source: src/molecules.hpp@ 375b458

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Last change on this file since 375b458 was ca2587, checked in by Frederik Heber <heber@…>, 17 years ago

Framework for embedding one molecule into another, now the embedding center finding is "only" missing
  • Property mode set to 100755
File size: 17.8 KB
Line 
1/** \file molecules.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_multimin.h>
13#include <gsl/gsl_vector.h>
14#include <gsl/gsl_matrix.h>
15#include <gsl/gsl_eigen.h>
16#include <gsl/gsl_heapsort.h>
17
18// STL headers
19#include <map>
20#include <set>
21#include <deque>
22#include <list>
23#include <vector>
24
25#include "helpers.hpp"
26#include "parser.hpp"
27#include "periodentafel.hpp"
28#include "stackclass.hpp"
29#include "vector.hpp"
30
31class atom;
32class bond;
33class config;
34class molecule;
35class MoleculeListClass;
36class Verbose;
37
38/******************************** Some definitions for easier reading **********************************/
39
40#define KeyStack deque<int>
41#define KeySet set<int>
42#define NumberValuePair pair<int, double>
43#define Graph map <KeySet, NumberValuePair, KeyCompare >
44#define GraphPair pair <KeySet, NumberValuePair >
45#define KeySetTestPair pair<KeySet::iterator, bool>
46#define GraphTestPair pair<Graph::iterator, bool>
47
48#define DistancePair pair < double, atom* >
49#define DistanceMap multimap < double, atom* >
50#define DistanceTestPair pair < DistanceMap::iterator, bool>
51
52#define Boundaries map <double, DistancePair >
53#define BoundariesPair pair<double, DistancePair >
54#define BoundariesTestPair pair< Boundaries::iterator, bool>
55
56#define PointMap map < int, class BoundaryPointSet * >
57#define PointPair pair < int, class BoundaryPointSet * >
58#define PointTestPair pair < PointMap::iterator, bool >
59
60#define LineMap map < int, class BoundaryLineSet * >
61#define LinePair pair < int, class BoundaryLineSet * >
62#define LineTestPair pair < LineMap::iterator, bool >
63
64#define TriangleMap map < int, class BoundaryTriangleSet * >
65#define TrianglePair pair < int, class BoundaryTriangleSet * >
66#define TriangleTestPair pair < TrianglePair::iterator, bool >
67
68#define DistanceMultiMap multimap <double, pair < PointMap::iterator, PointMap::iterator> >
69#define DistanceMultiMapPair pair <double, pair < PointMap::iterator, PointMap::iterator> >
70
71#define MoleculeList list <molecule *>
72#define MoleculeListTest pair <MoleculeList::iterator, bool>
73
74/******************************** Some small functions and/or structures **********************************/
75
76struct KeyCompare
77{
78 bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
79};
80
81struct Trajectory
82{
83 vector<Vector> R; //!< position vector
84 vector<Vector> U; //!< velocity vector
85 vector<Vector> F; //!< last force vector
86 atom *ptr; //!< pointer to atom whose trajectory we contain
87};
88
89//bool operator < (KeySet SubgraphA, KeySet SubgraphB); //note: this declaration is important, otherwise normal < is used (producing wrong order)
90inline void InsertFragmentIntoGraph(ofstream *out, struct UniqueFragments *Fragment); // Insert a KeySet into a Graph
91inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter); // Insert all KeySet's in a Graph into another Graph
92int CompareDoubles (const void * a, const void * b);
93
94
95/************************************* Class definitions ****************************************/
96
97
98// some algebraic matrix stuff
99#define RDET3(a) ((a)[0]*(a)[4]*(a)[8] + (a)[3]*(a)[7]*(a)[2] + (a)[6]*(a)[1]*(a)[5] - (a)[2]*(a)[4]*(a)[6] - (a)[5]*(a)[7]*(a)[0] - (a)[8]*(a)[1]*(a)[3]) //!< hard-coded determinant of a 3x3 matrix
100#define RDET2(a0,a1,a2,a3) ((a0)*(a3)-(a1)*(a2)) //!< hard-coded determinant of a 2x2 matrix
101
102
103/** Parameter structure for least square minimsation.
