Changeset bce72c

Timestamp:

Feb 24, 2011, 4:30:56 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:

54b42e

Parents:

c864a8

git-author:

Frederik Heber <heber@…> (02/07/11 18:35:30)

git-committer:

Frederik Heber <heber@…> (02/24/11 16:30:56)

Message:

AtomicInfo::AtomicVelocity and ::AtomicForce are now private.

• Access is granted via getters and setters.

Location:

src

Files:

• AtomicInfo.cpp (modified) (2 diffs)
• Parser/PcpParser.cpp (modified) (1 diff)
• Parser/TremoloParser.cpp (modified) (2 diffs)
• Parser/unittests/ParserTremoloUnitTest.cpp (modified) (1 diff)
• atom.cpp (modified) (3 diffs)
• atom_atominfo.cpp (modified) (1 diff)
• atom_atominfo.hpp (modified) (3 diffs)
• config.cpp (modified) (2 diffs)
• molecule.cpp (modified) (3 diffs)

src/AtomicInfo.cpp

@@ -35 +35 @@
     Position(_atom.getPosition()),
     Type(_atom.getType()),
-    Velocity(_atom.AtomicVelocity),
+    Velocity(_atom.getAtomicVelocity()),
     Father(_atom.father),
     Mol(_atom.getMolecule()),
@@ -51 +51 @@
   _atom.father = const_cast<atom *>(Father); // TODO: Actually, atom::father should be const atom *!
   _atom.setMolecule(const_cast<molecule *>(Mol)); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
-  _atom.AtomicVelocity = Velocity;
+  _atom.setAtomicVelocity(Velocity);
   if (_atom.getId() == Id)
     return true;

src/Parser/PcpParser.cpp

@@ -558 +558 @@
     *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);
     *file << "\t" << (*AtomRunner)->FixedIon;
-    if ((*AtomRunner)->AtomicVelocity.Norm() > MYEPSILON)
-      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->AtomicVelocity[0] << "\t" << (*AtomRunner)->AtomicVelocity[1] << "\t" << (*AtomRunner)->AtomicVelocity[2] << "\t";
+    if ((*AtomRunner)->getAtomicVelocity().Norm() > MYEPSILON)
+      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->getAtomicVelocity()[0] << "\t" << (*AtomRunner)->getAtomicVelocity()[1] << "\t" << (*AtomRunner)->getAtomicVelocity()[2] << "\t";
     *file << " # molecule nr " << nr++ << endl;
   }

src/Parser/TremoloParser.cpp

@@ -188 +188 @@
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
-        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->AtomicVelocity << std::endl);
-        *file << currentAtom->AtomicVelocity[0] << "\t";
-        *file << currentAtom->AtomicVelocity[1] << "\t";
-        *file << currentAtom->AtomicVelocity[2] << "\t";
+        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getAtomicVelocity() << std::endl);
+        *file << currentAtom->getAtomicVelocity()[0] << "\t";
+        *file << currentAtom->getAtomicVelocity()[1] << "\t";
+        *file << currentAtom->getAtomicVelocity()[2] << "\t";
         break;
       case TremoloKey::Type :
@@ -343 +343 @@
           ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for u["+toString(i)+"]!");
           //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
-          newAtom->AtomicVelocity[i] = toDouble(*tok_iter);
+          newAtom->getAtomicVelocity()[i] = toDouble(*tok_iter);
           tok_iter++;
         }

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -151 +151 @@
   input << Tremolo_velocity;
   testParser->load(&input);
-  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->AtomicVelocity[0] == 3.0);
+  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->getAtomicVelocity()[0] == 3.0);
   input.clear();
 }

src/atom.cpp

@@ -54 +54 @@
   setType(pointer->getType());  // copy element of atom
   setPosition(pointer->getPosition()); // copy coordination
-  AtomicVelocity = pointer->AtomicVelocity; // copy velocity
+  setAtomicVelocity(pointer->getAtomicVelocity()); // copy velocity
   FixedIon = pointer->FixedIon;
 };
@@ -153 +153 @@
     *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (AtomicVelocity.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
+    if (getAtomicVelocity().Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;
@@ -180 +180 @@
     *out << at(0) << "\t" << at(1) << "\t" << at(2);
     *out << "\t" << FixedIon;
-    if (AtomicVelocity.Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << AtomicVelocity[0] << "\t" << AtomicVelocity[1] << "\t" << AtomicVelocity[2] << "\t";
+    if (getAtomicVelocity().Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
     if (comment != NULL)
       *out << " # " << comment << endl;

src/atom_atominfo.cpp

@@ -83 +83 @@
 }
 
+Vector& AtomInfo::getAtomicVelocity()
+{
+  return AtomicVelocity;
+}
+
+const Vector& AtomInfo::getAtomicVelocity() const
+{
+  return AtomicVelocity;
+}
+
+void AtomInfo::setAtomicVelocity(const Vector &_newvelocity)
+{
+  AtomicVelocity = _newvelocity;
+}
+
+const Vector& AtomInfo::getAtomicForce() const
+{
+  return AtomicForce;
+}
+
+void AtomInfo::setAtomicForce(const Vector &_newforce)
+{
+  AtomicForce = _newforce;
+}
+
 void AtomInfo::setPosition(const Vector& _vector)
 {

src/atom_atominfo.hpp

@@ -33 +33 @@
 
 public:
-  Vector AtomicVelocity;       //!< velocity vector of atom, giving last velocity within cell
-  Vector AtomicForce;       //!< Force vector of atom, giving last force within cell
-
   AtomInfo();
   AtomInfo(const AtomInfo &_atom);
@@ -41 +38 @@
   virtual ~AtomInfo();
 
