source: molecuilder/src/molecule.hpp@ e71890

Last change on this file since e71890 was 3efb4a, checked in by Frederik Heber <heber@…>, 16 years ago

Implementing templated iterators done for molecule.cpp
  • Property mode set to 100755
File size: 18.3 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
59
60#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
61enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
62
63
64/** The complete molecule.
65 * Class incorporates number of types
66 */
67class molecule : public PointCloud {
68 public:
69 double cell_size[6];//!< cell size
70 periodentafel *elemente; //!< periodic table with each element
71 atom *start; //!< start of atom list
72 atom *end; //!< end of atom list
73 bond *first; //!< start of bond list
74 bond *last; //!< end of bond list
75 bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
76 int MDSteps; //!< The number of MD steps in Trajectories
77 int *NumberOfBondsPerAtom; //!< Number of Bonds each atom has
78 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
79 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
80 int ElementCount; //!< how many unique elements are therein
81 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
82 int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
83 int NoNonBonds; //!< number of non-hydrogen bonds in molecule
84 int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
85 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
86 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
87 Vector Center; //!< Center of molecule in a global box
88 char name[MAXSTRINGSIZE]; //!< arbitrary name
89 int IndexNr; //!< index of molecule in a MoleculeListClass
90 class Tesselation *TesselStruct;
91
92 molecule(periodentafel *teil);
93 virtual ~molecule();
94
95 // re-definition of virtual functions from PointCloud
96 Vector *GetCenter(ofstream *out);
97 TesselPoint *GetPoint();
98 TesselPoint *GetTerminalPoint();
99 void GoToNext();
100 void GoToPrevious();
101 void GoToFirst();
102 void GoToLast();
103 bool IsEmpty();
104 bool IsEnd();
105
106 // templates for allowing global manipulation of all vectors
107 template <typename res> void ActOnAllVectors( res (Vector::*f)() );
108 template <typename res> void ActOnAllVectors( res (Vector::*f)() const);
109 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
110 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
111 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t );
112 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t );
113 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
114 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
115 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u );
116 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u );
117 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
118 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
119 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v);
120 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v);
121 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
122 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;
123
124 // templates for allowing global manipulation of molecule with each atom as single argument
125 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) );
126 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const);
127 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
128 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
129
130 // templates for allowing global copying of molecule with each atom as single argument
131 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy);
132 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const , molecule *copy);
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> void ActOnAllAtoms( res (atom::*f)() );
138 template <typename res> void ActOnAllAtoms( res (atom::*f)() const );
139 template <typename res> void ActOnAllAtoms( res (atom::*f)() ) const;
140 template <typename res> void ActOnAllAtoms( res (atom::*f)() const) const;
141 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T), T t );
142 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T) const, T t );
143 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T), T t ) const;
144 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T) const, T t ) const;
145 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U), T t, U u );
146 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U) const, T t, U u );
147 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U), T t, U u ) const;
148 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U) const, T t, U u ) const;
149 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v);
150 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V) const, T t, U u, V v);
151 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v) const;
152 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V) const, T t, U u, V v) const;
153 template <typename res, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (atom::*f)(T, U, V, W), T t, U u, V v, W w);
154 template <typename res, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (atom::*f)(T, U, V, W) const, T t, U u, V v, W w);
155 template <typename res, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (atom::*f)(T, U, V, W), T t, U u, V v, W w) const;
156 template <typename res, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (atom::*f)(T, U, V, W) const, T t, U u, V v, W w) const;
157
158 // templates for allowing conditional global copying of molecule with each atom as single argument
159 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () );
160 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t );
161 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u );
162 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 );
163
164 // templates for allowing global manipulation of an array with one entry per atom
165 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T));
166 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T), T t);
167 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T));
168 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T), T t);
169 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, T (atom::*Setor)(Vector &), Vector atom::*value);
170 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::*index, T (atom::*Setor)(Vector &), Vector &vect );
171
172 /// remove atoms from molecule.
173 bool AddAtom(atom *pointer);
174 bool RemoveAtom(atom *pointer);
175 bool UnlinkAtom(atom *pointer);
176 bool CleanupMolecule();
177
178 /// Add/remove atoms to/from molecule.
179 atom * AddCopyAtom(atom *pointer);
180 bool AddXYZFile(string filename);
181 bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
182 bond * AddBond(atom *first, atom *second, int degree = 1);
183 bool RemoveBond(bond *pointer);
184 bool RemoveBonds(atom *BondPartner);
185
186 /// Find atoms.
187 atom * FindAtom(int Nr) const;
188 atom * AskAtom(string text);
189
190 /// Count and change present atoms' coordination.
