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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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 (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);
    float propertyValue;
    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;
    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:	1627
Committed:	Tue Sep 13 22:05:04 2011 UTC (13 years, 7 months ago) by gezelter
File size:	14135 byte(s)
Log Message:	Splitting out ifstrstream into a header and an implementation. This means that much of the code that depends on it can be compiled only once and the parallel I/O is concentrated into a few files. To do this, a number of files that relied on basic_ifstrstream to load the mpi header had to be modified to manage their own headers.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	277	*/
41
42	tim	283	#include <stack>
43	tim	277	#include "selection/SelectionEvaluator.hpp"
44	tim	283	#include "primitives/Atom.hpp"
45			#include "primitives/DirectionalAtom.hpp"
46			#include "primitives/RigidBody.hpp"
47			#include "primitives/Molecule.hpp"
48	gezelter	1627	#include "io/ifstrstream.hpp"
49	tim	283
50	gezelter	1390	namespace OpenMD {
51	tim	277
52
53	gezelter	507	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
54	gezelter	1412	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
55			indexFinder(info),
56	cli2	1364	isLoaded_(false){
57			nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
58	gezelter	507	}
59	tim	283
60	cli2	1364	bool SelectionEvaluator::loadScript(const std::string& filename,
61			const std::string& script) {
62	tim	288	clearDefinitionsAndLoadPredefined();
63	tim	278	this->filename = filename;
64			this->script = script;
65			if (! compiler.compile(filename, script)) {
66	gezelter	507	error = true;
67			errorMessage = compiler.getErrorMessage();
68	cli2	1364
69			sprintf( painCave.errMsg,
70			"SelectionCompiler Error: %s\n", errorMessage.c_str());
71	gezelter	1390	painCave.severity = OPENMD_ERROR;
72	cli2	1364	painCave.isFatal = 1;
73			simError();
74	gezelter	507	return false;
75	tim	278	}
76
77			pc = 0;
78			aatoken = compiler.getAatokenCompiled();
79			linenumbers = compiler.getLineNumbers();
80			lineIndices = compiler.getLineIndices();
81	tim	288
82			std::vector<std::vector<Token> >::const_iterator i;
83
84			isDynamic_ = false;
85			for (i = aatoken.begin(); i != aatoken.end(); ++i) {
86	gezelter	507	if (containDynamicToken(*i)) {
87			isDynamic_ = true;
88			break;
89			}
90	tim	288	}
91
92			isLoaded_ = true;
93	tim	278	return true;
94	gezelter	507	}
95	tim	278
96	gezelter	507	void SelectionEvaluator::clearState() {
97	tim	278	error = false;
98	tim	281	errorMessage = "";
99	gezelter	507	}
100	tim	278
101	gezelter	507	bool SelectionEvaluator::loadScriptString(const std::string& script) {
102	tim	278	clearState();
103	tim	281	return loadScript("", script);
104	gezelter	507	}
105	tim	278
106	gezelter	507	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
107	tim	278	clearState();
108			return loadScriptFileInternal(filename);
109	gezelter	507	}
110	tim	278
111	cli2	1364	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
112			ifstrstream ifs(filename.c_str());
113	tim	288	if (!ifs.is_open()) {
114	gezelter	507	return false;
115	tim	288	}
116	cli2	1364
117	tim	288	const int bufferSize = 65535;
118			char buffer[bufferSize];
119			std::string script;
120			while(ifs.getline(buffer, bufferSize)) {
121	gezelter	507	script += buffer;
122	tim	288	}
123			return loadScript(filename, script);
124	gezelter	507	}
125	cli2	1364
126	gezelter	1390	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
127	tim	288
128	tim	281	while ( pc < aatoken.size()) {
129	gezelter	507	statement = aatoken[pc++];
130			statementLength = statement.size();
131			Token token = statement[0];
132			switch (token.tok) {
133			case Token::define:
134			define();
135			break;
136			case Token::select:
137			select(bs);
138			break;
139			default:
140			unrecognizedCommand(token);
141			return;
142			}
143	tim	278	}
144	tim	288
145	gezelter	507	}
146	tim	278
147	gezelter	1390	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
148	cli2	1364	int pcStart) {
149	gezelter	1390	OpenMDBitSet bs;
150			std::stack<OpenMDBitSet> stack;
151	cli2	1364
152	tim	288	for (int pc = pcStart; pc < code.size(); ++pc) {
