Changeset 8c31865 for src/LinkedCell

Timestamp:

Jan 2, 2012, 1:34:42 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:

54f3d1

Parents:

e776dc

git-author:

Frederik Heber <heber@…> (12/20/11 14:28:33)

git-committer:

Frederik Heber <heber@…> (01/02/12 13:34:42)

Message:

Added new class LinkedCellArrayCache that performs the lazy updates on a LinkedCellArray.

• basically, we cache all write operations and perform them first when there is a read operation that requires an up-to-date structure.
• we cannot do this via the Cacheable pattern was there we always have a return value of the update structure. It is currently unknown how to initialize a cached pointer (apart from always checking for this in the update function).

Location:

src/LinkedCell

Files:

• LinkedCell_Model.cpp (modified) (11 diffs)
• LinkedCell_Model.hpp (modified) (2 diffs)
• LinkedCell_Model_LinkedCellArrayCache.cpp (added)
• LinkedCell_Model_LinkedCellArrayCache.hpp (added)
• LinkedCell_Model_changeModel.cpp (modified) (1 diff)
• LinkedCell_Model_changeModel.hpp (modified) (1 diff)
• LinkedCell_Model_inline.hpp (modified) (3 diffs)
• Makefile.am (modified) (2 diffs)
• unittests/LinkedCell_ModelUnitTest.cpp (modified) (6 diffs)

src/LinkedCell/LinkedCell_Model.cpp

@@ -41 +41 @@
 #include "LinkedCell/LinkedCell.hpp"
 #include "LinkedCell/LinkedCell_Model_changeModel.hpp"
+#include "LinkedCell/LinkedCell_Model_LinkedCellArrayCache.hpp"
 #include "World.hpp"
-
-#include "LinkedCell_Model_inline.hpp"
 
 // initialize static entities
@@ -58 +57 @@
     Changes( new changeModel(radius) ),
     internal_Sizes(NULL),
+    N(new LinkedCellArrayCache(Changes, boost::bind(&changeModel::performUpdates, Changes), std::string("N_cached"))),
     domain(_domain)
 {
@@ -83 +83 @@
     Changes( new changeModel(radius) ),
     internal_Sizes(NULL),
+    N(new LinkedCellArrayCache(Changes, boost::bind(&changeModel::performUpdates, Changes), std::string("N_cached"))),
     domain(_domain)
 {
@@ -146 +147 @@
   for (int i=0;i<NDIM;i++)
     index[i] = static_cast<LinkedCellArray::index>(Dimensions.at(i,i));
-  N.resize(index);
+  N->setN().resize(index);
   ASSERT(getSize(0)*getSize(1)*getSize(2) < MAX_LINKEDCELLNODES,
       "LinkedCell_Model::AllocateCells() - Number linked of linked cell nodes exceeded hard-coded limit, use greater edge length!");
@@ -155 +156 @@
       for(index[2] = 0; index[2] != static_cast<LinkedCellArray::index>(Dimensions.at(2,2)); ++index[2]) {
         LOG(5, "INFO: Creating cell at " << index[0] << " " << index[1] << " " << index[2] << ".");
-        N(index) = new LinkedCell(index);
+        N->setN()(index) = new LinkedCell(index);
       }
     }
@@ -167 +168 @@
 {
   // free all LinkedCell instances
-  for(iterator3 iter3 = N.begin(); iter3 != N.end(); ++iter3) {
+  for(iterator3 iter3 = N->setN().begin(); iter3 != N->setN().end(); ++iter3) {
     for(iterator2 iter2 = (*iter3).begin(); iter2 != (*iter3).end(); ++iter2) {
       for(iterator1 iter1 = (*iter2).begin(); iter1 != (*iter2).end(); ++iter1) {
@@ -175 +176 @@
   }
   // set dimensions to zero
-  N.resize(boost::extents[0][0][0]);
+  N->setN().resize(boost::extents[0][0][0]);
 }
 