+  /** Getter for AtomicElement.
+   *
+   * @return constant reference to AtomicElement
+   */
   const element *getType() const;
-  void setType(const element *);
-  void setType(const int);
+  /** Setter for AtomicElement.
+   *
+   * @param _type new element by pointer to set
+   */
+  void setType(const element *_type);
+  /** Setter for AtomicElement.
+   *
+   * @param _typenr new element by index to set
+   */
+  void setType(const int _typenr);
+
+  /** Getter for AtomicVelocity.
+   *
+   * @return constant reference to AtomicVelocity
+   */
+  Vector& getAtomicVelocity();
+  /** Getter for AtomicVelocity.
+   *
+   * @return constant reference to AtomicVelocity
+   */
+  const Vector& getAtomicVelocity() const;
+  /** Setter for AtomicVelocity.
+   *
+   * @param _newvelocity new velocity to set
+   */
+  void setAtomicVelocity(const Vector &_newvelocity);
+
+  /** Getter for AtomicForce.
+   *
+   * @return constant reference to AtomicForce
+   */
+  const Vector& getAtomicForce() const;
+  /** Setter for AtomicForce.
+   *
+   * @param _newvelocity new force vector to set
+   */
+  void setAtomicForce(const Vector &_newforce);
 
   ///// manipulation of the atomic position
@@ -80 +116 @@
 private:
   Vector AtomicPosition;       //!< coordinate vector of atom, giving last position within cell
+  Vector AtomicVelocity;       //!< velocity vector of atom, giving last velocity within cell
+  Vector AtomicForce;       //!< Force vector of atom, giving last force within cell
+
   const element *AtomicElement;  //!< pointing to element
 };

src/config.cpp

@@ -543 +543 @@
 
             // parse velocities if present
-            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->AtomicVelocity[0], 1,optional))
-              neues->AtomicVelocity[0] = 0.;
-            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->AtomicVelocity[1], 1,optional))
-              neues->AtomicVelocity[1] = 0.;
-            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->AtomicVelocity[2], 1,optional))
-              neues->AtomicVelocity[2] = 0.;
+            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->getAtomicVelocity()[0], 1,optional))
+              neues->getAtomicVelocity()[0] = 0.;
+            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->getAtomicVelocity()[1], 1,optional))
+              neues->getAtomicVelocity()[1] = 0.;
+            if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->getAtomicVelocity()[2], 1,optional))
+              neues->getAtomicVelocity()[2] = 0.;
             for (int d=0;d<NDIM;d++)
-              neues->Trajectory.U.at(repetition)[d] = neues->AtomicVelocity[d];
+              neues->Trajectory.U.at(repetition)[d] = neues->getAtomicVelocity()[d];
 
             // parse forces if present
@@ -608 +608 @@
           neues->setPosition(position);
           ParseForParameter(verbose,FileBuffer, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
-          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->AtomicVelocity[0], repetition,optional))
-            neues->AtomicVelocity[0] = 0.;
-          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->AtomicVelocity[1], repetition,optional))
-            neues->AtomicVelocity[1] = 0.;
-          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->AtomicVelocity[2], repetition,optional))
-            neues->AtomicVelocity[2] = 0.;
+          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 5, 1, double_type, &neues->getAtomicVelocity()[0], repetition,optional))
+            neues->getAtomicVelocity()[0] = 0.;
+          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 6, 1, double_type, &neues->getAtomicVelocity()[1], repetition,optional))
+            neues->getAtomicVelocity()[1] = 0.;
+          if(!ParseForParameter(verbose,FileBuffer, keyword, 0, 7, 1, double_type, &neues->getAtomicVelocity()[2], repetition,optional))
+            neues->getAtomicVelocity()[2] = 0.;
           // here we don't care if forces are present (last in trajectories is always equal to current position)
           neues->setType(elementhash[i]); // find element type

src/molecule.cpp

@@ -364 +364 @@
       FirstOtherAtom = World::getInstance().createAtom();    // new atom
       FirstOtherAtom->setType(1);  // element is Hydrogen
-      FirstOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
       if (TopReplacement->getType()->getAtomicNumber() == 1) { // neither rescale nor replace if it's already hydrogen
@@ -429 +429 @@
       FirstOtherAtom->setType(1);
       SecondOtherAtom->setType(1);
-      FirstOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
-      SecondOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
@@ -484 +484 @@
       SecondOtherAtom->setType(1);
       ThirdOtherAtom->setType(1);
-      FirstOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
-      SecondOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
-      ThirdOtherAtom->AtomicVelocity = TopReplacement->AtomicVelocity; // copy velocity
+      ThirdOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
       ThirdOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  //  we are just an added hydrogen with no father