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), finder(info), isLoaded_(false){

}            

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() {
    //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) {
    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;
        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(BitSet& bs){
    bs = 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){
    
    return finder.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_) {
        instructionDispatchLoop(bs);
    }

    return bs;
}
        
//BitSet SelectionEvaluator::evaluate(int frameNo) {
//
//}

}
Revision:	1972
Committed:	Fri Feb 4 22:39:26 2005 UTC (19 years, 4 months ago) by tim
File size:	11674 byte(s)
Log Message:	half of the selection utility is working need to debug within keyword and atomproperty keyword
#	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	1972	SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), finder(info), isLoaded_(false){
53
54	tim	1967	}
55
56	tim	1962	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
57	tim	1972	clearDefinitionsAndLoadPredefined();
58	tim	1962	this->filename = filename;
59			this->script = script;
60			if (! compiler.compile(filename, script)) {
61			error = true;
62			errorMessage = compiler.getErrorMessage();
63	tim	1972	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
64	tim	1962	return false;
65			}
66
67			pc = 0;
68			aatoken = compiler.getAatokenCompiled();
69			linenumbers = compiler.getLineNumbers();
70			lineIndices = compiler.getLineIndices();
71	tim	1972
72			std::vector<std::vector<Token> >::const_iterator i;
73
74			isDynamic_ = false;
75			for (i = aatoken.begin(); i != aatoken.end(); ++i) {
76			if (containDynamicToken(*i)) {
77			isDynamic_ = true;
78			break;
79			}
80			}
81
82			isLoaded_ = true;
83	tim	1962	return true;
84	tim	1961	}
85	tim	1962
86			void SelectionEvaluator::clearState() {
87	tim	1972	//for (int i = scriptLevelMax; --i >= 0; )
88			// stack[i].clear();
89			//scriptLevel = 0;
90	tim	1962	error = false;
91	tim	1965	errorMessage = "";
92	tim	1962	}
93
94			bool SelectionEvaluator::loadScriptString(const std::string& script) {
95			clearState();
96	tim	1965	return loadScript("", script);
97	tim	1962	}
98
99			bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
100			clearState();
101			return loadScriptFileInternal(filename);
102			}
103
104	tim	1967	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
105	tim	1972	ifstream ifs(filename.c_str());
106			if (!ifs.is_open()) {
107			return false;
108			}
109
110			const int bufferSize = 65535;
111			char buffer[bufferSize];
112			std::string script;
113			while(ifs.getline(buffer, bufferSize)) {
114			script += buffer;
115			}
116			return loadScript(filename, script);
117	tim	1966	}
118
119	tim	1972	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
120
121	tim	1965	while ( pc < aatoken.size()) {
122	tim	1962	statement = aatoken[pc++];
123	tim	1965	statementLength = statement.size();
124	tim	1962	Token token = statement[0];
125			switch (token.tok) {
126	tim	1965	case Token::define:
127	tim	1962	define();
128			break;
129	tim	1965	case Token::select:
130	tim	1972	select(bs);
131	tim	1962	break;
132			default:
133			unrecognizedCommand(token);
134			return;
135			}
136			}
137	tim	1972
138	tim	1962	}
139
140	tim	1967	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
141	tim	1962	BitSet bs;
142	tim	1967	std::stack<BitSet> stack;
143
144	tim	1972	for (int pc = pcStart; pc < code.size(); ++pc) {
145	tim	1962	Token instruction = code[pc];
146	tim	1966
147	tim	1962	switch (instruction.tok) {
148	tim	1965	case Token::expressionBegin:
149	tim	1962	break;
150	tim	1965	case Token::expressionEnd:
151	tim	1966	break;
152	tim	1965	case Token::all:
153	tim	1967	bs = BitSet(nStuntDouble);
154			bs.setAll();
155			stack.push(bs);
156	tim	1962	break;
157	tim	1965	case Token::none:
158	tim	1967	bs = BitSet(nStuntDouble);
159			stack.push(bs);
160	tim	1962	break;
161	tim	1965	case Token::opOr:
162	tim	1967	bs = stack.top();
163			stack.pop();
164			stack.top() \|= bs;
165	tim	1962	break;
166	tim	1965	case Token::opAnd:
167	tim	1967	bs = stack.top();
168			stack.pop();
169			stack.top() &= bs;
170	tim	1962	break;
171	tim	1965	case Token::opNot:
172	tim	1967	stack.top().flip();
173	tim	1962	break;
174	tim	1965	case Token::within:
175	tim	1967
176			withinInstruction(instruction, stack.top());
177	tim	1962	break;
178	tim	1967	//case Token::selected:
179			// stack.push(getSelectionSet());
180			// break;
181	tim	1965	case Token::name:
182	tim	1967	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
183	tim	1962	break;
184	tim	1965	break;
185			case Token::identifier:
186	tim	1967	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
187	tim	1965	break;
188			case Token::opLT:
189			case Token::opLE:
190			case Token::opGE:
191			case Token::opGT:
192			case Token::opEQ:
193			case Token::opNE:
194	tim	1967	stack.push(comparatorInstruction(instruction));
195	tim	1962	break;
196			default:
197			unrecognizedExpression();
198			}
199			}
200	tim	1967	if (stack.size() != 1)
201	tim	1962	evalError("atom expression compiler error - stack over/underflow");
202	tim	1967
203			return stack.top();
