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 "selection/SelectionEvaluator.hpp"
namespace oopse {


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);
}


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;
        }
    }
}

  void SelectionEvaluator::predefine(const std::string& script) {
    if (compiler.compile("#predefine", script)) {
      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
      if (aatoken.size() != 1) {
        viewer.scriptStatus("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 = (std::string)statement[1].value;
          variables.put(variable, statement);
        } else {
          viewer.scriptStatus("invalid variable name:" + script);
        }
      } else {
        viewer.scriptStatus("bad predefinition length:" + script);
      }
    } else {
      viewer.scriptStatus("predefined set compile error:" + script +
                          "\ncompile error:" + compiler.getErrorMessage());
    }
  }


  BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
    int numberOfAtoms = viewer.getAtomCount();
    BitSet bs;
    BitSet[] stack = new BitSet[10];
    int sp = 0;

    for (int pc = pcStart; ; ++pc) {
      Token instruction = code[pc];
      if (logMessages)
        viewer.scriptStatus("instruction=" + instruction);
      switch (instruction.tok) {
      case Token::expressionBegin:
        break;
      case Token::expressionEnd:
        break expression_loop;
      case Token::all:
        bs = stack[sp++] = new BitSet(numberOfAtoms);
        for (int i = numberOfAtoms; --i >= 0; )
          bs.set(i);
        break;
      case Token::none:
        stack[sp++] = new BitSet();
        break;
      case Token::opOr:
        bs = stack[--sp];
        stack[sp-1].or(bs);
        break;
      case Token::opAnd:
        bs = stack[--sp];
        stack[sp-1].and(bs);
        break;
      case Token::opNot:
        bs = stack[sp - 1];
        notSet(bs);
        break;
      case Token::within:
        bs = stack[sp - 1];
        stack[sp - 1] = new BitSet();
        withinInstruction(instruction, bs, stack[sp - 1]);
        break;
      case Token::selected:
        stack[sp++] = copyBitSet(viewer.getSelectionSet());
        break;
      case Token::name:

        break;
      case  Token::index:
        
        break;
      case Token::molname:  

        break;
      case Token::molindex:
        break;
      case Token::identifier:
        stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
        break;
      case Token::opLT:
      case Token::opLE:
      case Token::opGE:
      case Token::opGT:
      case Token::opEQ:
      case Token::opNE:
        bs = stack[sp++] = new BitSet();
        comparatorInstruction(instruction, bs);
        break;
      default:
        unrecognizedExpression();
      }
    }
    if (sp != 1)
      evalError("atom expression compiler error - stack over/underflow");
    return stack[0];
  }


  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
    int comparator = instruction.tok;
    int property = instruction.intValue;
    float propertyValue = 0; // just for temperature
    int comparisonValue = ((Integer)instruction.value).intValue();
    int numberOfAtoms = viewer.getAtomCount();
    Frame frame = viewer.getFrame();
    for (int i = 0; i < numberOfAtoms; ++i) {
      Atom atom = frame.getAtomAt(i);
      switch (property) {
      case Token::mass:
        //propertyValue = atom.getAtomNumber();
        break;
      case Token::charge:

        break;
      case Token::dipole:

        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.set(i);
    }
  }

void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)

    boost::any withinSpec = instruction.value;
    if (withinSpec instanceof Float) {
        withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
        return;
    }
    evalError("Unrecognized within parameter:" + withinSpec);
}

  void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
    Frame frame = viewer.getFrame();
    for (int i = frame.getAtomCount(); --i >= 0; ) {
      if (bs.get(i)) {
        Atom atom = frame.getAtomAt(i);
        AtomIterator iterWithin =
          frame.getWithinIterator(atom, distance);
        while (iterWithin.hasNext())
          bsResult.set(iterWithin.next().getAtomIndex());
      }
    }
  }

  void SelectionEvaluator::define() {
    std::string variable = (std::string)statement[1].value;
    variables.insert(std::make_pair(variable, expression(statement, 2)));
  }
}

  void SelectionEvaluator::predefine(Token[] statement) {
    std::string variable = (std::string)statement[1].value;
    variables.put(variable, statement);
  }

  void SelectionEvaluator::select(){
      viewer.setSelectionSet(expression(statement, 1));
  }
  
