ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/selection/NameFinder.cpp

Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 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		#include "utils/wildcards.hpp"
44		#include "utils/StringTokenizer.hpp"
45		#include "primitives/Molecule.hpp"
46		#include "utils/StringUtils.hpp"
47	<	namespace oopse {
47	>	namespace OpenMD {
48
49		TreeNode::~TreeNode(){
50		std::map<std::string, TreeNode*>::iterator i;
#	Line 53 | Line 54 | namespace oopse {
54		children.clear();
55		}
56
56	–
57		NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58	<	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
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	>	nObjects_.push_back(info_->getNGlobalMolecules());
64	>
65		loadNames();
66		}
67
62	–
68		NameFinder::~NameFinder(){
69		delete root_;
70		}
71
72		void NameFinder::loadNames() {
68	–
69	–	std::map<std::string, TreeNode*>::iterator foundIter;
73		SimInfo::MoleculeIterator mi;
71	–	Molecule* mol;
74		Molecule::AtomIterator ai;
73	–	Atom* atom;
75		Molecule::RigidBodyIterator rbIter;
76	+	Molecule::BondIterator bondIter;
77	+	Molecule::BendIterator bendIter;
78	+	Molecule::TorsionIterator torsionIter;
79	+	Molecule::InversionIterator inversionIter;
80	+
81	+	Molecule* mol;
82	+	Atom* atom;
83		RigidBody* rb;
84	+	Bond* bond;
85	+	Bend* bend;
86	+	Torsion* torsion;
87	+	Inversion* inversion;
88
89		root_ = new TreeNode;
90	<	root_->bs.resize(nStuntDouble_);
90	>	root_->bs.resize(nObjects_);
91		root_->bs.setAll(); //
92
93	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
93	>	for (mol = info_->beginMolecule(mi); mol != NULL;
94	>	mol = info_->nextMolecule(mi)) {
95
96		std::string molName = mol->getMoleculeName();
97	<	TreeNode* currentMolNode = createNode(root_, molName);
97	>	TreeNode* molNode = createNode(root_, molName);
98	>	molNode->bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
99
100		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
101		std::string atomName = atom->getType();
102	<	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
102	>	TreeNode* atomNode = createNode(molNode, atomName);
103
104	<	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
105	<	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
104	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
105	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
106		}
107
108	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
108	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
109	>	rb = mol->nextRigidBody(rbIter)) {
110		std::string rbName = rb->getType();
111	<	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
111	>	TreeNode* rbNode = createNode(molNode, rbName);
112
113	<	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
114	<	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
113	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
114	>	rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
115
116	<	//create nodes for atoms belong to this rigidbody
117	<	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
118	<	std::string rbAtomName = atom->getType();
119	<	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
116	>	// COMMENTED OUT because rigid bodies are IntegrableObjects
117	>	// (e.g. they are independently mobile, so selecting their
118	>	// member atoms will give some odd results if we are computing
119	>	// degrees of freedom elsewhere.
120
121	<	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
122	<	}
121	>	// //create nodes for atoms belong to this rigidbody
122	>	// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
123	>	//   std::string rbAtomName = atom->getType();
124	>	//   TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
125
126	+	//   rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
127	+	// }
128		}
129	+
130	+	for (bond = mol->beginBond(bondIter); bond != NULL;
131	+	bond = mol->nextBond(bondIter)) {
132	+
133	+	std::string bondName = bond->getName();
134	+	TreeNode* bondNode = createNode(molNode, bondName);
135	+
136	+	molNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
137	+	bondNode->bs.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
138	+
139	+	std::vector<Atom*> atoms = bond->getAtoms();
140	+	std::vector<Atom*>::iterator ai;
141
142	<	}
142	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
143	>	std::string atomName = (*ai)->getType();
144	>	TreeNode* atomNode = createNode(bondNode, atomName);
145	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
146	>	}
147	>	}
148	>	for (bend = mol->beginBend(bendIter); bend != NULL;
149	>	bend = mol->nextBend(bendIter)) {
150	>
151	>	std::string bendName = bend->getName();
