Changeset c80643 for src/LinkedCell

Timestamp:

Jan 2, 2012, 1:34:29 PM (13 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:

53d894

Parents:

4459fc

git-author:

Frederik Heber <heber@…> (12/19/11 21:49:53)

git-committer:

Frederik Heber <heber@…> (01/02/12 13:34:29)

Message:

LinkedCell_Controller::getView() now needs a PointCloud set.

• this will allow the World to initialise new LinkedCell_Model, which at the very start first need to know about all presents atoms in the World.

Location:

src/LinkedCell

Files:

• LinkedCell_Controller.cpp (modified) (3 diffs)
• LinkedCell_Controller.hpp (modified) (2 diffs)
• LinkedCell_Model.cpp (modified) (1 diff)
• LinkedCell_Model.hpp (modified) (2 diffs)
• unittests/LinkedCell_ControllerUnitTest.cpp (modified) (13 diffs)
• unittests/LinkedCell_ControllerUnitTest.hpp (modified) (2 diffs)

src/LinkedCell/LinkedCell_Controller.cpp

@@ -26 +26 @@
 #include "LinkedCell_Model.hpp"
 #include "LinkedCell_View.hpp"
+#include "IPointCloud.hpp"
 
 
@@ -153 +154 @@
  *
  * @param distance edge length of the requested linked cell structure
+ * @param set of initial points to insert when new model is created (not always), should be World's
  * @return LinkedCell_View wrapping the best LinkedCell_Model
  */
-LinkedCell_View LinkedCell_Controller::getView(const double distance)
+LinkedCell_View LinkedCell_Controller::getView(const double distance, IPointCloud &set)
 {
   /// Look for best instance.
@@ -163 +165 @@
   if (LCModel_best == NULL) {
     LinkedCell_Model *LCModel_new = new LinkedCell_Model(distance, domain);
+    LCModel_new->insertPointCloud(set);
     insertNewModel(distance, LCModel_new);
     LinkedCell_View view(const_cast<const LinkedCell_Model &>(*LCModel_new));

src/LinkedCell/LinkedCell_Controller.hpp

@@ -20 +20 @@
 
 class LinkedCell_ControllerTest;
+class IPointCloud;
 
 namespace LinkedCell {
@@ -47 +48 @@
     ~LinkedCell_Controller();
 
-    LinkedCell_View getView(const double distance);
+    LinkedCell_View getView(const double distance, IPointCloud &set);
 
   private:

src/LinkedCell/LinkedCell_Model.cpp

@@ -139 +139 @@
   N.resize(index);
   ASSERT(getSize(0)*getSize(1)*getSize(2) < MAX_LINKEDCELLNODES,
-      "LinkedCell_Model::AllocateCells() - Number linked of linked cell nodes exceded hard-coded limit, use greater edge length!");
+      "LinkedCell_Model::AllocateCells() - Number linked of linked cell nodes exceeded hard-coded limit, use greater edge length!");
 
   // allocate LinkedCell instances

src/LinkedCell/LinkedCell_Model.hpp

@@ -67 +67 @@
     void setPartition(double distance);
 
+    void insertPointCloud(IPointCloud &set);
+
     //!> static indices to get nearest neighbors as default argument
     static tripleIndex NearestNeighbors;
@@ -78 +80 @@
     void AllocateCells();
     void Reset();
-    void insertPointCloud(IPointCloud &set);
 
     void startListening();

src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp

@@ -24 +24 @@
 #include <cppunit/ui/text/TestRunner.h>
 
+#include "Atom/atom.hpp"
 #include "Box.hpp"
 #include "CodePatterns/Assert.hpp"
@@ -30 +31 @@
 #include "LinkedCell/LinkedCell_View.hpp"
 #include "LinkedCell/unittests/defs.hpp"
+#include "LinkedCell/PointCloudAdaptor.hpp"
 
 #include "LinkedCell_ControllerUnitTest.hpp"
@@ -57 +59 @@
 
   controller = new LinkedCell::LinkedCell_Controller(*domain);
+
+  // create empty set
+  emptyset = new PointCloudAdaptor< std::vector<atom *> >(&emptyvector, std::string("emptyset"));
 }
 