204	tim	1962	}
205
206
207
208	tim	1967	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
209	tim	1962	int comparator = instruction.tok;
210			int property = instruction.intValue;
211	tim	1967	float comparisonValue = boost::any_cast<float>(instruction.value);
212			float propertyValue;
213			BitSet bs(nStuntDouble);
214
215			SimInfo::MoleculeIterator mi;
216			Molecule* mol;
217			Molecule::AtomIterator ai;
218			Atom* atom;
219			Molecule::RigidBodyIterator rbIter;
220			RigidBody* rb;
221
222			for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
223	tim	1965
224	tim	1967	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
225			compareProperty(atom, bs, property, comparator, comparisonValue);
226			}
227
228			//change the positions of atoms which belong to the rigidbodies
229			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
230			compareProperty(rb, bs, property, comparator, comparisonValue);
231			}
232	tim	1962	}
233
234	tim	1967	return bs;
235			}
236	tim	1962
237	tim	1967	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
238			double propertyValue;
239			switch (property) {
240			case Token::mass:
241			propertyValue = sd->getMass();
242			break;
243			case Token::charge:
244			return;
245			//break;
246			case Token::dipole:
247			return;
248			//break;
249			default:
250			unrecognizedAtomProperty(property);
251			}
252
253			bool match = false;
254			switch (comparator) {
255			case Token::opLT:
256			match = propertyValue < comparisonValue;
257			break;
258			case Token::opLE:
259			match = propertyValue <= comparisonValue;
260			break;
261			case Token::opGE:
262			match = propertyValue >= comparisonValue;
263			break;
264			case Token::opGT:
265			match = propertyValue > comparisonValue;
266			break;
267			case Token::opEQ:
268			match = propertyValue == comparisonValue;
269			break;
270			case Token::opNE:
271			match = propertyValue != comparisonValue;
272			break;
273			}
274			if (match)
275			bs.setBitOn(sd->getGlobalIndex());
276
277			}
278
279			void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
280
281	tim	1965	boost::any withinSpec = instruction.value;
282	tim	1966	if (withinSpec.type() == typeid(float)){
283	tim	1967	//
284	tim	1962	return;
285			}
286	tim	1966
287	tim	1967	evalError("Unrecognized within parameter");
288	tim	1962	}
289
290	tim	1967	void SelectionEvaluator::define() {
291	tim	1966	assert(statement.size() >= 3);
292
293			std::string variable = boost::any_cast<std::string>(statement[1].value);
294	tim	1967
295	tim	1965	variables.insert(std::make_pair(variable, expression(statement, 2)));
296	tim	1962	}
297
298	tim	1967
299	tim	1966	/** @todo */
300			void SelectionEvaluator::predefine(const std::string& script) {
301	tim	1962
302	tim	1966	if (compiler.compile("#predefine", script)) {
303			std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
304			if (aatoken.size() != 1) {
305			evalError("predefinition does not have exactly 1 command:"
306			+ script);
307			return;
308			}
309			std::vector<Token> statement = aatoken[0];
310			if (statement.size() > 2) {
311			int tok = statement[1].tok;
312			if (tok == Token::identifier \|\| (tok & Token::predefinedset) == Token::predefinedset) {
313	tim	1967	std::string variable = boost::any_cast<std::string>(statement[1].value);
314	tim	1966	variables.insert(std::make_pair(variable, statement));
315
316			} else {
317			evalError("invalid variable name:" + script);
318			}
319			}else {
320			evalError("bad predefinition length:" + script);
321			}
322
323
324			} else {
325			evalError("predefined set compile error:" + script +
326			"\ncompile error:" + compiler.getErrorMessage());
327			}
328
329			}
330
331	tim	1972	void SelectionEvaluator::select(BitSet& bs){
332			bs = expression(statement, 1);
333	tim	1966	}
334
335			BitSet SelectionEvaluator::lookupValue(const std::string& variable){
336
337			std::map<std::string, boost::any>::iterator i = variables.find(variable);
338
339			if (i != variables.end()) {
340			if (i->second.type() == typeid(BitSet)) {
341			return boost::any_cast<BitSet>(i->second);
342			} else if (i->second.type() == typeid(std::vector<Token>)){
343	tim	1967	BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
344	tim	1966	i->second = bs; /*@todo fixme /
345			return bs;
346			}
347	tim	1967	} else {
348			unrecognizedIdentifier(variable);
349	tim	1966	}
350			}
351
352	tim	1967	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
353
354	tim	1972	return finder.match(name);
355
356	tim	1967	}
357
358	tim	1972	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
359			std::vector<Token>::const_iterator i;
360			for (i = tokens.begin(); i != tokens.end(); ++i) {
361			if (i->tok & Token::dynamic) {
362			return true;
363			}
364			}
365	tim	1967
366	tim	1972	return false;
367			}
368
369			void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
370			variables.clear();
371			//load predefine
372			//predefine();
373	tim	1966	}
374	tim	1972
375			BitSet SelectionEvaluator::evaluate() {
376			BitSet bs(nStuntDouble);
377			if (isLoaded_) {
378			instructionDispatchLoop(bs);
379			}
380
381			return bs;
382			}
383
384			//BitSet SelectionEvaluator::evaluate(int frameNo) {
385			//
386			//}
387
388			}