source: src/molecule.hpp@ 23b830

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Last change on this file since 23b830 was fcd7b6, checked in by Frederik Heber <heber@…>, 16 years ago

In molecule::OutputTrajectories() ActOnAllAtoms() with new function atom::OutputTrajectory() is used.

For this to work, I had to change the Trajectory struct that was so far included in molecule.hpp to be incorporated directly into the class atom.
NOTE: This incorporation is incomplete and a ticket (#34) has been filed to remind of this issue.
However, the trajectory is better suited to reside in atom anyway and was probably just put in molecule due to memory prejudices against STL vector<>.
Functions in molecule.cpp, config.cpp, molecule_geometry.cpp and molecule_dynamics.cpp were adapted (changed from Trajectories[atom *] to atom *->Trajectory).
And the atom pointer in the Trajectory structure was removed.
  • Property mode set to 100755
File size: 17.7 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// GSL headers
12#include <gsl/gsl_eigen.h>
13#include <gsl/gsl_heapsort.h>
14#include <gsl/gsl_linalg.h>
15#include <gsl/gsl_matrix.h>
16#include <gsl/gsl_multimin.h>
17#include <gsl/gsl_vector.h>
18#include <gsl/gsl_randist.h>
19
20//// STL headers
21#include <map>
22#include <set>
23#include <deque>
24#include <list>
25#include <vector>
26
27#include "atom.hpp"
28#include "bond.hpp"
29#include "element.hpp"
30#include "leastsquaremin.hpp"
31#include "linkedcell.hpp"
32#include "parser.hpp"
33#include "periodentafel.hpp"
34#include "stackclass.hpp"
35#include "tesselation.hpp"
36#include "vector.hpp"
37
38class molecule;
39class MoleculeLeafClass;
40class MoleculeListClass;
41
42/******************************** Some definitions for easier reading **********************************/
43
44#define KeyStack deque<int>
45#define KeySet set<int>
46#define NumberValuePair pair<int, double>
47#define Graph map <KeySet, NumberValuePair, KeyCompare >
48#define GraphPair pair <KeySet, NumberValuePair >
49#define KeySetTestPair pair<KeySet::iterator, bool>
50#define GraphTestPair pair<Graph::iterator, bool>
51
52#define MoleculeList list <molecule *>
53#define MoleculeListTest pair <MoleculeList::iterator, bool>
54
55#define DistancePair pair < double, atom* >
56#define DistanceMap multimap < double, atom* >
57#define DistanceTestPair pair < DistanceMap::iterator, bool>
58
59
60//#define LinkedAtoms list <atom *>
61
62/******************************** Some small functions and/or structures **********************************/
63
64struct KeyCompare
65{
66 bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
67};
68
69//bool operator < (KeySet SubgraphA, KeySet SubgraphB); //note: this declaration is important, otherwise normal < is used (producing wrong order)
70inline void InsertFragmentIntoGraph(ofstream *out, struct UniqueFragments *Fragment); // Insert a KeySet into a Graph
71inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter); // Insert all KeySet's in a Graph into another Graph
72int CompareDoubles (const void * a, const void * b);
73
74
75/************************************* Class definitions ****************************************/
76
77
78
79#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
80enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
81
82
83/** The complete molecule.