@@ -64 +69 @@
   delete controller;
   delete domain;
+  delete emptyset;
 }
 
@@ -113 +119 @@
   /// obtain a view
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(2.);
+  LinkedCell::LinkedCell_View view = controller->getView(2., *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
   {
     /// get same view again and check that now new instance appears
-    LinkedCell::LinkedCell_View view_again = controller->getView(2.);
+    LinkedCell::LinkedCell_View view_again = controller->getView(2., *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
@@ -129 +135 @@
   /// obtain a view
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(2.);
+  LinkedCell::LinkedCell_View view = controller->getView(2., *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
   {
     /// pick another view that is not close enough
-    LinkedCell::LinkedCell_View view_other = controller->getView(5.);
+    LinkedCell::LinkedCell_View view_other = controller->getView(5., *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)2, controller->ModelsMap.size() );
   }
@@ -146 +152 @@
   const double edgelength = 2.;
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(edgelength);
+  LinkedCell::LinkedCell_View view = controller->getView(edgelength, *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
@@ -153 +159 @@
   {
     /// ... at half lower interval half
-    LinkedCell::LinkedCell_View view_lowerhalf = controller->getView((edgelength + interval.first)/2.);
+    LinkedCell::LinkedCell_View view_lowerhalf = controller->getView((edgelength + interval.first)/2., *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
   {
     /// ... at half upper interval half
-    LinkedCell::LinkedCell_View view_upperhalf = controller->getView((interval.last + edgelength)/2.);
+    LinkedCell::LinkedCell_View view_upperhalf = controller->getView((interval.last + edgelength)/2., *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
   {
     /// ... close to lower boundary
-    LinkedCell::LinkedCell_View view_closelower = controller->getView(interval.first + std::numeric_limits<double>::round_error());
+    LinkedCell::LinkedCell_View view_closelower = controller->getView(interval.first + std::numeric_limits<double>::round_error(), *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
   {
     /// ... close to upper boundary
-    LinkedCell::LinkedCell_View view_closerupper = controller->getView(interval.last - std::numeric_limits<double>::round_error());
+    LinkedCell::LinkedCell_View view_closerupper = controller->getView(interval.last - std::numeric_limits<double>::round_error(), *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
   {
     /// on lower boundary
-    LinkedCell::LinkedCell_View view_onlower = controller->getView(interval.first);
+    LinkedCell::LinkedCell_View view_onlower = controller->getView(interval.first, *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
@@ -187 +193 @@
   /// obtain a view
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(edgelength);
+  LinkedCell::LinkedCell_View view = controller->getView(edgelength, *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
@@ -194 +200 @@
   {
     /// ... outside lower boundary
-    LinkedCell::LinkedCell_View view_outsidelower = controller->getView(interval.first - std::numeric_limits<double>::round_error());
+    LinkedCell::LinkedCell_View view_outsidelower = controller->getView(interval.first - std::numeric_limits<double>::round_error(), *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)2, controller->ModelsMap.size() );
   }
   {
     /// ... on upper boundary
-    LinkedCell::LinkedCell_View view_onupper = controller->getView(interval.last);
+    LinkedCell::LinkedCell_View view_onupper = controller->getView(interval.last, *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)3, controller->ModelsMap.size() );
   }
@@ -211 +217 @@
   const double edgelength = 1.9*controller->lower_threshold;
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(edgelength);
+  LinkedCell::LinkedCell_View view = controller->getView(edgelength, *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
   {
     /// get a view at threshold and check that no new instance has been created
-    LinkedCell::LinkedCell_View view_onlower = controller->getView(controller->lower_threshold);
+    LinkedCell::LinkedCell_View view_onlower = controller->getView(controller->lower_threshold, *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
   {
     /// pick a view below 1.
-    LinkedCell::LinkedCell_View view_beneathlower = controller->getView(0.1*controller->lower_threshold);
+    LinkedCell::LinkedCell_View view_beneathlower = controller->getView(0.1*controller->lower_threshold, *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
@@ -233 +239 @@
   const double edgelength = controller->upper_threshold;
   CPPUNIT_ASSERT_EQUAL( (size_t)0, controller->ModelsMap.size() );
-  LinkedCell::LinkedCell_View view = controller->getView(edgelength);
+  LinkedCell::LinkedCell_View view = controller->getView(edgelength, *emptyset);
   CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
 
   {
     /// get a view beyond threshold and check that no new instance has been created
-    LinkedCell::LinkedCell_View view_beyondupper = controller->getView(1.1*controller->upper_threshold);
+    LinkedCell::LinkedCell_View view_beyondupper = controller->getView(1.1*controller->upper_threshold, *emptyset);
     CPPUNIT_ASSERT_EQUAL( (size_t)1, controller->ModelsMap.size() );
   }
@@ -246 +252 @@
     range<double> interval = controller->getHeuristicRange(edgelength);
     if ( !interval.isInRange(0.1*controller->upper_threshold) ) {
-      LinkedCell::LinkedCell_View view_beneathupper = controller->getView(0.1*controller->upper_threshold);
+      LinkedCell::LinkedCell_View view_beneathupper = controller->getView(0.1*controller->upper_threshold, *emptyset);
       CPPUNIT_ASSERT_EQUAL( (size_t)2, controller->ModelsMap.size() );
     }

src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp

@@ -17 +17 @@
 #include <cppunit/extensions/HelperMacros.h>
 
+#include <vector>
+
+#include "LinkedCell/PointCloudAdaptor.hpp"
+
+class atom;
 class Box;
 class RealSpaceMatrix;
@@ -54 +59 @@
       Box *domain;
       RealSpaceMatrix *BoxM;
+      std::vector<atom *> emptyvector;
+      PointCloudAdaptor< std::vector<atom *> > *emptyset;
       LinkedCell::LinkedCell_Controller *controller;
 };