| 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. |
| 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, 24107 (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(){ |
| 49 |
> |
TreeNode::~TreeNode(){ |
| 50 |
|
std::map<std::string, TreeNode*>::iterator i; |
| 51 |
|
for ( i = children.begin(); i != children.end(); ++i) { |
| 52 |
< |
i->second->~TreeNode(); |
| 52 |
> |
i->second->~TreeNode(); |
| 53 |
|
} |
| 54 |
|
children.clear(); |
| 55 |
< |
} |
| 55 |
> |
} |
| 56 |
|
|
| 57 |
|
|
| 58 |
< |
NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
| 58 |
> |
NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
| 59 |
|
nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 60 |
|
loadNames(); |
| 61 |
< |
} |
| 61 |
> |
} |
| 62 |
|
|
| 63 |
|
|
| 64 |
< |
NameFinder::~NameFinder(){ |
| 64 |
> |
NameFinder::~NameFinder(){ |
| 65 |
|
delete root_; |
| 66 |
< |
} |
| 66 |
> |
} |
| 67 |
|
|
| 68 |
< |
void NameFinder::loadNames() { |
| 68 |
> |
void NameFinder::loadNames() { |
| 69 |
|
|
| 70 |
|
std::map<std::string, TreeNode*>::iterator foundIter; |
| 71 |
|
SimInfo::MoleculeIterator mi; |
| 81 |
|
|
| 82 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 83 |
|
|
| 84 |
< |
std::string molName = mol->getMoleculeName(); |
| 85 |
< |
TreeNode* currentMolNode = createNode(root_, molName); |
| 84 |
> |
std::string molName = mol->getMoleculeName(); |
| 85 |
> |
TreeNode* currentMolNode = createNode(root_, molName); |
| 86 |
|
|
| 87 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 88 |
< |
std::string atomName = atom->getType(); |
| 89 |
< |
TreeNode* currentAtomNode = createNode(currentMolNode, atomName); |
| 87 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 88 |
> |
std::string atomName = atom->getType(); |
| 89 |
> |
TreeNode* currentAtomNode = createNode(currentMolNode, atomName); |
| 90 |
|
|
| 91 |
< |
currentMolNode->bs.setBitOn(atom->getGlobalIndex()); |
| 92 |
< |
currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 93 |
< |
} |
| 91 |
> |
currentMolNode->bs.setBitOn(atom->getGlobalIndex()); |
| 92 |
> |
currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 93 |
> |
} |
| 94 |
|
|
| 95 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 96 |
< |
std::string rbName = rb->getType(); |
| 97 |
< |
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
| 95 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 96 |
> |
std::string rbName = rb->getType(); |
| 97 |
> |
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
| 98 |
|
|
| 99 |
< |
currentMolNode->bs.setBitOn(rb->getGlobalIndex()); |
| 100 |
< |
currentRbNode->bs.setBitOn(rb->getGlobalIndex()); |
| 99 |
> |
currentMolNode->bs.setBitOn(rb->getGlobalIndex()); |
| 100 |
> |
currentRbNode->bs.setBitOn(rb->getGlobalIndex()); |
| 101 |
|
|
| 102 |
< |
//create nodes for atoms belong to this rigidbody |
| 103 |
< |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 104 |
< |
std::string rbAtomName = atom->getType(); |
| 105 |
< |
TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);; |
| 102 |
> |
//create nodes for atoms belong to this rigidbody |
| 103 |
> |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 104 |
> |
std::string rbAtomName = atom->getType(); |
| 105 |
> |
TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);; |
| 106 |
|
|
| 107 |
< |
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 108 |
< |
} |
| 107 |
> |
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 108 |
> |
} |
| 109 |
|
|
| 110 |
< |
} |
| 110 |
> |
} |
| 111 |
|
|
| 112 |
|
} |
| 113 |
|
|
| 114 |
< |
} |
| 114 |
> |
} |
| 115 |
|
|
| 116 |
< |
TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
| 116 |
> |
TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
| 117 |
|
TreeNode* node; |
| 118 |
|
std::map<std::string, TreeNode*>::iterator foundIter; |
| 119 |
|
foundIter = parent->children.find(name); |
| 120 |
|
if ( foundIter == parent->children.end()) { |
| 121 |
< |
node = new TreeNode; |
| 122 |
< |
node->name = name; |
| 123 |
< |
node->bs.resize(nStuntDouble_); |
| 124 |
< |
parent->children.insert(std::make_pair(name, node)); |
| 121 |
> |
node = new TreeNode; |
| 122 |
> |
node->name = name; |
| 123 |
> |
node->bs.resize(nStuntDouble_); |
| 124 |
> |
parent->children.insert(std::make_pair(name, node)); |
