Index: c/TAGS
===================================================================
--- src/TAGS	(revision 133d56d645e8dd889bb7a2a950dd50a4b08afcaf)
+++ 	(revision )
@@ -1,376 +1,0 @@
-
-
-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
