src/selection/SelectionEvaluator.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 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.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * 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"
#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;
  }

}
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	14262 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	tim	277	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	277	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	277	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	277	*/
42
43	tim	283	#include <stack>
44	tim	277	#include "selection/SelectionEvaluator.hpp"
45	tim	283	#include "primitives/Atom.hpp"
46			#include "primitives/DirectionalAtom.hpp"
47			#include "primitives/RigidBody.hpp"
48			#include "primitives/Molecule.hpp"
49	gezelter	1782	#include "io/ifstrstream.hpp"
50	tim	283
51	gezelter	1390	namespace OpenMD {
52	tim	277
53
54	gezelter	507	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
55	gezelter	1412	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
56			indexFinder(info),
57	cli2	1364	isLoaded_(false){
58			nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
59	gezelter	507	}
60	tim	283
61	cli2	1364	bool SelectionEvaluator::loadScript(const std::string& filename,
62			const std::string& script) {
63	tim	288	clearDefinitionsAndLoadPredefined();
64	tim	278	this->filename = filename;
65			this->script = script;
66			if (! compiler.compile(filename, script)) {
67	gezelter	507	error = true;
68			errorMessage = compiler.getErrorMessage();
69	cli2	1364
70			sprintf( painCave.errMsg,
71			"SelectionCompiler Error: %s\n", errorMessage.c_str());
72	gezelter	1390	painCave.severity = OPENMD_ERROR;
73	cli2	1364	painCave.isFatal = 1;
74			simError();
75	gezelter	507	return false;
76	tim	278	}
77
78			pc = 0;
79			aatoken = compiler.getAatokenCompiled();
80			linenumbers = compiler.getLineNumbers();
81			lineIndices = compiler.getLineIndices();
82	tim	288
83			std::vector<std::vector<Token> >::const_iterator i;
84
85			isDynamic_ = false;
86			for (i = aatoken.begin(); i != aatoken.end(); ++i) {
87	gezelter	507	if (containDynamicToken(*i)) {
88			isDynamic_ = true;
89			break;
90			}
91	tim	288	}
92
93			isLoaded_ = true;
94	tim	278	return true;
95	gezelter	507	}
96	tim	278
97	gezelter	507	void SelectionEvaluator::clearState() {
98	tim	278	error = false;
99	tim	281	errorMessage = "";
100	gezelter	507	}
101	tim	278
102	gezelter	507	bool SelectionEvaluator::loadScriptString(const std::string& script) {
103	tim	278	clearState();
104	tim	281	return loadScript("", script);
105	gezelter	507	}
106	tim	278
107	gezelter	507	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
108	tim	278	clearState();
109			return loadScriptFileInternal(filename);
110	gezelter	507	}
111	tim	278
112	cli2	1364	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
113			ifstrstream ifs(filename.c_str());
114	tim	288	if (!ifs.is_open()) {
115	gezelter	507	return false;
116	tim	288	}
117	cli2	1364
118	tim	288	const int bufferSize = 65535;
119			char buffer[bufferSize];
120			std::string script;
121			while(ifs.getline(buffer, bufferSize)) {
122	gezelter	507	script += buffer;
123	tim	288	}
124			return loadScript(filename, script);
125	gezelter	507	}
126	cli2	1364
127	gezelter	1390	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
128	tim	288
129	tim	281	while ( pc < aatoken.size()) {
130	gezelter	507	statement = aatoken[pc++];
131			statementLength = statement.size();
132			Token token = statement[0];
133			switch (token.tok) {
134			case Token::define:
