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 = allInstruction();
        stack.push(bs);            
        break;
      case Token::none:
        bs = OpenMDBitSet(nStuntDouble);
        stack.push(bs);            
        break;
      case Token::opOr:
        bs = stack.top();
        stack.pop();
        stack.top() |= bs;
        break;
      case Token::opAnd:
        bs = stack.top();
        stack.pop();
        stack.top() &= bs;
        break;
      case Token::opNot:
        stack.top().flip();
        break;
      case Token::within:
        withinInstruction(instruction, stack.top());
        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::allInstruction() {
    OpenMDBitSet bs(nStuntDouble);

    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;

    // Doing the loop insures that we're actually on this processor.

    for (mol = info->beginMolecule(mi); mol != NULL; 
         mol = info->nextMolecule(mi)) {

      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        bs.setBitOn(atom->getGlobalIndex());
      }
     
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        bs.setBitOn(rb->getGlobalIndex());
      }
    }

    return bs;
  }

  OpenMDBitSet SelectionEvaluator::hull() {
    OpenMDBitSet bs(nStuntDouble);
    
    bs = hullFinder.findHull();
    
    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:	1803
Committed:	Wed Oct 3 14:20:07 2012 UTC (12 years, 6 months ago) by gezelter
File size:	14964 byte(s)
Log Message:	Merging trunk changes back to development branch
#	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	1665	* [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	1627	#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	1767	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	1803	bs = allInstruction();
163	tim	283	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	gezelter	1390	OpenMDBitSet bs(nStuntDouble);
225	tim	295	bs.clearAll();
226	tim	283
227			SimInfo::MoleculeIterator mi;
228			Molecule* mol;
229			Molecule::AtomIterator ai;
230			Atom* atom;
231			Molecule::RigidBodyIterator rbIter;
232			RigidBody* rb;
233	tim	281
234	cli2	1364	for (mol = info->beginMolecule(mi); mol != NULL;
235			mol = info->nextMolecule(mi)) {
236
237	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
238			compareProperty(atom, bs, property, comparator, comparisonValue);
239			}
240	cli2	1364
241			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242			rb = mol->nextRigidBody(rbIter)) {
243			compareProperty(rb, bs, property, comparator, comparisonValue);
244			}
245	tim	278	}
246
247	tim	283	return bs;
248	gezelter	507	}
249	tim	278
250	gezelter	1390	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
251	cli2	1364	int property, int comparator,
252			float comparisonValue) {
253	tim	963	RealType propertyValue = 0.0;
254	gezelter	507	switch (property) {
255			case Token::mass:
256			propertyValue = sd->getMass();
257			break;
258			case Token::charge:
259			if (sd->isAtom()){
260			Atom* atom = static_cast<Atom*>(sd);
261			propertyValue = getCharge(atom);
262			} else if (sd->isRigidBody()) {
263			RigidBody* rb = static_cast<RigidBody*>(sd);
264			RigidBody::AtomIterator ai;
265			Atom* atom;
266			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
267			propertyValue+= getCharge(atom);
268			}
269			}
270			break;
271	cli2	1360	case Token::x:
272			propertyValue = sd->getPos().x();
273			break;
274			case Token::y:
275			propertyValue = sd->getPos().y();
276			break;
277			case Token::z:
278			propertyValue = sd->getPos().z();
279			break;
280	gezelter	1629	case Token::r:
281			propertyValue = sd->getPos().length();
282			break;
283	gezelter	507	default:
284			unrecognizedAtomProperty(property);
285			}
286	tim	283
287	gezelter	507	bool match = false;
288			switch (comparator) {
289			case Token::opLT:
290			match = propertyValue < comparisonValue;
291			break;
292			case Token::opLE:
293			match = propertyValue <= comparisonValue;
294			break;
295			case Token::opGE:
296			match = propertyValue >= comparisonValue;
297			break;
298			case Token::opGT:
299			match = propertyValue > comparisonValue;
300			break;
301			case Token::opEQ:
302			match = propertyValue == comparisonValue;
303			break;
304			case Token::opNE:
305			match = propertyValue != comparisonValue;
306			break;
307			}
308			if (match)
309			bs.setBitOn(sd->getGlobalIndex());
310	cli2	1364
311	gezelter	507	}
312	tim	283
313	cli2	1364	void SelectionEvaluator::withinInstruction(const Token& instruction,
314	gezelter	1390	OpenMDBitSet& bs){
315	tim	295
316	tim	281	boost::any withinSpec = instruction.value;
317	tim	295	float distance;
318	tim	282	if (withinSpec.type() == typeid(float)){
319	gezelter	507	distance = boost::any_cast<float>(withinSpec);
320	tim	295	} else if (withinSpec.type() == typeid(int)) {
321	gezelter	507	distance = boost::any_cast<int>(withinSpec);
322	tim	295	} else {
323	gezelter	507	evalError("casting error in withinInstruction");
324			bs.clearAll();
325	tim	278	}
326	tim	282
327	tim	295	bs = distanceFinder.find(bs, distance);
328	gezelter	507	}
329	cli2	1364
330	gezelter	507	void SelectionEvaluator::define() {
331	tim	282	assert(statement.size() >= 3);
332	cli2	1364
333	tim	282	std::string variable = boost::any_cast<std::string>(statement[1].value);
334	cli2	1364
335			variables.insert(VariablesType::value_type(variable,
336			expression(statement, 2)));
337	gezelter	507	}
338	cli2	1364
339	tim	278
