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root/OpenMD/branches/development/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.
branches/development/src/selection/NameFinder.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 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	>	nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59		loadNames();
60	<	}
60	>	}
61
62	+	NameFinder::~NameFinder(){
63	+	delete root_;
64	+	}
65
66	+	void NameFinder::loadNames() {
67
50	–	void NameFinder::loadNames() {
51	–
52	–	root_ = new NameNode;
53	–	root_.type = rootNode;
54	–
55	–	NameNode* newNode;
68		SimInfo::MoleculeIterator mi;
69		Molecule* mol;
70		Molecule::AtomIterator ai;
71		Atom* atom;
72		Molecule::RigidBodyIterator rbIter;
73		RigidBody* rb;
74	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
75	<	newNode = new NameNode;
76	<	newNode.type = molNode;
77	<	newNode.name = mol->getMoleculeName();
74	>
75	>	root_ = new TreeNode;
76	>	root_->bs.resize(nStuntDouble_);
77	>	root_->bs.setAll(); //
78	>
79	>	for (mol = info_->beginMolecule(mi); mol != NULL;
80	>	mol = info_->nextMolecule(mi)) {
81	>
82	>	std::string molName = mol->getMoleculeName();
83	>	TreeNode* currentMolNode = createNode(root_, molName);
84
85	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86	<	atomNames_.insert(atom->getType());
87	<	}
88	<
89	<	//change the positions of atoms which belong to the rigidbodies
90	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
91	<	rbNames_.insert(rb->getType());
74	<	}
75	<	}
76	<	}
85	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86	>	std::string atomName = atom->getType();
87	>	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
88	>
89	>	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
90	>	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
91	>	}
92
93	<	bool NameFinder::match(const std::string& name, BitSet& bs){
93	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
94	>	rb = mol->nextRigidBody(rbIter)) {
95	>	std::string rbName = rb->getType();
96	>	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
97	>
98	>	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
99	>	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
100
101	<	bool error = true;
101	>	//create nodes for atoms belong to this rigidbody
102	>	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
103	>	std::string rbAtomName = atom->getType();
104	>	TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
105	>
106	>	currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
107	>	}
108	>	}
109	>	}
110	>	}
111	>
112	>	TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
113	>	TreeNode* node;
114	>	std::map<std::string, TreeNode*>::iterator foundIter;
115	>	foundIter = parent->children.find(name);
116	>	if ( foundIter  == parent->children.end()) {
117	>	node = new TreeNode;
118	>	node->name = name;
119	>	node->bs.resize(nStuntDouble_);
120	>	parent->children.insert(std::make_pair(name, node));
121	>	}else {
122	>	node = foundIter->second;
123	>	}
124	>	return node;
125	>	}
126	>
127	>	OpenMDBitSet NameFinder::match(const std::string& name){
128	>	OpenMDBitSet bs(nStuntDouble_);
129	>
130		StringTokenizer tokenizer(name, ".");
131
132		std::vector<std::string> names;
133		while(tokenizer.hasMoreTokens()) {
134	<	names.push_back(tokenizer.nextToken());
134	>	names.push_back(tokenizer.nextToken());
135		}
136
137		int size = names.size();
138		switch(size) {
139	<	case 1 :
140	<	//could be molecule name, atom name, rigidbody name
141	<	isMolName();
142	<	isAtomName();
94	<	isRigidBodyName();
95	<	break;
96	<	case 2:
97	<	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*
98	<	break;
99	<	case 3:
100	<	//must be molecule.rigidbody.*
139	>	case 1 :
140	>	//could be molecule name, atom name and rigidbody name
141	>	matchMolecule(names[0], bs);
142	>	matchStuntDouble("*", names[0], bs);
143
144	<	break;
145	<	default:
146	<	break;
144	>	break;
145	>	case 2:
146	>	//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
147	>
148	>	if (!isInteger(names[1])){
149	>	matchRigidAtoms("*", names[0], names[1], bs);
150	>	matchStuntDouble(names[0], names[1], bs);
151	>	} else {
152	>	int internalIndex = lexi_cast<int>(names[1]);
153	>	if (internalIndex < 0) {
154	>	std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;
155	>	} else {
156	>	matchInternalIndex(names[0], internalIndex, bs);
157	>	}
158	>	}
159	>
160	>	break;
161	>	case 3:
162	>	//must be molecule.rigidbody.*
163	>	matchRigidAtoms(names[0], names[1], names[2], bs);
164	>	break;
165	>	default:
166	>	std::cerr << "invalid name: " << name << std::endl;
167	>	break;
168		}
169
170	<	return matched;
171	<	}
170	>	return bs;
171	>	}
172
173	+	void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) {
174	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
175	+	std::vector<TreeNode*>::iterator i;
176	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
177	+	bs |= (*i)->bs;
178	+	}
179	+	}
180	+
181	+	void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){
182	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
183	+	std::vector<TreeNode*>::iterator i;
184	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
185	+	std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);
186	+	std::vector<TreeNode*>::iterator j;
187	+	for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
188	+	bs |= (*j)->bs;
189	+	}
190	+	}
191	+
192	+	}
193	+
194	+	void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){
195	+	std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);
196	+	std::vector<TreeNode*>::iterator i;
197	+	for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
198	+	std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);
199	+	std::vector<TreeNode*>::iterator j;
200	+	for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
201	+	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
202	+	std::vector<TreeNode*>::iterator k;
203	+	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
204	+	bs |= (*k)->bs;
205	+	}
206	+	}
207	+	}
208	+
209	+	}
210	+
211	+
212	+	std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
213	+	std::vector<TreeNode*> matchedNodes;
214	+	std::map<std::string, TreeNode*>::iterator i;
215	+	for (i = node->children.begin(); i != node->children.end(); ++i) {
216	+	if (isMatched( i->first, name)) {
217	+	matchedNodes.push_back(i->second);
218	+	}
219	+	}
220	+
221	+	return matchedNodes;
222	+	}
223	+
224	+	bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
225	+	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
226	+	}
227	+
228	+
229	+	void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){
230	+
231	+	SimInfo::MoleculeIterator mi;
232	+	Molecule* mol;
233	+
234	+	for (mol = info_->beginMolecule(mi); mol != NULL;
235	+	mol = info_->nextMolecule(mi)) {
236	+
237	+	if (isMatched(mol->getMoleculeName(), name) ) {
238	+	int natoms = mol->getNAtoms();
239	+	int nrigidbodies = mol->getNRigidBodies();
240	+	if (internalIndex >= natoms + nrigidbodies) {
241	+	continue;
242	+	} else if (internalIndex < natoms) {
243	+	bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
244	+	continue;
245	+	} else if ( internalIndex < natoms + nrigidbodies) {
246	+	bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
247	+	}
248	+	}
249	+	}
250	+	}
251	+
252	+	bool NameFinder::isInteger(const std::string &str) {
253	+	for(unsigned int i = 0; i < str.size(); ++i){
254	+	if (!std::isdigit(str[i])) {
255	+	return false;
256	+	}
257	+	}
258	+	return true;
259	+	}
260		}

Comparing:
trunk/src/selection/NameFinder.cpp (property svn:keywords), Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC vs.
branches/development/src/selection/NameFinder.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 0 | Line 1
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