source: src/molecule.hpp@ 9fe36b

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Last change on this file since 9fe36b was 6adb96, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Added possibility for views to catch name changes of molecules
  • Property mode set to 100755
File size: 20.6 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 <string>
30
31#include "graph.hpp"
32#include "stackclass.hpp"
33#include "tesselation.hpp"
34#include "Patterns/Observer.hpp"
35
36/****************************************** forward declarations *****************************/
37
38class atom;
39class bond;
40class BondedParticle;
41class BondGraph;
42class element;
43class ForceMatrix;
44class LinkedCell;
45class molecule;
46class MoleculeLeafClass;
47class MoleculeListClass;
48class periodentafel;
49class Vector;
50
51/******************************** Some definitions for easier reading **********************************/
52
53#define MoleculeList list <molecule *>
54#define MoleculeListTest pair <MoleculeList::iterator, bool>
55
56#define DistancePair pair < double, atom* >
57#define DistanceMap multimap < double, atom* >
58#define DistanceTestPair pair < DistanceMap::iterator, bool>
59
60
61/************************************* Class definitions ****************************************/
62
63/** Structure to contain parameters needed for evaluation of constraint potential.
64 */
65struct EvaluatePotential
66{
67 int startstep; //!< start configuration (MDStep in atom::trajectory)
68 int endstep; //!< end configuration (MDStep in atom::trajectory)
69 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
70 DistanceMap **DistanceList; //!< distance list of each atom to each atom
71 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
72 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
73 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
74 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
75 double *PenaltyConstants; //!< penalty constant in front of each term
76};
77
78#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
79enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
80
81
82/** The complete molecule.
83 * Class incorporates number of types
84 */
85class molecule : public PointCloud , public Observable {
86 public:
87 double cell_size[6];//!< cell size
88 const periodentafel * const elemente; //!< periodic table with each element
89 atom *start; //!< start of atom list
90 atom *end; //!< end of atom list
91 bond *first; //!< start of bond list
92 bond *last; //!< end of bond list
93 int MDSteps; //!< The number of MD steps in Trajectories
94 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
95 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
96 int ElementCount; //!< how many unique elements are therein
97 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
98 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
99 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
100 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
101 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
102 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
103 Vector Center; //!< Center of molecule in a global box
104 int IndexNr; //!< index of molecule in a MoleculeListClass
105 char name[MAXSTRINGSIZE]; //!< arbitrary name
106
107public:
108 molecule(const periodentafel * const teil);
109 virtual ~molecule();
110
111 //getter and setter
112 const std::string getName();
113 void setName(const std::string);
114
115 // re-definition of virtual functions from PointCloud
116 Vector *GetCenter() const ;
117 TesselPoint *GetPoint() const ;
118 TesselPoint *GetTerminalPoint() const ;
119 void GoToNext() const ;
120 void GoToPrevious() const ;
121 void GoToFirst() const ;
122 void GoToLast() const ;
123 bool IsEmpty() const ;
124 bool IsEnd() const ;
125
126 // templates for allowing global manipulation of all vectors
127 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
128 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
129 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
130 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
131 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
132 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
133 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
134 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;
135
136 // templates for allowing global manipulation of molecule with each atom as single argument
137 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
138 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
139
140 // templates for allowing global copying of molecule with each atom as single argument
141 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
142 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
143
144 // templates for allowing global manipulation of all atoms
145 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
146 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
147 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
148 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
149 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
150 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
151 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;
152 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;
153 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;
154 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;
155
156 // templates for allowing conditional global copying of molecule with each atom as single argument
157 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
158 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
159 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
160 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
161 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
162 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
163 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
164 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
165 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;
166 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;
167 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;
168 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;
169 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;
170 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;
171 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;
172 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;
173
174 // templates for allowing global manipulation of an array with one entry per atom
175 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
176 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
177 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
178 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
179 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
180 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
181 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
182 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
183 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
184 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
185 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
186
187 // templates for allowing global manipulation of each atom by entries in an array
188 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
189 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
190
191 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
192 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
193 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
194 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
195
196 /// remove atoms from molecule.
197 bool AddAtom(atom *pointer);
198 bool RemoveAtom(atom *pointer);
199 bool UnlinkAtom(atom *pointer);
200 bool CleanupMolecule();
201
202 /// Add/remove atoms to/from molecule.
203 atom * AddCopyAtom(atom *pointer);
204 bool AddXYZFile(string filename);
205 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
206 bond * AddBond(atom *first, atom *second, int degree = 1);
207 bool RemoveBond(bond *pointer);
208 bool RemoveBonds(atom *BondPartner);
209
210 /// Find atoms.
211 atom * FindAtom(int Nr) const;
212 atom * AskAtom(string text);
213
214 /// Count and change present atoms' coordination.