152	>	TreeNode* bendNode = createNode(molNode, bendName);
153	>
154	>	molNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
155	>	bendNode->bs.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
156	>
157	>	std::vector<Atom*> atoms = bend->getAtoms();
158	>	std::vector<Atom*>::iterator ai;
159	>
160	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
161	>	std::string atomName = (*ai)->getType();
162	>	TreeNode* atomNode = createNode(bendNode, atomName);
163	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
164	>	}
165	>
166	>	}
167	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	>	torsion = mol->nextTorsion(torsionIter)) {
169	>
170	>	std::string torsionName = torsion->getName();
171	>	TreeNode* torsionNode = createNode(molNode, torsionName);
172	>
173	>	molNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
174	>	torsionNode->bs.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
175	>
176	>	std::vector<Atom*> atoms = torsion->getAtoms();
177	>	std::vector<Atom*>::iterator ai;
178	>
179	>	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
180	>	std::string atomName = (*ai)->getType();
181	>	TreeNode* atomNode = createNode(torsionNode, atomName);
182	>	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
183	>	}
184
185	+	}
186	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
187	+	inversion = mol->nextInversion(inversionIter)) {
188	+
189	+	std::string inversionName = inversion->getName();
190	+	TreeNode* inversionNode = createNode(molNode, inversionName);
191	+
192	+	molNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
193	+	inversionNode->bs.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
194	+	std::vector<Atom*> atoms = inversion->getAtoms();
195	+	std::vector<Atom*>::iterator ai;
196	+
197	+	for (ai = atoms.begin(); ai != atoms.end(); ++ai) {
198	+	std::string atomName = (*ai)->getType();
199	+	TreeNode* atomNode = createNode(inversionNode, atomName);
200	+	atomNode->bs.bitsets_[STUNTDOUBLE].setBitOn((*ai)->getGlobalIndex());
201	+	}
202	+	}
203	+	}
204		}
205
206		TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
#	Line 119 | Line 210 | namespace oopse {
210		if ( foundIter  == parent->children.end()) {
211		node = new TreeNode;
212		node->name = name;
213	<	node->bs.resize(nStuntDouble_);
213	>	node->bs.resize(nObjects_);
214		parent->children.insert(std::make_pair(name, node));
215		}else {
216		node = foundIter->second;
#	Line 127 | Line 218 | namespace oopse {
218		return node;
219		}
220
221	<	OOPSEBitSet NameFinder::match(const std::string& name){
222	<	OOPSEBitSet bs(nStuntDouble_);
221	>	SelectionSet NameFinder::match(const std::string& name){
222	>	SelectionSet bs(nObjects_);
223
224		StringTokenizer tokenizer(name, ".");
225
#	Line 138 | Line 229 | namespace oopse {
229		}
230
231		int size = names.size();
232	+
233		switch(size) {
234		case 1 :
235		//could be molecule name, atom name and rigidbody name
236		matchMolecule(names[0], bs);
237		matchStuntDouble("*", names[0], bs);
238	+	matchBond("*", names[0], bs);
239	+	matchBend("*", names[0], bs);
240	+	matchTorsion("*", names[0], bs);
241	+	matchInversion("*", names[0], bs);
242
243		break;
244		case 2:
#	Line 173 | Line 269 | namespace oopse {
269		return bs;
270		}
271
272	<	void NameFinder::matchMolecule(const std::string& molName, OOPSEBitSet& bs) {
272	>	void NameFinder::matchMolecule(const std::string& molName, 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 ) {
#	Line 181 | Line 277 | namespace oopse {
277		}
278		}
279
280	<	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OOPSEBitSet& bs){
280	>	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, SelectionSet& bs){
281		std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
282		std::vector<TreeNode*>::iterator i;
283		for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
#	Line 194 | Line 290 | namespace oopse {
290
291		}
292
293	<	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OOPSEBitSet& bs){
293	>	void NameFinder::matchBond(const std::string& molName,
294	>	const std::string& bondName, SelectionSet& bs){
295		std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
296		std::vector<TreeNode*>::iterator i;
297		for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
298	+	std::vector<TreeNode*> bondNodes = getMatchedChildren(*i, bondName);
299	+	std::vector<TreeNode*>::iterator j;
300	+	for (j = bondNodes.begin(); j != bondNodes.end(); ++j) {
301	+	bs |= (*j)->bs;
302	+	std::vector<TreeNode*> bondAtomNodes = getAllChildren(*j);
303	+	std::vector<TreeNode*>::iterator k;
304	+	for(k = bondAtomNodes.begin(); k != bondAtomNodes.end(); ++k){
305	+	bs |= (*k)->bs;
306	+	}
307	+	}
308	+	}
309	+	}
310	+
