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root/group/trunk/OOPSE-4/src/selection/SelectionEvaluator.cpp
Revision: 1982
Committed: Mon Feb 7 20:06:00 2005 UTC (19 years, 4 months ago) by tim
File size: 12944 byte(s)
Log Message:
forget to reset the pc which cause reevaluate return NULL

File Contents

# 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 1979 SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), nameFinder(info), distanceFinder(info), isLoaded_(false){
53     nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
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 1979 case Token::index:
185     stack.push(indexInstruction(instruction.value));
186 tim 1965 break;
187     case Token::identifier:
188 tim 1967 stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
189 tim 1965 break;
190     case Token::opLT:
191     case Token::opLE:
192     case Token::opGE:
193     case Token::opGT:
194     case Token::opEQ:
195     case Token::opNE:
196 tim 1967 stack.push(comparatorInstruction(instruction));
197 tim 1962 break;
198     default:
199     unrecognizedExpression();
200     }
201     }
202 tim 1967 if (stack.size() != 1)
203 tim 1962 evalError("atom expression compiler error - stack over/underflow");
204 tim 1967
205     return stack.top();
206 tim 1962 }
207    
208    
209    
210 tim 1967 BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
211 tim 1962 int comparator = instruction.tok;
212     int property = instruction.intValue;
213 tim 1967 float comparisonValue = boost::any_cast<float>(instruction.value);
214     float propertyValue;
215     BitSet bs(nStuntDouble);
216 tim 1979 bs.clearAll();
217 tim 1967
218     SimInfo::MoleculeIterator mi;
219     Molecule* mol;
220     Molecule::AtomIterator ai;
221     Atom* atom;
222     Molecule::RigidBodyIterator rbIter;
223     RigidBody* rb;
224    
225     for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
226 tim 1965
227 tim 1967 for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
228     compareProperty(atom, bs, property, comparator, comparisonValue);
229     }
230    
231     //change the positions of atoms which belong to the rigidbodies
232     for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
233     compareProperty(rb, bs, property, comparator, comparisonValue);
234     }
235 tim 1962 }
236    
237 tim 1967 return bs;
238     }
239 tim 1962
240 tim 1967 void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
241     double propertyValue;
242     switch (property) {
243     case Token::mass:
244     propertyValue = sd->getMass();
245     break;
246     case Token::charge:
247     return;
248     //break;
249     case Token::dipole:
250     return;
251     //break;
252     default:
253     unrecognizedAtomProperty(property);
254     }
255    
256     bool match = false;
257     switch (comparator) {
258     case Token::opLT:
259     match = propertyValue < comparisonValue;
260     break;
261     case Token::opLE:
262     match = propertyValue <= comparisonValue;
263     break;
264     case Token::opGE:
265     match = propertyValue >= comparisonValue;
266     break;
267     case Token::opGT:
268     match = propertyValue > comparisonValue;
269     break;
270     case Token::opEQ:
271     match = propertyValue == comparisonValue;
272     break;
273     case Token::opNE:
274     match = propertyValue != comparisonValue;
275     break;
276     }
277     if (match)
278     bs.setBitOn(sd->getGlobalIndex());
279    
280     }
281    
282     void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
283 tim 1979
284 tim 1965 boost::any withinSpec = instruction.value;
285 tim 1979 float distance;
286 tim 1966 if (withinSpec.type() == typeid(float)){
287 tim 1979 distance = boost::any_cast<float>(withinSpec);
288     } else if (withinSpec.type() == typeid(int)) {
289     distance = boost::any_cast<int>(withinSpec);
290     } else {
291     evalError("casting error in withinInstruction");
292     bs.clearAll();
293 tim 1962 }
294 tim 1966
