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root/group/trunk/OOPSE-4/src/selection/SelectionEvaluator.cpp
Revision: 2034
Committed: Tue Feb 15 17:49:58 2005 UTC (19 years, 4 months ago) by tim
File size: 12958 byte(s)
Log Message:
replace std::make_pair by VariablesType::value_type to make Sun Compiler happy

File Contents

# Content
1 /*
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 <stack>
43 #include "selection/SelectionEvaluator.hpp"
44 #include "primitives/Atom.hpp"
45 #include "primitives/DirectionalAtom.hpp"
46 #include "primitives/RigidBody.hpp"
47 #include "primitives/Molecule.hpp"
48
49 namespace oopse {
50
51
52 SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), nameFinder(info), distanceFinder(info), isLoaded_(false){
53 nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
54 }
55
56 bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
57 clearDefinitionsAndLoadPredefined();
58 this->filename = filename;
59 this->script = script;
60 if (! compiler.compile(filename, script)) {
61 error = true;
62 errorMessage = compiler.getErrorMessage();
63 std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
64 return false;
65 }
66
67 pc = 0;
68 aatoken = compiler.getAatokenCompiled();
69 linenumbers = compiler.getLineNumbers();
70 lineIndices = compiler.getLineIndices();
71
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 return true;
84 }
85
86 void SelectionEvaluator::clearState() {
87 //for (int i = scriptLevelMax; --i >= 0; )
88 // stack[i].clear();
89 //scriptLevel = 0;
90 error = false;
91 errorMessage = "";
92 }
93
94 bool SelectionEvaluator::loadScriptString(const std::string& script) {
95 clearState();
96 return loadScript("", script);
97 }
98
99 bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
100 clearState();
101 return loadScriptFileInternal(filename);
102 }
103
104 bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
105 std::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 }
118
119 void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
120
121 while ( pc < aatoken.size()) {
122 statement = aatoken[pc++];
123 statementLength = statement.size();
124 Token token = statement[0];
125 switch (token.tok) {
126 case Token::define:
127 define();
128 break;
129 case Token::select:
130 select(bs);
131 break;
132 default:
133 unrecognizedCommand(token);
134 return;
135 }
136 }
137
138 }
139
140 BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
141 BitSet bs;
142 std::stack<BitSet> stack;
143
144 for (int pc = pcStart; pc < code.size(); ++pc) {
145 Token instruction = code[pc];
146
147 switch (instruction.tok) {
148 case Token::expressionBegin:
149 break;
150 case Token::expressionEnd:
151 break;
152 case Token::all:
153 bs = BitSet(nStuntDouble);
154 bs.setAll();
155 stack.push(bs);
156 break;
157 case Token::none:
158 bs = BitSet(nStuntDouble);
159 stack.push(bs);
160 break;
161 case Token::opOr:
162 bs = stack.top();
163 stack.pop();
164 stack.top() |= bs;
165 break;
166 case Token::opAnd:
167 bs = stack.top();
168 stack.pop();
169 stack.top() &= bs;
170 break;
171 case Token::opNot:
172 stack.top().flip();
173 break;
174 case Token::within:
175
176 withinInstruction(instruction, stack.top());
177 break;
178 //case Token::selected:
179 // stack.push(getSelectionSet());
180 // break;
181 case Token::name:
182 stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
183 break;
184 case Token::index:
185 stack.push(indexInstruction(instruction.value));
186 break;
187 case Token::identifier:
188 stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
189 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 stack.push(comparatorInstruction(instruction));
197 break;
198 default:
199 unrecognizedExpression();
200 }
201 }
202 if (stack.size() != 1)
203 evalError("atom expression compiler error - stack over/underflow");
204
205 return stack.top();
206 }
207
208
209
210 BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
211 int comparator = instruction.tok;
212 int property = instruction.intValue;
213 float comparisonValue = boost::any_cast<float>(instruction.value);
214 float propertyValue;
215 BitSet bs(nStuntDouble);
216 bs.clearAll();
217
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
227 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 }
236
237 return bs;
238 }
239
240 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
284 boost::any withinSpec = instruction.value;
285 float distance;
286 if (withinSpec.type() == typeid(float)){
287 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 }
294
295 bs = distanceFinder.find(bs, distance);
296 }
297
298 void SelectionEvaluator::define() {
299 assert(statement.size() >= 3);
300
301 std::string variable = boost::any_cast<std::string>(statement[1].value);
302
303 variables.insert(std::make_pair(variable, expression(statement, 2)));
304 }
305
306
307 /** @todo */
308 void SelectionEvaluator::predefine(const std::string& script) {
309
310 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 std::string variable = boost::any_cast<std::string>(statement[1].value);
322 variables.insert(VariablesType::value_type(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 void SelectionEvaluator::select(BitSet& bs){
340 bs = expression(statement, 1);
341 }
342
343 BitSet SelectionEvaluator::lookupValue(const std::string& variable){
344
345 BitSet bs(nStuntDouble);
346 std::map<std::string, boost::any>::iterator i = variables.find(variable);
347
348 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 bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
353 i->second = bs; /**@todo fixme */
354 return bs;
355 }
356 } else {
357 unrecognizedIdentifier(variable);
358 }
359
360 return bs;
361 }
362
363 BitSet SelectionEvaluator::nameInstruction(const std::string& name){
364
365 return nameFinder.match(name);
366
367 }
368
369 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
377 return false;
378 }
379
380 void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
381 variables.clear();
382 //load predefine
383 //predefine();
384 }
385
386 BitSet SelectionEvaluator::evaluate() {
387 BitSet bs(nStuntDouble);
388 if (isLoaded_) {
389 pc = 0;
390 instructionDispatchLoop(bs);
391 }
392
393 return bs;
394 }
395
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 //BitSet SelectionEvaluator::evaluate(int frameNo) {
420 //
421 //}
422
423 }