source: src/molecule.hpp@ bfce50

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Last change on this file since bfce50 was bfce50, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Moved method to rename molecules to a seperate Action
  • Property mode set to 100755
File size: 20.5 KB
Line 
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 "graph.hpp"
30#include "stackclass.hpp"
31#include "tesselation.hpp"
32#include "Patterns/Observer.hpp"
33
34/****************************************** forward declarations *****************************/
35
36class atom;
37class bond;
38class BondedParticle;
39class BondGraph;
40class element;
41class ForceMatrix;
42class LinkedCell;
43class molecule;
44class MoleculeLeafClass;
45class MoleculeListClass;
46class periodentafel;
47class Vector;
48
49/******************************** Some definitions for easier reading **********************************/
50
51#define MoleculeList list <molecule *>
52#define MoleculeListTest pair <MoleculeList::iterator, bool>
53
54#define DistancePair pair < double, atom* >
55#define DistanceMap multimap < double, atom* >
56#define DistanceTestPair pair < DistanceMap::iterator, bool>
57
58
59/************************************* Class definitions ****************************************/
60
61/** Structure to contain parameters needed for evaluation of constraint potential.
62 */
63struct EvaluatePotential
64{
65 int startstep; //!< start configuration (MDStep in atom::trajectory)
66 int endstep; //!< end configuration (MDStep in atom::trajectory)
67 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
68 DistanceMap **DistanceList; //!< distance list of each atom to each atom
69 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
70 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
71 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
72 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
73 double *PenaltyConstants; //!< penalty constant in front of each term
74};
75
76#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
77enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
78
79
80/** The complete molecule.
81 * Class incorporates number of types
82 */
83class molecule : public PointCloud {
84 public:
85 double cell_size[6];//!< cell size
86 const periodentafel * const elemente; //!< periodic table with each element
87 atom *start; //!< start of atom list
88 atom *end; //!< end of atom list
89 bond *first; //!< start of bond list
90 bond *last; //!< end of bond list
91 int MDSteps; //!< The number of MD steps in Trajectories
92 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
93 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
94 int ElementCount; //!< how many unique elements are therein
95 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
96 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
97 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
98 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
99 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
100 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
101 Vector Center; //!< Center of molecule in a global box
102 char name[MAXSTRINGSIZE]; //!< arbitrary name
103 int IndexNr; //!< index of molecule in a MoleculeListClass
104
105 molecule(const periodentafel * const teil);
106 virtual ~molecule();
107
108 // re-definition of virtual functions from PointCloud
109 const char * const GetName() const;
110 Vector *GetCenter() const ;
111 TesselPoint *GetPoint() const ;
112 TesselPoint *GetTerminalPoint() const ;
113 int GetMaxId() const;
114 void GoToNext() const ;
115 void GoToPrevious() const ;
116 void GoToFirst() const ;
117 void GoToLast() const ;
118 bool IsEmpty() const ;
119 bool IsEnd() const ;
120
121 // templates for allowing global manipulation of all vectors
122 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
123 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
124 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
125 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
126 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
127 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
128 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
129 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;
130
131 // templates for allowing global manipulation of molecule with each atom as single argument
132 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
133 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
134
135 // templates for allowing global copying of molecule with each atom as single argument
136 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
137 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
138
139 // templates for allowing global manipulation of all atoms
140 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
141 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
142 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
143 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
144 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
145 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
146 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;
147 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;
148 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;
149 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;
150
151 // templates for allowing conditional global copying of molecule with each atom as single argument
152 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
153 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
154 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
155 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
156 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
157 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
158 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
159 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
160 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;
161 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;
162 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;
163 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;
164 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;
165 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;
166 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;
167 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;
168
169 // templates for allowing global manipulation of an array with one entry per atom
170 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
171 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
172 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
173 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
174 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
175 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
176 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
177 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
178 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
179 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
180 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
181
182 // templates for allowing global manipulation of each atom by entries in an array
183 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
184 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
185
186 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
187 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
188 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
189 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
190
191 /// remove atoms from molecule.
192 bool AddAtom(atom *pointer);
193 bool RemoveAtom(atom *pointer);
194 bool UnlinkAtom(atom *pointer);
195 bool CleanupMolecule();
196
197 /// Add/remove atoms to/from molecule.
198 atom * AddCopyAtom(atom *pointer);
199 bool AddXYZFile(string filename);
200 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
201 bond * AddBond(atom *first, atom *second, int degree = 1);
202 bool RemoveBond(bond *pointer);
203 bool RemoveBonds(atom *BondPartner);
204
205 /// Find atoms.
206 atom * FindAtom(int Nr) const;
207 atom * AskAtom(string text);
208
209 /// Count and change present atoms' coordination.
