Changeset 54a746 for src/molecules.hpp

Timestamp:

Aug 18, 2009, 8:48:06 AM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

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

Children:

658efb

Parents:

093645

git-author:

Frederik Heber <heber@…> (08/18/09 08:38:46)

git-committer:

Frederik Heber <heber@…> (08/18/09 08:48:06)

Message:

Incorporation of Unit test on class Vector.

• new file leastsquaremin.[ch]pp has least square minimisation which is otherwise unclean between classes molecules and Vector

Unit test (later tests rely on good results of earlier ones)

• incorporation of cppunit into configure.ac and Makefile.am of molecuilder/src
• UnityTest: test IsZero and IsOne
• SimpleAlgebraTest: tests algebra
• OperatorAlgebraTest: tests algebra with operator implementations
• EuclidianTest: tests norms and distances

changes to class Vector:

• Vector::IsNull() -> IsZero()
• new function Vector::IsOne() similar to IsZero()
• BUGFIX: Vector::IsNULL() (thx to unit test :)

• Tesselation::getAngle() changed due to above rename

File:

• src/molecules.hpp (modified) (2 diffs)

src/molecules.hpp

@@ -28 +28 @@
 #include "bond.hpp"
 #include "element.hpp"
+#include "leastsquaremin.hpp"
 #include "linkedcell.hpp"
 #include "parser.hpp"
@@ -83 +84 @@
 
 
-// some algebraic matrix stuff
-#define RDET3(a) ((a)[0]*(a)[4]*(a)[8] + (a)[3]*(a)[7]*(a)[2] + (a)[6]*(a)[1]*(a)[5] - (a)[2]*(a)[4]*(a)[6] - (a)[5]*(a)[7]*(a)[0] - (a)[8]*(a)[1]*(a)[3])  //!< hard-coded determinant of a 3x3 matrix
-#define RDET2(a0,a1,a2,a3) ((a0)*(a3)-(a1)*(a2))                      //!< hard-coded determinant of a 2x2 matrix
-
-
-/** Parameter structure for least square minimsation.
- */
-struct LSQ_params {
-  Vector **vectors;
-  int num;
-};
-
-double LSQ(const gsl_vector * x, void * params);
-
-/** Parameter structure for least square minimsation.
- */
-struct lsq_params {
-  gsl_vector *x;
-  const molecule *mol;
-  element *type;
-};
 
 #define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented