source: src/molecule.hpp@ 9f3b85

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
Last change on this file since 9f3b85 was 257c77, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Merge branch 'stable' into QT4Refactoring

Conflicts:

molecuilder/src/Actions/TesselationAction/ConvexEnvelopeAction.hpp
molecuilder/src/Helpers/MemDebug.hpp
molecuilder/src/Makefile.am
molecuilder/src/UIElements/Dialog.cpp
molecuilder/src/UIElements/MainWindow.cpp
molecuilder/src/UIElements/TextUI/TextUIFactory.cpp
molecuilder/src/builder.cpp
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File size: 22.4 KB
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1/** \file molecule.hpp
2 *
3 * Class definitions of atom and molecule, element and periodentafel
4 */
5
6#ifndef MOLECULES_HPP_
7#define MOLECULES_HPP_
8
9using namespace std;
10
11/*********************************************** includes ***********************************/
12
13// GSL headers
14#include <gsl/gsl_eigen.h>
15#include <gsl/gsl_heapsort.h>
16#include <gsl/gsl_linalg.h>
17#include <gsl/gsl_matrix.h>
18#include <gsl/gsl_multimin.h>
19#include <gsl/gsl_vector.h>
20#include <gsl/gsl_randist.h>
21
22//// STL headers
23#include <map>
24#include <set>
25#include <deque>
26#include <list>
27#include <vector>
28
29#include <string>
30
31#include "types.hpp"
32#include "graph.hpp"
33#include "stackclass.hpp"
34#include "tesselation.hpp"
35#include "Patterns/Observer.hpp"
36#include "Patterns/ObservedIterator.hpp"
37#include "Patterns/Cacheable.hpp"
38
39#include "Descriptors/MoleculeDescriptor_impl.hpp"
40
41/****************************************** forward declarations *****************************/
42
43class atom;
44class bond;
45class BondedParticle;
46class BondGraph;
47class element;
48class ForceMatrix;
49class LinkedCell;
50class molecule;
51class MoleculeLeafClass;
52class MoleculeListClass;
53class periodentafel;
54class Vector;
55
56/******************************** Some definitions for easier reading **********************************/
57
58#define MoleculeList list <molecule *>
59#define MoleculeListTest pair <MoleculeList::iterator, bool>
60
61#define DistancePair pair < double, atom* >
62#define DistanceMap multimap < double, atom* >
63#define DistanceTestPair pair < DistanceMap::iterator, bool>
64
65
66/************************************* Class definitions ****************************************/
67
68/** Structure to contain parameters needed for evaluation of constraint potential.
69 */
70struct EvaluatePotential
71{
72 int startstep; //!< start configuration (MDStep in atom::trajectory)
73 int endstep; //!< end configuration (MDStep in atom::trajectory)
74 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
75 DistanceMap **DistanceList; //!< distance list of each atom to each atom
76 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
77 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
78 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
79 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
80 double *PenaltyConstants; //!< penalty constant in front of each term
81};
82
83#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
84enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
85
86
87/** The complete molecule.
88 * Class incorporates number of types
89 */
90class molecule : public PointCloud , public Observable {
91 friend molecule *NewMolecule();
92 friend void DeleteMolecule(molecule *);
93
94 public:
95 typedef std::set<atom*> atomSet;
96 typedef ObservedIterator<atomSet> iterator;
97 typedef atomSet::const_iterator const_iterator;
98
99 const periodentafel * const elemente; //!< periodic table with each element
100 // old deprecated atom handling
101 //atom *start; //!< start of atom list
102 //atom *end; //!< end of atom list
103 //bond *first; //!< start of bond list
104 //bond *last; //!< end of bond list
105 int MDSteps; //!< The number of MD steps in Trajectories
106 //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
107 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
108 int ElementCount; //!< how many unique elements are therein
109 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
110 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
111 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
112 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
113 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
114 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
115 Vector Center; //!< Center of molecule in a global box
116 int IndexNr; //!< index of molecule in a MoleculeListClass
117 char name[MAXSTRINGSIZE]; //!< arbitrary name
118
119 private:
120 Cacheable<string> formula;
121 Cacheable<int> AtomCount;
122 moleculeId_t id;
123 atomSet atoms; //<!set of atoms
124 protected:
125 //void CountAtoms();
126 /**
127 * this iterator type should be used for internal variables, \
128 * since it will not lock
129 */
130 typedef atomSet::iterator internal_iterator;
131
132
133 molecule(const periodentafel * const teil);
134 virtual ~molecule();
135
136
137public:
138 //getter and setter
139 const std::string getName();
140 int getAtomCount() const;
141 int doCountAtoms();
142 moleculeId_t getId();
143 void setId(moleculeId_t);
144 void setName(const std::string);
145 const std::string getFormula();
146 std::string calcFormula();
147
148 iterator begin();
149 const_iterator begin() const;
150 iterator end();
