source: src/molecule.hpp@ cc04b7

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Last change on this file since cc04b7 was 477bb2, checked in by Tillmann Crueger <crueger@…>, 16 years ago

Moved several Methods from Menu to MoleculeListClass
  • Property mode set to 100755
File size: 20.4 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
33/****************************************** forward declarations *****************************/
34
35class atom;
36class bond;
37class BondedParticle;
38class BondGraph;
39class element;
40class ForceMatrix;
41class LinkedCell;
42class molecule;
43class MoleculeLeafClass;
44class MoleculeListClass;
45class periodentafel;
46class Vector;
47
48/******************************** Some definitions for easier reading **********************************/
49
50#define MoleculeList list <molecule *>
51#define MoleculeListTest pair <MoleculeList::iterator, bool>
52
53#define DistancePair pair < double, atom* >
54#define DistanceMap multimap < double, atom* >
55#define DistanceTestPair pair < DistanceMap::iterator, bool>
56
57
58/************************************* Class definitions ****************************************/
59
60/** Structure to contain parameters needed for evaluation of constraint potential.
61 */
62struct EvaluatePotential
63{
64 int startstep; //!< start configuration (MDStep in atom::trajectory)
65 int endstep; //!< end configuration (MDStep in atom::trajectory)
66 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
67 DistanceMap **DistanceList; //!< distance list of each atom to each atom
68 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
69 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
70 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
71 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
72 double *PenaltyConstants; //!< penalty constant in front of each term
73};
74
75#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
76enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
77
78
79/** The complete molecule.
80 * Class incorporates number of types
81 */
82class molecule : public PointCloud {
83 public:
84 double cell_size[6];//!< cell size
85 const periodentafel * const elemente; //!< periodic table with each element
86 atom *start; //!< start of atom list
87 atom *end; //!< end of atom list
88 bond *first; //!< start of bond list
89 bond *last; //!< end of bond list
90 int MDSteps; //!< The number of MD steps in Trajectories
91 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
92 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
93 int ElementCount; //!< how many unique elements are therein
94 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
95 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
96 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
97 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
98 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
99 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
100 Vector Center; //!< Center of molecule in a global box
101 char name[MAXSTRINGSIZE]; //!< arbitrary name
102 int IndexNr; //!< index of molecule in a MoleculeListClass
103
104 molecule(const periodentafel * const teil);
105 virtual ~molecule();
106
107 // re-definition of virtual functions from PointCloud
108 Vector *GetCenter() const ;
109 TesselPoint *GetPoint() const ;
110 TesselPoint *GetTerminalPoint() const ;
111 void GoToNext() const ;
112 void GoToPrevious() const ;
113 void GoToFirst() const ;
114 void GoToLast() const ;
115 bool IsEmpty() const ;
116 bool IsEnd() const ;
117
118 // templates for allowing global manipulation of all vectors
119 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
120 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
121 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
122 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
123 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
124 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
125 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
126 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;
127
128 // templates for allowing global manipulation of molecule with each atom as single argument
129 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
130 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
131
132 // templates for allowing global copying of molecule with each atom as single argument
133 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
134 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
135
136 // templates for allowing global manipulation of all atoms
137 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
138 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
139 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
140 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
141 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
142 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
143 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;
144 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;
145 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;
146 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;
147
148 // templates for allowing conditional global copying of molecule with each atom as single argument
149 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
150 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
151 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
152 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
153 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
154 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
155 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
156 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
157 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;
158 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;
159 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;
160 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;
161 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;
162 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;
163 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;
164 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;
165
166 // templates for allowing global manipulation of an array with one entry per atom
167 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
168 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
169 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
170 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
171 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
172 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
173 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
174 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
175 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
176 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
177 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
178
179 // templates for allowing global manipulation of each atom by entries in an array
180 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
181 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
182
183 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
184 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
185 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
186 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
187
188 /// remove atoms from molecule.
189 bool AddAtom(atom *pointer);
190 bool RemoveAtom(atom *pointer);
191 bool UnlinkAtom(atom *pointer);
192 bool CleanupMolecule();
193
194 /// Add/remove atoms to/from molecule.
195 atom * AddCopyAtom(atom *pointer);
196 bool AddXYZFile(string filename);
197 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
198 bond * AddBond(atom *first, atom *second, int degree = 1);
199 bool RemoveBond(bond *pointer);
200 bool RemoveBonds(atom *BondPartner);
201
202 /// Find atoms.
203 atom * FindAtom(int Nr) const;
204 atom * AskAtom(string text);
205
206 /// Count and change present atoms' coordination.
