Changeset e2373df for src

Timestamp:

Feb 24, 2011, 6:36:33 PM (14 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:

fb9eba

Parents:

fb0b62

git-author:

Frederik Heber <heber@…> (02/24/11 14:48:51)

git-committer:

Frederik Heber <heber@…> (02/24/11 18:36:33)

Message:

TesselPoint, Atom and AtomInfo have virtual UpdateSteps() to allow consistent extending of trajectories.

• TesselPoint and Atom just implement it virtually.
• AtomInfo implements it by new function AppendTrajectoryStep() that adds steps.

Location:

src

Files:

• TesselPoint.cpp (modified) (2 diffs)
• TesselPoint.hpp (modified) (1 diff)
• atom.cpp (modified) (2 diffs)
• atom.hpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (5 diffs)
• atom_atominfo.hpp (modified) (2 diffs)

src/TesselPoint.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "CodePatterns/Log.hpp"
+
 #include "TesselPoint.hpp"
 
@@ -35 +37 @@
 {};
 
+void TesselPoint::UpdateSteps()
+{
+  ASSERT(0, "TesselPoint::UpdateSteps() should never be called, TesselPoints don't have trajectories.");
+  AtomInfo::AppendTrajectoryStep();
+};
+
 std::ostream & TesselPoint::operator << (std::ostream &ost) const
 {

src/TesselPoint.hpp

@@ -26 +26 @@
   ~TesselPoint();
 
+  /** Pushes back another step in all trajectory vectors.
+   *
+   * This allows to extend all trajectories contained in different classes
+   * consistently. This is implemented by the topmost class which calls the
+   * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
+   *
+   * Note that this function is actually not sensible with TesselPoints
+   * as they should not have trajectories but is implemented as they can be
+   * used stand-alone.
+   *
+   */
+  virtual void UpdateSteps();
+
   std::ostream & operator << (std::ostream &ost) const;
 };

src/atom.cpp

@@ -21 +21 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "CodePatterns/Log.hpp"
 #include "config.hpp"
 #include "element.hpp"
@@ -78 +79 @@
 };
 
+
+void atom::UpdateSteps()
+{
+  LOG(4,"atom::UpdateSteps() called.");
+  // append to position, velocity and force vector
+  AtomInfo::AppendTrajectoryStep();
+}
 
 /** Climbs up the father list until NULL, last is returned.

src/atom.hpp

@@ -52 +52 @@
 
   virtual atom *clone();
+
+  /** Pushes back another step in all trajectory vectors.
+   *
+   * This allows to extend all trajectories contained in different classes
+   * consistently. This is implemented by the topmost class which calls the
+   * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
+   */
+  virtual void UpdateSteps();
 
   bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;

src/atom_atominfo.cpp

@@ -74 +74 @@
 };
 
+void AtomInfo::AppendTrajectoryStep()
+{
+  AtomicPosition.push_back(zeroVec);
+  AtomicVelocity.push_back(zeroVec);
+  AtomicForce.push_back(zeroVec);
+}
+
 const element *AtomInfo::getType() const
 {
@@ -191 +198 @@
     AtomicVelocity[_step] = _newvelocity;
   } else if (_step == size) {
-    AtomicVelocity.push_back(_newvelocity);
+    UpdateSteps();
+    AtomicVelocity[_step] = _newvelocity;
   }
 }
@@ -232 +240 @@
     AtomicForce[_step] = _newforce;
   } else if (_step == size) {
-    AtomicForce.push_back(_newforce);
+    UpdateSteps();
+    AtomicForce[_step] = _newforce;
   }
 }
@@ -266 +275 @@
     AtomicPosition[_step] = _vector;
   } else if (_step == size) {
-    AtomicPosition.push_back(_vector);
+    UpdateSteps();
+    AtomicPosition[_step] = _vector;
   }
   //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
@@ -438 +448 @@
 void AtomInfo::ResizeTrajectory(size_t MaxSteps)
 {
-  if (AtomicPosition.size() <= (unsigned int)(MaxSteps)) {
-    DoLog(0) && (Log() << Verbose(0) << "Increasing size for trajectory array from " << AtomicPosition.size() << " to " << (MaxSteps+1) << "." << endl);
-    AtomicPosition.resize(MaxSteps+1, zeroVec);
-    AtomicVelocity.resize(MaxSteps+1, zeroVec);
-    AtomicForce.resize(MaxSteps+1, zeroVec);
-  }
-  for (size_t i = AtomicPosition.size(); i <= MaxSteps; ++i) {
-    AtomicPosition[i] = zeroVec;
-    AtomicVelocity[i] = zeroVec;
-    AtomicForce[i] = zeroVec;
-  }
-};
+  for (;AtomicPosition.size() <= (unsigned int)(MaxSteps);)
+    UpdateSteps();
+}
 
 size_t AtomInfo::getTrajectorySize() const

src/atom_atominfo.hpp

@@ -41 +41 @@
   AtomInfo(const VectorInterface &_v);
   virtual ~AtomInfo();
+
+  /** Pushes back another step in all trajectory vectors.
+   *
+   * This allows to extend all trajectories contained in different classes
+   * consistently. This is implemented by the topmost class which calls the
+   * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
+   */
+  virtual void UpdateSteps()=0;
 
   /** Getter for AtomicElement.
@@ -242 +250 @@
 
 protected:
+  /** Function used by this and inheriting classes to extend the trajectory
+   * vectors.
+   */
+  void AppendTrajectoryStep();
+
   // make these protected only such that deriving atom class still has full
   // access needed for clone and alike