Changeset 2e352f for src

Timestamp:

Oct 5, 2011, 9:18:21 AM (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:

37f9d4

Parents:

faca99

git-author:

Daniel Dueck <dueck@…> (04/06/11 17:17:41)

git-committer:

Frederik Heber <heber@…> (10/05/11 09:18:21)

Message:

Because of problems with columns in data-files, some changes were done.

• atom::CorrectFactor() does not set fathet to itself anymore in father's father case.
• molecule::CopyMolecule() does not correct fathers anymore

Changed due to rebase to v1.1.3:

• removed changes to TremoloParser.cpp and boundary.cpp.

Location:

src

Files:

• Actions/MoleculeAction/CreateMicelleAction.cpp (modified) (4 diffs)
• Parser/TremoloParser.cpp (modified) (6 diffs)
• atom.cpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)

src/Actions/MoleculeAction/CreateMicelleAction.cpp

@@ -56 +56 @@
 #include "Actions/ValueStorage.hpp"
 
-// memento to remember the state when undoing
-
-#include <iostream>
-#include <fstream>
-#include <config.h>
-#include "atom.hpp"
-#include "molecule.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/Line.hpp"
-#include "World.hpp"
-#include <gsl/gsl_poly.h>
-#include <gsl/gsl_eigen.h>
 //#define PATH "/home/dueck/workspace/tenside/tmp/"
 #define AtomVector std::vector <atom *>
@@ -175 +163 @@
   //double MYEPSILON=1e-10;
 
-  for (ka = 0; ka<params.N-1; ka++)
+  for (ka = 0; ka<pt.size()-1; ka++)
   {
     cout << "Creating " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ";
@@ -201 +189 @@
   cout << "rotating ...";
   Vector ZAxis(Vector(0.0,0.0,1.0));
-  Vector Axis(pt[params.N-1]);
+  Vector Axis(pt[pt.size()-1]);
   const double alpha = ZAxis.Angle(Axis);
   Axis.VectorProduct(ZAxis);
@@ -215 +203 @@
   Tensid=NULL;
 
-  GraphSubgraphDissection();
+  //GraphSubgraphDissection();
   return Action::success;
 }

src/Parser/TremoloParser.cpp

@@ -88 +88 @@
  */
 TremoloParser::~TremoloParser() {
+        std::cerr << "Clearing usedFields." << std::endl;
   usedFields.clear();
   additionalAtomData.clear();
@@ -105 +106 @@
   // reset atomIdMap, for we now get new serials
   atomIdMap.clear();
+        std::cerr << "Clearing usedFields." << std::endl;
   usedFields.clear();
 
@@ -126 +128 @@
   newmol->getAtomCount();
 
+  DoLog(3) && (Log() << Verbose(3) << "usedFields after load contains: " << usedFields << std::endl);
+
   processNeighborInformation();
   adaptImprData();
@@ -141 +145 @@
 
   vector<atom*>::const_iterator atomIt;
-  vector<string>::iterator it;
+  /*vector<string>::iterator it;*/
+  vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
+
+
+  DoLog(3) && (Log() << Verbose(3) << "usedFields before save contains: " << usedFields << std::endl);
+
+  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
 
   DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
@@ -174 +184 @@
  */
 void TremoloParser::saveLine(ostream* file, atom* currentAtom) {
-  vector<string>::iterator it;
+ /* vector<string>::iterator it;*/
+        vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
+
   TremoloKey::atomDataKey currentField;
 
@@ -295 +307 @@
 
   lineStream << line.substr(offset);
+        std::cerr << "Clearing usedFields in parseAtomDataKeysLine." << std::endl;
   usedFields.clear();
   while (lineStream.good()) {

src/atom.cpp

@@ -96 +96 @@
 void atom::CorrectFather()
 {
-  if (father->father == father)   // same atom in copy's father points to itself
-    father = this;  // set father to itself (copy of a whole molecule)
-  else
+  if (father->father != father)   // same atom in copy's father points to itself
+//    father = this;  // set father to itself (copy of a whole molecule)
+//  else
    father = father->father;  // set father to original's father
 

src/boundary.cpp

@@ -998 +998 @@
     DoLog(0) && (Log() << Verbose(0) << "Removing molecule " << Filling->getName() << ", all atoms have been removed." << std::endl);
     World::getInstance().destroyMolecule(Filling);
+    Filling = NULL;
   }
   return status;

src/molecule.cpp

@@ -690 +690 @@
   }
   // correct fathers
-  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
+  //for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
 
   return copy;