295 tim 1979 bs = distanceFinder.find(bs, distance);
296 tim 1962 }
297    
298 tim 1967 void SelectionEvaluator::define() {
299 tim 1966 assert(statement.size() >= 3);
300    
301     std::string variable = boost::any_cast<std::string>(statement[1].value);
302 tim 1967
303 tim 1965 variables.insert(std::make_pair(variable, expression(statement, 2)));
304 tim 1962 }
305    
306 tim 1967
307 tim 1966 /** @todo */
308     void SelectionEvaluator::predefine(const std::string& script) {
309 tim 1962
310 tim 1966 if (compiler.compile("#predefine", script)) {
311     std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
312     if (aatoken.size() != 1) {
313     evalError("predefinition does not have exactly 1 command:"
314     + script);
315     return;
316     }
317     std::vector<Token> statement = aatoken[0];
318     if (statement.size() > 2) {
319     int tok = statement[1].tok;
320     if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
321 tim 1967 std::string variable = boost::any_cast<std::string>(statement[1].value);
322 tim 1966 variables.insert(std::make_pair(variable, statement));
323    
324     } else {
325     evalError("invalid variable name:" + script);
326     }
327     }else {
328     evalError("bad predefinition length:" + script);
329     }
330    
331    
332     } else {
333     evalError("predefined set compile error:" + script +
334     "\ncompile error:" + compiler.getErrorMessage());
335     }
336    
337     }
338    
339 tim 1972 void SelectionEvaluator::select(BitSet& bs){
340     bs = expression(statement, 1);
341 tim 1966 }
342    
343     BitSet SelectionEvaluator::lookupValue(const std::string& variable){
344    
345 tim 1979 BitSet bs(nStuntDouble);
346 tim 1966 std::map<std::string, boost::any>::iterator i = variables.find(variable);
347 tim 1979
348 tim 1966 if (i != variables.end()) {
349     if (i->second.type() == typeid(BitSet)) {
350     return boost::any_cast<BitSet>(i->second);
351     } else if (i->second.type() == typeid(std::vector<Token>)){
352 tim 1979 bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
353 tim 1966 i->second = bs; /**@todo fixme */
354     return bs;
355     }
356 tim 1967 } else {
357     unrecognizedIdentifier(variable);
358 tim 1966 }
359 tim 1979
360     return bs;
361 tim 1966 }
362    
363 tim 1967 BitSet SelectionEvaluator::nameInstruction(const std::string& name){
364    
365 tim 1979 return nameFinder.match(name);
366 tim 1972
367 tim 1967 }
368    
369 tim 1972 bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
370     std::vector<Token>::const_iterator i;
371     for (i = tokens.begin(); i != tokens.end(); ++i) {
372     if (i->tok & Token::dynamic) {
373     return true;
374     }
375     }
376 tim 1967
377 tim 1972 return false;
378     }
379    
380     void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
381     variables.clear();
382     //load predefine
383     //predefine();
384 tim 1966 }
385 tim 1972
386     BitSet SelectionEvaluator::evaluate() {
387     BitSet bs(nStuntDouble);
388     if (isLoaded_) {
389 tim 1982 pc = 0;
390 tim 1972 instructionDispatchLoop(bs);
391     }
392    
393     return bs;
394     }
395 tim 1979
396     BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
397     BitSet bs(nStuntDouble);
398    
399     if (value.type() == typeid(int)) {
400     int index = boost::any_cast<int>(value);
401     if (index < 0 || index >= bs.size()) {
402     invalidIndex(index);
403     } else {
404     bs.setBitOn(index);
405     }
406     } else if (value.type() == typeid(std::pair<int, int>)) {
407     std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
408     assert(indexRange.first <= indexRange.second);
409     if (indexRange.first < 0 || indexRange.second >= bs.size()) {
410     invalidIndexRange(indexRange);
411     }else {
412     bs.setRangeOn(indexRange.first, indexRange.second);
413     }
414     }
415    
416     return bs;
417     }
418    
419 tim 1972 //BitSet SelectionEvaluator::evaluate(int frameNo) {
420     //
421     //}
422    
423     }