191 void CountAtoms(ofstream *out);
192 void CountElements();
193 void CalculateOrbitals(class config &configuration);
194 bool CenterInBox(ofstream *out);
195 bool BoundInBox(ofstream *out);
196 void CenterEdge(ofstream *out, Vector *max);
197 void CenterOrigin(ofstream *out);
198 void CenterPeriodic(ofstream *out);
199 void CenterAtVector(ofstream *out, Vector *newcenter);
200 void Translate(const Vector *x);
201 void TranslatePeriodically(const Vector *trans);
202 void Mirror(const Vector *x);
203 void Align(Vector *n);
204 void Scale(double **factor);
205 void DeterminePeriodicCenter(Vector &center);
206 Vector * DetermineCenterOfGravity(ofstream *out);
207 Vector * DetermineCenterOfAll(ofstream *out);
208 void SetNameFromFilename(const char *filename);
209 void SetBoxDimension(Vector *dim);
210 void ScanForPeriodicCorrection(ofstream *out);
211 bool VerletForceIntegration(ofstream *out, char *file, config &configuration);
212 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
213 void PrincipalAxisSystem(ofstream *out, bool DoRotate);
214 double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
215 Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
216
217
218 double ConstrainedPotential(ofstream *out, atom **permutation, int start, int end, double *constants, bool IsAngstroem);
219 double MinimiseConstrainedPotential(ofstream *out, atom **&permutation, int startstep, int endstep, bool IsAngstroem);
220 void EvaluateConstrainedForces(ofstream *out, int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
221 bool LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
222
223 bool CheckBounds(const Vector *x) const;
224 void GetAlignvector(struct lsq_params * par) const;
225
226 /// Initialising routines in fragmentation
227 void CreateAdjacencyList2(ofstream *out, ifstream *output);
228 void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
229 void CreateListOfBondsPerAtom(ofstream *out);
230
231 // Graph analysis
232 MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
233 void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
234 bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
235 bond * FindNextUnused(atom *vertex);
236 void SetNextComponentNumber(atom *vertex, int nr);
237 void InitComponentNumbers();
238 void OutputComponentNumber(ofstream *out, atom *vertex);
239 void ResetAllBondsToUnused();
240 void ResetAllAtomNumbers();
241 int CountCyclicBonds(ofstream *out);
242 bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
243 string GetColor(enum Shading color);
244
245 molecule *CopyMolecule();
246 molecule* CopyMoleculeFromSubRegion(Vector offset, double *parallelepiped);
247
248 /// Fragment molecule by two different approaches:
249 int FragmentMolecule(ofstream *out, int Order, config *configuration);
250 bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
251 bool StoreAdjacencyToFile(ofstream *out, char *path);
252 bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
253 bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
254 bool StoreOrderAtSiteFile(ofstream *out, char *path);
255 bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
256 bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
257 bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
258 bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
259 bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
260 void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
261 /// -# BOSSANOVA
262 void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
263 int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
264 bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
265 molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
266 void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
267 int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
268 int GuesstimateFragmentCount(ofstream *out, int order);
269
270 // Recognize doubly appearing molecules in a list of them
271 int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
272 int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
273
274 // Output routines.
275 bool Output(ofstream *out);
276 bool OutputTrajectories(ofstream *out);
277 void OutputListOfBonds(ofstream *out) const;
278 bool OutputXYZ(ofstream *out) const;
279 bool OutputTrajectoriesXYZ(ofstream *out);
280 bool Checkout(ofstream *out) const;
281 bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
282
283 private:
284 int last_atom; //!< number given to last atom
285 atom *InternalPointer; //!< internal pointer for PointCloud
286};
287
288#include "molecule_template.hpp"
289
290/** A list of \a molecule classes.
291 */
292class MoleculeListClass {
293 public:
294 MoleculeList ListOfMolecules; //!< List of the contained molecules
295 int MaxIndex;
296
297 MoleculeListClass();
298 ~MoleculeListClass();
299
300 bool AddHydrogenCorrection(ofstream *out, char *path);
301 bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
302 void insert(molecule *mol);
303 molecule * ReturnIndex(int index);
304 bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
305 int NumberOfActiveMolecules();
306 void Enumerate(ofstream *out);
307 void Output(ofstream *out);
308
309 // merging of molecules
310 bool SimpleMerge(molecule *mol, molecule *srcmol);
311 bool SimpleAdd(molecule *mol, molecule *srcmol);
312 bool SimpleMultiMerge(molecule *mol, int *src, int N);
313 bool SimpleMultiAdd(molecule *mol, int *src, int N);
314 bool ScatterMerge(molecule *mol, int *src, int N);
315 bool EmbedMerge(molecule *mol, molecule *srcmol);
316
317 private:
318};
319
320
321/** A leaf for a tree of \a molecule class
322 * Wraps molecules in a tree structure
323 */
324class MoleculeLeafClass {
325 public:
326 molecule *Leaf; //!< molecule of this leaf
327 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
328 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
329 MoleculeLeafClass *previous; //!< Previous leaf on this level
330 MoleculeLeafClass *next; //!< Next leaf on this level
331
332 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
333 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
334 ~MoleculeLeafClass();
335
336 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
337 bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
338 bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
339 bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
340 bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
341 void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
342 int Count() const;
343};
344
345
346#endif /*MOLECULES_HPP_*/
347
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