151 const_iterator end() const;
152 bool empty() const;
153 size_t size() const;
154 const_iterator erase( const_iterator loc );
155 const_iterator erase( atom * key );
156 const_iterator find ( atom * key ) const;
157 pair<iterator,bool> insert ( atom * const key );
158 bool containsAtom(atom* key);
159
160
161 // re-definition of virtual functions from PointCloud
162 const char * const GetName() const;
163 Vector *GetCenter() const ;
164 TesselPoint *GetPoint() const ;
165 int GetMaxId() const;
166 void GoToNext() const ;
167 void GoToFirst() const ;
168 bool IsEmpty() const ;
169 bool IsEnd() const ;
170
171 // templates for allowing global manipulation of all vectors
172 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
173 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
174 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
175 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
176 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&), T &t ) const;
177 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&) const, T &t ) const;
178 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
179 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
180 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
181 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v) const;
182
183 // templates for allowing global manipulation of molecule with each atom as single argument
184 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
185 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
186
187 // templates for allowing global copying of molecule with each atom as single argument
188 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
189 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
190
191 // templates for allowing global manipulation of all atoms
192 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
193 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
194 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
195 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
196 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
197 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
198 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V), T t, U u, V v) const;
199 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V) const, T t, U u, V v) const;
200 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W), T t, U u, V v, W w) const;
201 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W) const, T t, U u, V v, W w) const;
202
203 // templates for allowing conditional global copying of molecule with each atom as single argument
204 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
205 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
206 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
207 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
208 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
209 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
210 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
211 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
212 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
213 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
214 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
215 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
216 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
217 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
218 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
219 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
220
221 // templates for allowing global manipulation of an array with one entry per atom
222 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
223 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
224 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
225 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
226 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
227 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
228 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
229 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
230 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
231 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
232 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
233
234 // templates for allowing global manipulation of each atom by entries in an array
235 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
236 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
237
238 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
239 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
240 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
241 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
242
243 /// remove atoms from molecule.
244 bool AddAtom(atom *pointer);
245 bool RemoveAtom(atom *pointer);
246 bool UnlinkAtom(atom *pointer);
247 bool CleanupMolecule();
248
249 /// Add/remove atoms to/from molecule.
250 atom * AddCopyAtom(atom *pointer);
251 bool AddXYZFile(string filename);
252 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
253 bond * AddBond(atom *first, atom *second, int degree = 1);
254 bool RemoveBond(bond *pointer);
255 bool RemoveBonds(atom *BondPartner);
256 bool hasBondStructure();
257 unsigned int CountBonds() const;
258
259 /// Find atoms.
260 atom * FindAtom(int Nr) const;
261 atom * AskAtom(string text);
262
263 /// Count and change present atoms' coordination.
