel::AskElement(107,3041 bool periodentafel::Output(123,3370 bool periodentafel::Checkout(141,3816 bool periodentafel::LoadPeriodentafel(166,4629 bool periodentafel::StorePeriodentafel(305,9306 vector.cpp,1457 Vector::Vector(14,267 Vector::Vector(18,356 Vector::~Vector(22,484 double Vector::Distance(28,639 double Vector::PeriodicDistance(41,1061 void Vector::KeepPeriodic(78,2451 double Vector::ScalarProduct(109,3471 void Vector::VectorProduct(124,3904 void Vector::ProjectOntoPlane(139,4272 double Vector::Projection(151,4570 double Vector::Norm(159,4723 void Vector::Normalize(169,4900 void Vector::Zero(181,5133 void Vector::One(189,5257 void Vector::Init(197,5397 double Vector::Angle(208,5673 void Vector::RotateVector(217,5940 Vector& operator+=(operator+=241,6599 Vector& operator*=(operator*=251,6818 Vector& operator+(262,7028 Vector& operator*(275,7281 bool Vector::Output(287,7510 ofstream& operator<<(302,7767 void Vector::Scale(311,7966 void Vector::Scale(317,8064 void Vector::Scale(323,8156 void Vector::Translate(332,8328 void Vector::MatrixMultiplication(341,8507 void Vector::InverseMatrixMultiplication(356,8918 void Vector::LinearCombinationOfVectors(396,10441 void Vector::Mirror(405,10757 bool Vector::MakeNormalVector(427,11582 bool Vector::MakeNormalVector(463,12778 bool Vector::MakeNormalVector(493,13700 bool Vector::GetOneNormalVector(512,14285 double Vector::CutsPlaneAt(558,16093 bool Vector::LSQdistance(573,16650 void Vector::AddVector(655,18606 void Vector::SubtractVector(664,18772 void Vector::CopyVector(673,18943 void Vector::AskPosition(684,19258 bool Vector::SolveSystem(712,20440 verbose.cpp,120 ostream& Verbose::print 7,197 ostream& operator<<(22,682 ostream& Binary::print 33,1015 ostream& operator<<(56,1678 graph.cpp,0