| 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, 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 |
|
|
| 43 |
|
#include <stack> |
| 46 |
|
#include "primitives/DirectionalAtom.hpp" |
| 47 |
|
#include "primitives/RigidBody.hpp" |
| 48 |
|
#include "primitives/Molecule.hpp" |
| 49 |
+ |
#include "io/ifstrstream.hpp" |
| 50 |
+ |
#include "types/FixedChargeAdapter.hpp" |
| 51 |
+ |
#include "types/FluctuatingChargeAdapter.hpp" |
| 52 |
|
|
| 49 |
– |
namespace oopse { |
| 53 |
|
|
| 54 |
+ |
namespace OpenMD { |
| 55 |
|
|
| 52 |
– |
SelectionEvaluator::SelectionEvaluator(SimInfo* si) |
| 53 |
– |
: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){ |
| 54 |
– |
|
| 55 |
– |
nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies(); |
| 56 |
– |
} |
| 56 |
|
|
| 57 |
< |
bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) { |
| 57 |
> |
SelectionEvaluator::SelectionEvaluator(SimInfo* si) |
| 58 |
> |
: info(si), nameFinder(info), distanceFinder(info), hullFinder(info), |
| 59 |
> |
indexFinder(info), hasSurfaceArea_(false), |
| 60 |
> |
isLoaded_(false){ |
| 61 |
> |
nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies()); |
| 62 |
> |
nObjects.push_back(info->getNGlobalBonds()); |
| 63 |
> |
nObjects.push_back(info->getNGlobalBends()); |
| 64 |
> |
nObjects.push_back(info->getNGlobalTorsions()); |
| 65 |
> |
nObjects.push_back(info->getNGlobalInversions()); |
| 66 |
> |
} |
| 67 |
> |
|
| 68 |
> |
bool SelectionEvaluator::loadScript(const std::string& filename, |
| 69 |
> |
const std::string& script) { |
| 70 |
|
clearDefinitionsAndLoadPredefined(); |
| 71 |
|
this->filename = filename; |
| 72 |
|
this->script = script; |
| 73 |
|
if (! compiler.compile(filename, script)) { |
| 74 |
|
error = true; |
| 75 |
|
errorMessage = compiler.getErrorMessage(); |
| 76 |
< |
std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl; |
| 76 |
> |
|
| 77 |
> |
sprintf( painCave.errMsg, |
| 78 |
> |
"SelectionCompiler Error: %s\n", errorMessage.c_str()); |
| 79 |
> |
painCave.severity = OPENMD_ERROR; |
| 80 |
> |
painCave.isFatal = 1; |
| 81 |
> |
simError(); |
| 82 |
|
return false; |
| 83 |
|
} |
| 84 |
|
|
| 116 |
|
return loadScriptFileInternal(filename); |
| 117 |
|
} |
| 118 |
|
|
| 119 |
< |
bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
| 120 |
< |
std::ifstream ifs(filename.c_str()); |
| 119 |
> |
bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
| 120 |
> |
ifstrstream ifs(filename.c_str()); |
| 121 |
|
if (!ifs.is_open()) { |
| 122 |
|
return false; |
| 123 |
|
} |
| 124 |
< |
|
| 124 |
> |
|
| 125 |
|
const int bufferSize = 65535; |
| 126 |
|
char buffer[bufferSize]; |
| 127 |
|
std::string script; |
| 130 |
|
} |
| 131 |
|
return loadScript(filename, script); |
| 132 |
|
} |
| 133 |
< |
|
| 134 |
< |
void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){ |
| 133 |
> |
|
| 134 |
> |
void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){ |
| 135 |
|
|
| 136 |
|
while ( pc < aatoken.size()) { |
| 137 |
|
statement = aatoken[pc++]; |
| 152 |
|
|
| 153 |
|
} |
| 154 |
|
|
| 155 |
< |
OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) { |
| 140 |
< |
OOPSEBitSet bs; |
| 141 |
< |
std::stack<OOPSEBitSet> stack; |
| 155 |
> |
void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){ |
| 156 |
|
|
| 157 |
< |
for (int pc = pcStart; pc < code.size(); ++pc) { |