  }
Revision:	1965
Committed:	Wed Feb 2 23:13:11 2005 UTC (19 years, 4 months ago) by tim
File size:	9198 byte(s)
Log Message:	selection library in progress, except SelectionEvaluator, other files are compiled
#	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			#include "selection/SelectionEvaluator.hpp"
43			namespace oopse {
44
45
46	tim	1962	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
47			this->filename = filename;
48			this->script = script;
49			if (! compiler.compile(filename, script)) {
50			error = true;
51			errorMessage = compiler.getErrorMessage();
52			return false;
53			}
54
55			pc = 0;
56			aatoken = compiler.getAatokenCompiled();
57			linenumbers = compiler.getLineNumbers();
58			lineIndices = compiler.getLineIndices();
59			return true;
60	tim	1961	}
61	tim	1962
62			void SelectionEvaluator::clearState() {
63			for (int i = scriptLevelMax; --i >= 0; )
64	tim	1965	stack[i].clear();
65	tim	1962	scriptLevel = 0;
66			error = false;
67	tim	1965	errorMessage = "";
68	tim	1962	}
69
70			bool SelectionEvaluator::loadScriptString(const std::string& script) {
71			clearState();
72	tim	1965	return loadScript("", script);
73	tim	1962	}
74
75			bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
76			clearState();
77			return loadScriptFileInternal(filename);
78			}
79
80
81			void SelectionEvaluator::instructionDispatchLoop(){
82
83	tim	1965	while ( pc < aatoken.size()) {
84	tim	1962	statement = aatoken[pc++];
85	tim	1965	statementLength = statement.size();
86	tim	1962	Token token = statement[0];
87			switch (token.tok) {
88	tim	1965	case Token::define:
89	tim	1962	define();
90			break;
91	tim	1965	case Token::select:
92	tim	1962	select();
93			break;
94			default:
95			unrecognizedCommand(token);
96			return;
97			}
98			}
99			}
100
101	tim	1965	void SelectionEvaluator::predefine(const std::string& script) {
102	tim	1962	if (compiler.compile("#predefine", script)) {
103	tim	1965	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
104			if (aatoken.size() != 1) {
105	tim	1962	viewer.scriptStatus("predefinition does not have exactly 1 command:"
106			+ script);
107			return;
108			}
109	tim	1965
110			std::vector<Token> statement = aatoken[0];
111
112			if (statement.size() > 2) {
113	tim	1962	int tok = statement[1].tok;
114	tim	1965	if (tok == Token::identifier \|\|
115			(tok & Token::predefinedset) == Token::predefinedset) {
116			std::string variable = (std::string)statement[1].value;
117	tim	1962	variables.put(variable, statement);
118			} else {
119			viewer.scriptStatus("invalid variable name:" + script);
120			}
121			} else {
122			viewer.scriptStatus("bad predefinition length:" + script);
123			}
124			} else {
125			viewer.scriptStatus("predefined set compile error:" + script +
126			"\ncompile error:" + compiler.getErrorMessage());
127			}
128			}
129
130
131
132	tim	1965	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
133	tim	1962	int numberOfAtoms = viewer.getAtomCount();
134			BitSet bs;
135			BitSet[] stack = new BitSet[10];
136			int sp = 0;
137
138			for (int pc = pcStart; ; ++pc) {
139			Token instruction = code[pc];
140			if (logMessages)
141			viewer.scriptStatus("instruction=" + instruction);
142			switch (instruction.tok) {
143	tim	1965	case Token::expressionBegin:
144	tim	1962	break;
145	tim	1965	case Token::expressionEnd:
146	tim	1962	break expression_loop;
147	tim	1965	case Token::all:
148	tim	1962	bs = stack[sp++] = new BitSet(numberOfAtoms);
149			for (int i = numberOfAtoms; --i >= 0; )
150			bs.set(i);
151			break;
152	tim	1965	case Token::none:
153	tim	1962	stack[sp++] = new BitSet();
154			break;
155	tim	1965	case Token::opOr:
156	tim	1962	bs = stack[--sp];
157			stack[sp-1].or(bs);
158			break;
159	tim	1965	case Token::opAnd:
160	tim	1962	bs = stack[--sp];
