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Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "selection/NameFinder.hpp"
43	<	namespace oopse {
43	>	#include "utils/wildcards.hpp"
44	>	#include "utils/StringTokenizer.hpp"
45	>	#include "primitives/Molecule.hpp"
46	>	#include "utils/StringUtils.hpp"
47	>	namespace OpenMD {
48
49	<	NameFinder::NameFinder(SimInfo* info) {
49	>	TreeNode::~TreeNode(){
50	>	std::map<std::string, TreeNode*>::iterator i;
51	>	for ( i = children.begin(); i != children.end(); ++i) {
52	>	i->second->~TreeNode();
53	>	}
54	>	children.clear();
55	>	}
56	>
57	>	NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	>	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
59	>	nObjects_.push_back(info_->getNGlobalBonds());
60	>	nObjects_.push_back(info_->getNGlobalBends());
61	>	nObjects_.push_back(info_->getNGlobalTorsions());
62	>	nObjects_.push_back(info_->getNGlobalInversions());
63		loadNames();
64	<	}
64	>	}
65
66	+	NameFinder::~NameFinder(){
67	+	delete root_;
68	+	}
69
70	<
50	<	void NameFinder::loadNames() {
51	<
52	<	root_ = new NameNode;
53	<	root_.type = rootNode;
54	<
55	<	NameNode* newNode;
70	>	void NameFinder::loadNames() {
71		SimInfo::MoleculeIterator mi;
57	–	Molecule* mol;
72		Molecule::AtomIterator ai;
59	–	Atom* atom;
73		Molecule::RigidBodyIterator rbIter;
74	+	Molecule::BondIterator bondIter;
75	+	Molecule::BendIterator bendIter;
76	+	Molecule::TorsionIterator torsionIter;
77	+	Molecule::InversionIterator inversionIter;
78	+
79	+	Molecule* mol;
80	+	Atom* atom;
81		RigidBody* rb;
82	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
83	<	newNode = new NameNode;
84	<	newNode.type = molNode;
85	<	newNode.name = mol->getMoleculeName();
82	>	Bond* bond;
83	>	Bend* bend;
84	>	Torsion* torsion;
85	>	Inversion* inversion;
86	>
87	>	root_ = new TreeNode;
88	>	root_->bs.resize(nObjects_);
89	>	root_->bs.setAll(); //
90	>
91	>	for (mol = info_->beginMolecule(mi); mol != NULL;
92	>	mol = info_->nextMolecule(mi)) {
93	>
94	>	std::string molName = mol->getMoleculeName();
95	>	TreeNode* molNode = createNode(root_, molName);
96
97	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
98	<	atomNames_.insert(atom->getType());
97	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
98	>	std::string atomName = atom->getType();
99	>	TreeNode* atomNode = createNode(molNode, atomName);
100	>
101	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
102	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
103	>	}
104	>
105	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
106	>	rb = mol->nextRigidBody(rbIter)) {
107	>	std::string rbName = rb->getType();
108	>	TreeNode* rbNode = createNode(molNode, rbName);
109	>
110	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
111	>	rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
112	>
113	>	//create nodes for atoms belong to this rigidbody
114	>	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115	>	std::string rbAtomName = atom->getType();
116	>	TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
117	>
118	>	rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
119	>	}
120	>	}
121	>
122	>	for (bond = mol->beginBond(bondIter); bond != NULL;
123	>	bond = mol->nextBond(bondIter)) {
124	>
125	>	std::string bondName = bond->getName();
126	>	TreeNode* bondNode = createNode(molNode, bondName);
127	>
128	>	molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
129	>	bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
130	>
131	>	std::vector<Atom*> atoms = bond->getAtoms();
132	>	std::vector<Atom*>::iterator ai;
133	>
134	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
135	>	std::string atomName = (*ai)->getType();
136	>	TreeNode* atomNode = createNode(bondNode, atomName);
137	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
138		}
139	+	}
140	+	for (bend = mol->beginBend(bendIter); bend != NULL;
141	+	bend = mol->nextBend(bendIter)) {
142	+
143	+	std::string bendName = bend->getName();
144	+	TreeNode* bendNode = createNode(molNode, bendName);
145	+
146	+	molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
147	+	bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
148	+
149	+	std::vector<Atom*> atoms = bend->getAtoms();
150	+	std::vector<Atom*>::iterator ai;
151
152	<	//change the positions of atoms which belong to the rigidbodies
153	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
154	<	rbNames_.insert(rb->getType());
155	<	}
156	<	}
76	<	}
152	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
153	>	std::string atomName = (*ai)->getType();
154	>	TreeNode* atomNode = createNode(bendNode, atomName);
155	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
156	>	}
157
158	<	bool NameFinder::match(const std::string& name, BitSet& bs){
158	>	}
159	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
160	>	torsion = mol->nextTorsion(torsionIter)) {
161
162	<	bool error = true;
162	>	std::string torsionName = torsion->getName();
163	>	TreeNode* torsionNode = createNode(molNode, torsionName);
164	>
165	>	molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
166	>	torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
167	>
168	>	std::vector<Atom*> atoms = torsion->getAtoms();
169	>	std::vector<Atom*>::iterator ai;
170	>
171	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
172	>	std::string atomName = (*ai)->getType();
173	>	TreeNode* atomNode = createNode(torsionNode, atomName);
174	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
175	>	}
176	>
177	>	}
178	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
179	>	inversion = mol->nextInversion(inversionIter)) {
180	>
181	>	std::string inversionName = inversion->getName();
182	>	TreeNode* inversionNode = createNode(molNode, inversionName);
183	>
184	>	molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
185	>	inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
186	>	std::vector<Atom*> atoms = inversion->getAtoms();
187	>	std::vector<Atom*>::iterator ai;
188	>
189	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
190	>	std::string atomName = (*ai)->getType();
191	>	TreeNode* atomNode = createNode(inversionNode, atomName);
192	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
193	>	}
194	>	}
195	>	}
196	>	}
197	>
198	>	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
199	>	TreeNode* node;
200	>	std::map<std::string, TreeNode*>::iterator foundIter;
201	>	foundIter = parent->children.find(name);
202	>	if ( foundIter  == parent->children.end()) {
203	>	node = new TreeNode;
204	>	node->name = name;
205	>	node->bs.resize(nObjects_);
206	>	parent->children.insert(std::make_pair(name, node));
207	>	}else {
208	>	node = foundIter->second;
209	>	}
210	>	return node;
211	>	}
212	>
213	>	SelectionSet NameFinder::match(const std::string& name){
214	>	SelectionSet bs(nObjects_);
215	>
216		StringTokenizer tokenizer(name, ".");
217
218		std::vector<std::string> names;
219		while(tokenizer.hasMoreTokens()) {
220	<	names.push_back(tokenizer.nextToken());
220	>	names.push_back(tokenizer.nextToken());
221		}
222
223		int size = names.size();
224	+
225		switch(size) {
226	<	case 1 :
227	<	//could be molecule name, atom name, rigidbody name
228	<	isMolName();
229	<	isAtomName();
230	<	isRigidBodyName();
231	<	break;
232	<	case 2:
233	<	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*
98	<	break;
99	<	case 3:
100	<	//must be molecule.rigidbody.*
226	>	case 1 :
227	>	//could be molecule name, atom name and rigidbody name
228	>	matchMolecule(names[0], bs);
229	>	matchStuntDouble("*", names[0], bs);
230	>	matchBond("*", names[0], bs);
231	>	matchBend("*", names[0], bs);
232	>	matchTorsion("*", names[0], bs);
233	>	matchInversion("*", names[0], bs);
234
235	<	break;
236	<	default:
237	<	break;
235	>	break;
236	>	case 2:
237	>	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
238	>
239	>	if (!isInteger(names[1])){
240	>	matchRigidAtoms("*", names[0], names[1], bs);
241	>	matchStuntDouble(names[0], names[1], bs);
242	>	} else {
243	>	int internalIndex = lexi_cast<int>(names[1]);
244	>	if (internalIndex < 0) {
245	>	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
246	>	} else {
247	>	matchInternalIndex(names[0], internalIndex, bs);
248	>	}
249	>	}
250	>
251	>	break;
252	>	case 3:
253	>	//must be molecule.rigidbody.*
254	>	matchRigidAtoms(names[0], names[1], names[2], bs);
255	>	break;
256	>	default:
257	>	std::cerr << "invalid name: " << name << std::endl;
258	>	break;
259		}
260
261	<	return matched;
262	<	}
261	>	return bs;
262	>	}
263
264	+	void NameFinder::matchMolecule(const std::string& molName, SelectionSet& bs) {
265	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
266	+	std::vector<TreeNode*>::iterator i;
267	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
268	+	bs |= (*i)->bs;
269	+	}
270	+	}
271	+
272	+	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
273	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
274	+	std::vector<TreeNode*>::iterator i;
275	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
276	+	std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);
277	+	std::vector<TreeNode*>::iterator j;
278	+	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
279	+	bs |= (*j)->bs;
280	+	}
281	+	}
282	+
283	+	}
284	+
285	+	void NameFinder::matchBond(const std::string& molName,
286	+	const std::string& bondName, SelectionSet& bs){
287	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
288	+	std::vector<TreeNode*>::iterator i;
289	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
290	+	std::vector<TreeNode*> bondNodes = getMatchedChildren(*i, bondName);
291	+	std::vector<TreeNode*>::iterator j;
