source: src/molecule.hpp@ c6efc1

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 c6efc1 was 8cbb97, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Merge branch 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp
  • Property mode set to 100755
File size: 21.3 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 "defs.hpp"
32#include "graph.hpp"
33#include "stackclass.hpp"
34#include "tesselation.hpp"
35#include "Patterns/Observer.hpp"
36#include "Patterns/Cacheable.hpp"
37
38/****************************************** forward declarations *****************************/
39
40class atom;
41class bond;
42class BondedParticle;
43class BondGraph;
44class element;
45class ForceMatrix;
46class LinkedCell;
47class molecule;
48class MoleculeLeafClass;
49class MoleculeListClass;
50class periodentafel;
51class Vector;
52
53/******************************** Some definitions for easier reading **********************************/
54
55#define MoleculeList list <molecule *>
56#define MoleculeListTest pair <MoleculeList::iterator, bool>
57
58#define DistancePair pair < double, atom* >
59#define DistanceMap multimap < double, atom* >
60#define DistanceTestPair pair < DistanceMap::iterator, bool>
61
62
63/************************************* Class definitions ****************************************/
64
65/** Structure to contain parameters needed for evaluation of constraint potential.
66 */
67struct EvaluatePotential
68{
69 int startstep; //!< start configuration (MDStep in atom::trajectory)
70 int endstep; //!< end configuration (MDStep in atom::trajectory)
71 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
72 DistanceMap **DistanceList; //!< distance list of each atom to each atom
73 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
74 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
75 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
76 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
77 double *PenaltyConstants; //!< penalty constant in front of each term
78};
79
80#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
81enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
82
83
84/** The complete molecule.
85 * Class incorporates number of types
86 */
87class molecule : public PointCloud , public Observable {
88 friend molecule *NewMolecule();
89 friend void DeleteMolecule(molecule *);
90 public:
91 const periodentafel * const elemente; //!< periodic table with each element
92 atom *start; //!< start of atom list
93 atom *end; //!< end of atom list
94 bond *first; //!< start of bond list
95 bond *last; //!< end of bond list
96 int MDSteps; //!< The number of MD steps in Trajectories
97 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
98 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
99 int ElementCount; //!< how many unique elements are therein
100 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
101 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
102 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
103 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
104 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
105 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
106 Vector Center; //!< Center of molecule in a global box
107 int IndexNr; //!< index of molecule in a MoleculeListClass
108 char name[MAXSTRINGSIZE]; //!< arbitrary name
109
110 private:
111 Cacheable<string> formula;
112 moleculeId_t id;
113 protected:
114 molecule(const periodentafel * const teil);
115 virtual ~molecule();
116
117
118public:
119 //getter and setter
120 const std::string getName();
121 moleculeId_t getId();
122 void setId(moleculeId_t);
123 void setName(const std::string);
124 const std::string getFormula();
125 std::string calcFormula();
126
127
128 // re-definition of virtual functions from PointCloud
129 const char * const GetName() const;
130 Vector *GetCenter() const ;
131 TesselPoint *GetPoint() const ;
132 TesselPoint *GetTerminalPoint() const ;
133 int GetMaxId() const;
134 void GoToNext() const ;
135 void GoToPrevious() const ;
136 void GoToFirst() const ;
137 void GoToLast() const ;
138 bool IsEmpty() const ;
139 bool IsEnd() const ;
140
141 // templates for allowing global manipulation of all vectors
142 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
143 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
144 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
145 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
146 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&), T &t ) const;
147 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&) const, T &t ) const;
148 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
149 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
150 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
151 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;
152
153 // templates for allowing global manipulation of molecule with each atom as single argument
154 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
155 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
156
157 // templates for allowing global copying of molecule with each atom as single argument
158 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
159 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
160
161 // templates for allowing global manipulation of all atoms
162 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
163 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
164 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
165 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
166 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
167 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
168 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;
169 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;
170 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;
171 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;
172
173 // templates for allowing conditional global copying of molecule with each atom as single argument
174 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
175 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
176 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
177 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
178 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
179 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
180 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
181 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
182 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;
183 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;
184 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;
185 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;
186 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;
187 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;
188 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;
189 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;
190
191 // templates for allowing global manipulation of an array with one entry per atom
192 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
193 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
194 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
195 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
196 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
197 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
198 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
199 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
200 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
201 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
202 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
203
204 // templates for allowing global manipulation of each atom by entries in an array
205 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
206 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
207
208 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
209 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
210 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
211 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
212
213 /// remove atoms from molecule.
214 bool AddAtom(atom *pointer);
215 bool RemoveAtom(atom *pointer);
216 bool UnlinkAtom(atom *pointer);
217 bool CleanupMolecule();
218
219 /// Add/remove atoms to/from molecule.
220 atom * AddCopyAtom(atom *pointer);
221 bool AddXYZFile(string filename);
222 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
223 bond * AddBond(atom *first, atom *second, int degree = 1);
224 bool RemoveBond(bond *pointer);
225 bool RemoveBonds(atom *BondPartner);
226
227 /// Find atoms.
228 atom * FindAtom(int Nr) const;
229 atom * AskAtom(string text);
230
231 /// Count and change present atoms' coordination.