210 void CountAtoms();
211 void CountElements();
212 void CalculateOrbitals(class config &configuration);
213 bool CenterInBox();
214 bool BoundInBox();
215 void CenterEdge(Vector *max);
216 void CenterOrigin();
217 void CenterPeriodic();
218 void CenterAtVector(Vector *newcenter);
219 void Translate(const Vector *x);
220 void TranslatePeriodically(const Vector *trans);
221 void Mirror(const Vector *x);
222 void Align(Vector *n);
223 void Scale(const double ** const factor);
224 void DeterminePeriodicCenter(Vector &center);
225 Vector * DetermineCenterOfGravity();
226 Vector * DetermineCenterOfAll() const;
227 void SetNameFromFilename(const char *filename);
228 void SetBoxDimension(Vector *dim);
229 void ScanForPeriodicCorrection();
230 bool VerletForceIntegration(char *file, config &configuration);
231 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
232 void PrincipalAxisSystem(bool DoRotate);
233 double VolumeOfConvexEnvelope(bool IsAngstroem);
234
235 double ConstrainedPotential(struct EvaluatePotential &Params);
236 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
237 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
238 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
239
240 bool CheckBounds(const Vector *x) const;
241 void GetAlignvector(struct lsq_params * par) const;
242
243 /// Initialising routines in fragmentation
244 void CreateAdjacencyListFromDbondFile(ifstream *output);
245 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
246 int CorrectBondDegree() const;
247 void OutputBondsList() const;
248 void CyclicBondAnalysis() const;
249 void OutputGraphInfoPerAtom() const;
250 void OutputGraphInfoPerBond() const;
251
252
253 // Graph analysis
254 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
255 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
256 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
257 bond * FindNextUnused(atom *vertex) const;
258 void SetNextComponentNumber(atom *vertex, int nr) const;
259 void ResetAllBondsToUnused() const;
260 int CountCyclicBonds();
261 bool CheckForConnectedSubgraph(KeySet *Fragment);
262 string GetColor(enum Shading color) const;
263 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
264
265
266 molecule *CopyMolecule();
267 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
268
269 /// Fragment molecule by two different approaches:
270 int FragmentMolecule(int Order, config *configuration);
271 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
272 bool StoreAdjacencyToFile(char *path);
273 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
274 bool ParseOrderAtSiteFromFile(char *path);
275 bool StoreOrderAtSiteFile(char *path);
276 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
277 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
278 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
279 /// -# BOSSANOVA
280 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
281 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
282 bool BuildInducedSubgraph(const molecule *Father);
283 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
284 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
285 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
286 int GuesstimateFragmentCount(int order);
287
288 // Recognize doubly appearing molecules in a list of them
289 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
290 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
291
292 // Output routines.
293 bool Output(ofstream * const output);
294 bool OutputTrajectories(ofstream * const output);
295 void OutputListOfBonds() const;
296 bool OutputXYZ(ofstream * const output) const;
297 bool OutputTrajectoriesXYZ(ofstream * const output);
298 bool Checkout(ofstream * const output) const;
299 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
300
301 // Manipulation routines
302 void flipActiveFlag();
303
304 private:
305 int last_atom; //!< number given to last atom
306 mutable atom *InternalPointer; //!< internal pointer for PointCloud
307};
308
309#include "molecule_template.hpp"
310
311/** A list of \a molecule classes.
312 */
313class MoleculeListClass : public Observable {
314 public:
315 MoleculeList ListOfMolecules; //!< List of the contained molecules
316 int MaxIndex;
317
318 MoleculeListClass();
319 ~MoleculeListClass();
320
321 bool AddHydrogenCorrection(char *path);
322 bool StoreForcesFile(char *path, int *SortIndex);
323 void insert(molecule *mol);
324 molecule * ReturnIndex(int index);
325 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
326 int NumberOfActiveMolecules();
327 void Enumerate(ofstream *out);
328 void Output(ofstream *out);
329 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
330 int CountAllAtoms() const;
331
332 // Methods moved here from the menus
333 // TODO: more refactoring needed on these methods
334 void flipChosen();
335 void createNewMolecule(periodentafel *periode);
336 void loadFromXYZ(periodentafel *periode);
337 void setMoleculeFilename();
338 void parseXYZIntoMolecule();
339 void eraseMolecule();
340
341
342 // merging of molecules
343 bool SimpleMerge(molecule *mol, molecule *srcmol);
344 bool SimpleAdd(molecule *mol, molecule *srcmol);
345 bool SimpleMultiMerge(molecule *mol, int *src, int N);
346 bool SimpleMultiAdd(molecule *mol, int *src, int N);
347 bool ScatterMerge(molecule *mol, int *src, int N);
348 bool EmbedMerge(molecule *mol, molecule *srcmol);
349
350 private:
351};
352
353
354/** A leaf for a tree of \a molecule class
355 * Wraps molecules in a tree structure
356 */
357class MoleculeLeafClass {
358 public:
359 molecule *Leaf; //!< molecule of this leaf
360 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
361 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
362 MoleculeLeafClass *previous; //!< Previous leaf on this level
363 MoleculeLeafClass *next; //!< Next leaf on this level
364
365 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
366 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
367 ~MoleculeLeafClass();
368
369 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
370 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
371 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
372 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
373 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
374 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
375 int Count() const;
376};
377
378
379#endif /*MOLECULES_HPP_*/
380
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