Changeset 84c494 for src/analysis_correlation.cpp

Timestamp:

Jun 30, 2010, 1:55:42 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

4907a3

Parents:

9df5c6

Message:

Made the world store the cell_size within a Box object.

File:

• src/analysis_correlation.cpp (modified) (7 diffs)

src/analysis_correlation.cpp

@@ -22 +22 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Box.hpp"
 
 
@@ -35 +36 @@
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
-  double *domain = World::getInstance().getDomain();
+  const Matrix &domain = World::getInstance().getDomain().getM();
 
   if (molecules->ListOfMolecules.empty()) {
@@ -136 +137 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++){
     if ((*MolWalker)->ActiveFlag) {
-      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullInverseMatrix = FullMatrix.invert();
+      Matrix FullMatrix = World::getInstance().getDomain().getM();
+      Matrix FullInverseMatrix = World::getInstance().getDomain().getMinv();
       DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       eLog() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
@@ -190 +191 @@
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
-  double *cell_size = World::getInstance().getDomain();
+  const Matrix &domain = World::getInstance().getDomain().getM();
 
   if (molecules->ListOfMolecules.empty()) {
@@ -206 +207 @@
         for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
           if ((*type == NULL) || ((*iter)->type == *type)) {
-            distance = (*iter)->node->PeriodicDistance(*point, cell_size);
+            distance = (*iter)->node->PeriodicDistance(*point, domain);
             DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
             outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> ((*iter), point) ) );
@@ -241 +242 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullInverseMatrix = FullMatrix.invert();
+      Matrix FullMatrix = World::getInstance().getDomain().getM();
+      Matrix FullInverseMatrix = World::getInstance().getDomain().getMinv();
       DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
@@ -343 +344 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      Matrix FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-      Matrix FullInverseMatrix = FullMatrix.invert();
+      Matrix FullMatrix = World::getInstance().getDomain().getM();
+      Matrix FullInverseMatrix = World::getInstance().getDomain().getMinv();
       DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
       for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {