| 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 |
|
|
| 43 |
|
#include <stack> |
| 46 |
|
#include "primitives/DirectionalAtom.hpp" |
| 47 |
|
#include "primitives/RigidBody.hpp" |
| 48 |
|
#include "primitives/Molecule.hpp" |
| 49 |
+ |
#include "io/ifstrstream.hpp" |
| 50 |
|
|
| 51 |
< |
namespace oopse { |
| 51 |
> |
namespace OpenMD { |
| 52 |
|
|
| 53 |
|
|
| 54 |
|
SelectionEvaluator::SelectionEvaluator(SimInfo* si) |
| 55 |
< |
: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){ |
| 56 |
< |
|
| 57 |
< |
nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies(); |
| 55 |
> |
: info(si), nameFinder(info), distanceFinder(info), hullFinder(info), |
| 56 |
> |
indexFinder(info), |
| 57 |
> |
isLoaded_(false){ |
| 58 |
> |
nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies(); |
| 59 |
|
} |
| 60 |
|
|
| 61 |
< |
bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) { |
| 61 |
> |
bool SelectionEvaluator::loadScript(const std::string& filename, |
| 62 |
> |
const std::string& script) { |
| 63 |
|
clearDefinitionsAndLoadPredefined(); |
| 64 |
|
this->filename = filename; |
| 65 |
|
this->script = script; |
| 66 |
|
if (! compiler.compile(filename, script)) { |
| 67 |
|
error = true; |
| 68 |
|
errorMessage = compiler.getErrorMessage(); |
| 69 |
< |
std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl; |
| 69 |
> |
|
| 70 |
> |
sprintf( painCave.errMsg, |
| 71 |
> |
"SelectionCompiler Error: %s\n", errorMessage.c_str()); |
| 72 |
> |
painCave.severity = OPENMD_ERROR; |
| 73 |
> |
painCave.isFatal = 1; |
| 74 |
> |
simError(); |
| 75 |
|
return false; |
| 76 |
|
} |
| 77 |
|
|
| 109 |
|
return loadScriptFileInternal(filename); |
| 110 |
|
} |
| 111 |
|
|
| 112 |
< |
bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
| 113 |
< |
std::ifstream ifs(filename.c_str()); |
| 112 |
> |
bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
| 113 |
> |
ifstrstream ifs(filename.c_str()); |
| 114 |
|
if (!ifs.is_open()) { |
| 115 |
|
return false; |
| 116 |
|
} |
| 117 |
< |
|
| 117 |
> |
|
| 118 |
|
const int bufferSize = 65535; |
| 119 |
|
char buffer[bufferSize]; |
| 120 |
|
std::string script; |
| 123 |
|
} |
| 124 |
|
return loadScript(filename, script); |
| 125 |
|
} |
| 126 |
< |
|
| 127 |
< |
void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){ |
| 126 |
> |
|
| 127 |
> |
void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){ |
| 128 |
|
|
| 129 |
|
while ( pc < aatoken.size()) { |
| 130 |
|
statement = aatoken[pc++]; |
| 145 |
|
|
| 146 |
|
} |
| 147 |
|
|
| 148 |
< |
BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) { |
| 149 |
< |
BitSet bs; |
| 150 |
< |
std::stack<BitSet> stack; |
| 151 |
< |
|
| 152 |
< |
for (int pc = pcStart; pc < code.size(); ++pc) { |
| 148 |
> |
OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code, |
| 149 |
> |
int pcStart) { |
| 150 |
> |
OpenMDBitSet bs; |
| 151 |
> |
std::stack<OpenMDBitSet> stack; |
| 152 |
> |
|
| 153 |
> |
for (unsigned int pc = pcStart; pc < code.size(); ++pc) { |
| 154 |
|
Token instruction = code[pc]; |
| 155 |
|
|
| 156 |
|
switch (instruction.tok) { |
| 159 |
|
case Token::expressionEnd: |
| 160 |
|
break; |
| 161 |
|
case Token::all: |
| 162 |
< |
bs = BitSet(nStuntDouble); |
