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, const std::string& script) : info(si), finder(info){
}            

bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
    this->filename = filename;
    this->script = script;
    if (! compiler.compile(filename, script)) {
        error = true;
        errorMessage = compiler.getErrorMessage();
        return false;
    }

    pc = 0;
    aatoken = compiler.getAatokenCompiled();
    linenumbers = compiler.getLineNumbers();
    lineIndices = compiler.getLineIndices();
    return true;
}

void SelectionEvaluator::clearState() {
    for (int i = scriptLevelMax; --i >= 0; )
        stack[i].clear();
    scriptLevel = 0;
    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) {
    return true; /**@todo */
}

void SelectionEvaluator::instructionDispatchLoop(){

    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();
            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) {
      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;
        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);
    
    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);
        }
        
        //change the positions of atoms which belong to the rigidbodies
        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;
        switch (property) {
        case Token::mass:
            propertyValue = sd->getMass();
            break;
        case Token::charge:
            return;
            //break;
        case Token::dipole:
            return;
            //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;
    if (withinSpec.type() == typeid(float)){
        //
        return;
    }
    
    evalError("Unrecognized within parameter");
}

void SelectionEvaluator::define() {
    assert(statement.size() >= 3);

    std::string variable = boost::any_cast<std::string>(statement[1].value);

    variables.insert(std::make_pair(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(std::make_pair(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(){
    //viewer.setSelectionSet(expression(statement, 1));
}

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

    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>)){
            BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
            i->second =  bs; /**@todo fixme */
            return bs;
        }
    } else {
        unrecognizedIdentifier(variable);
    }
}

BitSet SelectionEvaluator::nameInstruction(const std::string& name){
    BitSet bs(nStuntDouble);
    
    bool hasError = finder.match(name, bs);
    
