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. 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
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include <stack>
#include "selection/SelectionEvaluator.hpp"
#include "primitives/Atom.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Molecule.hpp"

namespace oopse {


SelectionEvaluator::SelectionEvaluator(SimInfo* si) 
    : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
    
    nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
}            

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();
        std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
        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) {
  std::ifstream 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(BitSet& 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;
        }
    }

}

  BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
    BitSet bs;
    std::stack<BitSet> 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 = BitSet(nStuntDouble);
        bs.setAll();
        stack.push(bs);            
        break;
      case Token::none:
        bs = BitSet(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::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();
  }


BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
    int comparator = instruction.tok;
    int property = instruction.intValue;
    float comparisonValue = boost::any_cast<float>(instruction.value);
    float propertyValue;
    BitSet 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, BitSet& bs, int property, int comparator, float comparisonValue) {
        double 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;
        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, BitSet& 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(BitSet& bs){
    bs = expression(statement, 1);
}

BitSet SelectionEvaluator::lookupValue(const std::string& variable){

    BitSet bs(nStuntDouble);
    std::map<std::string, boost::any>::iterator i = variables.find(variable);
    
    if (i != variables.end()) {
        if (i->second.type() == typeid(BitSet)) {
            return boost::any_cast<BitSet>(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;
}

BitSet 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();
}

BitSet SelectionEvaluator::evaluate() {
    BitSet bs(nStuntDouble);
    if (isLoaded_) {
        pc = 0;
        instructionDispatchLoop(bs);
    }

    return bs;
}

BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
    BitSet 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;
}


double SelectionEvaluator::getCharge(Atom* atom) {
    double 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 = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
            }
        } 
    }

    return charge;
}

}
Revision:	432
Committed:	Fri Mar 11 15:00:20 2005 UTC (20 years, 1 month ago) by tim
Original Path:	*trunk/src/selection/SelectionEvaluator.cpp*
File size:	13940 byte(s)
Log Message:	clean up SimInfo; modify the images of SelectionExpression.html
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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
49	tim	277	namespace oopse {
50
51
52	tim	413	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
53			: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54
55	tim	295	nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56	tim	283	}
57
58	tim	278	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
59	tim	288	clearDefinitionsAndLoadPredefined();
60	tim	278	this->filename = filename;
61			this->script = script;
62			if (! compiler.compile(filename, script)) {
63			error = true;
64			errorMessage = compiler.getErrorMessage();
65	tim	288	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
66	tim	278	return false;
67			}
68
69			pc = 0;
70			aatoken = compiler.getAatokenCompiled();
71			linenumbers = compiler.getLineNumbers();
72			lineIndices = compiler.getLineIndices();
73	tim	288
74			std::vector<std::vector<Token> >::const_iterator i;
75
76			isDynamic_ = false;
77			for (i = aatoken.begin(); i != aatoken.end(); ++i) {
78			if (containDynamicToken(*i)) {
79			isDynamic_ = true;
80			break;
81			}
82			}
83
84			isLoaded_ = true;
85	tim	278	return true;
86	tim	277	}
87	tim	278
88			void SelectionEvaluator::clearState() {
89			error = false;
90	tim	281	errorMessage = "";
91	tim	278	}
92
93			bool SelectionEvaluator::loadScriptString(const std::string& script) {
94			clearState();
95	tim	281	return loadScript("", script);
96	tim	278	}
97
98			bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
99			clearState();
100			return loadScriptFileInternal(filename);
101			}
102
103	tim	283	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
104	chrisfen	301	std::ifstream ifs(filename.c_str());
105	tim	288	if (!ifs.is_open()) {
106			return false;
107			}
108
109			const int bufferSize = 65535;
110			char buffer[bufferSize];
111			std::string script;
112			while(ifs.getline(buffer, bufferSize)) {
113			script += buffer;
114			}
115			return loadScript(filename, script);
116	tim	282	}
117
118	tim	288	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
119
120	tim	281	while ( pc < aatoken.size()) {
121	tim	278	statement = aatoken[pc++];
122	tim	281	statementLength = statement.size();
123	tim	278	Token token = statement[0];
124			switch (token.tok) {
125	tim	281	case Token::define:
126	tim	278	define();
127			break;
128	tim	281	case Token::select:
129	tim	288	select(bs);
130	tim	278	break;
131			default:
132			unrecognizedCommand(token);
133			return;
134			}
135			}
136	tim	288
137	tim	278	}
138
139	tim	283	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
140	tim	278	BitSet bs;
141	tim	283	std::stack<BitSet> stack;
142
143	tim	288	for (int pc = pcStart; pc < code.size(); ++pc) {
144	tim	278	Token instruction = code[pc];
145	tim	282
146	tim	278	switch (instruction.tok) {
147	tim	281	case Token::expressionBegin:
148	tim	278	break;
149	tim	281	case Token::expressionEnd:
150	tim	282	break;
151	tim	281	case Token::all:
152	tim	283	bs = BitSet(nStuntDouble);
153			bs.setAll();
154			stack.push(bs);
155	tim	278	break;
156	tim	281	case Token::none:
157	tim	283	bs = BitSet(nStuntDouble);
158			stack.push(bs);
159	tim	278	break;
160	tim	281	case Token::opOr:
161	tim	283	bs = stack.top();
162			stack.pop();
163			stack.top() \|= bs;
164	tim	278	break;
165	tim	281	case Token::opAnd:
166	tim	283	bs = stack.top();
167			stack.pop();
168			stack.top() &= bs;
169	tim	278	break;
170	tim	281	case Token::opNot:
171	tim	283	stack.top().flip();
172	tim	278	break;
173	tim	281	case Token::within:
174	tim	283
175			withinInstruction(instruction, stack.top());
176	tim	278	break;
177	tim	283	//case Token::selected:
178			// stack.push(getSelectionSet());
179			// break;
180	tim	281	case Token::name:
181	tim	283	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
182	tim	278	break;
183	tim	295	case Token::index:
184			stack.push(indexInstruction(instruction.value));
185	tim	281	break;
186			case Token::identifier:
187	tim	283	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
188	tim	281	break;
189			case Token::opLT:
190			case Token::opLE:
191			case Token::opGE:
192			case Token::opGT:
193			case Token::opEQ:
194			case Token::opNE:
195	tim	283	stack.push(comparatorInstruction(instruction));
196	tim	278	break;
197			default:
198			unrecognizedExpression();
199			}
200			}
201	tim	283	if (stack.size() != 1)
202	tim	278	evalError("atom expression compiler error - stack over/underflow");
203	tim	283
204			return stack.top();
205	tim	278	}
206
207
208
209	tim	283	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
210	tim	278	int comparator = instruction.tok;
211			int property = instruction.intValue;
212	tim	283	float comparisonValue = boost::any_cast<float>(instruction.value);
213			float propertyValue;
214			BitSet bs(nStuntDouble);
215	tim	295	bs.clearAll();
216	tim	283
217			SimInfo::MoleculeIterator mi;
218			Molecule* mol;
219			Molecule::AtomIterator ai;
220			Atom* atom;
221			Molecule::RigidBodyIterator rbIter;
222			RigidBody* rb;
223
224			for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
225	tim	281
226	tim	283	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
227			compareProperty(atom, bs, property, comparator, comparisonValue);
228			}
229
230			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
231			compareProperty(rb, bs, property, comparator, comparisonValue);
232			}
233	tim	278	}
234
235	tim	283	return bs;
236			}
237	tim	278
238	tim	283	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
239	tim	432	double propertyValue = 0.0;
240	tim	283	switch (property) {
241			case Token::mass:
242			propertyValue = sd->getMass();
243			break;
244			case Token::charge:
245	tim	432	if (sd->isAtom()){