| 153 |
< |
bs.setAll(); |
| 162 |
> |
bs = allInstruction(); |
| 163 |
|
stack.push(bs); |
| 164 |
|
break; |
| 165 |
|
case Token::none: |
| 166 |
< |
bs = BitSet(nStuntDouble); |
| 166 |
> |
bs = OpenMDBitSet(nStuntDouble); |
| 167 |
|
stack.push(bs); |
| 168 |
|
break; |
| 169 |
|
case Token::opOr: |
| 180 |
|
stack.top().flip(); |
| 181 |
|
break; |
| 182 |
|
case Token::within: |
| 174 |
– |
|
| 183 |
|
withinInstruction(instruction, stack.top()); |
| 184 |
|
break; |
| 185 |
+ |
case Token::hull: |
| 186 |
+ |
stack.push(hull()); |
| 187 |
+ |
break; |
| 188 |
|
//case Token::selected: |
| 189 |
|
// stack.push(getSelectionSet()); |
| 190 |
|
// break; |
| 217 |
|
|
| 218 |
|
|
| 219 |
|
|
| 220 |
< |
BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 220 |
> |
OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 221 |
|
int comparator = instruction.tok; |
| 222 |
|
int property = instruction.intValue; |
| 223 |
|
float comparisonValue = boost::any_cast<float>(instruction.value); |
| 224 |
< |
float propertyValue; |
| 214 |
< |
BitSet bs(nStuntDouble); |
| 224 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 225 |
|
bs.clearAll(); |
| 226 |
|
|
| 227 |
|
SimInfo::MoleculeIterator mi; |
| 230 |
|
Atom* atom; |
| 231 |
|
Molecule::RigidBodyIterator rbIter; |
| 232 |
|
RigidBody* rb; |
| 223 |
– |
|
| 224 |
– |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 233 |
|
|
| 234 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 235 |
+ |
mol = info->nextMolecule(mi)) { |
| 236 |
+ |
|
| 237 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 238 |
|
compareProperty(atom, bs, property, comparator, comparisonValue); |
| 239 |
|
} |
| 240 |
< |
|
| 241 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 242 |
< |
compareProperty(rb, bs, property, comparator, comparisonValue); |
| 243 |
< |
} |
| 240 |
> |
|
| 241 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 242 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 243 |
> |
compareProperty(rb, bs, property, comparator, comparisonValue); |
| 244 |
> |
} |
| 245 |
|
} |
| 246 |
|
|
| 247 |
|
return bs; |
| 248 |
|
} |
| 249 |
|
|
| 250 |
< |
void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) { |
| 251 |
< |
double propertyValue = 0.0; |
| 250 |
> |
void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, |
| 251 |
> |
int property, int comparator, |
| 252 |
> |
float comparisonValue) { |
| 253 |
> |
RealType propertyValue = 0.0; |
| 254 |
|
switch (property) { |
| 255 |
|
case Token::mass: |
| 256 |
|
propertyValue = sd->getMass(); |
| 267 |
|
propertyValue+= getCharge(atom); |
| 268 |
|
} |
| 269 |
|
} |
| 270 |
+ |
break; |
| 271 |
+ |
case Token::x: |
| 272 |
+ |
propertyValue = sd->getPos().x(); |
| 273 |
+ |
break; |
| 274 |
+ |
case Token::y: |
| 275 |
+ |
propertyValue = sd->getPos().y(); |
| 276 |
+ |
break; |
| 277 |
+ |
case Token::z: |
| 278 |
+ |
propertyValue = sd->getPos().z(); |
| 279 |
+ |
break; |
| 280 |
+ |
case Token::r: |
| 281 |
+ |
propertyValue = sd->getPos().length(); |
| 282 |
|
break; |
| 283 |
|
default: |
| 284 |
|
unrecognizedAtomProperty(property); |
| 307 |
|
} |
| 308 |
|
if (match) |
| 309 |
|
bs.setBitOn(sd->getGlobalIndex()); |
| 310 |
< |
|
| 310 |
> |
|
| 311 |
|
} |
| 312 |
|
|
| 313 |
< |
void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){ |
| 313 |
> |
void SelectionEvaluator::withinInstruction(const Token& instruction, |
| 314 |
> |
OpenMDBitSet& bs){ |
| 315 |
|
|
| 316 |
|
boost::any withinSpec = instruction.value; |
| 317 |
|
float distance; |
| 326 |
|
|
| 327 |
|
bs = distanceFinder.find(bs, distance); |
| 328 |
|
} |
| 329 |
< |
|
| 329 |
> |
|
| 330 |
|
void SelectionEvaluator::define() { |
| 331 |
|
assert(statement.size() >= 3); |
| 332 |
< |
|
| 332 |
> |
|
| 333 |
|
std::string variable = boost::any_cast<std::string>(statement[1].value); |
| 334 |
< |
|
| 335 |
< |
variables.insert(VariablesType::value_type(variable, expression(statement, 2))); |
| 334 |
> |
|
| 335 |
> |
variables.insert(VariablesType::value_type(variable, |
| 336 |
> |
expression(statement, 2))); |
| 337 |
|
} |
| 338 |
+ |
|
| 339 |
|
|
| 311 |
– |
|
| 340 |
|
/** @todo */ |
| 341 |
|
void SelectionEvaluator::predefine(const std::string& script) { |
| 342 |
< |
|
| 342 |
> |
|
| 343 |
|
if (compiler.compile("#predefine", script)) { |
| 344 |
|
std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled(); |
| 345 |
|
if (aatoken.size() != 1) { |
| 350 |
|
std::vector<Token> statement = aatoken[0]; |
| 351 |
|
if (statement.size() > 2) { |
| 352 |
|
int tok = statement[1].tok; |
| 353 |
< |
if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) { |
| 353 |
> |
if (tok == Token::identifier || |
| 354 |
> |
(tok & Token::predefinedset) == Token::predefinedset) { |
| 355 |
|
std::string variable = boost::any_cast<std::string>(statement[1].value); |
| 356 |
|
variables.insert(VariablesType::value_type(variable, statement)); |
| 357 |
< |
|
| 357 |
> |
|
| 358 |
|
} else { |
| 359 |
|
evalError("invalid variable name:" + script); |
| 360 |
|
} |
| 361 |
|
}else { |
| 362 |
|
evalError("bad predefinition length:" + script); |
| 363 |
< |
} |
| 335 |
< |
|
| 363 |
> |
} |
| 364 |
|
|
| 365 |
|
} else { |
| 366 |
|
evalError("predefined set compile error:" + script + |
| 367 |
|
"\ncompile error:" + compiler.getErrorMessage()); |
| 368 |
|
} |
| 341 |
– |
|
| 369 |
|
} |
| 370 |
|
|
| 371 |
< |
void SelectionEvaluator::select(BitSet& bs){ |
| 371 |
> |
void SelectionEvaluator::select(OpenMDBitSet& bs){ |
| 372 |
|
bs = expression(statement, 1); |
| 373 |
|
} |
| 374 |
< |
|
| 375 |
< |
BitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 376 |
< |
|
| 377 |
< |
BitSet bs(nStuntDouble); |
| 374 |
> |
|
| 375 |
> |
OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 376 |
> |
|
| 377 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 378 |
|
std::map<std::string, boost::any>::iterator i = variables.find(variable); |
| 379 |
|
|
| 380 |
|
if (i != variables.end()) { |
| 381 |
< |
if (i->second.type() == typeid(BitSet)) { |
| 382 |
< |
return boost::any_cast<BitSet>(i->second); |
| 381 |
> |
if (i->second.type() == typeid(OpenMDBitSet)) { |
| 382 |
> |
return boost::any_cast<OpenMDBitSet>(i->second); |
| 383 |
|
} else if (i->second.type() == typeid(std::vector<Token>)){ |
| 384 |
|
bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
| 385 |
|
i->second = bs; /**@todo fixme */ |
| 388 |
|
} else { |
| 389 |
|
unrecognizedIdentifier(variable); |
