source: src/Matrix.cpp@ 1da5f5

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 1da5f5 was 1da5f5, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Added method that allows fast construction of Unity matrices

  • Property mode set to 100644
File size: 4.4 KB
Line 
1/*
2 * Matrix.cpp
3 *
4 * Created on: Jun 25, 2010
5 * Author: crueger
6 */
7
8#include "Matrix.hpp"
9#include "Helpers/Assert.hpp"
10#include "Exceptions/NotInvertibleException.hpp"
11#include "Helpers/fast_functions.hpp"
12#include "Helpers/Assert.hpp"
13
14#include <gsl/gsl_blas.h>
15#include <cmath>
16
17Matrix::Matrix()
18{
19 content = gsl_matrix_calloc(NDIM, NDIM);
20}
21
22Matrix::Matrix(const double* src){
23 content = gsl_matrix_alloc(NDIM, NDIM);
24 set(0,0, src[0]);
25 set(1,0, src[1]);
26 set(2,0, src[2]);
27
28 set(0,1, src[3]);
29 set(1,1, src[4]);
30 set(2,1, src[5]);
31
32 set(0,2, src[6]);
33 set(1,2, src[7]);
34 set(2,2, src[8]);
35}
36
37Matrix::Matrix(const Matrix &src){
38 content = gsl_matrix_alloc(NDIM, NDIM);
39 gsl_matrix_memcpy(content,src.content);
40}
41
42Matrix::Matrix(gsl_matrix* _content) :
43 content(_content)
44{}
45
46Matrix::~Matrix()
47{
48 gsl_matrix_free(content);
49}
50
51void Matrix::one(){
52 gsl_matrix_free(content);
53 content = gsl_matrix_calloc(NDIM, NDIM);
54 for(int i = NDIM;i--;){
55 set(i,i,1.);
56 }
57}
58
59Matrix &Matrix::operator=(const Matrix &src){
60 if(&src!=this){
61 gsl_matrix_memcpy(content,src.content);
62 }
63 return *this;
64}
65
66Matrix &Matrix::operator+=(const Matrix &rhs){
67 gsl_matrix_add(content, rhs.content);
68 return *this;
69}
70
71Matrix &Matrix::operator-=(const Matrix &rhs){
72 gsl_matrix_sub(content, rhs.content);
73 return *this;
74}
75
76Matrix &Matrix::operator*=(const Matrix &rhs){
77 (*this) = (*this)*rhs;
78 return *this;
79}
80
81Matrix Matrix::operator+(const Matrix &rhs) const{
82 Matrix tmp = *this;
83 tmp+=rhs;
84 return tmp;
85}
86
87Matrix Matrix::operator-(const Matrix &rhs) const{
88 Matrix tmp = *this;
89 tmp-=rhs;
90 return tmp;
91}
92
93Matrix Matrix::operator*(const Matrix &rhs) const{
94 gsl_matrix *res = gsl_matrix_alloc(NDIM, NDIM);
95 gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, this->content, rhs.content, 0.0, res);
96 return Matrix(res);
97}
98
99double &Matrix::at(size_t i, size_t j){
100 ASSERT(i>=0&&i<NDIM,"Index i for Matrix access out of range");
101 ASSERT(j>=0&&j<NDIM,"Index j for Matrix access out of range");
102 return *gsl_matrix_ptr (content, i, j);
103}
104
105const double Matrix::at(size_t i, size_t j) const{
106 ASSERT(i>=0&&i<NDIM,"Index i for Matrix access out of range");
107 ASSERT(j>=0&&j<NDIM,"Index j for Matrix access out of range");
108 return gsl_matrix_get(content, i, j);
109}
110
111void Matrix::set(size_t i, size_t j, const double value){
112 ASSERT(i>=0&&i<NDIM,"Index i for Matrix access out of range");
113 ASSERT(j>=0&&j<NDIM,"Index j for Matrix access out of range");
114 gsl_matrix_set(content,i,j,value);
115}
116
117double Matrix::determinant() const{
118 return at(0,0)*at(1,1)*at(2,2)
119 + at(0,1)*at(1,2)*at(2,0)
120 + at(0,2)*at(1,0)*at(2,1)
121 - at(2,0)*at(1,1)*at(0,2)
122 - at(2,1)*at(1,2)*at(0,0)
123 - at(2,2)*at(1,0)*at(0,1);
124}
125
126Matrix Matrix::invert() const{
127 double det = determinant();
128 if(fabs(det)<MYEPSILON){
129 throw NotInvertibleException(__FILE__,__LINE__);
130 }
131
132 double detReci = 1./det;
133 Matrix res;
134 res.set(0,0, detReci*RDET2(at(1,1),at(2,1),at(1,2),at(2,2))); // A_11
135 res.set(1,0, -detReci*RDET2(at(1,0),at(2,0),at(1,2),at(2,2))); // A_21
136 res.set(2,0, detReci*RDET2(at(1,0),at(2,0),at(1,1),at(2,1))); // A_31
137 res.set(0,1, -detReci*RDET2(at(0,1),at(2,1),at(0,2),at(2,2))); // A_12
138 res.set(1,1, detReci*RDET2(at(0,0),at(2,0),at(0,2),at(2,2))); // A_22
139 res.set(2,1, -detReci*RDET2(at(0,0),at(2,0),at(0,1),at(2,1))); // A_32
140 res.set(0,2, detReci*RDET2(at(0,1),at(1,1),at(0,2),at(1,2))); // A_13
141 res.set(1,2, -detReci*RDET2(at(0,0),at(1,0),at(0,2),at(1,2))); // A_23
142 res.set(2,2, detReci*RDET2(at(0,0),at(1,0),at(0,1),at(1,1))); // A_33
143 return res;
144}
145
146Matrix &Matrix::operator*=(const double factor){
147 gsl_matrix_scale(content, factor);
148 return *this;
149}
150
151Matrix operator*(const double factor,const Matrix& mat){
152 Matrix tmp = mat;
153 tmp*=factor;
154 return tmp;
155}
156
157Matrix operator*(const Matrix &mat,const double factor){
158 return factor*mat;
159}
160
161/** Blows the 6-dimensional \a cell_size array up to a full NDIM by NDIM matrix.
162 * \param *symm 6-dim array of unique symmetric matrix components
163 * \return allocated NDIM*NDIM array with the symmetric matrix
164 */
165Matrix ReturnFullMatrixforSymmetric(const double * const symm)
166{
167 Matrix matrix;
168 matrix.set(0,0, symm[0]);
169 matrix.set(1,0, symm[1]);
170 matrix.set(2,0, symm[3]);
171 matrix.set(0,1, symm[1]);
172 matrix.set(1,1, symm[2]);
173 matrix.set(2,1, symm[4]);
174 matrix.set(0,2, symm[3]);
175 matrix.set(1,2, symm[4]);
176 matrix.set(2,2, symm[5]);
177 return matrix;
178};
Note: See TracBrowser for help on using the repository browser.