207 void CountAtoms();
208 void CountElements();
209 void CalculateOrbitals(class config &configuration);
210 bool CenterInBox();
211 bool BoundInBox();
212 void CenterEdge(Vector *max);
213 void CenterOrigin();
214 void CenterPeriodic();
215 void CenterAtVector(Vector *newcenter);
216 void Translate(const Vector *x);
217 void TranslatePeriodically(const Vector *trans);
218 void Mirror(const Vector *x);
219 void Align(Vector *n);
220 void Scale(const double ** const factor);
221 void DeterminePeriodicCenter(Vector &center);
222 Vector * DetermineCenterOfGravity();
223 Vector * DetermineCenterOfAll() const;
224 void SetNameFromFilename(const char *filename);
225 void SetBoxDimension(Vector *dim);
226 void ScanForPeriodicCorrection();
227 bool VerletForceIntegration(char *file, config &configuration);
228 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
229 void PrincipalAxisSystem(bool DoRotate);
230 double VolumeOfConvexEnvelope(bool IsAngstroem);
231
232 double ConstrainedPotential(struct EvaluatePotential &Params);
233 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
234 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
235 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
236
237 bool CheckBounds(const Vector *x) const;
238 void GetAlignvector(struct lsq_params * par) const;
239
240 /// Initialising routines in fragmentation
241 void CreateAdjacencyListFromDbondFile(ifstream *output);
242 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
243 int CorrectBondDegree() const;
244 void OutputBondsList() const;
245 void CyclicBondAnalysis() const;
246 void OutputGraphInfoPerAtom() const;
247 void OutputGraphInfoPerBond() const;
248
249
250 // Graph analysis
251 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
252 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
253 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
254 bond * FindNextUnused(atom *vertex) const;
255 void SetNextComponentNumber(atom *vertex, int nr) const;
256 void ResetAllBondsToUnused() const;
257 int CountCyclicBonds();
258 bool CheckForConnectedSubgraph(KeySet *Fragment);
259 string GetColor(enum Shading color) const;
260 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
261
262
263 molecule *CopyMolecule();
264 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
265
266 /// Fragment molecule by two different approaches:
267 int FragmentMolecule(int Order, config *configuration);
268 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
269 bool StoreAdjacencyToFile(char *path);
270 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
271 bool ParseOrderAtSiteFromFile(char *path);
272 bool StoreOrderAtSiteFile(char *path);
273 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
274 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
275 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
276 /// -# BOSSANOVA
277 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
278 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
279 bool BuildInducedSubgraph(const molecule *Father);
280 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
281 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
282 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
283 int GuesstimateFragmentCount(int order);
284
285 // Recognize doubly appearing molecules in a list of them
286 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
287 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
288
289 // Output routines.
290 bool Output(ofstream * const output);
291 bool OutputTrajectories(ofstream * const output);
292 void OutputListOfBonds() const;
293 bool OutputXYZ(ofstream * const output) const;
294 bool OutputTrajectoriesXYZ(ofstream * const output);
295 bool Checkout(ofstream * const output) const;
296 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
297
298 // Manipulation routines
299 void flipActiveFlag();
300
301 private:
302 int last_atom; //!< number given to last atom
303 mutable atom *InternalPointer; //!< internal pointer for PointCloud
304};
305
306#include "molecule_template.hpp"
307
308/** A list of \a molecule classes.
309 */
310class MoleculeListClass {
311 public:
312 MoleculeList ListOfMolecules; //!< List of the contained molecules
313 int MaxIndex;
314
315 MoleculeListClass();
316 ~MoleculeListClass();
317
318 bool AddHydrogenCorrection(char *path);
319 bool StoreForcesFile(char *path, int *SortIndex);
320 void insert(molecule *mol);
321 molecule * ReturnIndex(int index);
322 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
323 int NumberOfActiveMolecules();
324 void Enumerate(ofstream *out);
325 void Output(ofstream *out);
326 void DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration);
327 int CountAllAtoms() const;
328
329 // Methods moved here from the menus
330 // TODO: more refactoring needed on these methods
331 void flipChosen();
332 void createNewMolecule(periodentafel *periode);
333 void loadFromXYZ(periodentafel *periode);
334 void changeName();
335 void setMoleculeFilename();
336 void parseXYZIntoMolecule();
337 void eraseMolecule();
338
339
340 // merging of molecules
341 bool SimpleMerge(molecule *mol, molecule *srcmol);
342 bool SimpleAdd(molecule *mol, molecule *srcmol);
343 bool SimpleMultiMerge(molecule *mol, int *src, int N);
344 bool SimpleMultiAdd(molecule *mol, int *src, int N);
345 bool ScatterMerge(molecule *mol, int *src, int N);
346 bool EmbedMerge(molecule *mol, molecule *srcmol);
347
348 private:
349};
350
351
352/** A leaf for a tree of \a molecule class
353 * Wraps molecules in a tree structure
354 */
355class MoleculeLeafClass {
356 public:
357 molecule *Leaf; //!< molecule of this leaf
358 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
359 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
360 MoleculeLeafClass *previous; //!< Previous leaf on this level
361 MoleculeLeafClass *next; //!< Next leaf on this level
362
363 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
364 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
365 ~MoleculeLeafClass();
366
367 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
368 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
369 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
370 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
371 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
372 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
373 int Count() const;
374};
375
376
377#endif /*MOLECULES_HPP_*/
378
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