153	tim	278	Token instruction = code[pc];
154	tim	282
155	tim	278	switch (instruction.tok) {
156	tim	281	case Token::expressionBegin:
157	tim	278	break;
158	tim	281	case Token::expressionEnd:
159	tim	282	break;
160	tim	281	case Token::all:
161	gezelter	1390	bs = OpenMDBitSet(nStuntDouble);
162	tim	283	bs.setAll();
163			stack.push(bs);
164	tim	278	break;
165	tim	281	case Token::none:
166	gezelter	1390	bs = OpenMDBitSet(nStuntDouble);
167	tim	283	stack.push(bs);
168	tim	278	break;
169	tim	281	case Token::opOr:
170	tim	283	bs = stack.top();
171			stack.pop();
172			stack.top() \|= bs;
173	tim	278	break;
174	tim	281	case Token::opAnd:
175	tim	283	bs = stack.top();
176			stack.pop();
177			stack.top() &= bs;
178	tim	278	break;
179	tim	281	case Token::opNot:
180	tim	283	stack.top().flip();
181	tim	278	break;
182	tim	281	case Token::within:
183	tim	283	withinInstruction(instruction, stack.top());
184	tim	278	break;
185	gezelter	1412	case Token::hull:
186			stack.push(hull());
187			break;
188	gezelter	507	//case Token::selected:
189			// stack.push(getSelectionSet());
190			// break;
191	tim	281	case Token::name:
192	tim	283	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
193	tim	278	break;
194	tim	295	case Token::index:
195			stack.push(indexInstruction(instruction.value));
196	tim	281	break;
197			case Token::identifier:
198	tim	283	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
199	tim	281	break;
200			case Token::opLT:
201			case Token::opLE:
202			case Token::opGE:
203			case Token::opGT:
204			case Token::opEQ:
205			case Token::opNE:
206	tim	283	stack.push(comparatorInstruction(instruction));
207	tim	278	break;
208			default:
209			unrecognizedExpression();
210			}
211			}
212	tim	283	if (stack.size() != 1)
213	tim	278	evalError("atom expression compiler error - stack over/underflow");
214	tim	283
215			return stack.top();
216	tim	278	}
217
218
219
220	gezelter	1390	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
221	tim	278	int comparator = instruction.tok;
222			int property = instruction.intValue;
223	tim	283	float comparisonValue = boost::any_cast<float>(instruction.value);
224			float propertyValue;
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	507	default:
282			unrecognizedAtomProperty(property);
283			}
284	tim	283
285	gezelter	507	bool match = false;
286			switch (comparator) {
287			case Token::opLT:
288			match = propertyValue < comparisonValue;
289			break;
290			case Token::opLE:
291			match = propertyValue <= comparisonValue;
292			break;
293			case Token::opGE:
294			match = propertyValue >= comparisonValue;
295			break;
296			case Token::opGT:
297			match = propertyValue > comparisonValue;
298			break;
299			case Token::opEQ:
300			match = propertyValue == comparisonValue;
301			break;
302			case Token::opNE:
303			match = propertyValue != comparisonValue;
304			break;
305			}
306			if (match)
307			bs.setBitOn(sd->getGlobalIndex());
308	cli2	1364
309	gezelter	507	}
310	tim	283
311	cli2	1364	void SelectionEvaluator::withinInstruction(const Token& instruction,
312	gezelter	1390	OpenMDBitSet& bs){
313	tim	295
314	tim	281	boost::any withinSpec = instruction.value;
315	tim	295	float distance;
316	tim	282	if (withinSpec.type() == typeid(float)){
317	gezelter	507	distance = boost::any_cast<float>(withinSpec);
318	tim	295	} else if (withinSpec.type() == typeid(int)) {
319	gezelter	507	distance = boost::any_cast<int>(withinSpec);
320	tim	295	} else {
321	gezelter	507	evalError("casting error in withinInstruction");
322			bs.clearAll();
323	tim	278	}
324	tim	282
325	tim	295	bs = distanceFinder.find(bs, distance);
326	gezelter	507	}
327	cli2	1364
328	gezelter	507	void SelectionEvaluator::define() {
329	tim	282	assert(statement.size() >= 3);
330	cli2	1364
331	tim	282	std::string variable = boost::any_cast<std::string>(statement[1].value);
332	cli2	1364
333			variables.insert(VariablesType::value_type(variable,
334			expression(statement, 2)));
335	gezelter	507	}
336	cli2	1364
337	tim	278
338	gezelter	507	/** @todo */
339			void SelectionEvaluator::predefine(const std::string& script) {
340	cli2	1364
341	tim	282	if (compiler.compile("#predefine", script)) {
342	gezelter	507	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
343			if (aatoken.size() != 1) {
344			evalError("predefinition does not have exactly 1 command:"
345			+ script);
346			return;