311	+	void NameFinder::matchBend(const std::string& molName, const std::string& bendName,  SelectionSet& bs){
312	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
313	+	std::vector<TreeNode*>::iterator i;
314	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
315	+	std::vector<TreeNode*> bendNodes = getMatchedChildren(*i, bendName);
316	+	std::vector<TreeNode*>::iterator j;
317	+	for (j = bendNodes.begin(); j != bendNodes.end(); ++j) {
318	+	std::vector<TreeNode*> bendAtomNodes = getAllChildren(*j);
319	+	std::vector<TreeNode*>::iterator k;
320	+	for(k = bendAtomNodes.begin(); k != bendAtomNodes.end(); ++k){
321	+	bs |= (*k)->bs;
322	+	}
323	+	}
324	+	}
325	+	}
326	+	void NameFinder::matchTorsion(const std::string& molName, const std::string& torsionName, SelectionSet& bs){
327	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
328	+	std::vector<TreeNode*>::iterator i;
329	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
330	+	std::vector<TreeNode*> torsionNodes = getMatchedChildren(*i, torsionName);
331	+	std::vector<TreeNode*>::iterator j;
332	+	for (j = torsionNodes.begin(); j != torsionNodes.end(); ++j) {
333	+	std::vector<TreeNode*> torsionAtomNodes = getAllChildren(*j);
334	+	std::vector<TreeNode*>::iterator k;
335	+	for(k = torsionAtomNodes.begin(); k != torsionAtomNodes.end(); ++k){
336	+	bs |= (*k)->bs;
337	+	}
338	+	}
339	+	}
340	+	}
341	+	void NameFinder::matchInversion(const std::string& molName, const std::string& inversionName, SelectionSet& bs){
342	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
343	+	std::vector<TreeNode*>::iterator i;
344	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
345	+	std::vector<TreeNode*> inversionNodes = getMatchedChildren(*i, inversionName);
346	+	std::vector<TreeNode*>::iterator j;
347	+	for (j = inversionNodes.begin(); j != inversionNodes.end(); ++j) {
348	+	std::vector<TreeNode*> inversionAtomNodes = getAllChildren(*j);
349	+	std::vector<TreeNode*>::iterator k;
350	+	for(k = inversionAtomNodes.begin(); k != inversionAtomNodes.end(); ++k){
351	+	bs |= (*k)->bs;
352	+	}
353	+	}
354	+	}
355	+	}
356	+
357	+	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, SelectionSet& bs){
358	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
359	+	std::vector<TreeNode*>::iterator i;
360	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
361		std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);
362		std::vector<TreeNode*>::iterator j;
363		for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
#	Line 211 | Line 371 | namespace oopse {
371
372		}
373
374	+	std::vector<TreeNode*> NameFinder::getAllChildren(TreeNode* node)  {
375	+	std::vector<TreeNode*> childNodes;
376	+	std::map<std::string, TreeNode*>::iterator i;
377	+	for (i = node->children.begin(); i != node->children.end(); ++i) {
378	+	childNodes.push_back(i->second);
379	+	}
380	+	return childNodes;
381	+	}
382
383		std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
384		std::vector<TreeNode*> matchedNodes;
#	Line 225 | Line 393 | namespace oopse {
393		}
394
395		bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
396	<	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
396	>	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
397		}
398
399
400	<	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OOPSEBitSet& bs){
400	>	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, SelectionSet& bs){
401
234	–	std::map<std::string, TreeNode*>::iterator foundIter;
402		SimInfo::MoleculeIterator mi;
403		Molecule* mol;
404
405	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
405	>	for (mol = info_->beginMolecule(mi); mol != NULL;
406	>	mol = info_->nextMolecule(mi)) {
407
408		if (isMatched(mol->getMoleculeName(), name) ) {
409		int natoms = mol->getNAtoms();
#	Line 243 | Line 411 | namespace oopse {
411		if (internalIndex >= natoms + nrigidbodies) {
412		continue;
413		} else if (internalIndex < natoms) {
414	<	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
414	>	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
415		continue;
416		} else if ( internalIndex < natoms + nrigidbodies) {
417	<	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
417	>	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
418		}
419		}
420	<
253	<	}
254	<
420	>	}
421		}
422
423	<	bool NameFinder::isInteger(const std::string str) {
424	<	for(int i =0; i < str.size(); ++i){
423	>	bool NameFinder::isInteger(const std::string &str) {
424	>	for(unsigned int i = 0; i < str.size(); ++i){
425		if (!std::isdigit(str[i])) {
426		return false;
427		}
428		}
263	–
429		return true;
430		}
266	–
431		}

Comparing trunk/src/selection/NameFinder.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines