Changeset e41951

Timestamp:

Oct 7, 2009, 2:29:57 PM (15 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:

f66195

Parents:

23b830

git-author:

Frederik Heber <heber@…> (10/07/09 14:26:53)

git-committer:

Frederik Heber <heber@…> (10/07/09 14:29:57)

Message:

used forward declaration to untangle atom and bond declarations, molecule::CreateListOfBondsPerAtom() uses ActOnAllAtoms

• a major problem is two classes depending on one another and we've often made constraints in order to accommodate for this. But there is an easier solution: Have forward declarations of the other class in each header file, only include the true other header file in each implementation (i.e. cpp file).
• This was done with atom and bond class to allow for a new function atom::OutputBondOfAtom()
• molecule::CreateListOfBondsPerAtom() uses ActOnAllAtoms with this new function.

Location:

src

Files:

• atom.cpp (modified) (6 diffs)
• atom.hpp (modified) (2 diffs)
• bond.cpp (modified) (1 diff)
• bond.hpp (modified) (1 diff)
• molecule.cpp (modified) (5 diffs)

src/atom.cpp

@@ -6 +6 @@
 
 #include "atom.hpp"
+#include "bond.hpp"
 #include "memoryallocator.hpp"
 
@@ -120 +121 @@
  * \param *out stream to output to
  * \param *comment commentary after '#' sign
+  * \return true - \a *out present, false - \a *out is NULL
  */
 bool atom::Output(ofstream *out, int ElementNo, int AtomNo, const char *comment) const
@@ -157 +159 @@
 /** Output of a single atom as one lin in xyz file.
  * \param *out stream to output to
+  * \return true - \a *out present, false - \a *out is NULL
  */
 bool atom::OutputXYZLine(ofstream *out) const
@@ -169 +172 @@
 /** Output of a single atom as one lin in xyz file.
  * \param *out stream to output to
+ * \param *ElementNo array with ion type number in the config file this atom's element shall have
+ * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
+ * \param step Trajectory time step to output
+  * \return true - \a *out present, false - \a *out is NULL
  */
 bool atom::OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const
@@ -189 +196 @@
 /** Output of a single atom as one lin in xyz file.
  * \param *out stream to output to
+ * \param step Trajectory time step to output
+ * \return true - \a *out present, false - \a *out is NULL
  */
 bool atom::OutputTrajectoryXYZ(ofstream *out, int step) const
@@ -202 +211 @@
 };
 
+/** Prints all bonds of this atom from given global lists.
+ * \param *out stream to output to
+ * \param *NumberOfBondsPerAtom array with number of bonds per atomic index
+ * \param ***ListOfBondsPerAtom array per atomic index of array with pointer to bond
+ * \return true - \a *out present, false - \a *out is NULL
+ */
+bool atom::OutputBondOfAtom(ofstream *out, int *NumberOfBondsPerAtom, bond ***ListOfBondsPerAtom) const
+{
+  if (out != NULL) {
+    *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << NumberOfBondsPerAtom[nr] << " bonds: ";
+    int TotalDegree = 0;
+    for (int j=0;j<NumberOfBondsPerAtom[nr];j++) {
+      *out << *ListOfBondsPerAtom[nr][j] << "\t";
+      TotalDegree += ListOfBondsPerAtom[nr][j]->BondDegree;
+    }
+    *out << " -- TotalDegree: " << TotalDegree << endl;
+    return true;
+  } else
+    return false;
+};
+
 ostream & operator << (ostream &ost, const atom &a)
 {

src/atom.hpp

@@ -23 +23 @@
 #include "tesselation.hpp"
 #include "vector.hpp"
+
+class bond;
 
 /** Single atom.
@@ -65 +67 @@
   bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
   bool OutputTrajectoryXYZ(ofstream *out, int step) const;
+  bool OutputBondOfAtom(ofstream *out, int *NumberOfBondsPerAtom, bond ***ListOfBondsPerAtom) const;
 
   void EqualsFather ( atom *ptr, atom **res );

src/bond.cpp

@@ -5 +5 @@
  */
 
+#include "atom.hpp"
 #include "bond.hpp"
 

src/bond.hpp

@@ -16 +16 @@
 #endif
 
-#include "atom.hpp"
+class atom;
 
 /** Bonds between atoms.

src/molecule.cpp

@@ -734 +734 @@
 bool molecule::OutputTrajectories(ofstream *out)
 {
-  atom *walker = NULL;
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
   CountElements();
@@ -799 +798 @@
 bool molecule::OutputTrajectoriesXYZ(ofstream *out)
 {
-  int No = 0;
   time_t now;
 
@@ -818 +816 @@
 bool molecule::OutputXYZ(ofstream *out) const
 {
-  atom *walker = NULL;
-  int AtomNo = 0;
   time_t now;
 
@@ -918 +914 @@
 {
   bond *Binder = NULL;
-  atom *Walker = NULL;
-  int TotalDegree;
   *out << Verbose(1) << "Begin of Creating ListOfBondsPerAtom: AtomCount = " << AtomCount << "\tBondCount = " << BondCount << "\tNoNonBonds = " << NoNonBonds << "." << endl;
 
@@ -960 +954 @@
   // output list for debugging
   *out << Verbose(3) << "ListOfBondsPerAtom for each atom:" << endl;
-  Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    *out << Verbose(4) << "Atom " << Walker->Name << "/" << Walker->nr << " with " << NumberOfBondsPerAtom[Walker->nr] << " bonds: ";
-    TotalDegree = 0;
-    for (int j=0;j<NumberOfBondsPerAtom[Walker->nr];j++) {
-      *out << *ListOfBondsPerAtom[Walker->nr][j] << "\t";
-      TotalDegree += ListOfBondsPerAtom[Walker->nr][j]->BondDegree;
-    }
-    *out << " -- TotalDegree: " << TotalDegree << endl;
-  }
+  ActOnAllAtoms( &atom::OutputBondOfAtom, out, NumberOfBondsPerAtom, ListOfBondsPerAtom );
+
   *out << Verbose(1) << "End of Creating ListOfBondsPerAtom." << endl << endl;
 };
-
 
 /** Blows the 6-dimensional \a cell_size array up to a full NDIM by NDIM matrix.