347			}
348			std::vector<Token> statement = aatoken[0];
349			if (statement.size() > 2) {
350			int tok = statement[1].tok;
351	cli2	1364	if (tok == Token::identifier \|\|
352			(tok & Token::predefinedset) == Token::predefinedset) {
353	gezelter	507	std::string variable = boost::any_cast<std::string>(statement[1].value);
354			variables.insert(VariablesType::value_type(variable, statement));
355	cli2	1364
356	gezelter	507	} else {
357			evalError("invalid variable name:" + script);
358			}
359			}else {
360			evalError("bad predefinition length:" + script);
361	cli2	1364	}
362	tim	282
363			} else {
364	gezelter	507	evalError("predefined set compile error:" + script +
365			"\ncompile error:" + compiler.getErrorMessage());
366	tim	282	}
367	gezelter	507	}
368	tim	282
369	gezelter	1390	void SelectionEvaluator::select(OpenMDBitSet& bs){
370	tim	288	bs = expression(statement, 1);
371	gezelter	507	}
372	cli2	1364
373	gezelter	1390	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
374	cli2	1364
375	gezelter	1390	OpenMDBitSet bs(nStuntDouble);
376	tim	282	std::map<std::string, boost::any>::iterator i = variables.find(variable);
377	tim	295
378	tim	282	if (i != variables.end()) {
379	gezelter	1390	if (i->second.type() == typeid(OpenMDBitSet)) {
380			return boost::any_cast<OpenMDBitSet>(i->second);
381	gezelter	507	} else if (i->second.type() == typeid(std::vector<Token>)){
382			bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
383			i->second = bs; /*@todo fixme /
384			return bs;
385			}
386	tim	283	} else {
387	gezelter	507	unrecognizedIdentifier(variable);
388	tim	282	}
389	cli2	1364
390	tim	295	return bs;
391	gezelter	507	}
392	cli2	1364
393	gezelter	1390	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
394	cli2	1364	return nameFinder.match(name);
395	gezelter	507	}
396	tim	283
397	gezelter	507	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
398	tim	288	std::vector<Token>::const_iterator i;
399			for (i = tokens.begin(); i != tokens.end(); ++i) {
400	gezelter	507	if (i->tok & Token::dynamic) {
401			return true;
402			}
403	tim	288	}
404	cli2	1364
405	tim	288	return false;
406	gezelter	507	}
407	tim	288
408	gezelter	507	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
409	tim	288	variables.clear();
410			//load predefine
411			//predefine();
412	gezelter	507	}
413	tim	288
414	gezelter	1390	OpenMDBitSet SelectionEvaluator::evaluate() {
415			OpenMDBitSet bs(nStuntDouble);
416	tim	288	if (isLoaded_) {
417	gezelter	507	pc = 0;
418			instructionDispatchLoop(bs);
419	tim	288	}
420
421			return bs;
422	gezelter	507	}
423	tim	295
424	gezelter	1390	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
425			OpenMDBitSet bs(nStuntDouble);
426	tim	295
427			if (value.type() == typeid(int)) {
428	gezelter	507	int index = boost::any_cast<int>(value);
429			if (index < 0 \|\| index >= bs.size()) {
430			invalidIndex(index);
431			} else {
432			bs = indexFinder.find(index);
433			}
434	tim	295	} else if (value.type() == typeid(std::pair<int, int>)) {
435	gezelter	507	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
436			assert(indexRange.first <= indexRange.second);
437			if (indexRange.first < 0 \|\| indexRange.second >= bs.size()) {
438			invalidIndexRange(indexRange);
439			}else {
440			bs = indexFinder.find(indexRange.first, indexRange.second);
441			}
442	tim	295	}
443
444			return bs;
445	gezelter	507	}
446	tim	295
447	tim	432
448	gezelter	1412	OpenMDBitSet SelectionEvaluator::hull() {
449			OpenMDBitSet bs(nStuntDouble);
450
451			bs = hullFinder.findHull();
452
453			return bs;
454			}
455
456
457
458	tim	963	RealType SelectionEvaluator::getCharge(Atom* atom) {
459			RealType charge =0.0;
460	tim	432	AtomType* atomType = atom->getAtomType();
461			if (atomType->isCharge()) {
462	gezelter	507	GenericData* data = atomType->getPropertyByName("Charge");
463			if (data != NULL) {
464			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
465	tim	432
466	gezelter	507	if (doubleData != NULL) {
467			charge = doubleData->getData();
468	tim	432
469	gezelter	507	} else {
470			sprintf( painCave.errMsg,
471			"Can not cast GenericData to DoubleGenericData\n");
472	gezelter	1390	painCave.severity = OPENMD_ERROR;
473	gezelter	507	painCave.isFatal = 1;
474			simError();
475			}
476			}
477	tim	432	}
478
479			return charge;
480	gezelter	507	}
481	tim	432
482			}