84 * Class incorporates number of types
85 */
86class molecule : public PointCloud {
87 public:
88 double cell_size[6];//!< cell size
89 periodentafel *elemente; //!< periodic table with each element
90 atom *start; //!< start of atom list
91 atom *end; //!< end of atom list
92 bond *first; //!< start of bond list
93 bond *last; //!< end of bond list
94 bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
95 int MDSteps; //!< The number of MD steps in Trajectories
96 int *NumberOfBondsPerAtom; //!< Number of Bonds each atom has
97 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
98 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
99 int ElementCount; //!< how many unique elements are therein
100 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
101 int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
102 int NoNonBonds; //!< number of non-hydrogen bonds in molecule
103 int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
104 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
105 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
106 Vector Center; //!< Center of molecule in a global box
107 char name[MAXSTRINGSIZE]; //!< arbitrary name
108 int IndexNr; //!< index of molecule in a MoleculeListClass
109 class Tesselation *TesselStruct;
110
111 molecule(periodentafel *teil);
112 virtual ~molecule();
113
114 // re-definition of virtual functions from PointCloud
115 Vector *GetCenter(ofstream *out);
116 TesselPoint *GetPoint();
117 TesselPoint *GetTerminalPoint();
118 void GoToNext();
119 void GoToPrevious();
120 void GoToFirst();
121 void GoToLast();
122 bool IsEmpty();
123 bool IsEnd();
124
125 // templates for allowing global manipulation of all vectors
126 template <typename res> void ActOnAllVectors( res (Vector::*f)() );
127 template <typename res> void ActOnAllVectors( res (Vector::*f)() const);
128 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
129 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t );
130 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t );
131 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
132 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u );
133 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u );
134 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
135 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v);
136 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v);
137 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
138
139 // templates for allowing global manipulation of molecule with each atom as single argument
140 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) );
141 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const);
142 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
143
144 // templates for allowing global copying of molecule with each atom as single argument
145 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy);
146 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const , molecule *copy);
147 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
148
149 // templates for allowing global manipulation of all atoms
150 template <typename res> void ActOnAllAtoms( res (atom::*f)() );
151 template <typename res> void ActOnAllAtoms( res (atom::*f)() const );
152 template <typename res> void ActOnAllAtoms( res (atom::*f)() ) const;
153 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T), T t );
154 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T) const, T t );
155 template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T) const, T t ) const;
156 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U), T t, U u );
157 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U) const, T t, U u );
158 template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U), T t, U u ) const;
159 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v);
160 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V) const, T t, U u, V v);
161 template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v) const;
162 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);
163 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);
164 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;
165
166 // templates for allowing conditional global copying of molecule with each atom as single argument
167 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () );
168 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t );
169 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u );
170 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 );
171
172 // templates for allowing global manipulation of an array with one entry per atom
173 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int atom::* index, void (*Setor)(T *, T));
174 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int atom::* index, void (*Setor)(T *, T), T);
175 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T));
176 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T), T);
177
178 /// remove atoms from molecule.
179 bool AddAtom(atom *pointer);
180 bool RemoveAtom(atom *pointer);
181 bool UnlinkAtom(atom *pointer);
182 bool CleanupMolecule();
183
184 /// Add/remove atoms to/from molecule.
185 atom * AddCopyAtom(atom *pointer);
186 bool AddXYZFile(string filename);
187 bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
188 bond * AddBond(atom *first, atom *second, int degree = 1);
189 bool RemoveBond(bond *pointer);
190 bool RemoveBonds(atom *BondPartner);
191
192 /// Find atoms.
193 atom * FindAtom(int Nr) const;
194 atom * AskAtom(string text);
195
196 /// Count and change present atoms' coordination.
197 void CountAtoms(ofstream *out);
198 void CountElements();
199 void CalculateOrbitals(class config &configuration);
200 bool CenterInBox(ofstream *out);
201 bool BoundInBox(ofstream *out);
202 void CenterEdge(ofstream *out, Vector *max);
203 void CenterOrigin(ofstream *out);
204 void CenterPeriodic(ofstream *out);
205 void CenterAtVector(ofstream *out, Vector *newcenter);
206 void Translate(const Vector *x);
207 void TranslatePeriodically(const Vector *trans);
208 void Mirror(const Vector *x);
209 void Align(Vector *n);