135			define();
136			break;
137			case Token::select:
138			select(bs);
139			break;
140			default:
141			unrecognizedCommand(token);
142			return;
143			}
144	tim	278	}
145	tim	288
146	gezelter	507	}
147	tim	278
148	gezelter	1390	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
149	cli2	1364	int pcStart) {
150	gezelter	1390	OpenMDBitSet bs;
151			std::stack<OpenMDBitSet> stack;
152	cli2	1364
153	gezelter	1782	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
154	tim	278	Token instruction = code[pc];
155	tim	282
156	tim	278	switch (instruction.tok) {
157	tim	281	case Token::expressionBegin:
158	tim	278	break;
159	tim	281	case Token::expressionEnd:
160	tim	282	break;
161	tim	281	case Token::all:
162	gezelter	1390	bs = OpenMDBitSet(nStuntDouble);
163	tim	283	bs.setAll();
164			stack.push(bs);
165	tim	278	break;
166	tim	281	case Token::none:
167	gezelter	1390	bs = OpenMDBitSet(nStuntDouble);
168	tim	283	stack.push(bs);
169	tim	278	break;
170	tim	281	case Token::opOr:
171	tim	283	bs = stack.top();
172			stack.pop();
173			stack.top() \|= bs;
174	tim	278	break;
175	tim	281	case Token::opAnd:
176	tim	283	bs = stack.top();
177			stack.pop();
178			stack.top() &= bs;
179	tim	278	break;
180	tim	281	case Token::opNot:
181	tim	283	stack.top().flip();
182	tim	278	break;
183	tim	281	case Token::within:
184	tim	283	withinInstruction(instruction, stack.top());
185	tim	278	break;
186	gezelter	1412	case Token::hull:
187			stack.push(hull());
188			break;
189	gezelter	507	//case Token::selected:
190			// stack.push(getSelectionSet());
191			// break;
192	tim	281	case Token::name:
193	tim	283	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
194	tim	278	break;
195	tim	295	case Token::index:
196			stack.push(indexInstruction(instruction.value));
197	tim	281	break;
198			case Token::identifier:
199	tim	283	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
200	tim	281	break;
201			case Token::opLT:
202			case Token::opLE:
203			case Token::opGE:
204			case Token::opGT:
205			case Token::opEQ:
206			case Token::opNE:
207	tim	283	stack.push(comparatorInstruction(instruction));
208	tim	278	break;
209			default:
210			unrecognizedExpression();
211			}
212			}
213	tim	283	if (stack.size() != 1)
214	tim	278	evalError("atom expression compiler error - stack over/underflow");
215	tim	283
216			return stack.top();
217	tim	278	}
218
219
220
221	gezelter	1390	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
222	tim	278	int comparator = instruction.tok;
223			int property = instruction.intValue;
224	tim	283	float comparisonValue = boost::any_cast<float>(instruction.value);
225	gezelter	1390	OpenMDBitSet bs(nStuntDouble);
226	tim	295	bs.clearAll();
227	tim	283
228			SimInfo::MoleculeIterator mi;
229			Molecule* mol;
230			Molecule::AtomIterator ai;
231			Atom* atom;
232			Molecule::RigidBodyIterator rbIter;
233			RigidBody* rb;
234	tim	281
235	cli2	1364	for (mol = info->beginMolecule(mi); mol != NULL;
236			mol = info->nextMolecule(mi)) {
237
238	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
239			compareProperty(atom, bs, property, comparator, comparisonValue);
240			}
241	cli2	1364
242			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
243			rb = mol->nextRigidBody(rbIter)) {
244			compareProperty(rb, bs, property, comparator, comparisonValue);
245			}
246	tim	278	}
247
248	tim	283	return bs;
249	gezelter	507	}
250	tim	278
251	gezelter	1390	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
252	cli2	1364	int property, int comparator,
253			float comparisonValue) {
254	tim	963	RealType propertyValue = 0.0;
255	gezelter	507	switch (property) {
256			case Token::mass:
257			propertyValue = sd->getMass();
258			break;
259			case Token::charge:
260			if (sd->isAtom()){
261			Atom* atom = static_cast<Atom*>(sd);
262			propertyValue = getCharge(atom);
263			} else if (sd->isRigidBody()) {
264			RigidBody* rb = static_cast<RigidBody*>(sd);
265			RigidBody::AtomIterator ai;
266			Atom* atom;
267			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
268			propertyValue+= getCharge(atom);
269			}
270			}
271			break;
272	cli2	1360	case Token::x:
273			propertyValue = sd->getPos().x();
274			break;
275			case Token::y:
276			propertyValue = sd->getPos().y();
277			break;
278			case Token::z:
279			propertyValue = sd->getPos().z();
280			break;
281	gezelter	1513	case Token::r:
282			propertyValue = sd->getPos().length();
283			break;
284	gezelter	507	default:
285			unrecognizedAtomProperty(property);
286			}
287	tim	283
288	gezelter	507	bool match = false;
289			switch (comparator) {
290			case Token::opLT:
291			match = propertyValue < comparisonValue;
292			break;
293			case Token::opLE:
294			match = propertyValue <= comparisonValue;
295			break;
296			case Token::opGE:
297			match = propertyValue >= comparisonValue;
298			break;
299			case Token::opGT:
300			match = propertyValue > comparisonValue;
301			break;
302			case Token::opEQ:
303			match = propertyValue == comparisonValue;
304			break;
305			case Token::opNE:
306			match = propertyValue != comparisonValue;
307			break;
308			}
309			if (match)
310			bs.setBitOn(sd->getGlobalIndex());
311	cli2	1364
312	gezelter	507	}
313	tim	283
314	cli2	1364	void SelectionEvaluator::withinInstruction(const Token& instruction,
315	gezelter	1390	OpenMDBitSet& bs){
316	tim	295
317	tim	281	boost::any withinSpec = instruction.value;
318	tim	295	float distance;
319	tim	282	if (withinSpec.type() == typeid(float)){
320	gezelter	507	distance = boost::any_cast<float>(withinSpec);
321	tim	295	} else if (withinSpec.type() == typeid(int)) {
322	gezelter	507	distance = boost::any_cast<int>(withinSpec);
323	tim	295	} else {
324	gezelter	507	evalError("casting error in withinInstruction");
325			bs.clearAll();
326	tim	278	}
327	tim	282
328	tim	295	bs = distanceFinder.find(bs, distance);
329	gezelter	507	}
330	cli2	1364
331	gezelter	507	void SelectionEvaluator::define() {
332	tim	282	assert(statement.size() >= 3);
333	cli2	1364
334	tim	282	std::string variable = boost::any_cast<std::string>(statement[1].value);
335	cli2	1364
336			variables.insert(VariablesType::value_type(variable,
337			expression(statement, 2)));
338	gezelter	507	}
339	cli2	1364
340	tim	278
341	gezelter	507	/** @todo */
342			void SelectionEvaluator::predefine(const std::string& script) {
343	cli2	1364
344	tim	282	if (compiler.compile("#predefine", script)) {
345	gezelter	507	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
346			if (aatoken.size() != 1) {
347			evalError("predefinition does not have exactly 1 command:"
348			+ script);
349			return;
350			}
351			std::vector<Token> statement = aatoken[0];
352			if (statement.size() > 2) {
353			int tok = statement[1].tok;
354	cli2	1364	if (tok == Token::identifier \|\|
355			(tok & Token::predefinedset) == Token::predefinedset) {
356	gezelter	507	std::string variable = boost::any_cast<std::string>(statement[1].value);
357			variables.insert(VariablesType::value_type(variable, statement));
358	cli2	1364
359	gezelter	507	} else {
360			evalError("invalid variable name:" + script);
361			}
362			}else {
363			evalError("bad predefinition length:" + script);
364	cli2	1364	}
365	tim	282
366			} else {
367	gezelter	507	evalError("predefined set compile error:" + script +
368			"\ncompile error:" + compiler.getErrorMessage());