340	gezelter	507	/** @todo */
341			void SelectionEvaluator::predefine(const std::string& script) {
342	cli2	1364
343	tim	282	if (compiler.compile("#predefine", script)) {
344	gezelter	507	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
345			if (aatoken.size() != 1) {
346			evalError("predefinition does not have exactly 1 command:"
347			+ script);
348			return;
349			}
350			std::vector<Token> statement = aatoken[0];
351			if (statement.size() > 2) {
352			int tok = statement[1].tok;
353	cli2	1364	if (tok == Token::identifier \|\|
354			(tok & Token::predefinedset) == Token::predefinedset) {
355	gezelter	507	std::string variable = boost::any_cast<std::string>(statement[1].value);
356			variables.insert(VariablesType::value_type(variable, statement));
357	cli2	1364
358	gezelter	507	} else {
359			evalError("invalid variable name:" + script);
360			}
361			}else {
362			evalError("bad predefinition length:" + script);
363	cli2	1364	}
364	tim	282
365			} else {
366	gezelter	507	evalError("predefined set compile error:" + script +
367			"\ncompile error:" + compiler.getErrorMessage());
368	tim	282	}
369	gezelter	507	}
370	tim	282
371	gezelter	1390	void SelectionEvaluator::select(OpenMDBitSet& bs){
372	tim	288	bs = expression(statement, 1);
373	gezelter	507	}
374	cli2	1364
375	gezelter	1390	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
376	cli2	1364
377	gezelter	1390	OpenMDBitSet bs(nStuntDouble);
378	tim	282	std::map<std::string, boost::any>::iterator i = variables.find(variable);
379	tim	295
380	tim	282	if (i != variables.end()) {
381	gezelter	1390	if (i->second.type() == typeid(OpenMDBitSet)) {
382			return boost::any_cast<OpenMDBitSet>(i->second);
383	gezelter	507	} else if (i->second.type() == typeid(std::vector<Token>)){
384			bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
385			i->second = bs; /*@todo fixme /
386			return bs;
387			}
388	tim	283	} else {
389	gezelter	507	unrecognizedIdentifier(variable);
390	tim	282	}
391	cli2	1364
392	tim	295	return bs;
393	gezelter	507	}
394	cli2	1364
395	gezelter	1390	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
396	cli2	1364	return nameFinder.match(name);
397	gezelter	507	}
398	tim	283
399	gezelter	507	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
400	tim	288	std::vector<Token>::const_iterator i;
401			for (i = tokens.begin(); i != tokens.end(); ++i) {
402	gezelter	507	if (i->tok & Token::dynamic) {
403			return true;
404			}
405	tim	288	}
406	cli2	1364
407	tim	288	return false;
408	gezelter	507	}
409	tim	288
410	gezelter	507	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
411	tim	288	variables.clear();
412			//load predefine
413			//predefine();
414	gezelter	507	}
415	tim	288
416	gezelter	1390	OpenMDBitSet SelectionEvaluator::evaluate() {
417			OpenMDBitSet bs(nStuntDouble);
418	tim	288	if (isLoaded_) {
419	gezelter	507	pc = 0;
420			instructionDispatchLoop(bs);
421	tim	288	}
422
423			return bs;
424	gezelter	507	}
425	tim	295
426	gezelter	1390	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
427			OpenMDBitSet bs(nStuntDouble);
428	tim	295
429			if (value.type() == typeid(int)) {
430	gezelter	507	int index = boost::any_cast<int>(value);
431			if (index < 0 \|\| index >= bs.size()) {
432			invalidIndex(index);
433			} else {
434			bs = indexFinder.find(index);
435			}
436	tim	295	} else if (value.type() == typeid(std::pair<int, int>)) {
437	gezelter	507	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
438			assert(indexRange.first <= indexRange.second);
439			if (indexRange.first < 0 \|\| indexRange.second >= bs.size()) {
440			invalidIndexRange(indexRange);
441			}else {
442			bs = indexFinder.find(indexRange.first, indexRange.second);
443			}
444	tim	295	}
445
446			return bs;
447	gezelter	507	}
448	tim	295
449	gezelter	1803	OpenMDBitSet SelectionEvaluator::allInstruction() {
450			OpenMDBitSet bs(nStuntDouble);
451	tim	432
452	gezelter	1803	SimInfo::MoleculeIterator mi;
453			Molecule* mol;
454			Molecule::AtomIterator ai;
455			Atom* atom;
456			Molecule::RigidBodyIterator rbIter;
457			RigidBody* rb;
458
459			// Doing the loop insures that we're actually on this processor.
460
461			for (mol = info->beginMolecule(mi); mol != NULL;
462			mol = info->nextMolecule(mi)) {
463
464			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
465			bs.setBitOn(atom->getGlobalIndex());
466			}
467
468			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
469			rb = mol->nextRigidBody(rbIter)) {
470			bs.setBitOn(rb->getGlobalIndex());
471			}
472			}
473
474			return bs;
475			}
476
477	gezelter	1412	OpenMDBitSet SelectionEvaluator::hull() {
478			OpenMDBitSet bs(nStuntDouble);
479
480			bs = hullFinder.findHull();
481
482			return bs;
483			}
484
485	tim	963	RealType SelectionEvaluator::getCharge(Atom* atom) {
486			RealType charge =0.0;
487	tim	432	AtomType* atomType = atom->getAtomType();
488			if (atomType->isCharge()) {
489	gezelter	507	GenericData* data = atomType->getPropertyByName("Charge");
490			if (data != NULL) {
491			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
492	tim	432
493	gezelter	507	if (doubleData != NULL) {
494			charge = doubleData->getData();
495	tim	432
496	gezelter	507	} else {
497			sprintf( painCave.errMsg,
498			"Can not cast GenericData to DoubleGenericData\n");
499	gezelter	1390	painCave.severity = OPENMD_ERROR;
500	gezelter	507	painCave.isFatal = 1;
501			simError();
502			}
503			}
504	tim	432	}
505
506			return charge;
507	gezelter	507	}
508	tim	432
509			}