Changeset 2034f3 for src/Atom

Timestamp:

Apr 5, 2012, 3:55:48 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:

259887

Parents:

3d0892

git-author:

Frederik Heber <heber@…> (03/27/12 12:37:05)

git-committer:

Frederik Heber <heber@…> (04/05/12 15:55:48)

Message:

Added AtomInfo::charge along with getter and setter.

• charge is used by both TremoloParser and XmlParser, hence needs to be exchanged.
• Added charge to state info in AtomicInfo.
• TESTFIX: regression tests Molecules/Copy, Molecules/CreateMicelle, and Filling/FillVoidWithMolecule's tensid.data file had to be changed due to present Charge info with precision different to the one arising from new AtomInfo::Charge.
• removed ParserXmlUnitTest from XFAIL_TESTS.

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (3 diffs)
• AtomicInfo.hpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (3 diffs)
• atom_atominfo.hpp (modified) (2 diffs)

src/Atom/AtomicInfo.cpp

@@ -33 +33 @@
 AtomicInfo::AtomicInfo() :
     Type(NULL),
+    charge(0.),
     FatherId(0),
     MolId(0),
@@ -41 +42 @@
     Position(_atom.getPosition()),
     Type(_atom.getType()),
+    charge(_atom.getCharge()),
     Velocity(_atom.getAtomicVelocity()),
     FatherId(_atom.father->getId()),
@@ -56 +58 @@
   _atom.setPosition(Position);
   _atom.setType(Type);
+  _atom.setCharge(charge);
   _atom.setAtomicVelocity(Velocity);
 

src/Atom/AtomicInfo.hpp

@@ -37 +37 @@
   Vector Position;
   const element * Type;
+  double charge;
   Vector Velocity;
   atomId_t FatherId;

src/Atom/atom_atominfo.cpp

@@ -37 +37 @@
 AtomInfo::AtomInfo() :
   AtomicElement(0),
-  FixedIon(false)
+  FixedIon(false),
+  charge(0.)
 {
   AtomicPosition.reserve(1);
@@ -53 +54 @@
     AtomicPosition(_atom.AtomicPosition),
     AtomicElement(_atom.AtomicElement),
-    FixedIon(false)
+    FixedIon(_atom.FixedIon),
+    charge(_atom.charge)
 {
   AtomicVelocity.reserve(1);
@@ -63 +65 @@
 AtomInfo::AtomInfo(const VectorInterface &_v) :
     AtomicElement(-1),
-    FixedIon(false)
+    FixedIon(false),
+    charge(0.)
 {
   AtomicPosition[0] = _v.getPosition();

src/Atom/atom_atominfo.hpp

@@ -271 +271 @@
   Vector getMomentum(const unsigned int step) const;
   double getMass() const;
+  double getCharge() const {
+    return charge;
+  }
+  void setCharge(const double _charge) {
+    charge = _charge;
+  }
 
   std::ostream & operator << (std::ostream &ost) const;
@@ -288 +294 @@
 private:
   atomicNumber_t AtomicElement;          //!< contains atomic number (i.e. Z of element) or "-1" if unset
-  bool FixedIon;
+  bool FixedIon;    //!< whether this nuclei is influenced by force integration or not
+  double charge;    //!< charge of this nuclei
 };