104 */
105struct LSQ_params {
106 Vector **vectors;
107 int num;
108};
109
110double LSQ(const gsl_vector * x, void * params);
111
112/** Parameter structure for least square minimsation.
113 */
114struct lsq_params {
115 gsl_vector *x;
116 const molecule *mol;
117 element *type;
118};
119
120/** Single atom.
121 * Class incoporates position, type
122 */
123class atom {
124 public:
125 Vector x; //!< coordinate array of atom, giving position within cell
126 Vector v; //!< velocity array of atom
127 element *type; //!< pointing to element
128 atom *previous; //!< previous atom in molecule list
129 atom *next; //!< next atom in molecule list
130 atom *father; //!< In many-body bond order fragmentations points to originating atom
131 atom *Ancestor; //!< "Father" in Depth-First-Search
132 char *Name; //!< unique name used during many-body bond-order fragmentation
133 int FixedIon; //!< config variable that states whether forces act on the ion or not
134 int *sort; //!< sort criteria
135 int nr; //!< continuous, unique number
136 int GraphNr; //!< unique number, given in DepthFirstSearchAnalysis()
137 int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
138 int LowpointNr; //!< needed in DepthFirstSearchAnalysis() to detect nonseparable components, is the lowest possible number of an atom to reach via tree edges only followed by at most one back edge.
139 bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
140 bool IsCyclic; //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
141 unsigned char AdaptiveOrder; //!< current present bond order at site (0 means "not set")
142 bool MaxOrder; //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
143
144 atom();
145 ~atom();
146
147 bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
148 bool OutputXYZLine(ofstream *out) const;
149 atom *GetTrueFather();
150 bool Compare(atom &ptr);
151
152 private:
153};
154
155ostream & operator << (ostream &ost, atom &a);
156
157/** Bonds between atoms.
158 * Class incorporates bonds between atoms in a molecule,
159 * used to derive tge fragments in many-body bond order
160 * calculations.
161 */
162class bond {
163 public:
164 atom *leftatom; //!< first bond partner
165 atom *rightatom; //!< second bond partner
166 bond *previous; //!< previous atom in molecule list
167 bond *next; //!< next atom in molecule list
168 int HydrogenBond; //!< Number of hydrogen atoms in the bond
169 int BondDegree; //!< single, double, triple, ... bond
170 int nr; //!< unique number in a molecule, updated by molecule::CreateAdjacencyList()
171 bool Cyclic; //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
172 enum EdgeType Type;//!< whether this is a tree or back edge
173
174 atom * GetOtherAtom(atom *Atom) const;
175 bond * GetFirstBond();
176 bond * GetLastBond();
177
178 bool MarkUsed(enum Shading color);
179 enum Shading IsUsed();
180 void ResetUsed();
181 bool Contains(const atom *ptr);
182 bool Contains(const int nr);
183
184 bond();
185 bond(atom *left, atom *right);
186 bond(atom *left, atom *right, int degree);
187 bond(atom *left, atom *right, int degree, int number);
188 ~bond();
189
190 private:
191 enum Shading Used; //!< marker in depth-first search, DepthFirstSearchAnalysis()
192};
193
194ostream & operator << (ostream &ost, bond &b);
195
196class MoleculeLeafClass;
197
198/** The complete molecule.
199 * Class incorporates number of types
200 */
201class molecule {
202 public:
203 double cell_size[6];//!< cell size
204 periodentafel *elemente; //!< periodic table with each element
205 atom *start; //!< start of atom list
206 atom *end; //!< end of atom list
207 bond *first; //!< start of bond list
208 bond *last; //!< end of bond list
209 bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
210 map<atom *, struct Trajectory> Trajectories; //!< contains old trajectory points
211 int MDSteps; //!< The number of MD steps in Trajectories
212 int *NumberOfBondsPerAtom; //!< Number of Bonds each atom has
213 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
214 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
215 int ElementCount; //!< how many unique elements are therein
216 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
217 int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
218 int NoNonBonds; //!< number of non-hydrogen bonds in molecule
219 int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
220 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
221 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
222 Vector Center; //!< Center of molecule in a global box
223 char name[MAXSTRINGSIZE]; //!< arbitrary name
224 int IndexNr; //!< index of molecule in a MoleculeListClass
225
226 molecule(periodentafel *teil);
227 ~molecule();
228
229 /// remove atoms from molecule.
230 bool AddAtom(atom *pointer);
231 bool RemoveAtom(atom *pointer);
232 bool UnlinkAtom(atom *pointer);
233 bool CleanupMolecule();
234
235 /// Add/remove atoms to/from molecule.
236 atom * AddCopyAtom(atom *pointer);
237 bool AddXYZFile(string filename);
238 bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
239 bond * AddBond(atom *first, atom *second, int degree);
240 bool RemoveBond(bond *pointer);
241 bool RemoveBonds(atom *BondPartner);
242
243 /// Find atoms.
244 atom * FindAtom(int Nr) const;
245 atom * AskAtom(string text);
246
247 /// Count and change present atoms' coordination.
248 void CountAtoms(ofstream *out);
249 void CountElements();
250 void CalculateOrbitals(class config &configuration);
251 bool CenterInBox(ofstream *out, Vector *BoxLengths);
252 void CenterEdge(ofstream *out, Vector *max);
253 void CenterOrigin(ofstream *out, Vector *max);
254 void CenterGravity(ofstream *out, Vector *max);
255 void Translate(const Vector *x);
256 void Mirror(const Vector *x);
257 void Align(Vector *n);
258 void Scale(double **factor);
259 void DetermineCenter(Vector &center);
260 Vector * DetermineCenterOfGravity(ofstream *out);
261 Vector * DetermineCenterOfAll(ofstream *out);
262 void SetNameFromFilename(char *filename);
263 void SetBoxDimension(Vector *dim);
264 double * ReturnFullMatrixforSymmetric(double *cell_size);
265 void ScanForPeriodicCorrection(ofstream *out);
266 void PrincipalAxisSystem(ofstream *out, bool DoRotate);
267 double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
268 Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
269
270 bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
271
272 bool CheckBounds(const Vector *x) const;
273 void GetAlignvector(struct lsq_params * par) const;
274
275 /// Initialising routines in fragmentation
276 void CreateAdjacencyList2(ofstream *out, ifstream *output);
277 void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
278 void CreateListOfBondsPerAtom(ofstream *out);
279
280 // Graph analysis
281 MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
282 void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
283 bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
284 bond * FindNextUnused(atom *vertex);
285 void SetNextComponentNumber(atom *vertex, int nr);
286 void InitComponentNumbers();
287 void OutputComponentNumber(ofstream *out, atom *vertex);
288 void ResetAllBondsToUnused();
289 void ResetAllAtomNumbers();
290 int CountCyclicBonds(ofstream *out);
291 bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
292 string GetColor(enum Shading color);
293
294 molecule *CopyMolecule();
295
296 /// Fragment molecule by two different approaches:
297 int FragmentMolecule(ofstream *out, int Order, config *configuration);
298 bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
299 bool StoreAdjacencyToFile(ofstream *out, char *path);
300 bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
301 bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
302 bool StoreOrderAtSiteFile(ofstream *out, char *path);
303 bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
304 bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
305 bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
306 bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
307 bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
308 void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
309 /// -# BOSSANOVA
310 void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
311 int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
312 bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
313 molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
314 void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
315 int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
316 int GuesstimateFragmentCount(ofstream *out, int order);
317
318 // Recognize doubly appearing molecules in a list of them
319 int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
320 int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
321
322 // Output routines.
323 bool Output(ofstream *out);
324 bool OutputTrajectories(ofstream *out);
325 void OutputListOfBonds(ofstream *out) const;
326 bool OutputXYZ(ofstream *out) const;
327 bool OutputTrajectoriesXYZ(ofstream *out);
328 bool Checkout(ofstream *out) const;
329 bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
330
331 private:
332 int last_atom; //!< number given to last atom
333};
334
335/** A list of \a molecule classes.