| 157 |
> |
while ( pc < aatoken.size()) { |
| 158 |
> |
statement = aatoken[pc++]; |
| 159 |
> |
statementLength = statement.size(); |
| 160 |
> |
Token token = statement[0]; |
| 161 |
> |
switch (token.tok) { |
| 162 |
> |
case Token::define: |
| 163 |
> |
define(); |
| 164 |
> |
break; |
| 165 |
> |
case Token::select: |
| 166 |
> |
select(bs, frame); |
| 167 |
> |
break; |
| 168 |
> |
default: |
| 169 |
> |
unrecognizedCommand(token); |
| 170 |
> |
return; |
| 171 |
> |
} |
| 172 |
> |
} |
| 173 |
> |
|
| 174 |
> |
} |
| 175 |
> |
|
| 176 |
> |
SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code, |
| 177 |
> |
int pcStart) { |
| 178 |
> |
SelectionSet bs = createSelectionSets(); |
| 179 |
> |
std::stack<SelectionSet> stack; |
| 180 |
> |
vector<int> bsSize = bs.size(); |
| 181 |
> |
|
| 182 |
> |
for (unsigned int pc = pcStart; pc < code.size(); ++pc) { |
| 183 |
|
Token instruction = code[pc]; |
| 184 |
|
|
| 185 |
|
switch (instruction.tok) { |
| 188 |
|
case Token::expressionEnd: |
| 189 |
|
break; |
| 190 |
|
case Token::all: |
| 191 |
< |
bs = OOPSEBitSet(nStuntDouble); |
| 192 |
< |
bs.setAll(); |
| 191 |
> |
bs = allInstruction(); |
| 192 |
> |
stack.push(bs); |
| 193 |
> |
break; |
| 194 |
> |
case Token::none: |
| 195 |
> |
bs = createSelectionSets(); |
| 196 |
> |
stack.push(bs); |
| 197 |
> |
break; |
| 198 |
> |
case Token::opOr: |
| 199 |
> |
bs= stack.top(); |
| 200 |
> |
stack.pop(); |
| 201 |
> |
stack.top() |= bs; |
| 202 |
> |
break; |
| 203 |
> |
case Token::opAnd: |
| 204 |
> |
bs = stack.top(); |
| 205 |
> |
stack.pop(); |
| 206 |
> |
stack.top() &= bs; |
| 207 |
> |
break; |
| 208 |
> |
case Token::opNot: |
| 209 |
> |
stack.top().flip(); |
| 210 |
> |
break; |
| 211 |
> |
case Token::within: |
| 212 |
> |
withinInstruction(instruction, stack.top()); |
| 213 |
> |
break; |
| 214 |
> |
case Token::hull: |
| 215 |
> |
stack.push(hull()); |
| 216 |
> |
break; |
| 217 |
> |
//case Token::selected: |
| 218 |
> |
// stack.push(getSelectionSet()); |
| 219 |
> |
// break; |
| 220 |
> |
case Token::name: |
| 221 |
> |
stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); |
| 222 |
> |
break; |
| 223 |
> |
case Token::index: |
| 224 |
> |
stack.push(indexInstruction(instruction.value)); |
| 225 |
> |
break; |
| 226 |
> |
case Token::identifier: |
| 227 |
> |
stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); |
| 228 |
> |
break; |
| 229 |
> |
case Token::opLT: |
| 230 |
> |
case Token::opLE: |
| 231 |
> |
case Token::opGE: |
| 232 |
> |
case Token::opGT: |
| 233 |
> |
case Token::opEQ: |
| 234 |
> |
case Token::opNE: |
| 235 |
> |
stack.push(comparatorInstruction(instruction)); |
| 236 |
> |
break; |
| 237 |
> |
default: |
| 238 |
> |
unrecognizedExpression(); |
| 239 |
> |
} |
| 240 |
> |
} |
| 241 |
> |
if (stack.size() != 1) |
| 242 |
> |
evalError("atom expression compiler error - stack over/underflow"); |
| 243 |
> |
|
| 244 |
> |
return stack.top(); |
| 245 |
> |
} |
| 246 |
> |
|
| 247 |
> |
|
| 248 |
> |
SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code, |
| 249 |
> |
int pcStart, int frame) { |
| 250 |
> |
SelectionSet bs = createSelectionSets(); |
| 251 |
> |
std::stack<SelectionSet> stack; |
| 252 |
> |
|
| 253 |
> |
for (unsigned int pc = pcStart; pc < code.size(); ++pc) { |
| 254 |
> |
Token instruction = code[pc]; |
| 255 |
> |
|
| 256 |
> |
switch (instruction.tok) { |
| 257 |
> |
case Token::expressionBegin: |
| 258 |
> |
break; |
| 259 |
> |
case Token::expressionEnd: |
| 260 |
> |
break; |
| 261 |
> |
case Token::all: |
| 262 |
> |
bs = allInstruction(); |
| 263 |
|
stack.push(bs); |
| 264 |
|
break; |
| 265 |
|
case Token::none: |
| 266 |
< |
bs = OOPSEBitSet(nStuntDouble); |
| 266 |
> |
bs = SelectionSet(nObjects); |
| 267 |
|
stack.push(bs); |
| 268 |
|
break; |
| 269 |
|
case Token::opOr: |
| 280 |
|
stack.top().flip(); |
| 281 |
|
break; |
| 282 |
|
case Token::within: |
| 283 |
< |
|
| 175 |
< |
withinInstruction(instruction, stack.top()); |
| 283 |
> |
withinInstruction(instruction, stack.top(), frame); |
| 284 |
|
break; |
| 285 |
+ |
case Token::hull: |
| 286 |
+ |
stack.push(hull(frame)); |
| 287 |
+ |
break; |
| 288 |
|
//case Token::selected: |
| 289 |
|
// stack.push(getSelectionSet()); |
| 290 |
|
// break; |
| 303 |
|
case Token::opGT: |
| 304 |
|
case Token::opEQ: |
| 305 |
|
case Token::opNE: |
| 306 |
< |
stack.push(comparatorInstruction(instruction)); |
| 306 |
> |
stack.push(comparatorInstruction(instruction, frame)); |
| 307 |
|
break; |
| 308 |
|
default: |
| 309 |
|
unrecognizedExpression(); |
| 317 |
|
|
| 318 |
|
|
| 319 |
|
|
| 320 |
< |
OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 320 |
> |
SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 321 |
|
int comparator = instruction.tok; |
| 322 |
|
int property = instruction.intValue; |
| 323 |
|
float comparisonValue = boost::any_cast<float>(instruction.value); |
| 324 |
< |
float propertyValue; |
| 214 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 324 |
> |
SelectionSet bs = createSelectionSets(); |
| 325 |
|
bs.clearAll(); |
| 326 |
|
|
| 327 |
|
SimInfo::MoleculeIterator mi; |
| 330 |
|
Atom* atom; |
| 331 |
|
Molecule::RigidBodyIterator rbIter; |
| 332 |
|
RigidBody* rb; |
| 223 |
– |
|
| 224 |
– |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 333 |
|
|
| 334 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 335 |
+ |
mol = info->nextMolecule(mi)) { |
| 336 |
+ |
|
| 337 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 338 |
|
compareProperty(atom, bs, property, comparator, comparisonValue); |
| 339 |
|
} |
| 340 |
< |
|
| 341 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 342 |
< |
compareProperty(rb, bs, property, comparator, comparisonValue); |
| 343 |
< |
} |
| 340 |
> |
|
| 341 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 342 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 343 |
> |
compareProperty(rb, bs, property, comparator, comparisonValue); |
| 344 |
> |
} |
| 345 |
|
} |
| 346 |
|
|
| 347 |
|
return bs; |
| 348 |
|
} |
| 349 |
|
|
| 350 |
< |
void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) { |
| 351 |
< |
double propertyValue = 0.0; |
| 350 |
> |
SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) { |
| 351 |
> |
int comparator = instruction.tok; |
| 352 |
> |
int property = instruction.intValue; |
| 353 |
> |
float comparisonValue = boost::any_cast<float>(instruction.value); |
| 354 |
> |
SelectionSet bs = createSelectionSets(); |
| 355 |
> |
bs.clearAll(); |
| 356 |
> |
|
| 357 |
> |
SimInfo::MoleculeIterator mi; |
| 358 |
> |
Molecule* mol; |
| 359 |
> |
Molecule::AtomIterator ai; |
| 360 |
> |
Atom* atom; |
| 361 |
> |
Molecule::RigidBodyIterator rbIter; |
