Changeset 66fd49 for src/LinearAlgebra

Timestamp:

Feb 3, 2011, 9:51:18 AM (14 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:

d6f886

Parents:

0b15bb

git-author:

Frederik Heber <heber@…> (12/30/10 20:52:17)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

Rewrite of FillVoidWithMoleculeAction.

FillVoidWithMoleculeAction:

• new parameter MinDistance and default value of 0.
• BUGFIX: filler is already created when parsing file, removed useless creation of it initially (also caused lots of confusion due to an "extra" molecule).
• Undo implemented, regression test inserted.
• Redo is somewhat hard to implement, as one would use performCall() if it only it would not retrieve its values from ValueStorage ...

FillVoidWithMolecule():

• filler is now the zeroth not the last molecule, marked by firstInsertion and firstInserter. Filler is removed if no molecules are filled.
• outsourced stuff into smaller functions
  • RandomizeMoleculePositions()
  • RemoveAtomsOutsideDomain()
  • isSpaceAroundPointVoid()
• removed FillIt to through every atom despite only CurrentPosition, indepedent of atom position, is checked.

TESTFIXES:

• Analysis/3: test.xyz changed because boundary is now 1.5 instead of 2.1 as 2.1 is not enough of molecules get filled in (and the filler already is).
• Analysis/3: tensid.data was actually lacking water at (0,0,0) which is after the rewrite present.

Location:

src/LinearAlgebra

Files:

• RealSpaceMatrix.cpp (modified) (1 diff)
• RealSpaceMatrix.hpp (modified) (1 diff)

src/LinearAlgebra/RealSpaceMatrix.cpp

@@ -121 +121 @@
   set(2,2, cos(x)*cos(y));
 }
+
+void RealSpaceMatrix::setRandomRotation()
+{
+  double phi[NDIM];
+
+  for (int i=0;i<NDIM;i++) {
+    phi[i] = rand()/(RAND_MAX/(2.*M_PI));
+  }
+
+  set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
+  set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
+  set(0,2,              cos(phi[1])*sin(phi[2])                                        );
+  set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
+  set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
+  set(1,2,              sin(phi[1])                                                    );
+  set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
+  set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
+  set(2,2,              cos(phi[1])*cos(phi[2])                                        );
+}
+
 
 RealSpaceMatrix &RealSpaceMatrix::operator=(const RealSpaceMatrix &src)

src/LinearAlgebra/RealSpaceMatrix.hpp

@@ -72 +72 @@
    */
   void setRotation(const double x, const double y, const double z);
+  void setRandomRotation();
 
   /**