Changeset 31021ab

Timestamp:

Mar 22, 2013, 12:04:17 AM (12 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:

d948b4

Parents:

cf1183

git-author:

Frederik Heber <heber@…> (03/01/13 19:25:36)

git-committer:

Frederik Heber <heber@…> (03/22/13 00:04:17)

Message:

Optimized Bondgraph detection.

• VectorSet::minDistance() now operators on the set (translating by -point).
• VectorSet::minDistSquared() removed as is the same as minDistance().
• LinearAlgebra version is now 3:2:0, API is 1.0.5.
• decrease log level of DepthFirstSearchAnalysis' msg about disconnected subgraphs.
• Box::internal_explode() does not clear() internal_list, avoing constructing Vectors all the time.
• BondGraph::CreateAdjacency gives some more message to tell when it does what.

Files:

• LinearAlgebra/configure.ac (modified) (1 diff)
• LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) (1 diff)
• LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) (2 diffs)
• LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (modified) (1 diff)
• src/Box.cpp (modified) (2 diffs)
• src/Graph/BondGraph.hpp (modified) (3 diffs)
• src/Graph/DepthFirstSearchAnalysis.cpp (modified) (1 diff)

LinearAlgebra/configure.ac

@@ -34 +34 @@
 # refer to the libtool manual, section "Updating library version information":
 # http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
-AC_SUBST([LINEARALGEBRA_SO_VERSION], [3:1:0])
-AC_SUBST([LINEARALGEBRA_API_VERSION], [1.0.4])
+AC_SUBST([LINEARALGEBRA_SO_VERSION], [3:2:0])
+AC_SUBST([LINEARALGEBRA_API_VERSION], [1.0.5])
 
 dnl this macro is used to get the arguments supplied

LinearAlgebra/src/LinearAlgebra/VectorSet.hpp

@@ -82 +82 @@
     if(!this->size())
       return zeroVec;
-    std::vector<Vector> helper;
-    helper.resize(this->size());
-    std::transform(this->begin(),this->end(),
-              helper.begin(),
-              std::bind2nd(std::mem_fun_ref(&Vector::operator-),point));
-    return *min_element(helper.begin(),helper.end(),
-        boost::lambda::_1 < boost::lambda::_2);
-        //(boost::lambda::bind(Vector::NormSquared,boost::lambda::_1) < boost::lambda::bind(Vector::NormSquared,boost::lambda::_2)));
-  }
-
-  /** Return the length of the Vector that is closest to \a point.
-   *
-   * @param point
-   * @return
-   */
-  double minDistSquared(const Vector &point){
-    if(!this->size())
-      return std::numeric_limits<double>::infinity();
-    std::vector<double> helper;
-    helper.resize(this->size());
-    std::transform(this->begin(),this->end(),
-              helper.begin(),
-              std::bind2nd(std::mem_fun_ref(&Vector::DistanceSquared),point));
-    return *min_element(helper.begin(),helper.end());
+    translate(-1.*point);
+//    std::transform(this->begin(),this->end(),
+//        this->begin(),
+//        std::bind2nd(std::mem_fun_ref(&Vector::operator-),point));
+    return *min_element(this->begin(),this->end(),
+//        boost::lambda::_1 < boost::lambda::_2);
+        (boost::lambda::bind(&Vector::NormSquared,boost::lambda::_1) < boost::lambda::bind(&Vector::NormSquared,boost::lambda::_2)));
   }
 };

LinearAlgebra/src/unittests/VectorSetUnitTest.cpp

@@ -127 +127 @@
     Vector mindist = somelist.minDistance(center);
     CPPUNIT_ASSERT_EQUAL (Vector(1., 0., 0.), mindist);
+    // check that vector has changed (by nothing)
+    for (size_t i=0;i<somelist.size();++i)
+      CPPUNIT_ASSERT_EQUAL (Vector(i+1.,0.,0.), somelist[i]);
   }
   {
     Vector center(5.,0.,0.);
-    Vector mindist = worklist.minDistance(center);
+    VECTORSET(std::vector) somelist(worklist);
+    Vector mindist = somelist.minDistance(center);
     CPPUNIT_ASSERT_EQUAL (Vector(2., 1., 0.)-center, mindist);
+    // check that vector has changed
+    for (size_t i=0;i<somelist.size();++i)
+      CPPUNIT_ASSERT_EQUAL (somelist[i], worklist[i]-center);
   }
   {
     for (VECTORSET(std::vector)::const_iterator iter = worklist.begin();
         iter != worklist.end(); ++iter) {
-      Vector mindist = worklist.minDistance(*iter);
+      // copy list as we change it
+      VECTORSET(std::vector) somelist(worklist);
+      Vector mindist = somelist.minDistance(*iter);
       CPPUNIT_ASSERT_EQUAL( Vector(0.,0.,0.), mindist );
     }
@@ -142 +151 @@
 }
 
-/** UnitTest for minDistance()
- */
-void VectorSetTest::minDistSquaredTest()
-{
-  VECTORSET(std::vector) worklist(list);
-  {
-    Vector center(5.,0.,0.);
-    double mindist = worklist.minDistSquared(center);
-    double check = Vector(2., 1., 0.).DistanceSquared(center);
-    CPPUNIT_ASSERT_EQUAL( check, mindist );
-  }
-  {
-    for (VECTORSET(std::vector)::const_iterator iter = worklist.begin();
-        iter != worklist.end(); ++iter) {
-      double mindist = worklist.minDistSquared(*iter);
-      CPPUNIT_ASSERT_EQUAL( 0., mindist );
-    }
-  }
-}

LinearAlgebra/src/unittests/VectorSetUnitTest.hpp

@@ -30 +30 @@
     CPPUNIT_TEST ( transformTest );
     CPPUNIT_TEST ( minDistanceTest );
-    CPPUNIT_TEST ( minDistSquaredTest );
     CPPUNIT_TEST_SUITE_END();
 

src/Box.cpp

@@ -214 +214 @@
 
 void Box::internal_explode(const Vector &point,int n) const{
-  internal_list.clear();
+//  internal_list.clear();
   size_t list_index = 0;
 
@@ -233 +233 @@
     dims++;
   } // there are max vectors in total we need to create
-  internal_list.resize(pow(2*n+1, dims));
+  const int new_size = pow(2*n+1, dims);
+  if (internal_list.size() != new_size)
+    internal_list.resize(new_size);
 
   if(!dims){

src/Graph/BondGraph.hpp

@@ -188 +188 @@
     }
     // get all elements
-    std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
+    const std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
 
     // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
@@ -194 +194 @@
     if (counter > 1) {
       LOG(1, "STATUS: Setting max bond distance.");
+      LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
       LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(PresentElements));
 
-      LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
-
-      Box &domain = getDomain();
-      unsigned int CurrentTime = getTime();
+      LOG(1, "STATUS: Evaluating distance criterion for each atom.");
+
+      const Box &domain = getDomain();
+      const unsigned int CurrentTime = getTime();
 
       unsigned int BondCount = 0;
@@ -243 +244 @@
                     << MinMaxDistanceSquared << ".");
               }
-
             } else {
               LOG(5, "REJECT: Not Adding: Wrong order.");

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -402 +402 @@
     std::stringstream output;
     output << CurrentSubgraph;
-    LOG(0, "STATUS: Disconnected subgraph ranges from " << OldGraphNr << " to "
+    LOG(1, "INFO: Disconnected subgraph ranges from " << OldGraphNr << " to "
         << CurrentGraphNr-1 << ": " << output.str());