| 362 |
> |
RigidBody* rb; |
| 363 |
> |
|
| 364 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 365 |
> |
mol = info->nextMolecule(mi)) { |
| 366 |
> |
|
| 367 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 368 |
> |
compareProperty(atom, bs, property, comparator, comparisonValue, frame); |
| 369 |
> |
} |
| 370 |
> |
|
| 371 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 372 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 373 |
> |
compareProperty(rb, bs, property, comparator, comparisonValue, frame); |
| 374 |
> |
} |
| 375 |
> |
} |
| 376 |
> |
|
| 377 |
> |
return bs; |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs, |
| 381 |
> |
int property, int comparator, |
| 382 |
> |
float comparisonValue) { |
| 383 |
> |
RealType propertyValue = 0.0; |
| 384 |
> |
Vector3d pos; |
| 385 |
> |
|
| 386 |
|
switch (property) { |
| 387 |
|
case Token::mass: |
| 388 |
|
propertyValue = sd->getMass(); |
| 400 |
|
} |
| 401 |
|
} |
| 402 |
|
break; |
| 403 |
+ |
case Token::x: |
| 404 |
+ |
propertyValue = sd->getPos().x(); |
| 405 |
+ |
break; |
| 406 |
+ |
case Token::y: |
| 407 |
+ |
propertyValue = sd->getPos().y(); |
| 408 |
+ |
break; |
| 409 |
+ |
case Token::z: |
| 410 |
+ |
propertyValue = sd->getPos().z(); |
| 411 |
+ |
break; |
| 412 |
+ |
case Token::wrappedX: |
| 413 |
+ |
pos = sd->getPos(); |
| 414 |
+ |
info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); |
| 415 |
+ |
propertyValue = pos.x(); |
| 416 |
+ |
break; |
| 417 |
+ |
case Token::wrappedY: |
| 418 |
+ |
pos = sd->getPos(); |
| 419 |
+ |
info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); |
| 420 |
+ |
propertyValue = pos.y(); |
| 421 |
+ |
break; |
| 422 |
+ |
case Token::wrappedZ: |
| 423 |
+ |
pos = sd->getPos(); |
| 424 |
+ |
info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); |
| 425 |
+ |
propertyValue = pos.z(); |
| 426 |
+ |
break; |
| 427 |
+ |
case Token::r: |
| 428 |
+ |
propertyValue = sd->getPos().length(); |
| 429 |
+ |
break; |
| 430 |
|
default: |
| 431 |
|
unrecognizedAtomProperty(property); |
| 432 |
|
} |
| 452 |
|
match = propertyValue != comparisonValue; |
| 453 |
|
break; |
| 454 |
|
} |
| 282 |
– |
if (match) |
| 283 |
– |
bs.setBitOn(sd->getGlobalIndex()); |
| 455 |
|
|
| 456 |
+ |
if (match) |
| 457 |
+ |
bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex()); |
| 458 |
+ |
|
| 459 |
+ |
|
| 460 |
|
} |
| 461 |
|
|
| 462 |
< |
void SelectionEvaluator::withinInstruction(const Token& instruction, OOPSEBitSet& bs){ |
| 462 |
> |
void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs, |
| 463 |
> |
int property, int comparator, |
| 464 |
> |
float comparisonValue, int frame) { |
| 465 |
> |
RealType propertyValue = 0.0; |
| 466 |
> |
Vector3d pos; |
| 467 |
> |
switch (property) { |
| 468 |
> |
case Token::mass: |
| 469 |
> |
propertyValue = sd->getMass(); |
| 470 |
> |
break; |
| 471 |
> |
case Token::charge: |
| 472 |
> |
if (sd->isAtom()){ |
| 473 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 474 |
> |
propertyValue = getCharge(atom,frame); |
| 475 |
> |
} else if (sd->isRigidBody()) { |
| 476 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 477 |
> |
RigidBody::AtomIterator ai; |
| 478 |
> |
Atom* atom; |
| 479 |
> |
for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 480 |
> |
propertyValue+= getCharge(atom,frame); |
| 481 |
