Changeset af2c424 for src/linkedcell.cpp

Timestamp:

Aug 28, 2010, 12:57:56 AM (15 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, Candidate_v1.7.0, 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:

c449d9

Parents:

21585f

git-author:

Frederik Heber <heber@…> (08/27/10 20:58:40)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:57:56)

Message:

LinkedCell constructor rewritten.

• had to introduce getValue(iterator) to: molecule, tesselation, LinkedCell::LinkedNodes
• LinkedCell::LinkedNodes is not a typedef anymore
• new class LinkedCell::LinkedNodes derived from stl::list<TesselPoint *> to add getValue(iterator).
• LinkedCell constructors changed:
  • use template for all classes that have begin(), end() and ... sigh ... getValue()
  • Argh! STL containers do all have begin() and end() but no consistent operator* (maps return pair<> ...)
  • specialized version for PointCloud derivatives
  • various functions had to be changed due to changed signature of LinkedCell constructor

File:

• src/linkedcell.cpp (modified) (8 diffs)

src/linkedcell.cpp

@@ -25 +25 @@
 #include "Helpers/Log.hpp"
 #include "molecule.hpp"
+#include "PointCloud.hpp"
 #include "tesselation.hpp"
 #include "LinearAlgebra/Vector.hpp"
@@ -30 +31 @@
 // ========================================================= class LinkedCell ===========================================
 
+/** Constructor for class LinkedCell::LinkedNodes.
+ */
+LinkedCell::LinkedNodes::LinkedNodes()
+{}
+
+/** Destructor for class LinkedCell::LinkedNodes.
+ */
+LinkedCell::LinkedNodes::~LinkedNodes()
+{}
+
+TesselPoint * LinkedCell::LinkedNodes::getValue (const_iterator &rhs) const
+{
+  return *rhs;
+}
+
+TesselPoint * LinkedCell::LinkedNodes::getValue (iterator &rhs) const
+{
+  return *rhs;
+}
 
 /** Constructor for class LinkedCell.
@@ -48 +68 @@
  * \param RADIUS edge length of cells
  */
-LinkedCell::LinkedCell(const PointCloud * const set, const double radius) :
+LinkedCell::LinkedCell(const PointCloud & set, const double radius) :
   LC(NULL),
   RADIUS(radius),
@@ -60 +80 @@
   min.Zero();
   DoLog(1) && (Log() << Verbose(1) << "Begin of LinkedCell" << endl);
-  if ((set == NULL) || (set->IsEmpty())) {
+  if (set.IsEmpty()) {
     DoeLog(1) && (eLog()<< Verbose(1) << "set is NULL or contains no linked cell nodes!" << endl);
     return;
   }
   // 1. find max and min per axis of atoms
-  set->GoToFirst();
-  Walker = set->GetPoint();
+  set.GoToFirst();
+  Walker = set.GetPoint();
   for (int i=0;i<NDIM;i++) {
     max[i] = Walker->at(i);
     min[i] = Walker->at(i);
   }
-  set->GoToFirst();
-  while (!set->IsEnd()) {
-    Walker = set->GetPoint();
+  set.GoToFirst();
+  while (!set.IsEnd()) {
+    Walker = set.GetPoint();
     for (int i=0;i<NDIM;i++) {
       if (max[i] < Walker->at(i))
@@ -80 +100 @@
         min[i] = Walker->at(i);
     }
-    set->GoToNext();
+    set.GoToNext();
   }
   DoLog(2) && (Log() << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl);
@@ -105 +125 @@
   // 4. put each atom into its respective cell
   DoLog(2) && (Log() << Verbose(2) << "Filling cells ... ");
-  set->GoToFirst();
-  while (!set->IsEnd()) {
-    Walker = set->GetPoint();
+  set.GoToFirst();
+  while (!set.IsEnd()) {
+    Walker = set.GetPoint();
     for (int i=0;i<NDIM;i++) {
       n[i] = static_cast<int>(floor((Walker->at(i) - min[i])/RADIUS));
@@ -114 +134 @@
     LC[index].push_back(Walker);
     //Log() << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
-    set->GoToNext();
+    set.GoToNext();
   }
   DoLog(0) && (Log() << Verbose(0) << "done."  << endl);
@@ -120 +140 @@
 };
 
-
-/** Puts all atoms in \a *mol into a linked cell list with cell's lengths of \a RADIUS
- * \param *set LCNodeSet class with all LCNode's
- * \param RADIUS edge length of cells
- */
-LinkedCell::LinkedCell(LinkedNodes *set, const double radius) :
-  LC(NULL),
-  RADIUS(radius),
-  index(-1)
-{
-  class TesselPoint *Walker = NULL;
-  for(int i=0;i<NDIM;i++)
-    N[i] = 0;
-  max.Zero();
-  min.Zero();
-  DoLog(1) && (Log() << Verbose(1) << "Begin of LinkedCell" << endl);
-  if (set->empty()) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "set contains no linked cell nodes!" << endl);
-    return;
-  }
-  // 1. find max and min per axis of atoms
-  LinkedNodes::iterator Runner = set->begin();
-  for (int i=0;i<NDIM;i++) {
-    max[i] = (*Runner)->at(i);
-    min[i] = (*Runner)->at(i);
-  }
-  for (LinkedNodes::iterator Runner = set->begin(); Runner != set->end(); Runner++) {
-    Walker = *Runner;
-    for (int i=0;i<NDIM;i++) {
-      if (max[i] < Walker->at(i))
-        max[i] = Walker->at(i);
-      if (min[i] > Walker->at(i))
-        min[i] = Walker->at(i);
-    }
-  }
-  DoLog(2) && (Log() << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl);
-
-  // 2. find then number of cells per axis
-  for (int i=0;i<NDIM;i++) {
-    N[i] = static_cast<int>(floor((max[i] - min[i])/RADIUS)+1);
-  }
-  DoLog(2) && (Log() << Verbose(2) << "Number of cells per axis are " << N[0] << ", " << N[1] << " and " << N[2] << "." << endl);
-
-  // 3. allocate the lists
-  DoLog(2) && (Log() << Verbose(2) << "Allocating cells ... ");
-  if (LC != NULL) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell list is already allocated, I do nothing." << endl);
-    return;
-  }
-  ASSERT(N[0]*N[1]*N[2] < MAX_LINKEDCELLNODES, "Number linked of linked cell nodes exceded hard-coded limit, use greater edge length!");
-  LC = new LinkedNodes[N[0]*N[1]*N[2]];
-  for (index=0;index<N[0]*N[1]*N[2];index++) {
-    LC [index].clear();
-  }
-  DoLog(0) && (Log() << Verbose(0) << "done."  << endl);
-
-  // 4. put each atom into its respective cell
-  DoLog(2) && (Log() << Verbose(2) << "Filling cells ... ");
-  for (LinkedNodes::iterator Runner = set->begin(); Runner != set->end(); Runner++) {
-    Walker = *Runner;
-    for (int i=0;i<NDIM;i++) {
-      n[i] = static_cast<int>(floor((Walker->at(i) - min[i])/RADIUS));
-    }
-    index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
-    LC[index].push_back(Walker);
-    //Log() << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
-  }
-  DoLog(0) && (Log() << Verbose(0) << "done."  << endl);
-  DoLog(1) && (Log() << Verbose(1) << "End of LinkedCell" << endl);
-};
 
 /** Destructor for class LinkedCell.