161			stack[sp-1].and(bs);
162			break;
163	tim	1965	case Token::opNot:
164	tim	1962	bs = stack[sp - 1];
165			notSet(bs);
166			break;
167	tim	1965	case Token::within:
168	tim	1962	bs = stack[sp - 1];
169			stack[sp - 1] = new BitSet();
170			withinInstruction(instruction, bs, stack[sp - 1]);
171			break;
172	tim	1965	case Token::selected:
173	tim	1962	stack[sp++] = copyBitSet(viewer.getSelectionSet());
174			break;
175	tim	1965	case Token::name:
176
177	tim	1962	break;
178	tim	1965	case Token::index:
179
180			break;
181			case Token::molname:
182
183			break;
184			case Token::molindex:
185			break;
186			case Token::identifier:
187			stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
188			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	1962	bs = stack[sp++] = new BitSet();
196			comparatorInstruction(instruction, bs);
197			break;
198			default:
199			unrecognizedExpression();
200			}
201			}
202			if (sp != 1)
203			evalError("atom expression compiler error - stack over/underflow");
204			return stack[0];
205			}
206
207
208
209			void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
210			int comparator = instruction.tok;
211			int property = instruction.intValue;
212			float propertyValue = 0; // just for temperature
213			int comparisonValue = ((Integer)instruction.value).intValue();
214			int numberOfAtoms = viewer.getAtomCount();
215			Frame frame = viewer.getFrame();
216			for (int i = 0; i < numberOfAtoms; ++i) {
217			Atom atom = frame.getAtomAt(i);
218			switch (property) {
219	tim	1965	case Token::mass:
220			//propertyValue = atom.getAtomNumber();
221	tim	1962	break;
222	tim	1965	case Token::charge:
223
224	tim	1962	break;
225	tim	1965	case Token::dipole:
226
227	tim	1962	break;
228			default:
229			unrecognizedAtomProperty(property);
230			}
231	tim	1965	bool match = false;
232	tim	1962	switch (comparator) {
233	tim	1965	case Token::opLT:
234	tim	1962	match = propertyValue < comparisonValue;
235			break;
236	tim	1965	case Token::opLE:
237	tim	1962	match = propertyValue <= comparisonValue;
238			break;
239	tim	1965	case Token::opGE:
240	tim	1962	match = propertyValue >= comparisonValue;
241			break;
242	tim	1965	case Token::opGT:
243	tim	1962	match = propertyValue > comparisonValue;
244			break;
245	tim	1965	case Token::opEQ:
246	tim	1962	match = propertyValue == comparisonValue;
247			break;
248	tim	1965	case Token::opNE:
249	tim	1962	match = propertyValue != comparisonValue;
250			break;
251			}
252			if (match)
253			bs.set(i);
254			}
255			}
256
257	tim	1965	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
258	tim	1962
259	tim	1965	boost::any withinSpec = instruction.value;
260	tim	1962	if (withinSpec instanceof Float) {
261			withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
262			return;
263			}
264			evalError("Unrecognized within parameter:" + withinSpec);
265			}
266
267			void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
268			Frame frame = viewer.getFrame();
269			for (int i = frame.getAtomCount(); --i >= 0; ) {
270			if (bs.get(i)) {
271			Atom atom = frame.getAtomAt(i);
272			AtomIterator iterWithin =
273			frame.getWithinIterator(atom, distance);
274			while (iterWithin.hasNext())
275			bsResult.set(iterWithin.next().getAtomIndex());
276			}
277			}
278			}
279
280	tim	1965	void SelectionEvaluator::define() {
281			std::string variable = (std::string)statement[1].value;
282			variables.insert(std::make_pair(variable, expression(statement, 2)));
283	tim	1962	}
284			}
285
286			void SelectionEvaluator::predefine(Token[] statement) {
287	tim	1965	std::string variable = (std::string)statement[1].value;
288	tim	1962	variables.put(variable, statement);
289			}
290
291			void SelectionEvaluator::select(){
292			viewer.setSelectionSet(expression(statement, 1));
293			}
294
295			}