| 125 |
|
}else { |
| 126 |
< |
node = foundIter->second; |
| 126 |
> |
node = foundIter->second; |
| 127 |
|
} |
| 128 |
|
return node; |
| 129 |
< |
} |
| 129 |
> |
} |
| 130 |
|
|
| 131 |
< |
BitSet NameFinder::match(const std::string& name){ |
| 132 |
< |
BitSet bs(nStuntDouble_); |
| 131 |
> |
OpenMDBitSet NameFinder::match(const std::string& name){ |
| 132 |
> |
OpenMDBitSet bs(nStuntDouble_); |
| 133 |
|
|
| 134 |
|
StringTokenizer tokenizer(name, "."); |
| 135 |
|
|
| 136 |
|
std::vector<std::string> names; |
| 137 |
|
while(tokenizer.hasMoreTokens()) { |
| 138 |
< |
names.push_back(tokenizer.nextToken()); |
| 138 |
> |
names.push_back(tokenizer.nextToken()); |
| 139 |
|
} |
| 140 |
|
|
| 141 |
|
int size = names.size(); |
| 142 |
|
switch(size) { |
| 143 |
< |
case 1 : |
| 144 |
< |
//could be molecule name, atom name and rigidbody name |
| 145 |
< |
matchMolecule(names[0], bs); |
| 146 |
< |
matchStuntDouble("*", names[0], bs); |
| 143 |
> |
case 1 : |
| 144 |
> |
//could be molecule name, atom name and rigidbody name |
| 145 |
> |
matchMolecule(names[0], bs); |
| 146 |
> |
matchStuntDouble("*", names[0], bs); |
| 147 |
|
|
| 148 |
< |
break; |
| 149 |
< |
case 2: |
| 150 |
< |
//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
| 148 |
> |
break; |
| 149 |
> |
case 2: |
| 150 |
> |
//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
| 151 |
|
|
| 152 |
< |
if (!isInteger(names[1])){ |
| 153 |
< |
matchRigidAtoms("*", names[0], names[1], bs); |
| 154 |
< |
matchStuntDouble(names[0], names[1], bs); |
| 155 |
< |
} else { |
| 156 |
< |
int internalIndex = lexi_cast<int>(names[1]); |
| 157 |
< |
if (internalIndex < 0) { |
| 158 |
< |
std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl; |
| 159 |
< |
} else { |
| 160 |
< |
matchInternalIndex(names[0], internalIndex, bs); |
| 161 |
< |
} |
| 162 |
< |
} |
| 152 |
> |
if (!isInteger(names[1])){ |
| 153 |
> |
matchRigidAtoms("*", names[0], names[1], bs); |
| 154 |
> |
matchStuntDouble(names[0], names[1], bs); |
| 155 |
> |
} else { |
| 156 |
> |
int internalIndex = lexi_cast<int>(names[1]); |
| 157 |
> |
if (internalIndex < 0) { |
| 158 |
> |
std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl; |
| 159 |
> |
} else { |
| 160 |
> |
matchInternalIndex(names[0], internalIndex, bs); |
| 161 |
> |
} |
| 162 |
> |
} |
| 163 |
|
|
| 164 |
< |
break; |
| 165 |
< |
case 3: |
| 166 |
< |
//must be molecule.rigidbody.* |
| 167 |
< |
matchRigidAtoms(names[0], names[1], names[2], bs); |
| 168 |
< |
break; |
| 169 |
< |
default: |
| 170 |
< |
std::cerr << "invalid name: " << name << std::endl; |
| 171 |
< |
break; |
| 164 |
> |
break; |
| 165 |
> |
case 3: |
| 166 |
> |
//must be molecule.rigidbody.* |
| 167 |
> |
matchRigidAtoms(names[0], names[1], names[2], bs); |
| 168 |
> |
break; |
| 169 |
> |
default: |
| 170 |
> |
std::cerr << "invalid name: " << name << std::endl; |
| 171 |
> |
break; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
|
return bs; |
| 175 |
< |
} |
| 175 |
> |
} |
| 176 |
|
|
| 177 |
< |
void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) { |
| 177 |
> |
void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) { |
| 178 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 179 |
|
std::vector<TreeNode*>::iterator i; |
| 180 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 181 |
< |
bs |= (*i)->bs; |
| 181 |
> |
bs |= (*i)->bs; |
| 182 |
|
} |
| 183 |
< |
} |
| 183 |
> |
} |
| 184 |
|
|
| 185 |
< |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){ |
| 185 |
> |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){ |
| 186 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 187 |
|
std::vector<TreeNode*>::iterator i; |
| 188 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 189 |
< |
std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName); |
| 190 |
< |
std::vector<TreeNode*>::iterator j; |
| 191 |
< |
for (j = sdNodes.begin(); j != sdNodes.end(); ++j) { |
| 192 |
< |
bs |= (*j)->bs; |
| 193 |
< |
} |
| 189 |
> |
std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName); |
| 190 |
> |
std::vector<TreeNode*>::iterator j; |
| 191 |
> |
for (j = sdNodes.begin(); j != sdNodes.end(); ++j) { |
| 192 |
> |
bs |= (*j)->bs; |
| 193 |
> |
} |
| 194 |
|
} |