210 void Scale(double **factor);
211 void DeterminePeriodicCenter(Vector &center);
212 Vector * DetermineCenterOfGravity(ofstream *out);
213 Vector * DetermineCenterOfAll(ofstream *out);
214 void SetNameFromFilename(const char *filename);
215 void SetBoxDimension(Vector *dim);
216 double * ReturnFullMatrixforSymmetric(double *cell_size);
217 void ScanForPeriodicCorrection(ofstream *out);
218 bool VerletForceIntegration(ofstream *out, char *file, config &configuration);
219 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
220 void PrincipalAxisSystem(ofstream *out, bool DoRotate);
221 double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
222 Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
223
224
225 double ConstrainedPotential(ofstream *out, atom **permutation, int start, int end, double *constants, bool IsAngstroem);
226 double MinimiseConstrainedPotential(ofstream *out, atom **&permutation, int startstep, int endstep, bool IsAngstroem);
227 void EvaluateConstrainedForces(ofstream *out, int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
228 bool LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
229
230 bool CheckBounds(const Vector *x) const;
231 void GetAlignvector(struct lsq_params * par) const;
232
233 /// Initialising routines in fragmentation
234 void CreateAdjacencyList2(ofstream *out, ifstream *output);
235 void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
236 void CreateListOfBondsPerAtom(ofstream *out);
237
238 // Graph analysis
239 MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
240 void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
241 bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
242 bond * FindNextUnused(atom *vertex);
243 void SetNextComponentNumber(atom *vertex, int nr);
244 void InitComponentNumbers();
245 void OutputComponentNumber(ofstream *out, atom *vertex);
246 void ResetAllBondsToUnused();
247 void ResetAllAtomNumbers();
248 int CountCyclicBonds(ofstream *out);
249 bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
250 string GetColor(enum Shading color);
251
252 molecule *CopyMolecule();
253 molecule* CopyMoleculeFromSubRegion(Vector offset, double *parallelepiped);
254
255 /// Fragment molecule by two different approaches:
256 int FragmentMolecule(ofstream *out, int Order, config *configuration);
257 bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
258 bool StoreAdjacencyToFile(ofstream *out, char *path);
259 bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
260 bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
261 bool StoreOrderAtSiteFile(ofstream *out, char *path);
262 bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
263 bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
264 bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
265 bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
266 bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
267 void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
268 /// -# BOSSANOVA
269 void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
270 int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
271 bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
272 molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
273 void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
274 int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
275 int GuesstimateFragmentCount(ofstream *out, int order);
276
277 // Recognize doubly appearing molecules in a list of them
278 int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
279 int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
280
281 // Output routines.
282 bool Output(ofstream *out);
283 bool OutputTrajectories(ofstream *out);
284 void OutputListOfBonds(ofstream *out) const;
285 bool OutputXYZ(ofstream *out) const;
286 bool OutputTrajectoriesXYZ(ofstream *out);
287 bool Checkout(ofstream *out) const;
288 bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
289
290 private:
291 int last_atom; //!< number given to last atom
292 atom *InternalPointer; //!< internal pointer for PointCloud
293};
294
295#include "molecule_template.hpp"
296
297/** A list of \a molecule classes.
298 */
299class MoleculeListClass {
300 public:
301 MoleculeList ListOfMolecules; //!< List of the contained molecules
302 int MaxIndex;
303
304 MoleculeListClass();
305 ~MoleculeListClass();
306
307 bool AddHydrogenCorrection(ofstream *out, char *path);
308 bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
309 void insert(molecule *mol);
310 molecule * ReturnIndex(int index);
311 bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
312 int NumberOfActiveMolecules();
313 void Enumerate(ofstream *out);
314 void Output(ofstream *out);
315
316 // merging of molecules
317 bool SimpleMerge(molecule *mol, molecule *srcmol);
318 bool SimpleAdd(molecule *mol, molecule *srcmol);
319 bool SimpleMultiMerge(molecule *mol, int *src, int N);
320 bool SimpleMultiAdd(molecule *mol, int *src, int N);
321 bool ScatterMerge(molecule *mol, int *src, int N);
322 bool EmbedMerge(molecule *mol, molecule *srcmol);
323
324 private:
325};
326
327
328/** A leaf for a tree of \a molecule class
329 * Wraps molecules in a tree structure
330 */
331class MoleculeLeafClass {
332 public:
333 molecule *Leaf; //!< molecule of this leaf
334 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
335 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
336 MoleculeLeafClass *previous; //!< Previous leaf on this level
337 MoleculeLeafClass *next; //!< Next leaf on this level
338
339 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
340 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
341 ~MoleculeLeafClass();
342
343 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
344 bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
345 bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
346 bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
347 bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
348 void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
349 int Count() const;
350};
351
352
353#endif /*MOLECULES_HPP_*/
354
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