source: src/analysis_correlation.cpp@ 0e01b4

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Last change on this file since 0e01b4 was 8cbb97, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Merge branch 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp

  • Property mode set to 100644
File size: 19.3 KB
Line 
1/*
2 * analysis.cpp
3 *
4 * Created on: Oct 13, 2009
5 * Author: heber
6 */
7
8#include <iostream>
9
10#include "analysis_correlation.hpp"
11#include "element.hpp"
12#include "info.hpp"
13#include "log.hpp"
14#include "molecule.hpp"
15#include "tesselation.hpp"
16#include "tesselationhelpers.hpp"
17#include "triangleintersectionlist.hpp"
18#include "vector.hpp"
19#include "verbose.hpp"
20#include "World.hpp"
21
22
23/** Calculates the pair correlation between given elements.
24 * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
25 * \param *out output stream for debugging
26 * \param *molecules list of molecules structure
27 * \param *type1 first element or NULL (if any element)
28 * \param *type2 second element or NULL (if any element)
29 * \return Map of doubles with values the pair of the two atoms.
30 */
31PairCorrelationMap *PairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2 )
32{
33 Info FunctionInfo(__func__);
34 PairCorrelationMap *outmap = NULL;
35 double distance = 0.;
36
37 if (molecules->ListOfMolecules.empty()) {
38 DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
39 return outmap;
40 }
41 outmap = new PairCorrelationMap;
42 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
43 if ((*MolWalker)->ActiveFlag) {
44 DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
45 atom *Walker = (*MolWalker)->start;
46 while (Walker->next != (*MolWalker)->end) {
47 Walker = Walker->next;
48 DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
49 if ((type1 == NULL) || (Walker->type == type1)) {
50 for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
51 if ((*MolOtherWalker)->ActiveFlag) {
52 DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
53 atom *OtherWalker = (*MolOtherWalker)->start;
54 while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
55 OtherWalker = OtherWalker->next;
56 DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl);
57 if (Walker->nr < OtherWalker->nr)
58 if ((type2 == NULL) || (OtherWalker->type == type2)) {
59 distance = Walker->node->PeriodicDistance(*OtherWalker->node, World::getInstance().getDomain());
60 //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
61 outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
62 }
63 }
64 }
65 }
66 }
67 }
68
69 return outmap;
70};
71
72/** Calculates the pair correlation between given elements.
73 * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
74 * \param *out output stream for debugging
75 * \param *molecules list of molecules structure
76 * \param *type1 first element or NULL (if any element)
77 * \param *type2 second element or NULL (if any element)
78 * \param ranges[NDIM] interval boundaries for the periodic images to scan also
79 * \return Map of doubles with values the pair of the two atoms.
80 */
81PairCorrelationMap *PeriodicPairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2, const int ranges[NDIM] )
82{
83 Info FunctionInfo(__func__);
84 PairCorrelationMap *outmap = NULL;
85 double distance = 0.;
86 int n[NDIM];
87 Vector checkX;
88 Vector periodicX;
89 int Othern[NDIM];
90 Vector checkOtherX;
91 Vector periodicOtherX;
92
93 if (molecules->ListOfMolecules.empty()) {
94 DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
95 return outmap;
96 }
97 outmap = new PairCorrelationMap;
98 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
99 if ((*MolWalker)->ActiveFlag) {
100 double * FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
101 double * FullInverseMatrix = InverseMatrix(FullMatrix);
102 DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
103 atom *Walker = (*MolWalker)->start;
104 while (Walker->next != (*MolWalker)->end) {
105 Walker = Walker->next;
106 DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
107 if ((type1 == NULL) || (Walker->type == type1)) {
108 periodicX = *(Walker->node);
109 periodicX.MatrixMultiplication(FullInverseMatrix); // x now in [0,1)^3
110 // go through every range in xyz and get distance
111 for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
112 for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
113 for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
114 checkX = Vector(n[0], n[1], n[2]) + periodicX;
115 checkX.MatrixMultiplication(FullMatrix);
116 for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
117 if ((*MolOtherWalker)->ActiveFlag) {
118 DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
119 atom *OtherWalker = (*MolOtherWalker)->start;
120 while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
121 OtherWalker = OtherWalker->next;
122 DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl);
123 if (Walker->nr < OtherWalker->nr)
124 if ((type2 == NULL) || (OtherWalker->type == type2)) {
125 periodicOtherX = *(OtherWalker->node);
126 periodicOtherX.MatrixMultiplication(FullInverseMatrix); // x now in [0,1)^3
127 // go through every range in xyz and get distance
128 for (Othern[0]=-ranges[0]; Othern[0] <= ranges[0]; Othern[0]++)
129 for (Othern[1]=-ranges[1]; Othern[1] <= ranges[1]; Othern[1]++)
130 for (Othern[2]=-ranges[2]; Othern[2] <= ranges[2]; Othern[2]++) {
131 checkOtherX = Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX;
132 checkOtherX.MatrixMultiplication(FullMatrix);
133 distance = checkX.Distance(checkOtherX);
134 //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
135 outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
136 }
137 }
138 }
139 }
140 }
141 }
142 }
143 Free(&FullMatrix);
144 Free(&FullInverseMatrix);
145 }
146
147 return outmap;
148};
149
150/** Calculates the distance (pair) correlation between a given element and a point.
