| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include <stack> |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
|
#include "io/basic_ifstrstream.hpp" |
| 49 |
|
|
| 50 |
< |
namespace oopse { |
| 50 |
> |
namespace OpenMD { |
| 51 |
|
|
| 52 |
|
|
| 53 |
|
SelectionEvaluator::SelectionEvaluator(SimInfo* si) |
| 67 |
|
|
| 68 |
|
sprintf( painCave.errMsg, |
| 69 |
|
"SelectionCompiler Error: %s\n", errorMessage.c_str()); |
| 70 |
< |
painCave.severity = OOPSE_ERROR; |
| 70 |
> |
painCave.severity = OPENMD_ERROR; |
| 71 |
|
painCave.isFatal = 1; |
| 72 |
|
simError(); |
| 73 |
|
return false; |
| 122 |
|
return loadScript(filename, script); |
| 123 |
|
} |
| 124 |
|
|
| 125 |
< |
void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){ |
| 125 |
> |
void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){ |
| 126 |
|
|
| 127 |
|
while ( pc < aatoken.size()) { |
| 128 |
|
statement = aatoken[pc++]; |
| 143 |
|
|
| 144 |
|
} |
| 145 |
|
|
| 146 |
< |
OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, |
| 146 |
> |
OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code, |
| 147 |
|
int pcStart) { |
| 148 |
< |
OOPSEBitSet bs; |
| 149 |
< |
std::stack<OOPSEBitSet> stack; |
| 148 |
> |
OpenMDBitSet bs; |
| 149 |
> |
std::stack<OpenMDBitSet> stack; |
| 150 |
|
|
| 151 |
|
for (int pc = pcStart; pc < code.size(); ++pc) { |
| 152 |
|
Token instruction = code[pc]; |
| 157 |
|
case Token::expressionEnd: |
| 158 |
|
break; |
| 159 |
|
case Token::all: |
| 160 |
< |
bs = OOPSEBitSet(nStuntDouble); |
| 160 |
> |
bs = OpenMDBitSet(nStuntDouble); |
| 161 |
|
bs.setAll(); |
| 162 |
|
stack.push(bs); |
| 163 |
|
break; |
| 164 |
|
case Token::none: |
| 165 |
< |
bs = OOPSEBitSet(nStuntDouble); |
| 165 |
> |
bs = OpenMDBitSet(nStuntDouble); |
| 166 |
|
stack.push(bs); |
| 167 |
|
break; |
| 168 |
|
case Token::opOr: |
| 213 |
|
|
| 214 |
|
|
| 215 |
|
|
| 216 |
< |
OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 216 |
> |
OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
| 217 |
|
int comparator = instruction.tok; |
| 218 |
|
int property = instruction.intValue; |
| 219 |
|
float comparisonValue = boost::any_cast<float>(instruction.value); |
| 220 |
|
float propertyValue; |
| 221 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 221 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 222 |
|
bs.clearAll(); |
| 223 |
|
|
| 224 |
|
SimInfo::MoleculeIterator mi; |
| 244 |
|
return bs; |
| 245 |
|
} |
| 246 |
|
|
| 247 |
< |
void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, |
| 247 |
> |
void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, |
| 248 |
|
int property, int comparator, |
| 249 |
|
float comparisonValue) { |
| 250 |
|
RealType propertyValue = 0.0; |
| 305 |
|
} |
| 306 |
|
|
| 307 |
|
void SelectionEvaluator::withinInstruction(const Token& instruction, |
| 308 |
< |
OOPSEBitSet& bs){ |
| 308 |
> |
OpenMDBitSet& bs){ |
| 309 |
|
|
| 310 |
|
boost::any withinSpec = instruction.value; |
| 311 |
|
float distance; |
| 362 |
|
} |
| 363 |
|
} |
| 364 |
|
|
| 365 |
< |
void SelectionEvaluator::select(OOPSEBitSet& bs){ |
| 365 |
> |
void SelectionEvaluator::select(OpenMDBitSet& bs){ |
| 366 |
|
bs = expression(statement, 1); |
| 367 |
|
} |
| 368 |
|
|
| 369 |
< |
OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 369 |
> |
OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 370 |
|
|
| 371 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 371 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 372 |
|
std::map<std::string, boost::any>::iterator i = variables.find(variable); |
| 373 |
|
|
| 374 |
|
if (i != variables.end()) { |
| 375 |
< |
if (i->second.type() == typeid(OOPSEBitSet)) { |
| 376 |
< |
return boost::any_cast<OOPSEBitSet>(i->second); |
| 375 |
> |
if (i->second.type() == typeid(OpenMDBitSet)) { |
| 376 |
> |
return boost::any_cast<OpenMDBitSet>(i->second); |
| 377 |
|
} else if (i->second.type() == typeid(std::vector<Token>)){ |
| 378 |
|
bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
| 379 |
|
i->second = bs; /**@todo fixme */ |
| 386 |
|
return bs; |
| 387 |
|
} |
| 388 |
|
|
| 389 |
< |
OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 389 |
> |
OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 390 |
|
return nameFinder.match(name); |
| 391 |
|
} |
| 392 |
|
|
| 407 |
|
//predefine(); |
| 408 |
|
} |
| 409 |
|
|
| 410 |
< |
OOPSEBitSet SelectionEvaluator::evaluate() { |
| 411 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 410 |
> |
OpenMDBitSet SelectionEvaluator::evaluate() { |
| 411 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 412 |
|
if (isLoaded_) { |
| 413 |
|
pc = 0; |
| 414 |
|
instructionDispatchLoop(bs); |
| 417 |
|
return bs; |
| 418 |
|
} |
| 419 |
|
|
| 420 |
< |
OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 421 |
< |
OOPSEBitSet bs(nStuntDouble); |
| 420 |
> |
OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 421 |
> |
OpenMDBitSet bs(nStuntDouble); |
| 422 |
|
|
| 423 |
|
if (value.type() == typeid(int)) { |
| 424 |
|
int index = boost::any_cast<int>(value); |
| 455 |
|
} else { |
| 456 |
|
sprintf( painCave.errMsg, |
| 457 |
|
"Can not cast GenericData to DoubleGenericData\n"); |
| 458 |
< |
painCave.severity = OOPSE_ERROR; |
| 458 |
> |
painCave.severity = OPENMD_ERROR; |
| 459 |
|
painCave.isFatal = 1; |
| 460 |
|
simError(); |
| 461 |
|
} |
