Changeset de29ad6

Timestamp:

Dec 28, 2011, 3:24:23 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:

68c923

Parents:

bde4a6

git-author:

Frederik Heber <heber@…> (12/28/11 14:58:52)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:24:23)

Message:

Some optimization to speed up Subgraph dissections.

• Replaced std::list by std::vector in VectorSet<>::minDistSquared() and Box::internal_explode() as it caused lots of dynamic allocation. This has been the main cause of the slowdown of Box::internal_explode().
• Box has internalized vector<int>s coords and index of internal_explode() to avoid dynamic allocation for them as well. This is worth it as it has a heavily used function.
• Made Box internal_list non-static. There is only one box anyway.
• changes caused in BoxUnitTest and Box cstor's and dstor.
• speedup of Subgraph

• enhanced verbosity of BondGraph::CreateAdjacency().

Files:

• LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) (2 diffs)
• src/Box.cpp (modified) (11 diffs)
• src/Box.hpp (modified) (5 diffs)
• src/Graph/BondGraph.cpp (modified) (2 diffs)
• src/unittests/BoxUnitTest.cpp (modified) (5 diffs)

LinearAlgebra/src/LinearAlgebra/VectorSet.hpp

@@ -27 +27 @@
 
 #include "Vector.hpp"
-#include <list>
+#include <vector>
 
 // this tests, whether we actually have a Vector
@@ -62 +62 @@
     if(!this->size())
       return std::numeric_limits<double>::infinity();
-    std::list<double> helper;
+    std::vector<double> helper;
     helper.resize(this->size());
     transform(this->begin(),this->end(),

src/Box.cpp

@@ -37 +37 @@
 
 
-using namespace std;
-
-VECTORSET(std::list) Box::internal_list;
-
 Box::Box() :
     M(new RealSpaceMatrix()),
     Minv(new RealSpaceMatrix())
 {
+  internal_list.reserve(pow(3,3));
+  coords.reserve(NDIM);
+  index.reserve(NDIM);
   M->setIdentity();
   Minv->setIdentity();
@@ -55 +54 @@
   M(new RealSpaceMatrix(*src.M)),
   Minv(new RealSpaceMatrix(*src.Minv))
-{}
+{
+  internal_list.reserve(pow(3,3));
+  coords.reserve(NDIM);
+  index.reserve(NDIM);
+}
 
 Box::Box(RealSpaceMatrix _M) :
@@ -61 +64 @@
     Minv(new RealSpaceMatrix())
 {
+  internal_list.reserve(pow(3,3));
+  coords.reserve(NDIM);
+  index.reserve(NDIM);
   ASSERT(M->determinant()!=0,"Matrix in Box construction was not invertible");
   *Minv = M->invert();
@@ -135 +141 @@
 
 
-VECTORSET(std::list) Box::explode(const Vector &point,int n) const{
+VECTORSET(std::vector) Box::explode(const Vector &point,int n) const{
   ASSERT(isInside(point),"Exploded point not inside Box");
   internal_explode(point, n);
-  VECTORSET(std::list) res(internal_list);
+  VECTORSET(std::vector) res(internal_list);
   return res;
 }
@@ -144 +150 @@
 void Box::internal_explode(const Vector &point,int n) const{
   internal_list.clear();
+  size_t list_index = 0;
 
   Vector translater = translateOut(point);
@@ -150 +157 @@
   // count the number of coordinates we need to do
   int dims = 0; // number of dimensions that are not ignored
-  vector<int> coords;
-  vector<int> index;
+  coords.clear();
+  index.clear();
   for(int i=0;i<NDIM;++i){
     if(conditions[i]==Ignore){
@@ -161 +168 @@
     dims++;
   } // there are max vectors in total we need to create
+  internal_list.resize(pow(2*n+1, dims));
 
   if(!dims){
     // all boundaries are ignored
-    internal_list.push_back(point);
+    internal_list[list_index++] = point;
     return;
   }
@@ -206 +214 @@
     // add back all ignored coordinates (not handled in above loop)
     helper+=mask;
-    internal_list.push_back(translateIn(helper));
+    ASSERT(list_index < internal_list.size(),
+        "Box::internal_explode() - we have estimated the number of vectors wrong: "
+        +toString(list_index) +" >= "+toString(internal_list.size())+".");
+    internal_list[list_index++] = translateIn(helper);
     // set the new indexes
     int pos=0;
@@ -221 +232 @@
 }
 
-VECTORSET(std::list) Box::explode(const Vector &point) const{
+VECTORSET(std::vector) Box::explode(const Vector &point) const{
   ASSERT(isInside(point),"Exploded point not inside Box");
   return explode(point,1);
@@ -268 +279 @@
 }
 
