Changeset 3d0892

Timestamp:

Apr 5, 2012, 3:55:47 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:

2034f3

Parents:

d2596b

git-author:

Frederik Heber <heber@…> (03/26/12 09:59:32)

git-committer:

Frederik Heber <heber@…> (04/05/12 15:55:47)

Message:

Added an additionalAtomInfo container to XmlParser.

• this stores the parser-specific information such as charge, ...

Location:

src/Parser

Files:

• FormatParserStorage.cpp (modified) (1 diff)
• XmlParser.cpp (modified) (5 diffs)
• XmlParser.hpp (modified) (3 diffs)

src/Parser/FormatParserStorage.cpp

@@ -37 +37 @@
 #include "Psi3Parser.hpp"
 #include "TremoloParser.hpp"
+#include "XmlParser.hpp"
 #include "XyzParser.hpp"
 

src/Parser/XmlParser.cpp

@@ -37 +37 @@
 
 #include "Parser/pugixml/pugixml.hpp"
+
+// static instances
+FormatParser< xml >::additionalAtomInfo FormatParser< xml >::defaultAtomInfo;
 
 // declare specialized static variables
@@ -162 +165 @@
     newAtom->setPosition(p.position);
     newmol->AddAtom(newAtom);
+    additionalAtomInfo atomInfo(p.q, p.potential, p.field);
+#ifndef NDEBUG
+    std::pair<AtomInfoMap_t::iterator, bool> inserter =
+#endif
+    additionalAtomData.insert( std::make_pair(newAtom->getId(), atomInfo) );
+    ASSERT( inserter.second,
+        "FormatParser< xml >::load() - atomInfo entry for atom "+toString(newAtom->getId())
+        +" already present.");
   }
 
@@ -188 +199 @@
   for(std::vector<atom*>::const_iterator it = atoms.begin(); it != atoms.end(); it++) {
     struct scafacos::configuration::particle p;
+    const additionalAtomInfo &atomInfo = getAtomData(*(*it));
     p.position = (*it)->getPosition();
-    p.q = 0.;
-    p.potential = 0.;
-    p.field = zeroVec;
+    p.q = atomInfo.charge;
+    p.potential = atomInfo.potential;
+    p.field = atomInfo.field;
     data.config.p.push_back(p);
   }
@@ -234 +246 @@
 }
 
+/** Observer callback when new atom is added to World.
+ *
+ * @param id of atom
+ */
+void FormatParser< xml >::AtomInserted(atomId_t id)
+{
+  std::map<const atomId_t, additionalAtomInfo>::iterator iter = additionalAtomData.find(id);
+  ASSERT(iter == additionalAtomData.end(),
+      "FormatParser< xml >::AtomInserted() - additionalAtomData already present for newly added atom "
+      +toString(id)+".");
+  // additionalAtomData.insert( std::make_pair(id, additionalAtomInfo()) );
+}
+
+/** Remove additional AtomData info, when atom has been removed from World.
+ *
+ * @param id of atom
+ */
+void FormatParser< xml >::AtomRemoved(atomId_t id)
+{
+  std::map<const atomId_t, additionalAtomInfo>::iterator iter = additionalAtomData.find(id);
+  // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
+//  ASSERT(iter != additionalAtomData.end(),
+//      "FormatParser< tremolo >::AtomRemoved() - additionalAtomData is not present for atom "
+//      +toString(id)+" to remove.");
+  if (iter != additionalAtomData.end())
+    additionalAtomData.erase(iter);
+}
+
+const FormatParser< xml >::additionalAtomInfo& FormatParser< xml >::getAtomData(const atom &_atom) const
+{
+  {
+    // has its own entry?
+    AtomInfoMap_t::const_iterator iter = additionalAtomData.find(_atom.getId());
+    if (iter != additionalAtomData.end()) {
+      return iter->second;
+    }
+  }
+  {
+    // father has an entry?
+    AtomInfoMap_t::const_iterator iter = additionalAtomData.find(_atom.GetTrueFather()->getId());
+    if (iter != additionalAtomData.end()) {
+      return iter->second;
+    }
+  }
+  return defaultAtomInfo;
+}
+
+
 #define comparator(x,y) if (x != y) { LOG(2, "DEBUG: Mismatch in " << #x << ": " << x << " != " << y); return false; }
 #define num_comparator(x,y) if (fabs(x - y) > MYEPSILON) { LOG(2, "DEBUG: Numeric mismatch in " << #x << ": " << x << " != " << y << " by " << fabs(x - y) << "."); return false; }
@@ -265 +325 @@
 }
 
+
 bool FormatParser< xml >::scafacos::operator==(const scafacos &s) const {
   comparator(name, s.name)

src/Parser/XmlParser.hpp

@@ -14 +14 @@
 #endif
 
+#include <map>
 #include <string>
 
@@ -53 +54 @@
   void save(std::ostream* file, const std::vector<atom *> &atoms);
 
+protected:
+  void AtomInserted(atomId_t);
+  void AtomRemoved(atomId_t);
+
 private:
   //!> structure that contains all information from the xml file
@@ -91 +96 @@
     }
   } data;
+
+  //!> additional parser-specific information for an atom.
+  struct additionalAtomInfo {
+    /** Default constructor for additionalAtomInfo.
+     *
+     * Sets all parser-specific values to zero.
+     */
+    additionalAtomInfo() :
+      charge(0.),
+      potential(0),
+      field(zeroVec)
+    {}
+
+    /** Default constructor for additionalAtomInfo.
+     *
+     */
+    additionalAtomInfo(double _charge, double _potential, const Vector& _field) :
+      charge(_charge),
+      potential(_potential),
+      field(_field)
+    {}
+
+    //!> charge of the atom
+    double charge;
+    //!> potential at position of atom
+    double potential;
+    //!> field at position of atom
+    Vector field;
+  };
+
+  //!> typedef for map to associate additional parser-specific information to each atom.
+  typedef std::map< atomId_t, additionalAtomInfo> AtomInfoMap_t;
+
+  //!> map to associate additional parser-specific information to each atom.
+  AtomInfoMap_t additionalAtomData;
+
+  //!> static instance with default additional atom information
+  static additionalAtomInfo defaultAtomInfo;
+
+  /** Getter for additionalAtomInfo.
+   *
+   * @param _atom constant ref to atom
+   * @return constant reference to additional atom info container,
+   *         otherwise to default atom info
+   */
+  const additionalAtomInfo& getAtomData(const atom &_atom) const;
 };