--- trunk/src/selection/SelectionEvaluator.cpp 2009/10/07 20:49:50 1364 +++ trunk/src/selection/SelectionEvaluator.cpp 2012/10/01 18:21:15 1801 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,16 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -45,13 +46,14 @@ #include "primitives/DirectionalAtom.hpp" #include "primitives/RigidBody.hpp" #include "primitives/Molecule.hpp" -#include "io/basic_ifstrstream.hpp" +#include "io/ifstrstream.hpp" -namespace oopse { +namespace OpenMD { SelectionEvaluator::SelectionEvaluator(SimInfo* si) - : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), + : info(si), nameFinder(info), distanceFinder(info), hullFinder(info), + indexFinder(info), isLoaded_(false){ nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies(); } @@ -67,7 +69,7 @@ namespace oopse { sprintf( painCave.errMsg, "SelectionCompiler Error: %s\n", errorMessage.c_str()); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); return false; @@ -122,7 +124,7 @@ namespace oopse { return loadScript(filename, script); } - void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){ + void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){ while ( pc < aatoken.size()) { statement = aatoken[pc++]; @@ -143,12 +145,12 @@ namespace oopse { } - OOPSEBitSet SelectionEvaluator::expression(const std::vector& code, + OpenMDBitSet SelectionEvaluator::expression(const std::vector& code, int pcStart) { - OOPSEBitSet bs; - std::stack stack; + OpenMDBitSet bs; + std::stack stack; - for (int pc = pcStart; pc < code.size(); ++pc) { + for (unsigned int pc = pcStart; pc < code.size(); ++pc) { Token instruction = code[pc]; switch (instruction.tok) { @@ -157,12 +159,11 @@ namespace oopse { case Token::expressionEnd: break; case Token::all: - bs = OOPSEBitSet(nStuntDouble); - bs.setAll(); + bs = allInstruction(); stack.push(bs); break; case Token::none: - bs = OOPSEBitSet(nStuntDouble); + bs = OpenMDBitSet(nStuntDouble); stack.push(bs); break; case Token::opOr: @@ -181,6 +182,9 @@ namespace oopse { case Token::within: withinInstruction(instruction, stack.top()); break; + case Token::hull: + stack.push(hull()); + break; //case Token::selected: // stack.push(getSelectionSet()); // break; @@ -213,12 +217,11 @@ namespace oopse { - OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { + OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { int comparator = instruction.tok; int property = instruction.intValue; float comparisonValue = boost::any_cast(instruction.value); - float propertyValue; - OOPSEBitSet bs(nStuntDouble); + OpenMDBitSet bs(nStuntDouble); bs.clearAll(); SimInfo::MoleculeIterator mi; @@ -244,7 +247,7 @@ namespace oopse { return bs; } - void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, + void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue) { RealType propertyValue = 0.0; @@ -274,6 +277,9 @@ namespace oopse { case Token::z: propertyValue = sd->getPos().z(); break; + case Token::r: + propertyValue = sd->getPos().length(); + break; default: unrecognizedAtomProperty(property); } @@ -305,7 +311,7 @@ namespace oopse { } void SelectionEvaluator::withinInstruction(const Token& instruction, - OOPSEBitSet& bs){ + OpenMDBitSet& bs){ boost::any withinSpec = instruction.value; float distance; @@ -362,18 +368,18 @@ namespace oopse { } } - void SelectionEvaluator::select(OOPSEBitSet& bs){ + void SelectionEvaluator::select(OpenMDBitSet& bs){ bs = expression(statement, 1); } - OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){ + OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){ - OOPSEBitSet bs(nStuntDouble); + OpenMDBitSet bs(nStuntDouble); std::map::iterator i = variables.find(variable); if (i != variables.end()) { - if (i->second.type() == typeid(OOPSEBitSet)) { - return boost::any_cast(i->second); + if (i->second.type() == typeid(OpenMDBitSet)) { + return boost::any_cast(i->second); } else if (i->second.type() == typeid(std::vector)){ bs = expression(boost::any_cast >(i->second), 2); i->second = bs; /**@todo fixme */ @@ -386,7 +392,7 @@ namespace oopse { return bs; } - OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){ + OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){ return nameFinder.match(name); } @@ -407,8 +413,8 @@ namespace oopse { //predefine(); } - OOPSEBitSet SelectionEvaluator::evaluate() { - OOPSEBitSet bs(nStuntDouble); + OpenMDBitSet SelectionEvaluator::evaluate() { + OpenMDBitSet bs(nStuntDouble); if (isLoaded_) { pc = 0; instructionDispatchLoop(bs); @@ -417,8 +423,8 @@ namespace oopse { return bs; } - OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { - OOPSEBitSet bs(nStuntDouble); + OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { + OpenMDBitSet bs(nStuntDouble); if (value.type() == typeid(int)) { int index = boost::any_cast(value); @@ -440,7 +446,42 @@ namespace oopse { return bs; } + OpenMDBitSet SelectionEvaluator::allInstruction() { + OpenMDBitSet bs(nStuntDouble); + SimInfo::MoleculeIterator mi; + Molecule* mol; + Molecule::AtomIterator ai; + Atom* atom; + Molecule::RigidBodyIterator rbIter; + RigidBody* rb; + + // Doing the loop insures that we're actually on this processor. + + for (mol = info->beginMolecule(mi); mol != NULL; + mol = info->nextMolecule(mi)) { + + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + bs.setBitOn(atom->getGlobalIndex()); + } + + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { + bs.setBitOn(rb->getGlobalIndex()); + } + } + + return bs; + } + + OpenMDBitSet SelectionEvaluator::hull() { + OpenMDBitSet bs(nStuntDouble); + + bs = hullFinder.findHull(); + + return bs; + } + RealType SelectionEvaluator::getCharge(Atom* atom) { RealType charge =0.0; AtomType* atomType = atom->getAtomType(); @@ -455,7 +496,7 @@ namespace oopse { } else { sprintf( painCave.errMsg, "Can not cast GenericData to DoubleGenericData\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); }