Changeset 4455f4 for src/config.cpp

Timestamp:

Oct 19, 2009, 1:09:29 PM (16 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, Candidate_v1.7.0, 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:

c75de1

Parents:

9eefda

Message:

Huge Refactoring: class atom split up into several inherited classes.

• There are now two parts: classes containing data (called ...Info) and classes containing associated functions:
  • new data classes: ParticleInfo (id and name), AtomInfo (element, position, velocity, force), TrajectoryParticleInfo, GraphNodeInfo (all graph variables), BondedParticleInfo (AdaptiveOrder, MaxOrder, ListOfBonds)
  • new associated function classes: TrajectoryParticle, GraphNode, BondedParticle

• template functions ActOnAllAtoms(), SumPerAtom() were adapted with another template type for the class of the member function
• template functions SetIndexedArrayForEachAtomTo() have their index as ParticleInfo::*index

File:

• src/config.cpp (modified) (4 diffs)

src/config.cpp

@@ -9 +9 @@
 #include "element.hpp"
 #include "helpers.hpp"
+#include "molecule.hpp"
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
@@ -1444 +1445 @@
 bool config::SaveMPQC(const char *filename, molecule *mol) const
 {
-  int ElementNo = 0;
   int AtomNo;
-  atom *Walker = NULL;
-  element *runner = NULL;
   Vector *center = NULL;
   ofstream *output = NULL;
@@ -1475 +1473 @@
   center = mol->DetermineCenterOfAll(output);
   // output of atoms
-  runner = mol->elemente->start;
-  while (runner->next != mol->elemente->end) { // go through every element
-    runner = runner->next;
-    if (mol->ElementsInMolecule[runner->Z]) { // if this element got atoms
-      ElementNo++;
-      AtomNo = 0;
-      Walker = mol->start;
-      while (Walker->next != mol->end) { // go through every atom of this element
-        Walker = Walker->next;
-        if (Walker->type == runner) { // if this atom fits to element
-          AtomNo++;
-          *output << "\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center->x[0] << "\t" << Walker->x.x[1]-center->x[1] << "\t" << Walker->x.x[2]-center->x[2] << " ]" << endl;
-        }
-      }
-    }
-  }
+  AtomNo = 0;
+  mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, center, &AtomNo );
   delete(center);
   *output << "\t}" << endl;
@@ -1524 +1508 @@
   center = mol->DetermineCenterOfAll(output);
   // output of atoms
-  runner = mol->elemente->start;
-  while (runner->next != mol->elemente->end) { // go through every element
-    runner = runner->next;
-    if (mol->ElementsInMolecule[runner->Z]) { // if this element got atoms
-      ElementNo++;
-      AtomNo = 0;
-      Walker = mol->start;
-      while (Walker->next != mol->end) { // go through every atom of this element
-        Walker = Walker->next;
-        if (Walker->type == runner) { // if this atom fits to element
-          AtomNo++;
-          *output << "\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center->x[0] << "\t" << Walker->x.x[1]-center->x[1] << "\t" << Walker->x.x[2]-center->x[2] << " ]" << endl;
-        }
-      }
-    }
-  }
+  AtomNo = 0;
+  mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, center, &AtomNo );
   delete(center);
   *output << "\t}" << endl;