264 void CountElements();
265 void CalculateOrbitals(class config &configuration);
266 bool CenterInBox();
267 bool BoundInBox();
268 void CenterEdge(Vector *max);
269 void CenterOrigin();
270 void CenterPeriodic();
271 void CenterAtVector(Vector *newcenter);
272 void Translate(const Vector *x);
273 void TranslatePeriodically(const Vector *trans);
274 void Mirror(const Vector *x);
275 void Align(Vector *n);
276 void Scale(const double ** const factor);
277 void DeterminePeriodicCenter(Vector &center);
278 Vector * DetermineCenterOfGravity();
279 Vector * DetermineCenterOfAll() const;
280 Vector * DetermineCenterOfBox() const;
281 void SetNameFromFilename(const char *filename);
282 void SetBoxDimension(Vector *dim);
283 void ScanForPeriodicCorrection();
284 bool VerletForceIntegration(char *file, config &configuration);
285 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
286 void PrincipalAxisSystem(bool DoRotate);
287 double VolumeOfConvexEnvelope(bool IsAngstroem);
288
289 double ConstrainedPotential(struct EvaluatePotential &Params);
290 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
291 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
292 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
293
294 bool CheckBounds(const Vector *x) const;
295 void GetAlignvector(struct lsq_params * par) const;
296
297 /// Initialising routines in fragmentation
298 void CreateAdjacencyListFromDbondFile(ifstream *output);
299 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
300 int CorrectBondDegree() const;
301 void OutputBondsList() const;
302 void CyclicBondAnalysis() const;
303 void OutputGraphInfoPerAtom() const;
304 void OutputGraphInfoPerBond() const;
305
306
307 // Graph analysis
308 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
309 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
310 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
311 bond * FindNextUnused(atom *vertex) const;
312 void SetNextComponentNumber(atom *vertex, int nr) const;
313 void ResetAllBondsToUnused() const;
314 int CountCyclicBonds();
315 bool CheckForConnectedSubgraph(KeySet *Fragment);
316 string GetColor(enum Shading color) const;
317 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
318
319
320 molecule *CopyMolecule();
321 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
322
323 /// Fragment molecule by two different approaches:
324 int FragmentMolecule(int Order, config *configuration);
325 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
326 bool StoreBondsToFile(char *path, char *filename);
327 bool StoreAdjacencyToFile(char *path, char *filename);
328 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
329 bool ParseOrderAtSiteFromFile(char *path);
330 bool StoreOrderAtSiteFile(char *path);
331 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
332 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
333 bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
334 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
335 /// -# BOSSANOVA
336 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
337 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
338 bool BuildInducedSubgraph(const molecule *Father);
339 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
340 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
341 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
342 int GuesstimateFragmentCount(int order);
343
344 // Recognize doubly appearing molecules in a list of them
345 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
346 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
347
348 // Output routines.
349 bool Output(ofstream * const output);
350 bool OutputTrajectories(ofstream * const output);
351 void OutputListOfBonds() const;
352 bool OutputXYZ(ofstream * const output) const;
353 bool OutputTrajectoriesXYZ(ofstream * const output);
354 bool Checkout(ofstream * const output) const;
355 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
356
357 // Manipulation routines
358 void flipActiveFlag();
359
360 private:
361 int last_atom; //!< number given to last atom
362 mutable internal_iterator InternalPointer; //!< internal pointer for PointCloud
363};
364
365molecule *NewMolecule();
366void DeleteMolecule(molecule* mol);
367
368#include "molecule_template.hpp"
369
370/** A list of \a molecule classes.
371 */
372class MoleculeListClass : public Observable {
373 public:
374 MoleculeList ListOfMolecules; //!< List of the contained molecules
375 int MaxIndex;
376
377 MoleculeListClass(World *world);
378 ~MoleculeListClass();
379
380 bool AddHydrogenCorrection(char *path);
381 bool StoreForcesFile(char *path, int *SortIndex);
382 void insert(molecule *mol);
383 void erase(molecule *mol);
384 molecule * ReturnIndex(int index);
385 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
386 int NumberOfActiveMolecules();
387 void Enumerate(ostream *out);
388 void Output(ofstream *out);
389 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
390 int CountAllAtoms() const;
391
392 // Methods moved here from the menus
393 // TODO: more refactoring needed on these methods
394 void flipChosen();
395 void createNewMolecule(periodentafel *periode);
396 void loadFromXYZ(periodentafel *periode);
397 void setMoleculeFilename();
398 void parseXYZIntoMolecule();
399 void eraseMolecule();
400
401
402 // merging of molecules
403 bool SimpleMerge(molecule *mol, molecule *srcmol);
404 bool SimpleAdd(molecule *mol, molecule *srcmol);
405 bool SimpleMultiMerge(molecule *mol, int *src, int N);
406 bool SimpleMultiAdd(molecule *mol, int *src, int N);
407 bool ScatterMerge(molecule *mol, int *src, int N);
408 bool EmbedMerge(molecule *mol, molecule *srcmol);
409
410 private:
411 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
412};
413
414
415/** A leaf for a tree of \a molecule class
416 * Wraps molecules in a tree structure
417 */
418class MoleculeLeafClass {
419 public:
420 molecule *Leaf; //!< molecule of this leaf
421 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
422 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
423 MoleculeLeafClass *previous; //!< Previous leaf on this level
424 MoleculeLeafClass *next; //!< Next leaf on this level
425
426 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
427 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
428 ~MoleculeLeafClass();
429
430 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
431 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
432 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
433 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
434 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
435 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
436 int Count() const;
437};
438
439
440#endif /*MOLECULES_HPP_*/
441
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