source: src/molecule.hpp@ 5be0eb

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Last change on this file since 5be0eb was 24a5e0, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Added -Wall flag and fixed several small hickups
  • Property mode set to 100755
File size: 21.2 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 "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 double cell_size[6];//!< cell size
92 const periodentafel * const elemente; //!< periodic table with each element
93 atom *start; //!< start of atom list
94 atom *end; //!< end of atom list
95 bond *first; //!< start of bond list
96 bond *last; //!< end of bond list
97 int MDSteps; //!< The number of MD steps in Trajectories
98 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
99 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
100 int ElementCount; //!< how many unique elements are therein
101 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
102 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
103 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
104 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
105 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
106 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
107 Vector Center; //!< Center of molecule in a global box
108 int IndexNr; //!< index of molecule in a MoleculeListClass
109 char name[MAXSTRINGSIZE]; //!< arbitrary name
110
111 private:
112 Cacheable<string> formula;
113 moleculeId_t id;
114 protected:
115 molecule(const periodentafel * const teil);
116 virtual ~molecule();
117
118
119public:
120 //getter and setter
121 const std::string getName();
122 moleculeId_t getId();
123 void setId(moleculeId_t);
124 void setName(const std::string);
125 const std::string getFormula();
126 std::string calcFormula();
127
128
129 // re-definition of virtual functions from PointCloud
130 const char * const GetName() const;
131 Vector *GetCenter() const ;
132 TesselPoint *GetPoint() const ;
133 TesselPoint *GetTerminalPoint() const ;
134 int GetMaxId() const;
135 void GoToNext() const ;
136 void GoToPrevious() const ;
137 void GoToFirst() const ;
138 void GoToLast() const ;
139 bool IsEmpty() const ;
140 bool IsEnd() const ;
141
142 // templates for allowing global manipulation of all vectors
143 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
144 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
145 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
146 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
147 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
148 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
149 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
150 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;
151
152 // templates for allowing global manipulation of molecule with each atom as single argument
153 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
154 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
155
156 // templates for allowing global copying of molecule with each atom as single argument
157 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
158 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
159
160 // templates for allowing global manipulation of all atoms
161 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
162 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
163 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
164 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
165 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
166 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
167 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;
168 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;
169 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;
170 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;
171
172 // templates for allowing conditional global copying of molecule with each atom as single argument
173 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
174 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
175 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
176 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
177 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
178 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
179 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
180 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
181 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;
182 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;
183 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;
184 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;
185 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;
186 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;
187 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;
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) const, T t, U u, V v ) const;
189
190 // templates for allowing global manipulation of an array with one entry per atom
191 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
192 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
193 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), 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 element::* index, void (*Setor)(T *, T *)) const;
196 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), 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, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
199 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
200 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
201 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
202
203 // templates for allowing global manipulation of each atom by entries in an array
204 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
205 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
206
207 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
208 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
209 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
210 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
211
212 /// remove atoms from molecule.
213 bool AddAtom(atom *pointer);
214 bool RemoveAtom(atom *pointer);
215 bool UnlinkAtom(atom *pointer);
216 bool CleanupMolecule();
217
218 /// Add/remove atoms to/from molecule.
219 atom * AddCopyAtom(atom *pointer);
220 bool AddXYZFile(string filename);
221 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
222 bond * AddBond(atom *first, atom *second, int degree = 1);
223 bool RemoveBond(bond *pointer);
224 bool RemoveBonds(atom *BondPartner);
225
226 /// Find atoms.
227 atom * FindAtom(int Nr) const;
228 atom * AskAtom(string text);
229
230 /// Count and change present atoms' coordination.
231 void CountAtoms();
232 void CountElements();
233 void CalculateOrbitals(class config &configuration);
234 bool CenterInBox();
235 bool BoundInBox();
236 void CenterEdge(Vector *max);
237 void CenterOrigin();
238 void CenterPeriodic();
239 void CenterAtVector(Vector *newcenter);
240 void Translate(const Vector *x);
241 void TranslatePeriodically(const Vector *trans);
242 void Mirror(const Vector *x);
243 void Align(Vector *n);
244 void Scale(const double ** const factor);
245 void DeterminePeriodicCenter(Vector &center);
246 Vector * DetermineCenterOfGravity();
247 Vector * DetermineCenterOfAll() const;
248 void SetNameFromFilename(const char *filename);
249 void SetBoxDimension(Vector *dim);
250 void ScanForPeriodicCorrection();
251 bool VerletForceIntegration(char *file, config &configuration);
252 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
253 void PrincipalAxisSystem(bool DoRotate);
254 double VolumeOfConvexEnvelope(bool IsAngstroem);
255
256 double ConstrainedPotential(struct EvaluatePotential &Params);
257 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
258 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
259 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
260
261 bool CheckBounds(const Vector *x) const;
262 void GetAlignvector(struct lsq_params * par) const;
263
264 /// Initialising routines in fragmentation
265 void CreateAdjacencyListFromDbondFile(ifstream *output);
266 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
267 int CorrectBondDegree() const;
268 void OutputBondsList() const;
269 void CyclicBondAnalysis() const;
270 void OutputGraphInfoPerAtom() const;
271 void OutputGraphInfoPerBond() const;
272
273
274 // Graph analysis
275 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
276 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
277 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
278 bond * FindNextUnused(atom *vertex) const;
279 void SetNextComponentNumber(atom *vertex, int nr) const;
280 void ResetAllBondsToUnused() const;
281 int CountCyclicBonds();
282 bool CheckForConnectedSubgraph(KeySet *Fragment);
283 string GetColor(enum Shading color) const;
284 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
285
286
287 molecule *CopyMolecule();
288 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
289
290 /// Fragment molecule by two different approaches:
291 int FragmentMolecule(int Order, config *configuration);
292 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
293 bool StoreBondsToFile(char *path);
294 bool StoreAdjacencyToFile(char *path);
295 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
296 bool ParseOrderAtSiteFromFile(char *path);
297 bool StoreOrderAtSiteFile(char *path);
298 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
299 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
300 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
301 /// -# BOSSANOVA
302 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
303 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
304 bool BuildInducedSubgraph(const molecule *Father);
305 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
306 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
307 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
308 int GuesstimateFragmentCount(int order);
309
310 // Recognize doubly appearing molecules in a list of them
311 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
312 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
313
314 // Output routines.
315 bool Output(ofstream * const output);
316 bool OutputTrajectories(ofstream * const output);
317 void OutputListOfBonds() const;
318 bool OutputXYZ(ofstream * const output) const;
319 bool OutputTrajectoriesXYZ(ofstream * const output);
320 bool Checkout(ofstream * const output) const;
321 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
322
323 // Manipulation routines
324 void flipActiveFlag();
325
326 private:
327 int last_atom; //!< number given to last atom
328 mutable atom *InternalPointer; //!< internal pointer for PointCloud
329};
330
331molecule *NewMolecule();
332void DeleteMolecule(molecule* mol);
333
334#include "molecule_template.hpp"
335
336/** A list of \a molecule classes.
337 */
338class MoleculeListClass : public Observable {
339 public:
340 MoleculeList ListOfMolecules; //!< List of the contained molecules
341 int MaxIndex;
342
343 MoleculeListClass(World *world);
344 ~MoleculeListClass();
345
346 bool AddHydrogenCorrection(char *path);
347 bool StoreForcesFile(char *path, int *SortIndex);
348 void insert(molecule *mol);
349 molecule * ReturnIndex(int index);
350 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
351 int NumberOfActiveMolecules();
352 void Enumerate(ostream *out);
353 void Output(ofstream *out);
354 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
355 int CountAllAtoms() const;
356
357 // Methods moved here from the menus
358 // TODO: more refactoring needed on these methods
359 void flipChosen();
360 void createNewMolecule(periodentafel *periode);
361 void loadFromXYZ(periodentafel *periode);
362 void setMoleculeFilename();
363 void parseXYZIntoMolecule();
364 void eraseMolecule();
365
366
367 // merging of molecules
368 bool SimpleMerge(molecule *mol, molecule *srcmol);
369 bool SimpleAdd(molecule *mol, molecule *srcmol);
370 bool SimpleMultiMerge(molecule *mol, int *src, int N);
371 bool SimpleMultiAdd(molecule *mol, int *src, int N);
372 bool ScatterMerge(molecule *mol, int *src, int N);
373 bool EmbedMerge(molecule *mol, molecule *srcmol);
374
375 private:
376 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
377};
378
379
380/** A leaf for a tree of \a molecule class
381 * Wraps molecules in a tree structure
382 */
383class MoleculeLeafClass {
384 public:
385 molecule *Leaf; //!< molecule of this leaf
386 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
387 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
388 MoleculeLeafClass *previous; //!< Previous leaf on this level
389 MoleculeLeafClass *next; //!< Next leaf on this level
390
391 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
392 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
393 ~MoleculeLeafClass();
394
395 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
396 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
397 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
398 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
399 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
400 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
401 int Count() const;
402};
403
404
405#endif /*MOLECULES_HPP_*/
406
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