| 195 |
|
|
| 196 |
< |
} |
| 196 |
> |
} |
| 197 |
|
|
| 198 |
< |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){ |
| 198 |
> |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){ |
| 199 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 200 |
|
std::vector<TreeNode*>::iterator i; |
| 201 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 202 |
< |
std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName); |
| 203 |
< |
std::vector<TreeNode*>::iterator j; |
| 204 |
< |
for (j = rbNodes.begin(); j != rbNodes.end(); ++j) { |
| 205 |
< |
std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
| 206 |
< |
std::vector<TreeNode*>::iterator k; |
| 207 |
< |
for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){ |
| 208 |
< |
bs |= (*k)->bs; |
| 209 |
< |
} |
| 210 |
< |
} |
| 202 |
> |
std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName); |
| 203 |
> |
std::vector<TreeNode*>::iterator j; |
| 204 |
> |
for (j = rbNodes.begin(); j != rbNodes.end(); ++j) { |
| 205 |
> |
std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
| 206 |
> |
std::vector<TreeNode*>::iterator k; |
| 207 |
> |
for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){ |
| 208 |
> |
bs |= (*k)->bs; |
| 209 |
> |
} |
| 210 |
> |
} |
| 211 |
|
} |
| 212 |
|
|
| 213 |
< |
} |
| 213 |
> |
} |
| 214 |
|
|
| 215 |
|
|
| 216 |
< |
std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) { |
| 216 |
> |
std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) { |
| 217 |
|
std::vector<TreeNode*> matchedNodes; |
| 218 |
|
std::map<std::string, TreeNode*>::iterator i; |
| 219 |
|
for (i = node->children.begin(); i != node->children.end(); ++i) { |
| 220 |
< |
if (isMatched( i->first, name)) { |
| 221 |
< |
matchedNodes.push_back(i->second); |
| 222 |
< |
} |
| 220 |
> |
if (isMatched( i->first, name)) { |
| 221 |
> |
matchedNodes.push_back(i->second); |
| 222 |
> |
} |
| 223 |
|
} |
| 224 |
|
|
| 225 |
|
return matchedNodes; |
| 226 |
< |
} |
| 226 |
> |
} |
| 227 |
|
|
| 228 |
< |
bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
| 228 |
> |
bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
| 229 |
|
return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); |
| 230 |
< |
} |
| 230 |
> |
} |
| 231 |
|
|
| 232 |
|
|
| 233 |
< |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){ |
| 233 |
> |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){ |
| 234 |
|
|
| 235 |
|
std::map<std::string, TreeNode*>::iterator foundIter; |
| 236 |
|
SimInfo::MoleculeIterator mi; |
| 238 |
|
|
| 239 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 240 |
|
|
| 241 |
< |
if (isMatched(mol->getMoleculeName(), name) ) { |
| 242 |
< |
int natoms = mol->getNAtoms(); |
| 243 |
< |
int nrigidbodies = mol->getNRigidBodies(); |
| 244 |
< |
if (internalIndex >= natoms + nrigidbodies) { |
| 245 |
< |
continue; |
| 246 |
< |
} else if (internalIndex < natoms) { |
| 247 |
< |
bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex()); |
| 248 |
< |
continue; |
| 249 |
< |
} else if ( internalIndex < natoms + nrigidbodies) { |
| 250 |
< |
bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
| 251 |
< |
} |
| 252 |
< |
} |
| 241 |
> |
if (isMatched(mol->getMoleculeName(), name) ) { |
| 242 |
> |
int natoms = mol->getNAtoms(); |
| 243 |
> |
int nrigidbodies = mol->getNRigidBodies(); |
| 244 |
> |
if (internalIndex >= natoms + nrigidbodies) { |
| 245 |
> |
continue; |
| 246 |
> |
} else if (internalIndex < natoms) { |
| 247 |
> |
bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex()); |
| 248 |
> |
continue; |
| 249 |
> |
} else if ( internalIndex < natoms + nrigidbodies) { |
| 250 |
> |
bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
| 251 |
> |
} |
| 252 |
> |
} |
| 253 |
|
|
| 254 |
|
} |
| 255 |
|
|
| 256 |
< |
} |
| 256 |
> |
} |
| 257 |
|
|
| 258 |
< |
bool NameFinder::isInteger(const std::string str) { |
| 258 |
> |
bool NameFinder::isInteger(const std::string str) { |
| 259 |
|
for(int i =0; i < str.size(); ++i){ |
| 260 |
< |
if (!std::isdigit(str[i])) { |
| 261 |
< |
return false; |
| 262 |
< |
} |
| 260 |
> |
if (!std::isdigit(str[i])) { |
| 261 |
> |
return false; |
| 262 |
> |
} |
| 263 |
|
} |
| 264 |
|
|
| 265 |
|
return true; |
| 266 |
< |
} |
| 266 |
> |
} |
| 267 |
|
|
| 268 |
|
} |
