source: src/molecule.hpp@ 70ff32

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Last change on this file since 70ff32 was b453f9, checked in by Frederik Heber <heber@…>, 15 years ago

Begun with ticket #38 (make const what is const).

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