source: src/TAGS@ 03e57a

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 03e57a was 69eb71, checked in by Christian Neuen <neuen@…>, 17 years ago

Multiple changes to boundary, currently not fully operational.
Molecules has a new routine to create adjacency lists, reading bonds from a dbond file instead of looking for the distances by itself.
Vector function Project onto plane has been updated.
  • Property mode set to 100644
File size: 13.1 KB
Line 
1
2
3analyzer.cpp,17
4int main(23,516
5
6
7atom.cpp,262
8atom::atom(13,258
9atom::~atom(35,653
10atom *atom::GetTrueFather(atom::GetTrueFather45,973
11bool atom::Output(61,1416
12bool atom::OutputXYZLine(78,2040
13ostream & operator << operator <<87,2262
14bool atom::Compare(97,2547
15bool operator < operator <105,2652
16
17
18bond.cpp,385
19bond::bond(14,290
20bond::bond(34,691
21bond::bond(52,1136
22bond::~bond(73,1597
23ostream & operator << operator <<84,1788
24atom * bond::GetOtherAtom(94,2199
25bond * bond::GetFirstBond(107,2583
26bond * bond::GetLastBond(116,2865
27enum Shading bond::IsUsed(124,3000
28bool bond::Contains(133,3217
29bool bond::Contains(142,3475
30bool bond::MarkUsed(150,3691
31void bond::ResetUsed(163,3973
32
33
34border.cpp,229
35void Find_next_suitable_point(5,51
36void Tesselation::Find_next_suitable_triangle(63,2078
37void Find_second_point_for_Tesselation(141,4691
38void Tesselation::Find_starting_triangle(173,5558
39void Find_non_convex_border(287,8778
40
41
42boundary.cpp,1347
43BoundaryPointSet::BoundaryPointSet(12,397
44BoundaryPointSet::BoundaryPointSet(18,469
45BoundaryPointSet::~BoundaryPointSet(25,578
46void BoundaryPointSet::AddLine(31,704
47ostream & operator << operator <<42,1045
48BoundaryLineSet::BoundaryLineSet(50,1273
49BoundaryLineSet::BoundaryLineSet(58,1396
50BoundaryLineSet::~BoundaryLineSet(72,1836
51void BoundaryLineSet::AddTriangle(87,2407
52ostream & operator << operator <<94,2656
53BoundaryTriangleSet::BoundaryTriangleSet(103,2939
54BoundaryTriangleSet::BoundaryTriangleSet(112,3075
55BoundaryTriangleSet::~BoundaryTriangleSet(144,4167
56void BoundaryTriangleSet::GetNormalVector(159,4691
57ostream & operator << operator <<169,5082
58class BoundaryPointSet * GetCommonEndpoint(182,5559
59Boundaries * GetBoundaryPoints(209,6893
60double * GetDiametersOfCluster(384,15165
61double VolumeOfConvexEnvelope(470,20313
62void PrepareClustersinWater(610,27033
63Tesselation::Tesselation(692,31276
64Tesselation::~Tesselation(702,31494
65void Tesselation::GuessStartingTriangle(714,31995
66void Tesselation::TesselateOnBoundary(849,39116
67void Tesselation::AddPoint(1003,49558
68void Find_next_suitable_point(1024,50156
69void Tesselation::Find_next_suitable_triangle(1082,52183
70void Find_second_point_for_Tesselation(1160,54796
71void Tesselation::Find_starting_triangle(1192,55663
72void Find_non_convex_border(1306,58883
73
74
75builder.cpp,378
76static void AddAtoms(62,2281
77static void CenterAtoms(259,10538
78static void AlignAtoms(314,12598
79static void MirrorAtoms(382,15117
80static void RemoveAtoms(429,16855
81static void MeasureAtoms(487,18852
82static void FragmentAtoms(598,23710
83static void testroutine(619,24543
84static void SaveConfig(692,27108
85static int ParseCommandLineOptions(771,29725
86int main(1303,56039
87
88
89config.cpp,445
90config::config(13,261
91config::~config(89,2039
92void config::Edit(102,2590
93int config::TestSyntax(367,16198
94bool config::GetIsAngstroem(389,16806
95char * config::GetDefaultPath(397,16955
96void config::SetDefaultPath(406,17101
97void config::RetrieveConfigPathAndName(414,17286
98void config::Load(444,18309
99void config::LoadOld(773,36012
