Changeset 0ba410

Timestamp:

Aug 5, 2010, 3:46:01 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

0eea14

Parents:

bf8e20

Message:

made the molecule::Output() method use STL algorithms

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• atom.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)

src/atom.cpp

@@ -19 +19 @@
 
 #include <iomanip>
+#include <iostream>
 
 /************************************* Functions for class atom *************************************/
@@ -165 +166 @@
   * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
+bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
 {
   AtomNo[type->Z]++;  // increment number
   if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+    cout << "Looking for atom with element " << *type << endl;
+    ASSERT(elementLookup.there.find(type)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
+    *out << "Ion_Type" << elementLookup.there.find(type)->second << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;

src/atom.hpp

@@ -52 +52 @@
 
   bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
-  bool OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
+  bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
   bool OutputXYZLine(ofstream *out) const;
   bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;

src/molecule.cpp

@@ -860 +860 @@
  * \param *out output stream
  */
-bool molecule::Output(ofstream * const output)
-{
-  int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-
-  for (int i=0;i<MAX_ELEMENTS;++i) {
-    AtomNo[i] = 0;
-    ElementNo[i] = 0;
-  }
+bool molecule::Output(ostream * const output)
+{
   if (output == NULL) {
     return false;
   } else {
+    int AtomNo[MAX_ELEMENTS];
+    memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
+    enumeration<const element*> elementLookup = formula.enumerateElements();
+    for(map<const element*,unsigned int>::iterator iter=elementLookup.there.begin();
+        iter!=elementLookup.there.end();++iter){
+      cout << "Enumerated element " << *iter->first << " with number " << iter->second << endl;
+    }
     *output << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
-    SetIndexedArrayForEachAtomTo ( ElementNo, &element::Z, &AbsoluteValue, 1);
-    int current=1;
-    for (int i=0;i<MAX_ELEMENTS;++i) {
-      if (ElementNo[i] == 1)
-        ElementNo[i] = current++;
-    }
-    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
+    for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
     return true;
   }

src/molecule.hpp

@@ -341 +341 @@
 
   // Output routines.
-  bool Output(ofstream * const output);
+  bool Output(std::ostream * const output);
   bool OutputTrajectories(ofstream * const output);
   void OutputListOfBonds() const;