[ViewVC] Diff of: OpenMD/trunk/src/selection/SelectionEvaluator.cpp

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

+ * 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.
+ * 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 <stack>
+#include "selection/SelectionEvaluator.hpp"
-<
+namespace oopse {
->
+#include "primitives/Atom.hpp"
->
+#include "primitives/DirectionalAtom.hpp"
->
+#include "primitives/RigidBody.hpp"
->
+#include "primitives/Molecule.hpp"
->
+#include "io/ifstrstream.hpp"
-+
+namespace OpenMD {
-+
-+
+  SelectionEvaluator::SelectionEvaluator(SimInfo* si)
-+
+    : info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
-+
+      indexFinder(info),
-+
+      isLoaded_(false){
-+
+      nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
-+
+    }
-+
-+
+  bool SelectionEvaluator::loadScript(const std::string& filename,
-+
+                                      const std::string& script) {
-+
+    clearDefinitionsAndLoadPredefined();
-+
+    this->filename = filename;
-+
+    this->script = script;
-+
+    if (! compiler.compile(filename, script)) {
-+
+      error = true;
-+
+      errorMessage = compiler.getErrorMessage();
-+
-+
+      sprintf( painCave.errMsg,
-+
+               "SelectionCompiler Error: %s\n", errorMessage.c_str());
-+
+      painCave.severity = OPENMD_ERROR;
-+
+      painCave.isFatal = 1;
-+
+      simError();
-+
+      return false;
-+
+    }
-+
-+
+    pc = 0;
-+
+    aatoken = compiler.getAatokenCompiled();
-+
+    linenumbers = compiler.getLineNumbers();
-+
+    lineIndices = compiler.getLineIndices();
-+
-+
+    std::vector<std::vector<Token> >::const_iterator i;
-+
-+
+    isDynamic_ = false;
-+
+    for (i = aatoken.begin(); i != aatoken.end(); ++i) {
-+
+      if (containDynamicToken(*i)) {
-+
+        isDynamic_ = true;
-+
+        break;
-+
+      }
-+
+    }
-+
-+
+    isLoaded_ = true;
-+
+    return true;
-+
+  }
-+
-+
+  void SelectionEvaluator::clearState() {
-+
+    error = false;
-+
+    errorMessage = "";
-+
+  }
-+
-+
+  bool SelectionEvaluator::loadScriptString(const std::string& script) {
-+
+    clearState();
-+
+    return loadScript("", script);
-+
+  }
-+
-+
+  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
-+
+    clearState();
-+
+    return loadScriptFileInternal(filename);
-+
+  }
-+
-+
+  bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
-+
+    ifstrstream ifs(filename.c_str());
-+
+    if (!ifs.is_open()) {
-+
+      return false;
-+
+    }
-+
-+
+    const int bufferSize = 65535;
-+
+    char buffer[bufferSize];
-+
+    std::string script;
-+
+    while(ifs.getline(buffer, bufferSize)) {
-+
+      script += buffer;
-+
+    }
-+
+    return loadScript(filename, script);
-+
+  }
-+
-+
+  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
-+
-+
+    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);
-+
+        break;
-+
+      default:
-+
+        unrecognizedCommand(token);
-+
+        return;
-+
+      }
-+
+    }
-+
-+
+  }
-+
-+
+  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
-+
+                                             int pcStart) {
-+
+    OpenMDBitSet bs;
-+
+    std::stack<OpenMDBitSet> stack;
-+
-+
+    for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
-+
+      Token instruction = code[pc];
-+
-+
+      switch (instruction.tok) {
-+
+      case Token::expressionBegin:
-+
+        break;
-+
+      case Token::expressionEnd:
-+
+        break;
-+
+      case Token::all:
-+
+        bs = OpenMDBitSet(nStuntDouble);
-+
+        bs.setAll();
-+
+        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());
-+
+        break;
-+
+      case Token::hull:
-+
+        stack.push(hull());
-+
+        break;
-+
+        //case Token::selected:
-+
+        //  stack.push(getSelectionSet());
-+
+        //  break;
-+
+      case Token::name:
-+
+        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
-+
+        break;
-+
+      case Token::index:
-+
+        stack.push(indexInstruction(instruction.value));
-+
+        break;
-+
+      case Token::identifier:
-+
+        stack.push(lookupValue(boost::any_cast<std::string>(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));
-+
+        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<float>(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);
-+
+      }
-+
-+
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
-+
+           rb = mol->nextRigidBody(rbIter)) {
-+
+        compareProperty(rb, bs, property, comparator, comparisonValue);
-+
+      }
-+
+    }
-+
-+
+    return bs;
-+
+  }
-+
-+
+  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
-+
+                                           int property, int comparator,
-+
+                                           float comparisonValue) {
-+
+    RealType propertyValue = 0.0;
-+
+    switch (property) {
-+
+    case Token::mass:
-+
+      propertyValue = sd->getMass();
-+
+      break;
-+
+    case Token::charge:
-+
+      if (sd->isAtom()){
-+
+        Atom* atom = static_cast<Atom*>(sd);
-+
+        propertyValue = getCharge(atom);
-+
+      } else if (sd->isRigidBody()) {
-+
+        RigidBody* rb = static_cast<RigidBody*>(sd);
-+
+        RigidBody::AtomIterator ai;
-+
+        Atom* atom;
-+
+        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
-+
+          propertyValue+=  getCharge(atom);
-+
+        }
-+
+      }
-+
+      break;
-+
+    case Token::x:
-+
+      propertyValue = sd->getPos().x();
-+
+      break;
-+
+    case Token::y:
-+
+      propertyValue = sd->getPos().y();
-+
+      break;
-+
+    case Token::z:
-+
+      propertyValue = sd->getPos().z();