| 390 |
|
} |
| 391 |
< |
|
| 391 |
> |
|
| 392 |
|
return bs; |
| 393 |
|
} |
| 394 |
< |
|
| 395 |
< |
BitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 396 |
< |
|
| 370 |
< |
return nameFinder.match(name); |
| 371 |
< |
|
| 394 |
> |
|
| 395 |
> |
OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 396 |
> |
return nameFinder.match(name); |
| 397 |
|
} |
| 398 |
|
|
| 399 |
|
bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){ |
| 403 |
|
return true; |
| 404 |
|
} |
| 405 |
|
} |
| 406 |
< |
|
| 406 |
> |
|
| 407 |
|
return false; |
| 408 |
|
} |
| 409 |
|
|
| 413 |
|
//predefine(); |
| 414 |
|
} |
| 415 |
|
|
| 416 |
< |
BitSet SelectionEvaluator::evaluate() { |
| 417 |
< |
BitSet bs(nStuntDouble); |
| 416 |
> |
OpenMDBitSet SelectionEvaluator::evaluate() { |
| 417 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 418 |
|
if (isLoaded_) { |
| 419 |
|
pc = 0; |
| 420 |
|
instructionDispatchLoop(bs); |
| 423 |
|
return bs; |
| 424 |
|
} |
| 425 |
|
|
| 426 |
< |
BitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 427 |
< |
BitSet bs(nStuntDouble); |
| 426 |
> |
OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 427 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 428 |
|
|
| 429 |
|
if (value.type() == typeid(int)) { |
| 430 |
|
int index = boost::any_cast<int>(value); |
| 446 |
|
return bs; |
| 447 |
|
} |
| 448 |
|
|
| 449 |
+ |
OpenMDBitSet SelectionEvaluator::allInstruction() { |
| 450 |
+ |
OpenMDBitSet bs(nStuntDouble); |
| 451 |
|
|
| 452 |
< |
double SelectionEvaluator::getCharge(Atom* atom) { |
| 453 |
< |
double charge =0.0; |
| 452 |
> |
SimInfo::MoleculeIterator mi; |
| 453 |
> |
Molecule* mol; |
| 454 |
> |
Molecule::AtomIterator ai; |
| 455 |
> |
Atom* atom; |
| 456 |
> |
Molecule::RigidBodyIterator rbIter; |
| 457 |
> |
RigidBody* rb; |
| 458 |
> |
|
| 459 |
> |
// Doing the loop insures that we're actually on this processor. |
| 460 |
> |
|
| 461 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 462 |
> |
mol = info->nextMolecule(mi)) { |
| 463 |
> |
|
| 464 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 465 |
> |
bs.setBitOn(atom->getGlobalIndex()); |
| 466 |
> |
} |
| 467 |
> |
|
| 468 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 469 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 470 |
> |
bs.setBitOn(rb->getGlobalIndex()); |
| 471 |
> |
} |
| 472 |
> |
} |
| 473 |
> |
|
| 474 |
> |
return bs; |
| 475 |
> |
} |
| 476 |
> |
|
| 477 |
> |
OpenMDBitSet SelectionEvaluator::hull() { |
| 478 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 479 |
> |
|
| 480 |
> |
bs = hullFinder.findHull(); |
| 481 |
> |
|
| 482 |
> |
return bs; |
| 483 |
> |
} |
| 484 |
> |
|
| 485 |
> |
RealType SelectionEvaluator::getCharge(Atom* atom) { |
| 486 |
> |
RealType charge =0.0; |
| 487 |
|
AtomType* atomType = atom->getAtomType(); |
| 488 |
|
if (atomType->isCharge()) { |
| 489 |
|
GenericData* data = atomType->getPropertyByName("Charge"); |
| 496 |
|
} else { |
| 497 |
|
sprintf( painCave.errMsg, |
| 498 |
|
"Can not cast GenericData to DoubleGenericData\n"); |
| 499 |
< |
painCave.severity = OOPSE_ERROR; |
| 499 |
> |
painCave.severity = OPENMD_ERROR; |
| 500 |
|
painCave.isFatal = 1; |
| 501 |
|
simError(); |
| 502 |
|
} |