100bool config::Save(977,45063
101bool config::SaveMPQC(1084,52722
102int config::ParseForParameter(1213,58282
103
104
105datacreator.cpp,954
106bool OpenOutputFile(19,468
107bool AppendOutputFile(37,1009
108bool CreateDataEnergyOrder(56,1690
109bool CreateDataDeltaEnergyOrder(89,3244
110bool CreateDataForcesOrder(126,5185
111bool CreateDataDeltaForcesOrder(158,6656
112bool CreateDataDeltaForcesOrderPerAtom(190,8202
113bool CreateDataForcesOrderPerAtom(237,10288
114bool CreateDataFragment(266,11393
115void CreateMaxFragmentOrder(294,12696
116void CreateMinFragmentOrder(311,13550
117bool CreateDataFragmentOrder(331,14537
118void CreateEnergy(358,15708
119void CreateMinimumForce(369,16220
120void CreateMeanForce(403,17598
121void CreateMaximumForce(428,18520
122void CreateSameForce(450,19299
123void CreateVectorSumForce(460,19630
124void CreatePlotHeader(480,20389
125bool CreatePlotOrder(517,21999
126void AbsEnergyPlotLine(538,23154
127void EnergyPlotLine(562,23997
128void ForceMagnitudePlotLine(586,24845
129void AbsFirstForceValuePlotLine(617,26051
130void BoxesForcePlotLine(648,27192
131void BoxesFirstForceValuePlotLine(680,28575
132
133
134element.cpp,112
135element::element(13,270
136element::~element(23,412
137bool element::Output(28,507
138bool element::Checkout(43,1115
139
140
141helpers.cpp,325
142double ask_value(15,316
143void debug_in(30,757
144void debug_in(34,918
145void * Malloc(42,1223
146void * Calloc(56,1671
147void * ReAlloc(71,2182
148void Free(88,2787
149char* MallocString(103,3192
150void bound(121,3685
151void flip(134,3996
152int pot(147,4205
153char *FixedDigitNumber(FixedDigitNumber161,4624
154bool IsValidNumber(188,5558
155
156
157joiner.cpp,17
158int main(17,429
159
160
161moleculelist.cpp,859
162MoleculeListClass::MoleculeListClass(13,290
163MoleculeListClass::MoleculeListClass(21,496
164MoleculeListClass::~MoleculeListClass(33,889
165int MolCompare(52,1584
166void MoleculeListClass::Output(127,3994
167bool MoleculeListClass::AddHydrogenCorrection(142,4664
168bool MoleculeListClass::StoreForcesFile(329,12009
169bool MoleculeListClass::OutputConfigForListOfFragments(382,14293
170MoleculeLeafClass::MoleculeLeafClass(492,18874
171MoleculeLeafClass::~MoleculeLeafClass(512,19382
172bool MoleculeLeafClass::AddLeaf(550,20693
173bool MoleculeLeafClass::FillBondStructureFromReference(564,21475
174bool MoleculeLeafClass::FillRootStackForSubgraphs(622,24472
175bool MoleculeLeafClass::FillListOfLocalAtoms(662,26126
176bool MoleculeLeafClass::AssignKeySetsToFragment(696,27829
177void MoleculeLeafClass::TranslateIndicesToGlobalIDs(762,31354
178int MoleculeLeafClass::Count(786,32584
179
180
181molecules.cpp,4521
182double LSQ 16,351
183molecule::molecule(36,961
184molecule::~molecule(69,1815
185bool molecule::AddAtom(88,2550
186atom * molecule::AddCopyAtom(116,3584
187bool molecule::AddHydrogenReplacementAtom(174,7697
188bool molecule::AddXYZFile(438,21482
189molecule *molecule::CopyMolecule(molecule::CopyMolecule499,23453
190bond * molecule::AddBond(563,25434
191bool molecule::RemoveBond(582,26231
192bool molecule::RemoveBonds(594,26664
193void molecule::SetBoxDimension(603,26931
194bool molecule::CenterInBox(617,27297
195void molecule::CenterEdge(666,28615
196void molecule::CenterOrigin(702,29700
197Vector * molecule::DetermineCenterOfAll(725,30355
198Vector * molecule::DetermineCenterOfGravity(753,31098
199void molecule::CenterGravity(782,31922
200void molecule::Scale(796,32208
201void molecule::Translate(811,32523
202void molecule::Mirror(826,32863
203void molecule::DetermineCenter(841,33204
204void molecule::PrincipalAxisSystem(909,35771
205bool molecule::VerletForceIntegration(1020,39893