292	+	for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
293	+	bs |= (*j)->bs;
294	+	std::vector<TreeNode*> bondAtomNodes = getAllChildren(*j);
295	+	std::vector<TreeNode*>::iterator k;
296	+	for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
297	+	bs |= (*k)->bs;
298	+	}
299	+	}
300	+	}
301	+	}
302	+
303	+	void NameFinder::matchBend(const std::string& molName, const std::string& bendName,  SelectionSet& bs){
304	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
305	+	std::vector<TreeNode*>::iterator i;
306	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
307	+	std::vector<TreeNode*> bendNodes = getMatchedChildren(*i, bendName);
308	+	std::vector<TreeNode*>::iterator j;
309	+	for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
310	+	std::vector<TreeNode*> bendAtomNodes = getAllChildren(*j);
311	+	std::vector<TreeNode*>::iterator k;
312	+	for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
313	+	bs |= (*k)->bs;
314	+	}
315	+	}
316	+	}
317	+	}
318	+	void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
319	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
320	+	std::vector<TreeNode*>::iterator i;
321	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
322	+	std::vector<TreeNode*> torsionNodes = getMatchedChildren(*i, torsionName);
323	+	std::vector<TreeNode*>::iterator j;
324	+	for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
325	+	std::vector<TreeNode*> torsionAtomNodes = getAllChildren(*j);
326	+	std::vector<TreeNode*>::iterator k;
327	+	for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
328	+	bs |= (*k)->bs;
329	+	}
330	+	}
331	+	}
332	+	}
333	+	void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
334	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
335	+	std::vector<TreeNode*>::iterator i;
336	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
337	+	std::vector<TreeNode*> inversionNodes = getMatchedChildren(*i, inversionName);
338	+	std::vector<TreeNode*>::iterator j;
339	+	for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
340	+	std::vector<TreeNode*> inversionAtomNodes = getAllChildren(*j);
341	+	std::vector<TreeNode*>::iterator k;
342	+	for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
343	+	bs |= (*k)->bs;
344	+	}
345	+	}
346	+	}
347	+	}
348	+
349	+	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
350	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
351	+	std::vector<TreeNode*>::iterator i;
352	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
353	+	std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);
354	+	std::vector<TreeNode*>::iterator j;
355	+	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
356	+	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
357	+	std::vector<TreeNode*>::iterator k;
358	+	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
359	+	bs |= (*k)->bs;
360	+	}
361	+	}
362	+	}
363	+
364	+	}
365	+
366	+	std::vector<TreeNode*> NameFinder::getAllChildren(TreeNode* node)  {
367	+	std::vector<TreeNode*> childNodes;
368	+	std::map<std::string, TreeNode*>::iterator i;
369	+	for (i = node->children.begin(); i != node->children.end(); ++i) {
370	+	childNodes.push_back(i->second);
371	+	}
372	+	return childNodes;
373	+	}
374	+
375	+	std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
376	+	std::vector<TreeNode*> matchedNodes;
377	+	std::map<std::string, TreeNode*>::iterator i;
378	+	for (i = node->children.begin(); i != node->children.end(); ++i) {
379	+	if (isMatched( i->first, name)) {
380	+	matchedNodes.push_back(i->second);
381	+	}
382	+	}
383	+
384	+	return matchedNodes;
385	+	}
386	+
387	+	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
388	+	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
389	+	}
390	+
391	+
392	+	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){
393	+
394	+	SimInfo::MoleculeIterator mi;
395	+	Molecule* mol;
396	+
397	+	for (mol = info_->beginMolecule(mi); mol != NULL;
398	+	mol = info_->nextMolecule(mi)) {
399	+
400	+	if (isMatched(mol->getMoleculeName(), name) ) {
401	+	int natoms = mol->getNAtoms();
402	+	int nrigidbodies = mol->getNRigidBodies();
403	+	if (internalIndex >= natoms + nrigidbodies) {
404	+	continue;
405	+	} else if (internalIndex < natoms) {
406	+	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
407	+	continue;
408	+	} else if ( internalIndex < natoms + nrigidbodies) {
409	+	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
410	+	}
411	+	}
412	+	}
413	+	}
414	+
415	+	bool NameFinder::isInteger(const std::string &str) {
416	+	for(unsigned int i = 0; i < str.size(); ++i){
417	+	if (!std::isdigit(str[i])) {
418	+	return false;
419	+	}
420	+	}
421	+	return true;
422	+	}
423		}

Comparing trunk/src/selection/NameFinder.cpp (property svn:keywords):
Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 0 | Line 1
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