215 void CountAtoms();
216 void CountElements();
217 void CalculateOrbitals(class config &configuration);
218 bool CenterInBox();
219 bool BoundInBox();
220 void CenterEdge(Vector *max);
221 void CenterOrigin();
222 void CenterPeriodic();
223 void CenterAtVector(Vector *newcenter);
224 void Translate(const Vector *x);
225 void TranslatePeriodically(const Vector *trans);
226 void Mirror(const Vector *x);
227 void Align(Vector *n);
228 void Scale(const double ** const factor);
229 void DeterminePeriodicCenter(Vector &center);
230 Vector * DetermineCenterOfGravity();
231 Vector * DetermineCenterOfAll() const;
232 void SetNameFromFilename(const char *filename);
233 void SetBoxDimension(Vector *dim);
234 void ScanForPeriodicCorrection();
235 bool VerletForceIntegration(char *file, config &configuration);
236 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
237 void PrincipalAxisSystem(bool DoRotate);
238 double VolumeOfConvexEnvelope(bool IsAngstroem);
239
240 double ConstrainedPotential(struct EvaluatePotential &Params);
241 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
242 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
243 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
244
245 bool CheckBounds(const Vector *x) const;
246 void GetAlignvector(struct lsq_params * par) const;
247
248 /// Initialising routines in fragmentation
249 void CreateAdjacencyListFromDbondFile(ifstream *output);
250 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
251 int CorrectBondDegree() const;
252 void OutputBondsList() const;
253 void CyclicBondAnalysis() const;
254 void OutputGraphInfoPerAtom() const;
255 void OutputGraphInfoPerBond() const;
256
257
258 // Graph analysis
259 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
260 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
261 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
262 bond * FindNextUnused(atom *vertex) const;
263 void SetNextComponentNumber(atom *vertex, int nr) const;
264 void ResetAllBondsToUnused() const;
265 int CountCyclicBonds();
266 bool CheckForConnectedSubgraph(KeySet *Fragment);
267 string GetColor(enum Shading color) const;
268 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
269
270
271 molecule *CopyMolecule();
272 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
273
274 /// Fragment molecule by two different approaches:
275 int FragmentMolecule(int Order, config *configuration);
276 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
277 bool StoreAdjacencyToFile(char *path);
278 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
279 bool ParseOrderAtSiteFromFile(char *path);
280 bool StoreOrderAtSiteFile(char *path);
281 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
282 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
283 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
284 /// -# BOSSANOVA
285 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
286 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
287 bool BuildInducedSubgraph(const molecule *Father);
288 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
289 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
290 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
291 int GuesstimateFragmentCount(int order);
292
293 // Recognize doubly appearing molecules in a list of them
294 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
295 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
296
297 // Output routines.
298 bool Output(ofstream * const output);
299 bool OutputTrajectories(ofstream * const output);
300 void OutputListOfBonds() const;
301 bool OutputXYZ(ofstream * const output) const;
302 bool OutputTrajectoriesXYZ(ofstream * const output);
303 bool Checkout(ofstream * const output) const;
304 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
305
306 // Manipulation routines
307 void flipActiveFlag();
308
309 private:
310 int last_atom; //!< number given to last atom
311 mutable atom *InternalPointer; //!< internal pointer for PointCloud
312};
313
314#include "molecule_template.hpp"
315
316/** A list of \a molecule classes.
317 */
318class MoleculeListClass : public Observable {
319 public:
320 MoleculeList ListOfMolecules; //!< List of the contained molecules
321 int MaxIndex;
322
323 MoleculeListClass();
324 ~MoleculeListClass();
325
326 bool AddHydrogenCorrection(char *path);
327 bool StoreForcesFile(char *path, int *SortIndex);
328 void insert(molecule *mol);
329 molecule * ReturnIndex(int index);
330 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
331 int NumberOfActiveMolecules();
332 void Enumerate(ofstream *out);
333 void Output(ofstream *out);
334 void DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration);
335 int CountAllAtoms() const;
336
337 // Methods moved here from the menus
338 // TODO: more refactoring needed on these methods
339 void flipChosen();
340 void createNewMolecule(periodentafel *periode);
341 void loadFromXYZ(periodentafel *periode);
342 void setMoleculeFilename();
343 void parseXYZIntoMolecule();
344 void eraseMolecule();
345
346
347 // merging of molecules
348 bool SimpleMerge(molecule *mol, molecule *srcmol);
349 bool SimpleAdd(molecule *mol, molecule *srcmol);
350 bool SimpleMultiMerge(molecule *mol, int *src, int N);
351 bool SimpleMultiAdd(molecule *mol, int *src, int N);
352 bool ScatterMerge(molecule *mol, int *src, int N);
353 bool EmbedMerge(molecule *mol, molecule *srcmol);
354
355 private:
356};
357
358
359/** A leaf for a tree of \a molecule class
360 * Wraps molecules in a tree structure
361 */
362class MoleculeLeafClass {
363 public:
364 molecule *Leaf; //!< molecule of this leaf
365 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
366 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
367 MoleculeLeafClass *previous; //!< Previous leaf on this level
368 MoleculeLeafClass *next; //!< Next leaf on this level
369
370 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
371 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
372 ~MoleculeLeafClass();
373
374 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
375 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
376 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
377 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
378 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
379 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
380 int Count() const;
381};
382
383
384#endif /*MOLECULES_HPP_*/
385
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