@@ -314 +315 @@
   LOG(2, "INFO: " << *Walker << " goes into cell " << index[0] << ", " << index[1] << ", " << index[2] << ".");
   LOG(2, "INFO: Cell's indices are "
-      << N(index)->getIndex(0) << " "
-      << N(index)->getIndex(1) << " "
-      << N(index)->getIndex(2) << ".");
+      << (N->getN())(index)->getIndex(0) << " "
+      << (N->getN())(index)->getIndex(1) << " "
+      << (N->getN())(index)->getIndex(2) << ".");
   // add to cell
-  N(index)->addPoint(Walker);
+  (N->setN())(index)->addPoint(Walker);
   // add to index with check for presence
-  std::pair<MapPointToCell::iterator, bool> inserter = CellLookup.insert( std::make_pair(Walker, N(index)) );
+  std::pair<MapPointToCell::iterator, bool> inserter = CellLookup.insert( std::make_pair(Walker, (N->setN())(index)) );
   ASSERT( inserter.second,
       "LinkedCell_Model::addNode() - Walker "
@@ -341 +342 @@
       "LinkedCell_Model::deleteNode() - Walker not present in cell stored under CellLookup.");
   if (iter != CellLookup.end()) {
+    // remove from lookup
     CellLookup.erase(iter);
+    // remove from cell
     iter->second->deletePoint(Walker);
   }
@@ -361 +364 @@
       iter->second->deletePoint(Walker);
       // add to new cell
-      N(index)->addPoint(Walker);
+      N->setN()(index)->addPoint(Walker);
       // update lookup
-      iter->second = N(index);
+      iter->second = N->setN()(index);
     }
   }
@@ -482 +485 @@
 }
 
+/** Returns a reference to the cell indicated by LinkedCell_Model::internal_index.
+ *
+ * \return LinkedCell ref to current cell
+ */
+const LinkedCell::LinkedCell& LinkedCell::LinkedCell_Model::getCell(const tripleIndex &index) const
+{
+  return *(N->getN()(index));
+}
+
+
+/** Returns size of array for given \a dim.
+ *
+ * @param dim desired dimension
+ * @return size of array along dimension
+ */
+LinkedCell::LinkedCellArray::index LinkedCell::LinkedCell_Model::getSize(const size_t dim) const
+{
+  ASSERT((dim >= 0) && (dim < NDIM),
+      "LinkedCell_Model::getSize() - dimension "
+      +toString(dim)+" is out of bounds.");
+  return N->getN().shape()[dim];
+}
+
 /** Callback function for Observer mechanism.
  *

src/LinkedCell/LinkedCell_Model.hpp

@@ -118 +118 @@
     boost::array<double, 3> EdgeLength;
 
-    //!> Linked cell array
-    LinkedCellArray N;
+    // forward declaration for LinkedCellArrayContainer, containing cached LinkedCellArray
+    class LinkedCellArrayCache;
+    //!> Linked cell array cache
+    LinkedCellArrayCache *N;
 
     //!> matrix to divide Box with
@@ -133 +135 @@
 }
 
-// inlined functions
-#include "LinkedCell_Model_inline.hpp"
-
 #endif /* LINKEDCELL_MODEL_HPP_ */

src/LinkedCell/LinkedCell_Model_changeModel.cpp

@@ -21 +21 @@
 
 #include "LinkedCell_Model_changeModel.hpp"
+
+#include "CodePatterns/toString.hpp"
 
 /** Constructor of LinkedCell_Model::changeModel.

