source: src/vector.hpp@ 5f612ee

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 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 5f612ee was 5f612ee, checked in by Frederik Heber <heber@…>, 15 years ago

Merge branch 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

  • new molecule() replaced by World::getInstance().createMolecule()
  • new atom() replaced by World::getInstance().createAtom() where appropriate.
  • Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
  • DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
  • ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

  • Property mode set to 100755
File size: 4.1 KB
Line 
1#ifndef VECTOR_HPP_
2#define VECTOR_HPP_
3
4using namespace std;
5
6/*********************************************** includes ***********************************/
7
8// include config.h
9#ifdef HAVE_CONFIG_H
10#include <config.h>
11#endif
12
13#include <iostream>
14#include <gsl/gsl_vector.h>
15#include <gsl/gsl_multimin.h>
16
17#include "defs.hpp"
18
19/********************************************** declarations *******************************/
20
21/** Single vector.
22 * basically, just a x[3] but with helpful functions
23 */
24class Vector {
25 public:
26 double x[NDIM];
27
28 Vector();
29 Vector(const Vector * const a);
30 Vector(const Vector &a);
31 Vector(const double x1, const double x2, const double x3);
32 ~Vector();
33
34 double Distance(const Vector * const y) const;
35 double DistanceSquared(const Vector * const y) const;
36 double DistanceToPlane(const Vector * const PlaneNormal, const Vector * const PlaneOffset) const;
37 double PeriodicDistance(const Vector * const y, const double * const cell_size) const;
38 double PeriodicDistanceSquared(const Vector * const y, const double * const cell_size) const;
39 double ScalarProduct(const Vector * const y) const;
40 double Norm() const;
41 double NormSquared() const;
42 double Angle(const Vector * const y) const;
43 bool IsZero() const;
44 bool IsOne() const;
45 bool IsNormalTo(const Vector * const normal) const;
46 bool IsEqualTo(const Vector * const a) const;
47
48 void AddVector(const Vector * const y);
49 void SubtractVector(const Vector * const y);
50 void CopyVector(const Vector * const y);
51 void CopyVector(const Vector &y);
52 void RotateVector(const Vector * const y, const double alpha);
53 void VectorProduct(const Vector * const y);
54 void ProjectOntoPlane(const Vector * const y);
55 void ProjectIt(const Vector * const y);
56 Vector Projection(const Vector * const y) const;
57 void Zero();
58 void One(const double one);
59 void Init(const double x1, const double x2, const double x3);
60 void Normalize();
61 void Translate(const Vector * const x);
62 void Mirror(const Vector * const x);
63 void Scale(const double ** const factor);
64 void Scale(const double * const factor);
65 void Scale(const double factor);
66 void MatrixMultiplication(const double * const M);
67 void InverseMatrixMultiplication(const double * const M);
68 void KeepPeriodic(const double * const matrix);
69 void LinearCombinationOfVectors(const Vector * const x1, const Vector * const x2, const Vector * const x3, const double * const factors);
70 double CutsPlaneAt(const Vector * const A, const Vector * const B, const Vector * const C) const;
71 Vector GetDistanceVectorToPlane(const Vector * const PlaneNormal, const Vector * const PlaneOffset) const;
72 bool GetIntersectionWithPlane(const Vector * const PlaneNormal, const Vector * const PlaneOffset, const Vector * const Origin, const Vector * const LineVector);
73 bool GetIntersectionOfTwoLinesOnPlane(const Vector * const Line1a, const Vector * const Line1b, const Vector * const Line2a, const Vector * const Line2b, const Vector *Normal = NULL);
74 bool GetOneNormalVector(const Vector * const x1);
75 bool MakeNormalVector(const Vector * const y1);
76 bool MakeNormalVector(const Vector * const y1, const Vector * const y2);
77 bool MakeNormalVector(const Vector * const x1, const Vector * const x2, const Vector * const x3);
78 bool SolveSystem(Vector * x1, Vector * x2, Vector * y, const double alpha, const double beta, const double c);
79 bool LSQdistance(const Vector ** vectors, int dim);
80 void AskPosition(const double * const cell_size, const bool check);
81 void Output() const;
82 bool IsInParallelepiped(const Vector &offset, const double * const parallelepiped) const;
83 void WrapPeriodically(const double * const M, const double * const Minv);
84
85};
86
87ostream & operator << (ostream& ost, const Vector &m);
88bool operator==(const Vector& a, const Vector& b);
89const Vector& operator+=(Vector& a, const Vector& b);
90const Vector& operator-=(Vector& a, const Vector& b);
91const Vector& operator*=(Vector& a, const double m);
92Vector const operator*(const Vector& a, const double m);
93Vector const operator*(const double m, const Vector& a);
94Vector const operator+(const Vector& a, const Vector& b);
95Vector const operator-(const Vector& a, const Vector& b);
96
97
98#endif /*VECTOR_HPP_*/
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