--- trunk/src/selection/SelectionEvaluator.cpp 2009/10/07 20:49:50 1364 +++ trunk/src/selection/SelectionEvaluator.cpp 2013/08/19 19:20:32 1931 @@ -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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -45,13 +46,17 @@ #include "primitives/DirectionalAtom.hpp" #include "primitives/RigidBody.hpp" #include "primitives/Molecule.hpp" -#include "io/basic_ifstrstream.hpp" +#include "io/ifstrstream.hpp" +#include "types/FixedChargeAdapter.hpp" +#include "types/FluctuatingChargeAdapter.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), hasSurfaceArea_(false), isLoaded_(false){ nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies(); } @@ -67,7 +72,7 @@ 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 +127,7 @@ 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 +148,33 @@ namespace oopse { } - OOPSEBitSet SelectionEvaluator::expression(const std::vector& code, + void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){ + + while ( pc < aatoken.size()) { + statement = aatoken[pc++]; + statementLength = statement.size(); + Token token = statement[0]; + switch (token.tok) { + case Token::define: + define(); + break; + case Token::select: + select(bs, frame); + break; + default: + unrecognizedCommand(token); + return; + } + } + + } + + 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 +183,11 @@ 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 +206,9 @@ namespace oopse { case Token::within: withinInstruction(instruction, stack.top()); break; + case Token::hull: + stack.push(hull()); + break; //case Token::selected: // stack.push(getSelectionSet()); // break; @@ -212,13 +240,83 @@ namespace oopse { } + OpenMDBitSet SelectionEvaluator::expression(const std::vector& code, + int pcStart, int frame) { + OpenMDBitSet bs; + std::stack stack; + + for (unsigned int pc = pcStart; pc < code.size(); ++pc) { + Token instruction = code[pc]; - OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { + switch (instruction.tok) { + case Token::expressionBegin: + break; + case Token::expressionEnd: + break; + case Token::all: + bs = allInstruction(); + stack.push(bs); + break; + case Token::none: + bs = OpenMDBitSet(nStuntDouble); + stack.push(bs); + break; + case Token::opOr: + bs = stack.top(); + stack.pop(); + stack.top() |= bs; + break; + case Token::opAnd: + bs = stack.top(); + stack.pop(); + stack.top() &= bs; + break; + case Token::opNot: + stack.top().flip(); + break; + case Token::within: + withinInstruction(instruction, stack.top(), frame); + break; + case Token::hull: + stack.push(hull(frame)); + break; + //case Token::selected: + // stack.push(getSelectionSet()); + // break; + case Token::name: + stack.push(nameInstruction(boost::any_cast(instruction.value))); + break; + case Token::index: + stack.push(indexInstruction(instruction.value)); + break; + case Token::identifier: + stack.push(lookupValue(boost::any_cast(instruction.value))); + break; + case Token::opLT: + case Token::opLE: + case Token::opGE: + case Token::opGT: + case Token::opEQ: + case Token::opNE: + stack.push(comparatorInstruction(instruction, frame)); + break; + default: + unrecognizedExpression(); + } + } + if (stack.size() != 1) + evalError("atom expression compiler error - stack over/underflow"); + + return stack.top(); + } + + + + 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; @@ -244,10 +342,42 @@ namespace oopse { return bs; } - void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, + OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) { + int comparator = instruction.tok; + int property = instruction.intValue; + float comparisonValue = boost::any_cast(instruction.value); + OpenMDBitSet bs(nStuntDouble); + bs.clearAll(); + + SimInfo::MoleculeIterator mi; + Molecule* mol; + Molecule::AtomIterator ai; + Atom* atom; + Molecule::RigidBodyIterator rbIter; + RigidBody* rb; + + for (mol = info->beginMolecule(mi); mol != NULL; + mol = info->nextMolecule(mi)) { + + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + compareProperty(atom, bs, property, comparator, comparisonValue, frame); + } + + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { + compareProperty(rb, bs, property, comparator, comparisonValue, frame); + } + } + + return bs; + } + + void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue) { RealType propertyValue = 0.0; + Vector3d pos; + switch (property) { case Token::mass: propertyValue = sd->getMass(); @@ -274,6 +404,24 @@ namespace oopse { case Token::z: propertyValue = sd->getPos().z(); break; + case Token::wrappedX: + pos = sd->getPos(); + info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); + propertyValue = pos.x(); + break; + case Token::wrappedY: + pos = sd->getPos(); + info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); + propertyValue = pos.y(); + break; + case Token::wrappedZ: + pos = sd->getPos(); + info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); + propertyValue = pos.z(); + break; + case Token::r: + propertyValue = sd->getPos().length(); + break; default: unrecognizedAtomProperty(property); } @@ -299,14 +447,97 @@ namespace oopse { match = propertyValue != comparisonValue; break; } - if (match) + + if (match) bs.setBitOn(sd->getGlobalIndex()); + } - void SelectionEvaluator::withinInstruction(const Token& instruction, - OOPSEBitSet& bs){ + void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, + int property, int comparator, + float comparisonValue, int frame) { + RealType propertyValue = 0.0; + Vector3d pos; + switch (property) { + case Token::mass: + propertyValue = sd->getMass(); + break; + case Token::charge: + if (sd->isAtom()){ + Atom* atom = static_cast(sd); + propertyValue = getCharge(atom,frame); + } else if (sd->isRigidBody()) { + RigidBody* rb = static_cast(sd); + RigidBody::AtomIterator ai; + Atom* atom; + for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { + propertyValue+= getCharge(atom,frame); + } + } + break; + case Token::x: + propertyValue = sd->getPos(frame).x(); + break; + case Token::y: + propertyValue = sd->getPos(frame).y(); + break; + case Token::z: + propertyValue = sd->getPos(frame).z(); + break; + case Token::wrappedX: + pos = sd->getPos(frame); + info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); + propertyValue = pos.x(); + break; + case Token::wrappedY: + pos = sd->getPos(frame); + info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); + propertyValue = pos.y(); + break; + case Token::wrappedZ: + pos = sd->getPos(frame); + info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); + propertyValue = pos.z(); + break; + + case Token::r: + propertyValue = sd->getPos(frame).length(); + break; + default: + unrecognizedAtomProperty(property); + } + + bool match = false; + switch (comparator) { + case Token::opLT: + match = propertyValue < comparisonValue; + break; + case Token::opLE: + match = propertyValue <= comparisonValue; + break; + case Token::opGE: + match = propertyValue >= comparisonValue; + break; + case Token::opGT: + match = propertyValue > comparisonValue; + break; + case Token::opEQ: + match = propertyValue == comparisonValue; + break; + case Token::opNE: + match = propertyValue != comparisonValue; + break; + } + if (match) + bs.setBitOn(sd->getGlobalIndex()); + + } + + void SelectionEvaluator::withinInstruction(const Token& instruction, + OpenMDBitSet& bs){ + boost::any withinSpec = instruction.value; float distance; if (withinSpec.type() == typeid(float)){ @@ -320,6 +551,23 @@ namespace oopse { bs = distanceFinder.find(bs, distance); } + + void SelectionEvaluator::withinInstruction(const Token& instruction, + OpenMDBitSet& bs, int frame){ + + boost::any withinSpec = instruction.value; + float distance; + if (withinSpec.type() == typeid(float)){ + distance = boost::any_cast(withinSpec); + } else if (withinSpec.type() == typeid(int)) { + distance = boost::any_cast(withinSpec); + } else { + evalError("casting error in withinInstruction"); + bs.clearAll(); + } + + bs = distanceFinder.find(bs, distance, frame); + } void SelectionEvaluator::define() { assert(statement.size() >= 3); @@ -362,18 +610,22 @@ namespace oopse { } } - void SelectionEvaluator::select(OOPSEBitSet& bs){ + void SelectionEvaluator::select(OpenMDBitSet& bs){ bs = expression(statement, 1); } + + void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){ + bs = expression(statement, 1, frame); + } - 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 +638,7 @@ namespace oopse { return bs; } - OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){ + OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){ return nameFinder.match(name); } @@ -407,18 +659,26 @@ namespace oopse { //predefine(); } - OOPSEBitSet SelectionEvaluator::evaluate() { - OOPSEBitSet bs(nStuntDouble); + OpenMDBitSet SelectionEvaluator::evaluate() { + OpenMDBitSet bs(nStuntDouble); if (isLoaded_) { pc = 0; instructionDispatchLoop(bs); } + return bs; + } + OpenMDBitSet SelectionEvaluator::evaluate(int frame) { + OpenMDBitSet bs(nStuntDouble); + if (isLoaded_) { + pc = 0; + instructionDispatchLoop(bs, frame); + } 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); @@ -440,28 +700,81 @@ 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(); + surfaceArea_ = hullFinder.getSurfaceArea(); + hasSurfaceArea_ = true; + return bs; + } + + + OpenMDBitSet SelectionEvaluator::hull(int frame) { + OpenMDBitSet bs(nStuntDouble); + + bs = hullFinder.findHull(frame); + + return bs; + } + RealType SelectionEvaluator::getCharge(Atom* atom) { - RealType charge =0.0; + RealType charge = 0.0; AtomType* atomType = atom->getAtomType(); - if (atomType->isCharge()) { - GenericData* data = atomType->getPropertyByName("Charge"); - if (data != NULL) { - DoubleGenericData* doubleData= dynamic_cast(data); - if (doubleData != NULL) { - charge = doubleData->getData(); - - } else { - sprintf( painCave.errMsg, - "Can not cast GenericData to DoubleGenericData\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } - } + FixedChargeAdapter fca = FixedChargeAdapter(atomType); + if ( fca.isFixedCharge() ) { + charge = fca.getCharge(); } + + FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); + if ( fqa.isFluctuatingCharge() ) { + charge += atom->getFlucQPos(); + } + return charge; + } + RealType SelectionEvaluator::getCharge(Atom* atom, int frame) { + RealType charge = 0.0; + AtomType* atomType = atom->getAtomType(); + + FixedChargeAdapter fca = FixedChargeAdapter(atomType); + if ( fca.isFixedCharge() ) { + charge = fca.getCharge(); + } + + FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); + if ( fqa.isFluctuatingCharge() ) { + charge += atom->getFlucQPos(frame); + } return charge; }