-+
+      break;
-+
+    case Token::r:
-+
+      propertyValue = sd->getPos().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)){
-+
+      distance = boost::any_cast<float>(withinSpec);
-+
+    } else if (withinSpec.type() == typeid(int)) {
-+
+      distance = boost::any_cast<int>(withinSpec);
-+
+    } else {
-+
+      evalError("casting error in withinInstruction");
-+
+      bs.clearAll();
-+
+    }
-+
-+
+    bs = distanceFinder.find(bs, distance);
-+
+  }
-+
-+
+  void SelectionEvaluator::define() {
-+
+    assert(statement.size() >= 3);
-+
-+
+    std::string variable = boost::any_cast<std::string>(statement[1].value);
-+
-+
+    variables.insert(VariablesType::value_type(variable,
-+
+                                               expression(statement, 2)));
-+
+  }
-+
-+
-+
+  /** @todo */
-+
+  void SelectionEvaluator::predefine(const std::string& script) {
-+
-+
+    if (compiler.compile("#predefine", script)) {
-+
+      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
-+
+      if (aatoken.size() != 1) {
-+
+        evalError("predefinition does not have exactly 1 command:"
-+
+                  + script);
-+
+        return;
-+
+      }
-+
+      std::vector<Token> statement = aatoken[0];
-+
+      if (statement.size() > 2) {
-+
+        int tok = statement[1].tok;
-+
+        if (tok == Token::identifier ||
-+
+            (tok & Token::predefinedset) == Token::predefinedset) {
-+
+          std::string variable = boost::any_cast<std::string>(statement[1].value);
-+
+          variables.insert(VariablesType::value_type(variable, statement));
-+
-+
+        } else {
-+
+          evalError("invalid variable name:" + script);
-+
+        }
-+
+      }else {
-+
+        evalError("bad predefinition length:" + script);
-+
+      }
-+
-+
+    } else {
-+
+      evalError("predefined set compile error:" + script +
-+
+                "\ncompile error:" + compiler.getErrorMessage());
-+
+    }
-+
+  }
-+
-+
+  void SelectionEvaluator::select(OpenMDBitSet& bs){
-+
+    bs = expression(statement, 1);
-+
+  }
-+
-+
+  OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
-+
-+
+    OpenMDBitSet bs(nStuntDouble);
-+
+    std::map<std::string, boost::any>::iterator i = variables.find(variable);
-+
-+
+    if (i != variables.end()) {
-+
+      if (i->second.type() == typeid(OpenMDBitSet)) {
-+
+        return boost::any_cast<OpenMDBitSet>(i->second);
-+
+      } else if (i->second.type() ==  typeid(std::vector<Token>)){
-+
+        bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
-+
+        i->second =  bs; /**@todo fixme */
-+
+        return bs;
-+
+      }
-+
+    } else {
-+
+      unrecognizedIdentifier(variable);
-+
+    }
-+
-+
+    return bs;
-+
+  }
-+
-+
+  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
-+
+    return nameFinder.match(name);
-+
+  }
-+
-+
+  bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
-+
+    std::vector<Token>::const_iterator i;
-+
+    for (i = tokens.begin(); i != tokens.end(); ++i) {
-+
+      if (i->tok & Token::dynamic) {
-+
+        return true;
-+
+      }
-+
+    }
-+
-+
+    return false;
-+
+  }
-+
-+
+  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
-+
+    variables.clear();
-+
+    //load predefine
-+
+    //predefine();
-+
+  }
-+
-+
+  OpenMDBitSet SelectionEvaluator::evaluate() {
-+
+    OpenMDBitSet bs(nStuntDouble);
-+
+    if (isLoaded_) {
-+
+      pc = 0;
-+
+      instructionDispatchLoop(bs);
-+
+    }
-+
-+
+    return bs;
-+
+  }
-+
-+
+  OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
-+
+    OpenMDBitSet bs(nStuntDouble);
-+
-+
+    if (value.type() == typeid(int)) {
-+
+      int index = boost::any_cast<int>(value);
-+
+      if (index < 0 || index >= bs.size()) {
-+
+        invalidIndex(index);
-+
+      } else {
-+
+        bs = indexFinder.find(index);
-+
+      }
-+
+    } else if (value.type() == typeid(std::pair<int, int>)) {
-+
+      std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
-+
+      assert(indexRange.first <= indexRange.second);
-+
+      if (indexRange.first < 0 || indexRange.second >= bs.size()) {
-+
+        invalidIndexRange(indexRange);
-+
+      }else {
-+
+        bs = indexFinder.find(indexRange.first, indexRange.second);
-+
+      }
-+
+    }
-+
-+
+    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();
-+
+    if (atomType->isCharge()) {
-+
+      GenericData* data = atomType->getPropertyByName("Charge");
-+
+      if (data != NULL) {
-+
+        DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
-+
-+
+        if (doubleData != NULL) {
-+
+          charge = doubleData->getData();
-+
-+
+        } else {
-+
+          sprintf( painCave.errMsg,
-+
+                   "Can not cast GenericData to DoubleGenericData\n");
-+
+          painCave.severity = OPENMD_ERROR;
-+
+          painCave.isFatal = 1;
-+
+          simError();
-+
+        }
-+
+      }
-+
+    }
-+
-+
+    return charge;
-+
+  }
-+

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 \| Line 1
1	+	Author Id Revision Date

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+Removed lines
-+
+Added lines
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+Changed lines
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+Changed lines

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents): Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs. Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords): Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs. Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

Diff Legend

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC