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 283 by tim, Thu Feb 3 23:14:05 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	<	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	>	nObjects_.push_back(info_->getNGlobalMolecules());
64	>
65		loadNames();
66	<	}
66	>	}
67
68	+	NameFinder::~NameFinder(){
69	+	delete root_;
70	+	}
71
72	<
50	<	void NameFinder::loadNames() {
51	<
52	<	root_ = new NameNode;
53	<	root_.type = rootNode;
54	<
55	<	NameNode* newNode;
72	>	void NameFinder::loadNames() {
73		SimInfo::MoleculeIterator mi;
57	–	Molecule* mol;
74		Molecule::AtomIterator ai;
59	–	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	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
85	<	newNode = new NameNode;
86	<	newNode.type = molNode;
87	<	newNode.name = mol->getMoleculeName();
84	>	Bond* bond;
85	>	Bend* bend;
86	>	Torsion* torsion;
87	>	Inversion* inversion;
88	>
89	>	root_ = new TreeNode;
90	>	root_->bs.resize(nObjects_);
91	>	root_->bs.setAll(); //
92	>
93	>	for (mol = info_->beginMolecule(mi); mol != NULL;
94	>	mol = info_->nextMolecule(mi)) {
95	>
96	>	std::string molName = mol->getMoleculeName();
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	<	atomNames_.insert(atom->getType());
100	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
101	>	std::string atomName = atom->getType();
102	>	TreeNode* atomNode = createNode(molNode, atomName);
103	>
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;
109	>	rb = mol->nextRigidBody(rbIter)) {
110	>	std::string rbName = rb->getType();
111	>	TreeNode* rbNode = createNode(molNode, rbName);
112	>
113	>	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
114	>	rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
115	>
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	>	// //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	>	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	<	//change the positions of atoms which belong to the rigidbodies
161	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
162	<	rbNames_.insert(rb->getType());
163	<	}
164	<	}
76	<	}
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	<	bool NameFinder::match(const std::string& name, BitSet& bs){
166	>	}
167	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	>	torsion = mol->nextTorsion(torsionIter)) {
169
170	<	bool error = true;
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) {
207	>	TreeNode* node;
208	>	std::map<std::string, TreeNode*>::iterator foundIter;
209	>	foundIter = parent->children.find(name);
210	>	if ( foundIter  == parent->children.end()) {
211	>	node = new TreeNode;
212	>	node->name = name;
213	>	node->bs.resize(nObjects_);
214	>	parent->children.insert(std::make_pair(name, node));
215	>	}else {
216	>	node = foundIter->second;
217	>	}
218	>	return node;
219	>	}
220	>
221	>	SelectionSet NameFinder::match(const std::string& name){
222	>	SelectionSet bs(nObjects_);
223	>
224		StringTokenizer tokenizer(name, ".");
225
226		std::vector<std::string> names;
227		while(tokenizer.hasMoreTokens()) {
228	<	names.push_back(tokenizer.nextToken());
228	>	names.push_back(tokenizer.nextToken());
229		}
230
231		int size = names.size();
232	+
233		switch(size) {
234	<	case 1 :
235	<	//could be molecule name, atom name, rigidbody name
236	<	isMolName();
237	<	isAtomName();
238	<	isRigidBodyName();
239	<	break;
240	<	case 2:
241	<	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*
98	<	break;
99	<	case 3:
100	<	//must be molecule.rigidbody.*
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	<	default:
245	<	break;
243	>	break;
244	>	case 2:
245	>	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
246	>
247	>	if (!isInteger(names[1])){
248	>	matchRigidAtoms("*", names[0], names[1], bs);
249	>	matchStuntDouble(names[0], names[1], bs);
250	>	} else {
251	>	int internalIndex = lexi_cast<int>(names[1]);
252	>	if (internalIndex < 0) {
253	>	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
254	>	} else {
255	>	matchInternalIndex(names[0], internalIndex, bs);
256	>	}
257	>	}
258	>
259	>	break;
260	>	case 3:
261	>	//must be molecule.rigidbody.*
262	>	matchRigidAtoms(names[0], names[1], names[2], bs);
263	>	break;
264	>	default:
265	>	std::cerr << "invalid name: " << name << std::endl;
266	>	break;
267		}
268
269	<	return matched;
270	<	}
269	>	return bs;
270	>	}
271
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 ) {
276	+	bs |= (*i)->bs;
277	+	}
278	+	}
279	+
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 ) {
284	+	std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);
285	+	std::vector<TreeNode*>::iterator j;
286	+	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
287	+	bs |= (*j)->bs;
288	+	}
289	+	}
290	+
291	+	}
292	+
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) {
364	+	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
365	+	std::vector<TreeNode*>::iterator k;
366	+	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
367	+	bs |= (*k)->bs;
368	+	}
369	+	}
370	+	}
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;
385	+	std::map<std::string, TreeNode*>::iterator i;
386	+	for (i = node->children.begin(); i != node->children.end(); ++i) {
387	+	if (isMatched( i->first, name)) {
388	+	matchedNodes.push_back(i->second);
389	+	}
390	+	}
391	+
392	+	return matchedNodes;
393	+	}
394	+
395	+	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
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, SelectionSet& bs){
401	+
402	+	SimInfo::MoleculeIterator mi;
403	+	Molecule* mol;
404	+
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();
410	+	int nrigidbodies = mol->getNRigidBodies();
411	+	if (internalIndex >= natoms + nrigidbodies) {
412	+	continue;
413	+	} else if (internalIndex < natoms) {
414	+	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
415	+	continue;
416	+	} else if ( internalIndex < natoms + nrigidbodies) {
417	+	bs.bitsets_[STUNTDOUBLE].setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
418	+	}
419	+	}
420	+	}
421	+	}
422	+
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	+	}
429	+	return true;
430	+	}
431		}

Comparing trunk/src/selection/NameFinder.cpp (property svn:keywords):
Revision 283 by tim, Thu Feb 3 23:14:05 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