> |
} |
| 482 |
> |
} |
| 483 |
> |
break; |
| 484 |
> |
case Token::x: |
| 485 |
> |
propertyValue = sd->getPos(frame).x(); |
| 486 |
> |
break; |
| 487 |
> |
case Token::y: |
| 488 |
> |
propertyValue = sd->getPos(frame).y(); |
| 489 |
> |
break; |
| 490 |
> |
case Token::z: |
| 491 |
> |
propertyValue = sd->getPos(frame).z(); |
| 492 |
> |
break; |
| 493 |
> |
case Token::wrappedX: |
| 494 |
> |
pos = sd->getPos(frame); |
| 495 |
> |
info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); |
| 496 |
> |
propertyValue = pos.x(); |
| 497 |
> |
break; |
| 498 |
> |
case Token::wrappedY: |
| 499 |
> |
pos = sd->getPos(frame); |
| 500 |
> |
info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); |
| 501 |
> |
propertyValue = pos.y(); |
| 502 |
> |
break; |
| 503 |
> |
case Token::wrappedZ: |
| 504 |
> |
pos = sd->getPos(frame); |
| 505 |
> |
info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); |
| 506 |
> |
propertyValue = pos.z(); |
| 507 |
> |
break; |
| 508 |
> |
|
| 509 |
> |
case Token::r: |
| 510 |
> |
propertyValue = sd->getPos(frame).length(); |
| 511 |
> |
break; |
| 512 |
> |
default: |
| 513 |
> |
unrecognizedAtomProperty(property); |
| 514 |
> |
} |
| 515 |
> |
|
| 516 |
> |
bool match = false; |
| 517 |
> |
switch (comparator) { |
| 518 |
> |
case Token::opLT: |
| 519 |
> |
match = propertyValue < comparisonValue; |
| 520 |
> |
break; |
| 521 |
> |
case Token::opLE: |
| 522 |
> |
match = propertyValue <= comparisonValue; |
| 523 |
> |
break; |
| 524 |
> |
case Token::opGE: |
| 525 |
> |
match = propertyValue >= comparisonValue; |
| 526 |
> |
break; |
| 527 |
> |
case Token::opGT: |
| 528 |
> |
match = propertyValue > comparisonValue; |
| 529 |
> |
break; |
| 530 |
> |
case Token::opEQ: |
| 531 |
> |
match = propertyValue == comparisonValue; |
| 532 |
> |
break; |
| 533 |
> |
case Token::opNE: |
| 534 |
> |
match = propertyValue != comparisonValue; |
| 535 |
> |
break; |
| 536 |
> |
} |
| 537 |
> |
if (match) |
| 538 |
> |
bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex()); |
| 539 |
> |
|
| 540 |
|
|
| 541 |
+ |
} |
| 542 |
+ |
|
| 543 |
+ |
void SelectionEvaluator::withinInstruction(const Token& instruction, |
| 544 |
+ |
SelectionSet& bs){ |
| 545 |
+ |
|
| 546 |
|
boost::any withinSpec = instruction.value; |
| 547 |
|
float distance; |
| 548 |
|
if (withinSpec.type() == typeid(float)){ |
| 557 |
|
bs = distanceFinder.find(bs, distance); |
| 558 |
|
} |
| 559 |
|
|
| 560 |
+ |
void SelectionEvaluator::withinInstruction(const Token& instruction, |
| 561 |
+ |
SelectionSet& bs, int frame){ |
| 562 |
+ |
|
| 563 |
+ |
boost::any withinSpec = instruction.value; |
| 564 |
+ |
float distance; |
| 565 |
+ |
if (withinSpec.type() == typeid(float)){ |
| 566 |
+ |
distance = boost::any_cast<float>(withinSpec); |
| 567 |
+ |
} else if (withinSpec.type() == typeid(int)) { |
| 568 |
+ |
distance = boost::any_cast<int>(withinSpec); |
| 569 |
+ |
} else { |
| 570 |
+ |
evalError("casting error in withinInstruction"); |
| 571 |
+ |
bs.clearAll(); |
| 572 |
+ |
} |
| 573 |
+ |
|
| 574 |
+ |
bs = distanceFinder.find(bs, distance, frame); |
| 575 |
+ |
} |
| 576 |
+ |
|
| 577 |
|
void SelectionEvaluator::define() { |
| 578 |
|
assert(statement.size() >= 3); |
| 579 |
< |
|
| 579 |
> |
|
| 580 |
|
std::string variable = boost::any_cast<std::string>(statement[1].value); |
| 581 |