206void molecule::Align(1131,44421
207bool molecule::RemoveAtom(1193,46676
208bool molecule::CleanupMolecule(1208,47333
209atom * molecule::FindAtom(1217,47566
210atom * molecule::AskAtom(1231,47958
211bool molecule::CheckBounds(1250,48510
212double LeastSquareDistance 1267,49011
213void molecule::GetAlignvector(1300,50133
214bool molecule::Output(1374,52004
215bool molecule::OutputTrajectories(1409,53012
216void molecule::OutputListOfBonds(1457,55095
217bool molecule::Checkout(1480,55797
218bool molecule::OutputTrajectoriesXYZ(1488,56002
219bool molecule::OutputXYZ(1517,56942
220void molecule::CountAtoms(1544,57672
221void molecule::CountElements(1579,58991
222int molecule::CountCyclicBonds(1601,59545
223string molecule::GetColor(1630,60399
224void molecule::CalculateOrbitals(1655,60877
225void molecule::CreateAdjacencyList(1696,63214
226MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(1884,73778
227void molecule::CyclicStructureAnalysis(2078,84349
228void molecule::SetNextComponentNumber(2284,95178
229void molecule::OutputComponentNumber(2305,95927
230void molecule::InitComponentNumbers(2313,96194
231bond * molecule::FindNextUnused(2330,96839
232void molecule::ResetAllBondsToUnused(2341,97177
233void molecule::ResetAllAtomNumbers(2352,97396
234void OutputAlreadyVisited(2365,97689
235int molecule::GuesstimateFragmentCount(2382,98216
236bool molecule::ScanBufferIntoKeySet(2403,99047
237bool molecule::ParseKeySetFile(2435,100271
238bool molecule::StoreKeySetFile(2515,103341
239bool molecule::StoreAdjacencyToFile(2571,105077
240bool molecule::CheckAdjacencyFileAgainstMolecule(2606,106282
241bool molecule::CheckOrderAtSite(2684,109955
242bool molecule::CreateMappingLabelsToConfigSequence(2847,118616
243int molecule::FragmentMolecule(2892,120867
244bool molecule::PickLocalBackEdges(3084,130811
245bool molecule::StoreOrderAtSiteFile(3121,132491
246bool molecule::ParseOrderAtSiteFromFile(3152,133743
247void molecule::CreateListOfBondsPerAtom(3209,136178
248void molecule::BreadthFirstSearchAdd(3280,139568
249bool molecule::BuildInducedSubgraph(3404,147541
250int molecule::LookForRemovalCandidate(3459,149968
251molecule * molecule::StoreFragmentFromKeySet(3487,151103
252struct UniqueFragments 3782,166770
253 config *configuration;UniqueFragments::configuration3783,166795
254 atom *Root;UniqueFragments::Root3784,166820
255 Graph *Leaflet;UniqueFragments::Leaflet3785,166834
256 KeySet *FragmentSet;UniqueFragments::FragmentSet3786,166852
257 int ANOVAOrder;UniqueFragments::ANOVAOrder3787,166875
258 int FragmentCounter;UniqueFragments::FragmentCounter3788,166893
259 int CurrentIndex;UniqueFragments::CurrentIndex3789,166916
260 double TEFactor;UniqueFragments::TEFactor3790,166936
261 int *ShortestPathList;UniqueFragments::ShortestPathList3791,166955
262 bool **UsedList;UniqueFragments::UsedList3792,166980
263 bond **BondsPerSPList;UniqueFragments::BondsPerSPList3793,166999
264 int *BondsPerSPCount;UniqueFragments::BondsPerSPCount3794,167024
265void molecule::SPFragmentGenerator(3811,168011
266bool molecule::CheckForConnectedSubgraph(3945,176059
267int molecule::PowerSetGenerator(4004,178457
268void molecule::ScanForPeriodicCorrection(4156,186870
269double * molecule::ReturnFullMatrixforSymmetric(4242,190359
270bool KeyCompare::operator() KeyCompare::operator()4257,190766
271inline void InsertFragmentIntoGraph(4294,192008
272inline void InsertGraphIntoGraph(4323,193480
273void molecule::FragmentBOSSANOVA(4357,195580
274inline int CompareDoubles 4547,207047
275int * molecule::IsEqualToWithinThreshold(4563,207650
276int * molecule::GetFatherSonAtomicMap(4688,213580
277bool molecule::OutputTemperatureFromTrajectories(4734,215516
278
279
280parser.cpp,1173
281bool FilePresent(24,588
282bool TestParams(43,1017
283MatrixContainer::MatrixContainer(56,1344
284MatrixContainer::~MatrixContainer(69,1863
285bool MatrixContainer::ParseMatrix(109,3580
286bool MatrixContainer::ParseFragmentMatrix(210,7695
287bool MatrixContainer::AllocateMatrix(260,9629
288bool MatrixContainer::ResetMatrix(284,10737
289double MatrixContainer::FindMaxValue(296,11067
290double MatrixContainer::FindMinValue(312,11530
291bool MatrixContainer::SetLastMatrix(330,12035
292bool MatrixContainer::SetLastMatrix(343,12489
293bool MatrixContainer::SumSubManyBodyTerms(358,13130
294bool MatrixContainer::WriteTotalFragments(412,16895
295bool MatrixContainer::WriteLastMatrix(445,17902
296bool EnergyMatrix::ParseIndices(473,18785
297bool EnergyMatrix::SumSubEnergy(494,19731
298bool EnergyMatrix::ParseFragmentMatrix(518,20903
299bool ForceMatrix::ParseIndices(550,22485
300bool ForceMatrix::SumSubForces(597,24393
301bool ForceMatrix::ParseFragmentMatrix(628,25589
302KeySetsContainer::KeySetsContainer(679,27595
303KeySetsContainer::~KeySetsContainer(690,27804
304bool KeySetsContainer::ParseKeySets(707,28606
305bool KeySetsContainer::ParseManyBodyTerms(751,30268
306bool KeySetsContainer::Contains(814,32310
307
308
309periodentafel.cpp,516
310periodentafel::periodentafel(16,396
311periodentafel::~periodentafel(29,703
312bool periodentafel::AddElement(40,947
313bool periodentafel::RemoveElement(52,1308
314bool periodentafel::CleanupPeriodtable(60,1520
315element * periodentafel::FindElement(70,1786
316element * periodentafel::FindElement(94,2687
317element * periodentafel::AskElement(107,3041
318bool periodentafel::Output(123,3370
319bool periodentafel::Checkout(141,3816
320bool periodentafel::LoadPeriodentafel(166,4629
321bool periodentafel::StorePeriodentafel(305,9306
322
323
324vector.cpp,1457
325Vector::Vector(14,267
326Vector::Vector(18,356
327Vector::~Vector(22,484
328double Vector::Distance(28,639
329double Vector::PeriodicDistance(41,1061
330void Vector::KeepPeriodic(78,2451
331double Vector::ScalarProduct(109,3471
332void Vector::VectorProduct(124,3904
333void Vector::ProjectOntoPlane(139,4272
334double Vector::Projection(151,4570
335double Vector::Norm(159,4723
336void Vector::Normalize(169,4900
337void Vector::Zero(181,5133
338void Vector::One(189,5257
339void Vector::Init(197,5397
340double Vector::Angle(208,5673
341void Vector::RotateVector(217,5940
342Vector& operator+=(operator+=241,6599
343Vector& operator*=(operator*=251,6818
344Vector& operator+(262,7028
345Vector& operator*(275,7281
346bool Vector::Output(287,7510
347ofstream& operator<<(302,7767
348void Vector::Scale(311,7966
349void Vector::Scale(317,8064
350void Vector::Scale(323,8156
351void Vector::Translate(332,8328
352void Vector::MatrixMultiplication(341,8507
353void Vector::InverseMatrixMultiplication(356,8918
354void Vector::LinearCombinationOfVectors(396,10441
355void Vector::Mirror(405,10757
356bool Vector::MakeNormalVector(427,11582
357bool Vector::MakeNormalVector(463,12778
358bool Vector::MakeNormalVector(493,13700
359bool Vector::GetOneNormalVector(512,14285
360double Vector::CutsPlaneAt(558,16093
361bool Vector::LSQdistance(573,16650
362void Vector::AddVector(655,18606
363void Vector::SubtractVector(664,18772
364void Vector::CopyVector(673,18943
365void Vector::AskPosition(684,19258
366bool Vector::SolveSystem(712,20440
367
368
369verbose.cpp,120
370ostream& Verbose::print 7,197
371ostream& operator<<(22,682
372ostream& Binary::print 33,1015
373ostream& operator<<(56,1678
374
375
376graph.cpp,0
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