src/LinkedCell/LinkedCell_Model_changeModel.hpp

@@ -41 +41 @@
         boost::function<void (const TesselPoint *)> _updateMethod
         );
-  protected:
+  private:
+    //!> grant LinkedCell_Model access to bind LinkedCellArrayCache to update funcation
+    friend class LinkedCell_Model;
     void performUpdates();
   private:

src/LinkedCell/LinkedCell_Model_inline.hpp

@@ -14 +14 @@
 #endif
 
+#include "LinkedCell_Model_LinkedCellArrayCache.hpp"
+
 // have all includes only needed here extra
 #ifdef HAVE_INLINE
@@ -28 +30 @@
 const LinkedCell::LinkedCell& LinkedCell::LinkedCell_Model::getCell(const tripleIndex &index) const
 {
-  return *N(index);
+  return *(N->getN()(index));
 }
 
@@ -45 +47 @@
       "LinkedCell_Model::getSize() - dimension "
       +toString(dim)+" is out of bounds.");
-  return N.shape()[dim];
+  return N->getN().shape()[dim];
 }
 

src/LinkedCell/Makefile.am

@@ -8 +8 @@
   LinkedCell/LinkedCell_Model.cpp \
   LinkedCell/LinkedCell_Model_changeModel.cpp \
+  LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp \
   LinkedCell/LinkedCell_Model_Update.cpp \
   LinkedCell/LinkedCell_View.cpp \
@@ -19 +20 @@
   LinkedCell/LinkedCell_Model.hpp \
   LinkedCell/LinkedCell_Model_changeModel.hpp \
-  LinkedCell/LinkedCell_Model_inline.hpp \
+  LinkedCell/LinkedCell_Model_LinkedCellArrayCache.hpp \
   LinkedCell/LinkedCell_Model_Update.hpp \
   LinkedCell/LinkedCell_View.hpp \

src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp

@@ -32 +32 @@
 #include "LinkedCell/LinkedCell.hpp"
 #include "LinkedCell/LinkedCell_Model.hpp"
+#include "LinkedCell/LinkedCell_Model_LinkedCellArrayCache.hpp"
 #include "LinkedCell/PointCloudAdaptor.hpp"
 #include "LinkedCell/unittests/defs.hpp"
@@ -99 +100 @@
   LinkedCell::tripleIndex index;
   index[0] = index[1] = index[2] = 0;
-  CPPUNIT_ASSERT(LC->N(index) != NULL);
+  CPPUNIT_ASSERT(LC->N->getN()(index) != NULL);
 
   // check that very last cell is allocated
   index[0] = index[1] = index[2] = (size_t)floor(NUMBERCELLS)-1;
-  CPPUNIT_ASSERT(LC->N(index) != NULL);
+  CPPUNIT_ASSERT(LC->N->getN()(index) != NULL);
 
 }
@@ -146 +147 @@
     index[0] = index[1] = index[2] = i;
     // assert that in the destined cell we have one Walker
-    CPPUNIT_ASSERT_EQUAL((size_t)1, LC->N(index)->size());
+    CPPUNIT_ASSERT_EQUAL((size_t)1, LC->N->getN()(index)->size());
   }
   index[0] = 9;
   index[1] = index[2] = 0;
   // assert that in the destined cell we have one Walker
-  CPPUNIT_ASSERT_EQUAL((size_t)0, LC->N(index)->size());
-
-}
-
-/** UnitTest for insertPointCloud()
+  CPPUNIT_ASSERT_EQUAL((size_t)0, LC->N->getN()(index)->size());
+
+}
+
+/** UnitTest for setPartition()
  */
 void LinkedCell_ModelTest::setPartitionTest()
@@ -173 +174 @@
 }
 
-/** UnitTest for insertPointCloud()
+/** UnitTest for getStep()
  */
 void LinkedCell_ModelTest::getStepTest()
@@ -197 +198 @@
 }
 
-/** UnitTest for insertPointCloud()
+/** UnitTest for getIndexToVector()
  */
 void LinkedCell_ModelTest::getIndexToVectorTest()
@@ -221 +222 @@
 }
 
-/** UnitTest for insertPointCloud()
+/** UnitTest for updating nodes
  */
 void LinkedCell_ModelTest::nodeTest()