< |
|
| 582 |
< |
variables.insert(VariablesType::value_type(variable, expression(statement, 2))); |
| 581 |
> |
|
| 582 |
> |
variables.insert(VariablesType::value_type(variable, |
| 583 |
> |
expression(statement, 2))); |
| 584 |
|
} |
| 585 |
+ |
|
| 586 |
|
|
| 311 |
– |
|
| 587 |
|
/** @todo */ |
| 588 |
|
void SelectionEvaluator::predefine(const std::string& script) { |
| 589 |
< |
|
| 589 |
> |
|
| 590 |
|
if (compiler.compile("#predefine", script)) { |
| 591 |
|
std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled(); |
| 592 |
|
if (aatoken.size() != 1) { |
| 597 |
|
std::vector<Token> statement = aatoken[0]; |
| 598 |
|
if (statement.size() > 2) { |
| 599 |
|
int tok = statement[1].tok; |
| 600 |
< |
if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) { |
| 600 |
> |
if (tok == Token::identifier || |
| 601 |
> |
(tok & Token::predefinedset) == Token::predefinedset) { |
| 602 |
|
std::string variable = boost::any_cast<std::string>(statement[1].value); |
| 603 |
|
variables.insert(VariablesType::value_type(variable, statement)); |
| 604 |
< |
|
| 604 |
> |
|
| 605 |
|
} else { |
| 606 |
|
evalError("invalid variable name:" + script); |
| 607 |
|
} |
| 608 |
|
}else { |
| 609 |
|
evalError("bad predefinition length:" + script); |
| 610 |
< |
} |
| 335 |
< |
|
| 610 |
> |
} |
| 611 |
|
|
| 612 |
|
} else { |
| 613 |
|
evalError("predefined set compile error:" + script + |
| 614 |
|
"\ncompile error:" + compiler.getErrorMessage()); |
| 615 |
|
} |
| 341 |
– |
|
| 616 |
|
} |
| 617 |
|
|
| 618 |
< |
void SelectionEvaluator::select(OOPSEBitSet& bs){ |
| 618 |
> |
void SelectionEvaluator::select(SelectionSet& bs){ |
| 619 |
|
bs = expression(statement, 1); |
| 620 |
|
} |
| 621 |
|
|
| 622 |
< |
OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 623 |
< |
|
| 624 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 622 |
> |
void SelectionEvaluator::select(SelectionSet& bs, int frame){ |
| 623 |
> |
bs = expression(statement, 1, frame); |
| 624 |
> |
} |
| 625 |
> |
|
| 626 |
> |
SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 627 |
> |
|
| 628 |
> |
SelectionSet bs = createSelectionSets(); |
| 629 |
|
std::map<std::string, boost::any>::iterator i = variables.find(variable); |
| 630 |
|
|
| 631 |
|
if (i != variables.end()) { |
| 632 |
< |
if (i->second.type() == typeid(OOPSEBitSet)) { |
| 633 |
< |
return boost::any_cast<OOPSEBitSet>(i->second); |
| 632 |
> |
if (i->second.type() == typeid(SelectionSet)) { |
| 633 |
> |
return boost::any_cast<SelectionSet>(i->second); |
| 634 |
|
} else if (i->second.type() == typeid(std::vector<Token>)){ |
| 635 |
|
bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
| 636 |
|
i->second = bs; /**@todo fixme */ |
| 639 |
|
} else { |
| 640 |
|
unrecognizedIdentifier(variable); |
| 641 |
|
} |
| 642 |
< |
|
| 642 |
> |
|
| 643 |
|
return bs; |
| 644 |
|
} |
| 645 |
< |
|
| 646 |
< |
OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 647 |
< |
|
| 370 |
< |
return nameFinder.match(name); |
| 371 |
< |
|
| 645 |
> |
|
| 646 |
> |
SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 647 |
> |
return nameFinder.match(name); |
| 648 |
|
} |
| 649 |
|
|
| 650 |
|
bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){ |
| 654 |
|
return true; |
| 655 |
|
} |
| 656 |
|
} |
| 657 |
< |
|
| 657 |
> |
|
| 658 |
|
return false; |
| 659 |
|
} |
| 660 |
|
|
| 664 |
|
//predefine(); |
| 665 |
|
} |
| 666 |
|
|
| 667 |
< |
OOPSEBitSet SelectionEvaluator::evaluate() { |
| 668 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 667 |
> |
SelectionSet SelectionEvaluator::createSelectionSets() { |
| 668 |
> |
SelectionSet ss(nObjects); |
| 669 |
> |
return ss; |
| 670 |
> |
} |
| 671 |
> |
|
| 672 |
> |
SelectionSet SelectionEvaluator::evaluate() { |
| 673 |
> |
SelectionSet bs = createSelectionSets(); |
| 674 |
|
if (isLoaded_) { |
| 675 |
|
pc = 0; |
| 676 |
|
instructionDispatchLoop(bs); |
| 677 |
|
} |
| 678 |
+ |
return bs; |
| 679 |
+ |
} |
| 680 |
|
|
| 681 |
+ |
SelectionSet SelectionEvaluator::evaluate(int frame) { |
| 682 |
+ |
SelectionSet bs = createSelectionSets(); |
| 683 |
+ |
if (isLoaded_) { |
| 684 |
+ |
pc = 0; |
| 685 |
+ |
instructionDispatchLoop(bs, frame); |
| 686 |
+ |
} |
| 687 |
|
return bs; |
| 688 |
|
} |
| 689 |
|
|
| 690 |
< |
OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 691 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 690 |
> |
SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 691 |
> |
SelectionSet bs = createSelectionSets(); |
| 692 |
|
|
| 693 |
|
if (value.type() == typeid(int)) { |
| 694 |
|
int index = boost::any_cast<int>(value); |
| 695 |
< |
if (index < 0 || index >= bs.size()) { |
| 695 |
> |
if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) { |
| 696 |
|
invalidIndex(index); |
| 697 |
|
} else { |
| 698 |
|
bs = indexFinder.find(index); |
| 700 |
|
} else if (value.type() == typeid(std::pair<int, int>)) { |
| 701 |
|
std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value); |
| 702 |
|
assert(indexRange.first <= indexRange.second); |
| 703 |
< |
if (indexRange.first < 0 || indexRange.second >= bs.size()) { |
| 703 |
> |
if (indexRange.first < 0 || |
| 704 |
> |
indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) { |
| 705 |
|
invalidIndexRange(indexRange); |
| 706 |
|
}else { |
| 707 |
|
bs = indexFinder.find(indexRange.first, indexRange.second); |
| 711 |
|
return bs; |
| 712 |
|
} |
| 713 |
|
|
| 714 |
+ |
SelectionSet SelectionEvaluator::allInstruction() { |
| 715 |
+ |
SelectionSet ss = createSelectionSets(); |
| 716 |
|
|
| 717 |
< |
double SelectionEvaluator::getCharge(Atom* atom) { |
| 718 |
< |
double charge =0.0; |
| 719 |
< |
AtomType* atomType = atom->getAtomType(); |
| 720 |
< |
if (atomType->isCharge()) { |
| 721 |
< |
GenericData* data = atomType->getPropertyByName("Charge"); |
| 722 |
< |
if (data != NULL) { |
| 723 |
< |
DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data); |
| 717 |
> |
SimInfo::MoleculeIterator mi; |
| 718 |
> |
Molecule::AtomIterator ai; |
| 719 |
> |
Molecule::RigidBodyIterator rbIter; |
| 720 |
> |
Molecule::BondIterator bondIter; |
| 721 |
> |
Molecule::BendIterator bendIter; |
| 722 |
> |
Molecule::TorsionIterator torsionIter; |
| 723 |
> |
Molecule::InversionIterator inversionIter; |
| 724 |
|
|
| 725 |
< |
if (doubleData != NULL) { |
| 726 |
< |
charge = doubleData->getData(); |
| 725 |
> |
Molecule* mol; |
| 726 |
> |
Atom* atom; |
| 727 |
> |
RigidBody* rb; |
| 728 |
> |
Bond* bond; |
| 729 |
> |
Bend* bend; |
| 730 |
> |
Torsion* torsion; |
| 731 |
> |
Inversion* inversion; |
| 732 |
|
|
| 733 |
< |
} else { |
| 734 |
< |
sprintf( painCave.errMsg, |
| 735 |
< |
"Can not cast GenericData to DoubleGenericData\n"); |
| 736 |
< |
painCave.severity = OOPSE_ERROR; |
| 737 |
< |
painCave.isFatal = 1; |
| 738 |
< |
simError(); |
| 739 |
< |
} |
| 740 |
< |
} |
| 733 |
> |
// Doing the loop insures that we're actually on this processor. |
| 734 |
> |
|
| 735 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 736 |
> |
mol = info->nextMolecule(mi)) { |
| 737 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 738 |
> |
ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
| 739 |
> |
} |
| 740 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 741 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 742 |
> |
ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
| 743 |
> |
} |
| 744 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 745 |
> |
bond = mol->nextBond(bondIter)) { |
| 746 |
> |
ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); |
| 747 |
> |
} |
| 748 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 749 |
> |
bend = mol->nextBend(bendIter)) { |
| 750 |
> |
ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); |
| 751 |
> |
} |
| 752 |
> |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 753 |
> |
torsion = mol->nextTorsion(torsionIter)) { |
| 754 |
> |
ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); |
| 755 |
> |
} |
| 756 |
> |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 757 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 758 |
> |
ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); |
| 759 |
> |
} |
| 760 |
|
} |
| 761 |
|
|
| 762 |
+ |
return ss; |
| 763 |
+ |
} |
| 764 |
+ |
|
| 765 |
+ |
SelectionSet SelectionEvaluator::hull() { |
| 766 |
+ |
SelectionSet bs = createSelectionSets(); |
| 767 |
+ |
|
| 768 |
+ |
bs = hullFinder.findHull(); |
| 769 |
+ |
surfaceArea_ = hullFinder.getSurfaceArea(); |
| 770 |
+ |
hasSurfaceArea_ = true; |
| 771 |
+ |
return bs; |
| 772 |
+ |
} |
| 773 |
+ |
|
| 774 |
+ |
|
| 775 |
+ |
SelectionSet SelectionEvaluator::hull(int frame) { |
| 776 |
+ |
SelectionSet bs = createSelectionSets(); |
| 777 |
+ |
|
| 778 |
+ |
bs = hullFinder.findHull(frame); |
| 779 |
+ |
|
| 780 |
+ |
return bs; |
| 781 |
+ |
} |
| 782 |
+ |
|
| 783 |
+ |
RealType SelectionEvaluator::getCharge(Atom* atom) { |
| 784 |
+ |
RealType charge = 0.0; |
| 785 |
+ |
AtomType* atomType = atom->getAtomType(); |
| 786 |
+ |
|
| 787 |
+ |
FixedChargeAdapter fca = FixedChargeAdapter(atomType); |
| 788 |
+ |
if ( fca.isFixedCharge() ) { |
| 789 |
+ |
charge = fca.getCharge(); |
| 790 |
+ |
} |
| 791 |
+ |
|
| 792 |
+ |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); |
| 793 |
+ |
if ( fqa.isFluctuatingCharge() ) { |
| 794 |
+ |
charge += atom->getFlucQPos(); |
| 795 |
+ |
} |
| 796 |
|
return charge; |
| 797 |
|
} |
| 798 |
|
|
| 799 |
+ |
RealType SelectionEvaluator::getCharge(Atom* atom, int frame) { |
| 800 |
+ |
RealType charge = 0.0; |
| 801 |
+ |
AtomType* atomType = atom->getAtomType(); |
| 802 |
+ |
|
| 803 |
+ |
FixedChargeAdapter fca = FixedChargeAdapter(atomType); |
| 804 |
+ |
if ( fca.isFixedCharge() ) { |
| 805 |
+ |
charge = fca.getCharge(); |
| 806 |
+ |
} |
| 807 |
+ |
|
| 808 |
+ |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); |
| 809 |
+ |
if ( fqa.isFluctuatingCharge() ) { |
| 810 |
+ |
charge += atom->getFlucQPos(frame); |
| 811 |
+ |
} |
| 812 |
+ |
return charge; |
| 813 |
+ |
} |
| 814 |
+ |
|
| 815 |
|
} |