    return bs;    
}    


}
Revision:	1967
Committed:	Thu Feb 3 23:14:05 2005 UTC (19 years, 4 months ago) by tim
File size:	10430 byte(s)
Log Message:	more work in selection library
#	User	Rev	Content
1	tim	1961	/*
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	1967	#include <stack>
43	tim	1961	#include "selection/SelectionEvaluator.hpp"
44	tim	1967	#include "primitives/Atom.hpp"
45			#include "primitives/DirectionalAtom.hpp"
46			#include "primitives/RigidBody.hpp"
47			#include "primitives/Molecule.hpp"
48
49	tim	1961	namespace oopse {
50
51
52	tim	1967	SelectionEvaluator::SelectionEvaluator(SimInfo* si, const std::string& script) : info(si), finder(info){
53			}
54
55	tim	1962	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
56			this->filename = filename;
57			this->script = script;
58			if (! compiler.compile(filename, script)) {
59			error = true;
60			errorMessage = compiler.getErrorMessage();
61			return false;
62			}
63
64			pc = 0;
65			aatoken = compiler.getAatokenCompiled();
66			linenumbers = compiler.getLineNumbers();
67			lineIndices = compiler.getLineIndices();
68			return true;
69	tim	1961	}
70	tim	1962
71			void SelectionEvaluator::clearState() {
72			for (int i = scriptLevelMax; --i >= 0; )
73	tim	1965	stack[i].clear();
74	tim	1962	scriptLevel = 0;
75			error = false;
76	tim	1965	errorMessage = "";
77	tim	1962	}
78
79			bool SelectionEvaluator::loadScriptString(const std::string& script) {
80			clearState();
81	tim	1965	return loadScript("", script);
82	tim	1962	}
83
84			bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
85			clearState();
86			return loadScriptFileInternal(filename);
87			}
88
89	tim	1967	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
90			return true; /*@todo /
91	tim	1966	}
92
93	tim	1962	void SelectionEvaluator::instructionDispatchLoop(){
94
95	tim	1965	while ( pc < aatoken.size()) {
96	tim	1962	statement = aatoken[pc++];
97	tim	1965	statementLength = statement.size();
98	tim	1962	Token token = statement[0];
99			switch (token.tok) {
100	tim	1965	case Token::define:
101	tim	1962	define();
102			break;
103	tim	1965	case Token::select:
104	tim	1962	select();
105			break;
106			default:
107			unrecognizedCommand(token);
108			return;
109			}
110			}
111			}
112
113	tim	1967	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
114	tim	1962	BitSet bs;
115	tim	1967	std::stack<BitSet> stack;
116
117	tim	1962	for (int pc = pcStart; ; ++pc) {
118			Token instruction = code[pc];
119	tim	1966
120	tim	1962	switch (instruction.tok) {
121	tim	1965	case Token::expressionBegin:
122	tim	1962	break;
123	tim	1965	case Token::expressionEnd:
124	tim	1966	break;
125	tim	1965	case Token::all:
126	tim	1967	bs = BitSet(nStuntDouble);
127			bs.setAll();
128			stack.push(bs);
129	tim	1962	break;
130	tim	1965	case Token::none:
131	tim	1967	bs = BitSet(nStuntDouble);
132			stack.push(bs);
133	tim	1962	break;
134	tim	1965	case Token::opOr:
135	tim	1967	bs = stack.top();
136			stack.pop();
137			stack.top() \|= bs;
138	tim	1962	break;
139	tim	1965	case Token::opAnd:
140	tim	1967	bs = stack.top();
141			stack.pop();
142			stack.top() &= bs;
143	tim	1962	break;
144	tim	1965	case Token::opNot:
145	tim	1967	stack.top().flip();
146	tim	1962	break;
147	tim	1965	case Token::within:
148	tim	1967
149			withinInstruction(instruction, stack.top());
150	tim	1962	break;
151	tim	1967	//case Token::selected:
152			// stack.push(getSelectionSet());
153			// break;
154	tim	1965	case Token::name:
155	tim	1967	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
156	tim	1962	break;
157	tim	1965	break;
158			case Token::identifier:
159	tim	1967	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
160	tim	1965	break;
161			case Token::opLT:
162			case Token::opLE:
163			case Token::opGE:
164			case Token::opGT:
165			case Token::opEQ:
166			case Token::opNE:
167	tim	1967	stack.push(comparatorInstruction(instruction));
168	tim	1962	break;
169			default:
170			unrecognizedExpression();
171			}
172			}
173	tim	1967	if (stack.size() != 1)
174	tim	1962	evalError("atom expression compiler error - stack over/underflow");
175	tim	1967
176			return stack.top();
177	tim	1962	}
178
179
180
181	tim	1967	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
182	tim	1962	int comparator = instruction.tok;
183			int property = instruction.intValue;
184	tim	1967	float comparisonValue = boost::any_cast<float>(instruction.value);
185			float propertyValue;
186			BitSet bs(nStuntDouble);
187
188			SimInfo::MoleculeIterator mi;
189			Molecule* mol;
190			Molecule::AtomIterator ai;
191			Atom* atom;
192			Molecule::RigidBodyIterator rbIter;
193			RigidBody* rb;
194
195			for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
196	tim	1965
197	tim	1967	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
198			compareProperty(atom, bs, property, comparator, comparisonValue);
199			}
200
201			//change the positions of atoms which belong to the rigidbodies
202			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
203			compareProperty(rb, bs, property, comparator, comparisonValue);
204			}
205	tim	1962	}
206
207	tim	1967	return bs;
208			}
209	tim	1962
210	tim	1967	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
211			double propertyValue;
212			switch (property) {
213			case Token::mass:
214			propertyValue = sd->getMass();
215			break;
216			case Token::charge:
217			return;
218			//break;
219			case Token::dipole:
220			return;
221			//break;
222			default:
223			unrecognizedAtomProperty(property);
224			}
225
226			bool match = false;
227			switch (comparator) {
228			case Token::opLT:
229			match = propertyValue < comparisonValue;
230			break;
231			case Token::opLE:
232			match = propertyValue <= comparisonValue;
233			break;
234			case Token::opGE:
235			match = propertyValue >= comparisonValue;
236			break;
237			case Token::opGT:
238			match = propertyValue > comparisonValue;
239			break;
240			case Token::opEQ:
241			match = propertyValue == comparisonValue;
242			break;
243			case Token::opNE:
244			match = propertyValue != comparisonValue;
245			break;
246			}
247			if (match)
248			bs.setBitOn(sd->getGlobalIndex());
249
250			}
251
252			void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
253
254	tim	1965	boost::any withinSpec = instruction.value;
255	tim	1966	if (withinSpec.type() == typeid(float)){
256	tim	1967	//
257	tim	1962	return;
258			}
259	tim	1966
260	tim	1967	evalError("Unrecognized within parameter");
261	tim	1962	}
262
263	tim	1967	void SelectionEvaluator::define() {
264	tim	1966	assert(statement.size() >= 3);
265
266			std::string variable = boost::any_cast<std::string>(statement[1].value);
267	tim	1967
268	tim	1965	variables.insert(std::make_pair(variable, expression(statement, 2)));
269	tim	1962	}
270
271	tim	1967
272	tim	1966	/** @todo */
273			void SelectionEvaluator::predefine(const std::string& script) {
274	tim	1962
275	tim	1966	if (compiler.compile("#predefine", script)) {
276			std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
277			if (aatoken.size() != 1) {
278			evalError("predefinition does not have exactly 1 command:"
279			+ script);
280			return;
281			}
282			std::vector<Token> statement = aatoken[0];
283			if (statement.size() > 2) {
284			int tok = statement[1].tok;
285			if (tok == Token::identifier \|\| (tok & Token::predefinedset) == Token::predefinedset) {
286	tim	1967	std::string variable = boost::any_cast<std::string>(statement[1].value);
287	tim	1966	variables.insert(std::make_pair(variable, statement));
288
289			} else {
290			evalError("invalid variable name:" + script);
291			}
292			}else {
293			evalError("bad predefinition length:" + script);
294			}
295
296
297			} else {
298			evalError("predefined set compile error:" + script +
299			"\ncompile error:" + compiler.getErrorMessage());
300			}
301
302			}
303
304			void SelectionEvaluator::select(){
305	tim	1967	//viewer.setSelectionSet(expression(statement, 1));
306	tim	1966	}
307
308			BitSet SelectionEvaluator::lookupValue(const std::string& variable){
309
310			std::map<std::string, boost::any>::iterator i = variables.find(variable);
311
312			if (i != variables.end()) {
313			if (i->second.type() == typeid(BitSet)) {
314			return boost::any_cast<BitSet>(i->second);
315			} else if (i->second.type() == typeid(std::vector<Token>)){
316	tim	1967	BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
317	tim	1966	i->second = bs; /*@todo fixme /
318			return bs;
319			}
320	tim	1967	} else {
321			unrecognizedIdentifier(variable);
322	tim	1966	}
323			}
324
325	tim	1967	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
326			BitSet bs(nStuntDouble);
327
328			bool hasError = finder.match(name, bs);
329
330			return bs;
331			}
332
333
334	tim	1966	}