232 void CountAtoms();
233 void CountElements();
234 void CalculateOrbitals(class config &configuration);
235 bool CenterInBox();
236 bool BoundInBox();
237 void CenterEdge(Vector *max);
238 void CenterOrigin();
239 void CenterPeriodic();
240 void CenterAtVector(Vector *newcenter);
241 void Translate(const Vector *x);
242 void TranslatePeriodically(const Vector *trans);
243 void Mirror(const Vector *x);
244 void Align(Vector *n);
245 void Scale(const double ** const factor);
246 void DeterminePeriodicCenter(Vector &center);
247 Vector * DetermineCenterOfGravity();
248 Vector * DetermineCenterOfAll() const;
249 void SetNameFromFilename(const char *filename);
250 void SetBoxDimension(Vector *dim);
251 void ScanForPeriodicCorrection();
252 bool VerletForceIntegration(char *file, config &configuration);
253 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
254 void PrincipalAxisSystem(bool DoRotate);
255 double VolumeOfConvexEnvelope(bool IsAngstroem);
256
257 double ConstrainedPotential(struct EvaluatePotential &Params);
258 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
259 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
260 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
261
262 bool CheckBounds(const Vector *x) const;
263 void GetAlignvector(struct lsq_params * par) const;
264
265 /// Initialising routines in fragmentation
266 void CreateAdjacencyListFromDbondFile(ifstream *output);
267 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
268 int CorrectBondDegree() const;
269 void OutputBondsList() const;
270 void CyclicBondAnalysis() const;
271 void OutputGraphInfoPerAtom() const;
272 void OutputGraphInfoPerBond() const;
273
274
275 // Graph analysis
276 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
277 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
278 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
279 bond * FindNextUnused(atom *vertex) const;
280 void SetNextComponentNumber(atom *vertex, int nr) const;
281 void ResetAllBondsToUnused() const;
282 int CountCyclicBonds();
283 bool CheckForConnectedSubgraph(KeySet *Fragment);
284 string GetColor(enum Shading color) const;
285 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
286
287
288 molecule *CopyMolecule();
289 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
290
291 /// Fragment molecule by two different approaches:
292 int FragmentMolecule(int Order, config *configuration);
293 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
294 bool StoreBondsToFile(char *path, char *filename);
295 bool StoreAdjacencyToFile(char *path, char *filename);
296 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
297 bool ParseOrderAtSiteFromFile(char *path);
298 bool StoreOrderAtSiteFile(char *path);
299 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
300 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
301 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
302 /// -# BOSSANOVA
303 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
304 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
305 bool BuildInducedSubgraph(const molecule *Father);
306 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
307 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
308 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
309 int GuesstimateFragmentCount(int order);
310
311 // Recognize doubly appearing molecules in a list of them
312 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
313 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
314
315 // Output routines.
316 bool Output(ofstream * const output);
317 bool OutputTrajectories(ofstream * const output);
318 void OutputListOfBonds() const;
319 bool OutputXYZ(ofstream * const output) const;
320 bool OutputTrajectoriesXYZ(ofstream * const output);
321 bool Checkout(ofstream * const output) const;
322 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
323
324 // Manipulation routines
325 void flipActiveFlag();
326
327 private:
328 int last_atom; //!< number given to last atom
329 mutable atom *InternalPointer; //!< internal pointer for PointCloud
330};
331
332molecule *NewMolecule();
333void DeleteMolecule(molecule* mol);
334
335#include "molecule_template.hpp"
336
337/** A list of \a molecule classes.
338 */
339class MoleculeListClass : public Observable {
340 public:
341 MoleculeList ListOfMolecules; //!< List of the contained molecules
342 int MaxIndex;
343
344 MoleculeListClass(World *world);
345 ~MoleculeListClass();
346
347 bool AddHydrogenCorrection(char *path);
348 bool StoreForcesFile(char *path, int *SortIndex);
349 void insert(molecule *mol);
350 molecule * ReturnIndex(int index);
351 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
352 int NumberOfActiveMolecules();
353 void Enumerate(ostream *out);
354 void Output(ofstream *out);
355 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
356 int CountAllAtoms() const;
357
358 // Methods moved here from the menus
359 // TODO: more refactoring needed on these methods
360 void flipChosen();
361 void createNewMolecule(periodentafel *periode);
362 void loadFromXYZ(periodentafel *periode);
363 void setMoleculeFilename();
364 void parseXYZIntoMolecule();
365 void eraseMolecule();
366
367
368 // merging of molecules
369 bool SimpleMerge(molecule *mol, molecule *srcmol);
370 bool SimpleAdd(molecule *mol, molecule *srcmol);
371 bool SimpleMultiMerge(molecule *mol, int *src, int N);
372 bool SimpleMultiAdd(molecule *mol, int *src, int N);
373 bool ScatterMerge(molecule *mol, int *src, int N);
374 bool EmbedMerge(molecule *mol, molecule *srcmol);
375
376 private:
377 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
378};
379
380
381/** A leaf for a tree of \a molecule class
382 * Wraps molecules in a tree structure
383 */
384class MoleculeLeafClass {
385 public:
386 molecule *Leaf; //!< molecule of this leaf
387 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
388 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
389 MoleculeLeafClass *previous; //!< Previous leaf on this level
390 MoleculeLeafClass *next; //!< Next leaf on this level
391
392 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
393 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
394 ~MoleculeLeafClass();
395
396 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
397 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
398 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
399 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
400 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
401 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
402 int Count() const;
403};
404
405
406#endif /*MOLECULES_HPP_*/
407
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