-const vector<pair<Plane,Plane> >  Box::getBoundingPlanes() const
-{
-  vector<pair<Plane,Plane> > res;
+const std::vector<std::pair<Plane,Plane> >  Box::getBoundingPlanes() const
+{
+  std::vector<std::pair<Plane,Plane> > res;
   for(int i=0;i<NDIM;++i){
     Vector base1,base2,base3;
@@ -314 +325 @@
 }
 
-ostream & operator << (ostream& ost, const Box &m)
+std::ostream & operator << (std::ostream& ost, const Box &m)
 {
   ost << m.getM();

src/Box.hpp

@@ -41 +41 @@
   } BoundaryCondition_t;
 
-  typedef vector<BoundaryCondition_t> Conditions_t;
+  typedef std::vector<BoundaryCondition_t> Conditions_t;
 
   Box();
@@ -92 +92 @@
    * Carefull, needs O(n^3) time and produces as many vectors.
    */
-  VECTORSET(std::list) explode(const Vector &point,int n) const;
-  VECTORSET(std::list) explode(const Vector &point) const;
+  VECTORSET(std::vector) explode(const Vector &point,int n) const;
+  VECTORSET(std::vector) explode(const Vector &point) const;
 
   /**
@@ -117 +117 @@
   void setCondition(int,BoundaryCondition_t);
 
-  const vector<pair<Plane,Plane> > getBoundingPlanes() const;
+  const std::vector<std::pair<Plane,Plane> > getBoundingPlanes() const;
 
   void setCuboid(const Vector&);
@@ -134 +134 @@
   void internal_explode(const Vector &point,int n) const;
 
-  //!> Internal vector list for exploding vectors and checking.
-  static VECTORSET(std::list) internal_list;
+  //!> Internal vector list for exploding vectors used in Box::internal_explode().
+  mutable VECTORSET(std::vector) internal_list;
+
+  //!> Internal vector for coordinates used in Box::internal_explode()
+  mutable std::vector<int> coords;
+  //!> Internal vector for indices used in Box::internal_explode()
+  mutable std::vector<int> index;
 
   Conditions_t conditions;
@@ -142 +147 @@
 };
 
-ostream & operator << (ostream& ost, const Box &m);
+std::ostream & operator << (std::ostream& ost, const Box &m);
 
 #endif /* BOX_HPP_ */

src/Graph/BondGraph.cpp

@@ -197 +197 @@
                   const TesselPointSTLList *OtherList = LC.GetRelativeToCurrentCell(n);
                   if (OtherList != NULL) {
-                    LOG(3, "INFO: Current relative cell is " << LC.n[0] << ", " << LC.n[1] << ", " << LC.n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
+                    LOG(3, "INFO: Current relative cell is " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
                     for (TesselPointSTLList::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                       if ((*OtherRunner) > Walker) {  // just to not add bonds from both sides
@@ -203 +203 @@
                         ASSERT(OtherWalker != NULL,
                             "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
+                        LOG(3, "INFO: Current other atom is " << *OtherWalker << ".");
                         if (OtherWalker->father > Walker->father ) { // just to not add bonds from both sides
                           const range<double> MinMaxDistanceSquared(

src/unittests/BoxUnitTest.cpp

@@ -476 +476 @@
 }
 
-bool testWrapExplode(VECTORSET(std::list) &set,Vector &point, Box* box){
+bool testWrapExplode(VECTORSET(std::vector) &set,Vector &point, Box* box){
   bool res = true;
   Vector wrappedPoint = box->WrapPeriodically(point);
-  for(std::list<Vector>::iterator iter = set.begin(); iter!=set.end();++iter){
+  for(std::vector<Vector>::iterator iter = set.begin(); iter!=set.end();++iter){
     Vector wrapped = box->WrapPeriodically(*iter);
     bool equals = (wrapped == wrappedPoint);
@@ -492 +492 @@
 void BoxUnittest::WrapExplodeTest(){
   Vector testVector(0,0,0);
-  VECTORSET(std::list) res;
+  VECTORSET(std::vector) res;
 
   // we only can explode those vectors that are actually inside the box
@@ -892 +892 @@
 void BoxUnittest::BoundaryBounceTest(){
   Vector testVector(0,0,0);
-  VECTORSET(std::list) res;
+  VECTORSET(std::vector) res;
 
   unitBox->setCondition(0,Box::Bounce);
@@ -1191 +1191 @@
 void BoxUnittest::BoundaryIgnoreTest(){
   Vector testVector(0,0,0);
-  VECTORSET(std::list) res;
+  VECTORSET(std::vector) res;
 
   unitBox->setCondition(0,Box::Ignore);
@@ -1490 +1490 @@
 void BoxUnittest::BoundaryMixedTest(){
   Vector testVector(0,0,0);
-  VECTORSET(std::list) res;
+  VECTORSET(std::vector) res;
 
   unitBox->setCondition(0,Box::Bounce);