246			Atom* atom = static_cast<Atom*>(sd);
247			propertyValue = getCharge(atom);
248			} else if (sd->isRigidBody()) {
249			RigidBody* rb = static_cast<RigidBody*>(sd);
250			RigidBody::AtomIterator ai;
251			Atom* atom;
252			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
253			propertyValue+= getCharge(atom);
254			}
255			}
256			break;
257	tim	283	default:
258			unrecognizedAtomProperty(property);
259			}
260
261			bool match = false;
262			switch (comparator) {
263			case Token::opLT:
264			match = propertyValue < comparisonValue;
265			break;
266			case Token::opLE:
267			match = propertyValue <= comparisonValue;
268			break;
269			case Token::opGE:
270			match = propertyValue >= comparisonValue;
271			break;
272			case Token::opGT:
273			match = propertyValue > comparisonValue;
274			break;
275			case Token::opEQ:
276			match = propertyValue == comparisonValue;
277			break;
278			case Token::opNE:
279			match = propertyValue != comparisonValue;
280			break;
281			}
282			if (match)
283			bs.setBitOn(sd->getGlobalIndex());
284
285			}
286
287			void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
288	tim	295
289	tim	281	boost::any withinSpec = instruction.value;
290	tim	295	float distance;
291	tim	282	if (withinSpec.type() == typeid(float)){
292	tim	295	distance = boost::any_cast<float>(withinSpec);
293			} else if (withinSpec.type() == typeid(int)) {
294			distance = boost::any_cast<int>(withinSpec);
295			} else {
296			evalError("casting error in withinInstruction");
297			bs.clearAll();
298	tim	278	}
299	tim	282
300	tim	295	bs = distanceFinder.find(bs, distance);
301	tim	278	}
302
303	tim	283	void SelectionEvaluator::define() {
304	tim	282	assert(statement.size() >= 3);
305
306			std::string variable = boost::any_cast<std::string>(statement[1].value);
307	tim	283
308	tim	351	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
309	tim	278	}
310
311	tim	283
312	tim	282	/** @todo */
313			void SelectionEvaluator::predefine(const std::string& script) {
314	tim	278
315	tim	282	if (compiler.compile("#predefine", script)) {
316			std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
317			if (aatoken.size() != 1) {
318			evalError("predefinition does not have exactly 1 command:"
319			+ script);
320			return;
321			}
322			std::vector<Token> statement = aatoken[0];
323			if (statement.size() > 2) {
324			int tok = statement[1].tok;
325			if (tok == Token::identifier \|\| (tok & Token::predefinedset) == Token::predefinedset) {
326	tim	283	std::string variable = boost::any_cast<std::string>(statement[1].value);
327	tim	350	variables.insert(VariablesType::value_type(variable, statement));
328	tim	282
329			} else {
330			evalError("invalid variable name:" + script);
331			}
332			}else {
333			evalError("bad predefinition length:" + script);
334			}
335
336
337			} else {
338			evalError("predefined set compile error:" + script +
339			"\ncompile error:" + compiler.getErrorMessage());
340			}
341
342			}
343
344	tim	288	void SelectionEvaluator::select(BitSet& bs){
345			bs = expression(statement, 1);
346	tim	282	}
347
348			BitSet SelectionEvaluator::lookupValue(const std::string& variable){
349
350	tim	295	BitSet bs(nStuntDouble);
351	tim	282	std::map<std::string, boost::any>::iterator i = variables.find(variable);
352	tim	295
353	tim	282	if (i != variables.end()) {
354			if (i->second.type() == typeid(BitSet)) {
355			return boost::any_cast<BitSet>(i->second);
356			} else if (i->second.type() == typeid(std::vector<Token>)){
357	tim	295	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
358	tim	282	i->second = bs; /*@todo fixme /
359			return bs;
360			}
361	tim	283	} else {
362			unrecognizedIdentifier(variable);
363	tim	282	}
364	tim	295
365			return bs;
366	tim	282	}
367
368	tim	283	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
369
370	tim	295	return nameFinder.match(name);
371	tim	288
372	tim	283	}
373
374	tim	288	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
375			std::vector<Token>::const_iterator i;
376			for (i = tokens.begin(); i != tokens.end(); ++i) {
377			if (i->tok & Token::dynamic) {
378			return true;
379			}
380			}
381	tim	283
382	tim	288	return false;
383			}
384
385			void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
386			variables.clear();
387			//load predefine
388			//predefine();
389	tim	282	}
390	tim	288
391			BitSet SelectionEvaluator::evaluate() {
392			BitSet bs(nStuntDouble);
393			if (isLoaded_) {
394	tim	298	pc = 0;
395	tim	288	instructionDispatchLoop(bs);
396			}
397
398			return bs;
399			}
400	tim	295
401			BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
402			BitSet bs(nStuntDouble);
403
404			if (value.type() == typeid(int)) {
405			int index = boost::any_cast<int>(value);
406			if (index < 0 \|\| index >= bs.size()) {
407			invalidIndex(index);
408			} else {
409	tim	415	bs = indexFinder.find(index);
410	tim	295	}
411			} else if (value.type() == typeid(std::pair<int, int>)) {
412			std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
413			assert(indexRange.first <= indexRange.second);
414			if (indexRange.first < 0 \|\| indexRange.second >= bs.size()) {
415			invalidIndexRange(indexRange);
416			}else {
417	tim	415	bs = indexFinder.find(indexRange.first, indexRange.second);
418	tim	295	}
419			}
420
421			return bs;
422			}
423
424	tim	432
425			double SelectionEvaluator::getCharge(Atom* atom) {
426			double charge =0.0;
427			AtomType* atomType = atom->getAtomType();
428			if (atomType->isCharge()) {
429			GenericData* data = atomType->getPropertyByName("Charge");
430			if (data != NULL) {
431			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
432
433			if (doubleData != NULL) {
434			charge = doubleData->getData();
435
436			} else {
437			sprintf( painCave.errMsg,
438			"Can not cast GenericData to DoubleGenericData\n");
439			painCave.severity = OOPSE_ERROR;
440			painCave.isFatal = 1;
441			simError();
442			}
443			}
444			}
445
446			return charge;
447	tim	288	}
448	tim	432
449			}