336 */
337class MoleculeListClass {
338 public:
339 MoleculeList ListOfMolecules; //!< List of the contained molecules
340 int MaxIndex;
341
342 MoleculeListClass();
343 ~MoleculeListClass();
344
345 bool AddHydrogenCorrection(ofstream *out, char *path);
346 bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
347 bool insert(molecule *mol);
348 molecule * ReturnIndex(int index);
349 bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
350 int NumberOfActiveMolecules();
351 void Enumerate(ofstream *out);
352 void Output(ofstream *out);
353
354 // merging of molecules
355 bool SimpleMerge(molecule *mol, molecule *srcmol);
356 bool SimpleAdd(molecule *mol, molecule *srcmol);
357 bool SimpleMultiMerge(molecule *mol, int *src, int N);
358 bool SimpleMultiAdd(molecule *mol, int *src, int N);
359 bool ScatterMerge(molecule *mol, int *src, int N);
360 bool EmbedMerge(molecule *mol, molecule *srcmol);
361
362 private:
363};
364
365
366/** A leaf for a tree of \a molecule class
367 * Wraps molecules in a tree structure
368 */
369class MoleculeLeafClass {
370 public:
371 molecule *Leaf; //!< molecule of this leaf
372 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
373 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
374 MoleculeLeafClass *previous; //!< Previous leaf on this level
375 MoleculeLeafClass *next; //!< Next leaf on this level
376
377 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
378 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
379 ~MoleculeLeafClass();
380
381 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
382 bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
383 bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
384 bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
385 bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
386 void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
387 int Count() const;
388};
389
390/** The config file.
391 * The class contains all parameters that control a dft run also functions to load and save.
392 */
393class config {
394 public:
395 int PsiType;
396 int MaxPsiDouble;
397 int PsiMaxNoUp;
398 int PsiMaxNoDown;
399 int MaxMinStopStep;
400 int InitMaxMinStopStep;
401 int ProcPEGamma;
402 int ProcPEPsi;
403 char *configpath;
404 char *configname;
405 bool FastParsing;
406 double Deltat;
407 string basis;
408
409 private:
410 char *mainname;
411 char *defaultpath;
412 char *pseudopotpath;
413
414 int DoOutVis;
415 int DoOutMes;
416 int DoOutNICS;
417 int DoOutOrbitals;
418 int DoOutCurrent;
419 int DoFullCurrent;
420 int DoPerturbation;
421 int DoWannier;
422 int CommonWannier;
423 double SawtoothStart;
424 int VectorPlane;
425 double VectorCut;
426 int UseAddGramSch;
427 int Seed;
428
429 int MaxOuterStep;
430 int OutVisStep;
431 int OutSrcStep;
432 double TargetTemp;
433 int ScaleTempStep;
434 int MaxPsiStep;
435 double EpsWannier;
436
437 int MaxMinStep;
438 double RelEpsTotalEnergy;
439 double RelEpsKineticEnergy;
440 int MaxMinGapStopStep;
441 int MaxInitMinStep;
442 double InitRelEpsTotalEnergy;
443 double InitRelEpsKineticEnergy;
444 int InitMaxMinGapStopStep;
445
446 //double BoxLength[NDIM*NDIM];
447
448 double ECut;
449 int MaxLevel;
450 int RiemannTensor;
451 int LevRFactor;
452 int RiemannLevel;
453 int Lev0Factor;
454 int RTActualUse;
455 int AddPsis;
456
457 double RCut;
458 int StructOpt;
459 int IsAngstroem;
460 int RelativeCoord;
461 int MaxTypes;
462
463
464 int ParseForParameter(int verbose, ifstream *file, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
465
466 public:
467 config();
468 ~config();
469
470 int TestSyntax(char *filename, periodentafel *periode, molecule *mol);
471 void Load(char *filename, periodentafel *periode, molecule *mol);
472 void LoadOld(char *filename, periodentafel *periode, molecule *mol);
473 void RetrieveConfigPathAndName(string filename);
474 bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
475 bool SaveMPQC(const char *filename, molecule *mol) const;
476 void Edit();
477 bool GetIsAngstroem() const;
478 char *GetDefaultPath() const;
479 void SetDefaultPath(const char *path);
480};
481
482#endif /*MOLECULES_HPP_*/
483
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