Changeset 4d2b33 for src

Timestamp:

Mar 27, 2012, 3:53:35 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:

46c832

Parents:

955b91

git-author:

Frederik Heber <heber@…> (03/19/12 16:42:39)

git-committer:

Frederik Heber <heber@…> (03/27/12 15:53:35)

Message:

FIX: molecule does not need a periodentafel.

• removed periodentafel param from cstor.
• removed member variable elemente
• removed AddXyzFile which was sole user of elemente.
• removed depending functions in MoleculeListClass which were all remnants from old menu interface.

Location:

src

Files:

• MoleculeListClass.hpp (modified) (1 diff)
• molecule.cpp (modified) (4 diffs)
• molecule.hpp (modified) (3 diffs)
• moleculelist.cpp (modified) (1 diff)

src/MoleculeListClass.hpp

@@ -53 +53 @@
   int CountAllAtoms() const;
 
-  // Methods moved here from the menus
-  // TODO: more refactoring needed on these methods
-  void createNewMolecule(periodentafel *periode);
-  void loadFromXYZ(periodentafel *periode);
-  void setMoleculeFilename();
-  void parseXYZIntoMolecule();
-  void eraseMolecule();
-
 private:
   World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor

src/molecule.cpp

@@ -36 +36 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Element/element.hpp"
-#include "Element/periodentafel.hpp"
 #include "Graph/BondGraph.hpp"
 #include "LinearAlgebra/Exceptions.hpp"
@@ -55 +54 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(const periodentafel * const teil) :
+molecule::molecule() :
   Observable("molecule"),
-  elemente(teil),
   MDSteps(0),
   NoNonHydrogen(0),
@@ -74 +72 @@
 
 molecule *NewMolecule(){
-  return new molecule(World::getInstance().getPeriode());
+  return new molecule();
 }
 
@@ -590 +588 @@
 };
 
-/** Adds given atom \a *pointer from molecule list.
- * Increases molecule::last_atom and gives last number to added atom.
- * \param filename name and path of xyz file
- * \return true - succeeded, false - file not found
- */
-bool molecule::AddXYZFile(std::string filename)
-{
-
-  istringstream *input = NULL;
-  int NumberOfAtoms = 0; // atom number in xyz read
-  int i; // loop variables
-  atom *Walker = NULL;  // pointer to added atom
-  char shorthand[3];  // shorthand for atom name
-  ifstream xyzfile;   // xyz file
-  string line;    // currently parsed line
-  double x[3];    // atom coordinates
-
-  xyzfile.open(filename.c_str());
-  if (!xyzfile)
-    return false;
-
-  OBSERVE;
-  getline(xyzfile,line,'\n'); // Read numer of atoms in file
-  input = new istringstream(line);
-  *input >> NumberOfAtoms;
-  LOG(0, "Parsing " << NumberOfAtoms << " atoms in file.");
-  getline(xyzfile,line,'\n'); // Read comment
-  LOG(1, "Comment: " << line);
-
-  if (MDSteps == 0) // no atoms yet present
-    MDSteps++;
-  for(i=0;i<NumberOfAtoms;i++){
-    Walker = World::getInstance().createAtom();
-    getline(xyzfile,line,'\n');
-    istringstream *item = new istringstream(line);
-    //istringstream input(line);
-    //LOG(1, "Reading: " << line);
-    *item >> shorthand;
-    *item >> x[0];
-    *item >> x[1];
-    *item >> x[2];
-    Walker->setType(elemente->FindElement(shorthand));
-    if (Walker->getType() == NULL) {
-      ELOG(1, "Could not parse the element at line: '" << line << "', setting to H.");
-      Walker->setType(1);
-    }
-
-    Walker->setPosition(Vector(x));
-    Walker->setPositionAtStep(MDSteps-1, Vector(x));
-    Walker->setAtomicVelocityAtStep(MDSteps-1, zeroVec);
-    Walker->setAtomicForceAtStep(MDSteps-1, zeroVec);
-    AddAtom(Walker);  // add to molecule
-    delete(item);
-  }
-  xyzfile.close();
-  delete(input);
-  return true;
-};
-
 /** Creates a copy of this molecule.
  * \return copy of molecule

src/molecule.hpp

@@ -84 +84 @@
   typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator;
 
-  const periodentafel * const elemente; //!< periodic table with each element
   int MDSteps; //!< The number of MD steps in Trajectories
   mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
@@ -103 +102 @@
 protected:
 
-  molecule(const periodentafel * const teil);
+  molecule();
   virtual ~molecule();
 
@@ -188 +187 @@
   /// Add/remove atoms to/from molecule.
   atom * AddCopyAtom(atom *pointer);
-  bool AddXYZFile(std::string filename);
   bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
   bond * AddBond(atom *first, atom *second, int degree = 1);

src/moleculelist.cpp

@@ -633 +633 @@
   return AtomNo;
 }
-
-/***********
- * Methods Moved here from the menus
- */
-
-void MoleculeListClass::createNewMolecule(periodentafel *periode) {
-  OBSERVE;
-  molecule *mol = NULL;
-  mol = World::getInstance().createMolecule();
-  insert(mol);
-};
-
-void MoleculeListClass::loadFromXYZ(periodentafel *periode){
-  molecule *mol = NULL;
-  Vector center;
-  char filename[MAXSTRINGSIZE];
-  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  mol = World::getInstance().createMolecule();
-  do {
-    std::cout << "Enter file name: ";
-    cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-  // center at set box dimensions
-  mol->CenterEdge(&center);
-  RealSpaceMatrix domain;
-  for(int i =0;i<NDIM;++i)
-    domain.at(i,i) = center[i];
-  World::getInstance().setDomain(domain);
-  insert(mol);
-}
-
-void MoleculeListClass::setMoleculeFilename() {
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  do {
-    std::cout << "Enter index of molecule: ";
-    cin >> nr;
-    mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  std::cout << "Enter name: ";
-  cin >> filename;
-  mol->SetNameFromFilename(filename);
-}
-
-void MoleculeListClass::parseXYZIntoMolecule(){
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  mol = NULL;
-  do {
-    std::cout << "Enter index of molecule: ";
-   cin >> nr;
-   mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  do {
-    std::cout << "Enter file name: ";
-   cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-};
-
-void MoleculeListClass::eraseMolecule(){
-  int nr;
-  molecule *mol = NULL;
-  std::cout << "Enter index of molecule: ";
-  cin >> nr;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if (nr == (*ListRunner)->IndexNr) {
-      mol = *ListRunner;
-      ListOfMolecules.erase(ListRunner);
-      World::getInstance().destroyMolecule(mol);
-      break;
-    }
-};