369	tim	282	}
370	gezelter	507	}
371	tim	282
372	gezelter	1390	void SelectionEvaluator::select(OpenMDBitSet& bs){
373	tim	288	bs = expression(statement, 1);
374	gezelter	507	}
375	cli2	1364
376	gezelter	1390	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
377	cli2	1364
378	gezelter	1390	OpenMDBitSet bs(nStuntDouble);
379	tim	282	std::map<std::string, boost::any>::iterator i = variables.find(variable);
380	tim	295
381	tim	282	if (i != variables.end()) {
382	gezelter	1390	if (i->second.type() == typeid(OpenMDBitSet)) {
383			return boost::any_cast<OpenMDBitSet>(i->second);
384	gezelter	507	} else if (i->second.type() == typeid(std::vector<Token>)){
385			bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
386			i->second = bs; /*@todo fixme /
387			return bs;
388			}
389	tim	283	} else {
390	gezelter	507	unrecognizedIdentifier(variable);
391	tim	282	}
392	cli2	1364
393	tim	295	return bs;
394	gezelter	507	}
395	cli2	1364
396	gezelter	1390	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
397	cli2	1364	return nameFinder.match(name);
398	gezelter	507	}
399	tim	283
400	gezelter	507	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
401	tim	288	std::vector<Token>::const_iterator i;
402			for (i = tokens.begin(); i != tokens.end(); ++i) {
403	gezelter	507	if (i->tok & Token::dynamic) {
404			return true;
405			}
406	tim	288	}
407	cli2	1364
408	tim	288	return false;
409	gezelter	507	}
410	tim	288
411	gezelter	507	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
412	tim	288	variables.clear();
413			//load predefine
414			//predefine();
415	gezelter	507	}
416	tim	288
417	gezelter	1390	OpenMDBitSet SelectionEvaluator::evaluate() {
418			OpenMDBitSet bs(nStuntDouble);
419	tim	288	if (isLoaded_) {
420	gezelter	507	pc = 0;
421			instructionDispatchLoop(bs);
422	tim	288	}
423
424			return bs;
425	gezelter	507	}
426	tim	295
427	gezelter	1390	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
428			OpenMDBitSet bs(nStuntDouble);
429	tim	295
430			if (value.type() == typeid(int)) {
431	gezelter	507	int index = boost::any_cast<int>(value);
432			if (index < 0 \|\| index >= bs.size()) {
433			invalidIndex(index);
434			} else {
435			bs = indexFinder.find(index);
436			}
437	tim	295	} else if (value.type() == typeid(std::pair<int, int>)) {
438	gezelter	507	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
439			assert(indexRange.first <= indexRange.second);
440			if (indexRange.first < 0 \|\| indexRange.second >= bs.size()) {
441			invalidIndexRange(indexRange);
442			}else {
443			bs = indexFinder.find(indexRange.first, indexRange.second);
444			}
445	tim	295	}
446
447			return bs;
448	gezelter	507	}
449	tim	295
450	tim	432
451	gezelter	1412	OpenMDBitSet SelectionEvaluator::hull() {
452			OpenMDBitSet bs(nStuntDouble);
453
454			bs = hullFinder.findHull();
455
456			return bs;
457			}
458
459
460
461	tim	963	RealType SelectionEvaluator::getCharge(Atom* atom) {
462			RealType charge =0.0;
463	tim	432	AtomType* atomType = atom->getAtomType();
464			if (atomType->isCharge()) {
465	gezelter	507	GenericData* data = atomType->getPropertyByName("Charge");
466			if (data != NULL) {
467			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
468	tim	432
469	gezelter	507	if (doubleData != NULL) {
470			charge = doubleData->getData();
471	tim	432
472	gezelter	507	} else {
473			sprintf( painCave.errMsg,
474			"Can not cast GenericData to DoubleGenericData\n");
475	gezelter	1390	painCave.severity = OPENMD_ERROR;
476	gezelter	507	painCave.isFatal = 1;
477			simError();
478			}
479			}
480	tim	432	}
481
482			return charge;
483	gezelter	507	}
484	tim	432
485			}