151 * \param *out output stream for debugging
152 * \param *molecules list of molecules structure
153 * \param *type element or NULL (if any element)
154 * \param *point vector to the correlation point
155 * \return Map of dobules with values as pairs of atom and the vector
156 */
157CorrelationToPointMap *CorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point )
158{
159 Info FunctionInfo(__func__);
160 CorrelationToPointMap *outmap = NULL;
161 double distance = 0.;
162
163 if (molecules->ListOfMolecules.empty()) {
164 DoLog(1) && (Log() << Verbose(1) <<"No molecule given." << endl);
165 return outmap;
166 }
167 outmap = new CorrelationToPointMap;
168 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
169 if ((*MolWalker)->ActiveFlag) {
170 DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
171 atom *Walker = (*MolWalker)->start;
172 while (Walker->next != (*MolWalker)->end) {
173 Walker = Walker->next;
174 DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
175 if ((type == NULL) || (Walker->type == type)) {
176 distance = Walker->node->PeriodicDistance(*point, World::getInstance().getDomain());
177 DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
178 outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
179 }
180 }
181 }
182
183 return outmap;
184};
185
186/** Calculates the distance (pair) correlation between a given element, all its periodic images and a point.
187 * \param *out output stream for debugging
188 * \param *molecules list of molecules structure
189 * \param *type element or NULL (if any element)
190 * \param *point vector to the correlation point
191 * \param ranges[NDIM] interval boundaries for the periodic images to scan also
192 * \return Map of dobules with values as pairs of atom and the vector
193 */
194CorrelationToPointMap *PeriodicCorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point, const int ranges[NDIM] )
195{
196 Info FunctionInfo(__func__);
197 CorrelationToPointMap *outmap = NULL;
198 double distance = 0.;
199 int n[NDIM];
200 Vector periodicX;
201 Vector checkX;
202
203 if (molecules->ListOfMolecules.empty()) {
204 DoLog(1) && (Log() << Verbose(1) <<"No molecule given." << endl);
205 return outmap;
206 }
207 outmap = new CorrelationToPointMap;
208 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
209 if ((*MolWalker)->ActiveFlag) {
210 double * FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
211 double * FullInverseMatrix = InverseMatrix(FullMatrix);
212 DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
213 atom *Walker = (*MolWalker)->start;
214 while (Walker->next != (*MolWalker)->end) {
215 Walker = Walker->next;
216 DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
217 if ((type == NULL) || (Walker->type == type)) {
218 periodicX = *(Walker->node);
219 periodicX.MatrixMultiplication(FullInverseMatrix); // x now in [0,1)^3
220 // go through every range in xyz and get distance
221 for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
222 for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
223 for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
224 checkX = Vector(n[0], n[1], n[2]) + periodicX;
225 checkX.MatrixMultiplication(FullMatrix);
226 distance = checkX.Distance(*point);
227 DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
228 outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
229 }
230 }
231 }
232 Free(&FullMatrix);
233 Free(&FullInverseMatrix);
234 }
235
236 return outmap;
237};
238
239/** Calculates the distance (pair) correlation between a given element and a surface.
240 * \param *out output stream for debugging
241 * \param *molecules list of molecules structure
242 * \param *type element or NULL (if any element)
243 * \param *Surface pointer to Tesselation class surface
244 * \param *LC LinkedCell structure to quickly find neighbouring atoms
245 * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
246 */
247CorrelationToSurfaceMap *CorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
248{
249 Info FunctionInfo(__func__);
250 CorrelationToSurfaceMap *outmap = NULL;
251 double distance = 0;
252 class BoundaryTriangleSet *triangle = NULL;
253 Vector centroid;
254
255 if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
256 DoeLog(1) && (eLog()<< Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl);
257 return outmap;
258 }
259 outmap = new CorrelationToSurfaceMap;
260 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
261 if ((*MolWalker)->ActiveFlag) {
262 DoLog(1) && (Log() << Verbose(1) << "Current molecule is " << (*MolWalker)->name << "." << endl);
263 atom *Walker = (*MolWalker)->start;
264 while (Walker->next != (*MolWalker)->end) {
265 Walker = Walker->next;
266 //Log() << Verbose(1) << "Current atom is " << *Walker << "." << endl;
267 if ((type == NULL) || (Walker->type == type)) {
268 TriangleIntersectionList Intersections(Walker->node,Surface,LC);
269 distance = Intersections.GetSmallestDistance();
270 triangle = Intersections.GetClosestTriangle();
271 outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
272 }
273 }
274 } else
275 DoLog(1) && (Log() << Verbose(1) << "molecule " << (*MolWalker)->name << " is not active." << endl);
276
277 return outmap;
278};
279
280/** Calculates the distance (pair) correlation between a given element, all its periodic images and and a surface.
281 * Note that we also put all periodic images found in the cells given by [ -ranges[i], ranges[i] ] and i=0,...,NDIM-1.
282 * I.e. We multiply the atom::node with the inverse of the domain matrix, i.e. transform it to \f$[0,0^3\f$, then add per
283 * axis an integer from [ -ranges[i], ranges[i] ] onto it and multiply with the domain matrix to bring it back into
284 * the real space. Then, we Tesselation::FindClosestTriangleToPoint() and DistanceToTrianglePlane().
285 * \param *out output stream for debugging
286 * \param *molecules list of molecules structure
287 * \param *type element or NULL (if any element)
288 * \param *Surface pointer to Tesselation class surface
289 * \param *LC LinkedCell structure to quickly find neighbouring atoms
290 * \param ranges[NDIM] interval boundaries for the periodic images to scan also
291 * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
292 */
293CorrelationToSurfaceMap *PeriodicCorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
294{
295 Info FunctionInfo(__func__);
296 CorrelationToSurfaceMap *outmap = NULL;
297 double distance = 0;
298 class BoundaryTriangleSet *triangle = NULL;
299 Vector centroid;
300 int n[NDIM];
301 Vector periodicX;
302 Vector checkX;
303
304 if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
305 DoLog(1) && (Log() << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl);
306 return outmap;
307 }
308 outmap = new CorrelationToSurfaceMap;
309 double ShortestDistance = 0.;
310 BoundaryTriangleSet *ShortestTriangle = NULL;
311 for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
312 if ((*MolWalker)->ActiveFlag) {
313 double * FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
314 double * FullInverseMatrix = InverseMatrix(FullMatrix);
315 DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
316 atom *Walker = (*MolWalker)->start;
317 while (Walker->next != (*MolWalker)->end) {
318 Walker = Walker->next;
319 DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
320 if ((type == NULL) || (Walker->type == type)) {
321 periodicX = *(Walker->node);
322 periodicX.MatrixMultiplication(FullInverseMatrix); // x now in [0,1)^3
323 // go through every range in xyz and get distance
324 ShortestDistance = -1.;
325 for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
326 for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
327 for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
328 checkX = Vector(n[0], n[1], n[2]) + periodicX;
329 checkX.MatrixMultiplication(FullMatrix);
330 TriangleIntersectionList Intersections(&checkX,Surface,LC);
331 distance = Intersections.GetSmallestDistance();
332 triangle = Intersections.GetClosestTriangle();
333 if ((ShortestDistance == -1.) || (distance < ShortestDistance)) {
334 ShortestDistance = distance;
335 ShortestTriangle = triangle;
336 }
337 }
338 // insert
339 outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (Walker, ShortestTriangle) ) );
340 //Log() << Verbose(1) << "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << "." << endl;
341 }
342 }
343 Free(&FullMatrix);
344 Free(&FullInverseMatrix);
345 }
346
347 return outmap;
348};
349
350/** Returns the index of the bin for a given value.
351 * \param value value whose bin to look for
352 * \param BinWidth width of bin
353 * \param BinStart first bin
354 */
355int GetBin ( const double value, const double BinWidth, const double BinStart )
356{
357 Info FunctionInfo(__func__);
358 int bin =(int) (floor((value - BinStart)/BinWidth));
359 return (bin);
360};
361
362
363/** Prints correlation (double, int) pairs to file.
364 * \param *file file to write to
365 * \param *map map to write
366 */
367void OutputCorrelation( ofstream * const file, const BinPairMap * const map )
368{
369 Info FunctionInfo(__func__);
370 *file << "BinStart\tCount" << endl;
371 for (BinPairMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
372 *file << setprecision(8) << runner->first << "\t" << runner->second << endl;
373 }
374};
375
376/** Prints correlation (double, (atom*,atom*) ) pairs to file.
377 * \param *file file to write to
378 * \param *map map to write
379 */
380void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map )
381{
382 Info FunctionInfo(__func__);
383 *file << "BinStart\tAtom1\tAtom2" << endl;
384 for (PairCorrelationMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
385 *file << setprecision(8) << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
386 }
387};
388
389/** Prints correlation (double, int) pairs to file.
390 * \param *file file to write to
391 * \param *map map to write
392 */
393void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map )
394{
395 Info FunctionInfo(__func__);
396 *file << "BinStart\tAtom::x[i]-point.x[i]" << endl;
397 for (CorrelationToPointMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
398 *file << runner->first;
399 for (int i=0;i<NDIM;i++)
400 *file << "\t" << setprecision(8) << (runner->second.first->node->at(i) - runner->second.second->at(i));
401 *file << endl;
402 }
403};
404
405/** Prints correlation (double, int) pairs to file.
406 * \param *file file to write to
407 * \param *map map to write
408 */
409void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map )
410{
411 Info FunctionInfo(__func__);
412 *file << "BinStart\tTriangle" << endl;
413 if (!map->empty())
414 for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
415 *file << setprecision(8) << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
416 }
417};
418
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