Changeset 0d1ad0 for src/molecule.hpp

Timestamp:

Jun 25, 2010, 9:42:28 AM (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, 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:

04488a, 0c5eeb, 93987b

Parents:

6d574a (diff), a356f2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into StructureRefactoring

Conflicts:

molecuilder/src/World.cpp

File:

• src/molecule.hpp (modified) (5 diffs)

src/molecule.hpp

@@ -80 +80 @@
   double *PenaltyConstants;   //!<  penalty constant in front of each term
 };
-
-#define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
-enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover };   //!< Thermostat names for output
-
 
 /** The complete molecule.
@@ -265 +261 @@
   /// Count and change present atoms' coordination.
   void CountElements();
-  void CalculateOrbitals(class config &configuration);
   bool CenterInBox();
   bool BoundInBox();
@@ -292 +287 @@
   double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
   void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
-  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
+  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
         
   bool CheckBounds(const Vector *x) const;
@@ -324 +319 @@
 
   /// Fragment molecule by two different approaches:
-  int FragmentMolecule(int Order, config *configuration);
-  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path, char *filename);
-  bool StoreAdjacencyToFile(char *path, char *filename);
-  bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
-  bool ParseOrderAtSiteFromFile(char *path);
-  bool StoreOrderAtSiteFile(char *path);
-  bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
+  int FragmentMolecule(int Order, std::string &prefix);
+  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
+  bool StoreBondsToFile(std::string &filename, std::string path = "");
+  bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
+  bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
+  bool ParseOrderAtSiteFromFile(std::string &path);
+  bool StoreOrderAtSiteFile(std::string &path);
+  bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
   bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
@@ -380 +375 @@
   ~MoleculeListClass();
 
-  bool AddHydrogenCorrection(char *path);
-  bool StoreForcesFile(char *path, int *SortIndex);
+  bool AddHydrogenCorrection(std::string &path);
+  bool StoreForcesFile(std::string &path, int *SortIndex);
   void insert(molecule *mol);
   void erase(molecule *mol);
   molecule * ReturnIndex(int index);
-  bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
+  bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
   int NumberOfActiveMolecules();
   void Enumerate(ostream *out);