ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-3.0/src/selection/SelectionEvaluator.cpp
Revision: 2099
Committed: Wed Mar 9 18:46:16 2005 UTC (19 years, 4 months ago) by tim
File size: 12955 byte(s)
Log Message:
fix compilation issue

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)
53 : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54
55 nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56 }
57
58 bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
59 clearDefinitionsAndLoadPredefined();
60 this->filename = filename;
61 this->script = script;
62 if (! compiler.compile(filename, script)) {
63 error = true;
64 errorMessage = compiler.getErrorMessage();
65 std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
66 return false;
67 }
68
69 pc = 0;
70 aatoken = compiler.getAatokenCompiled();
71 linenumbers = compiler.getLineNumbers();
72 lineIndices = compiler.getLineIndices();
73
74 std::vector<std::vector<Token> >::const_iterator i;
75
76 isDynamic_ = false;
77 for (i = aatoken.begin(); i != aatoken.end(); ++i) {
78 if (containDynamicToken(*i)) {
79 isDynamic_ = true;
80 break;
81 }
82 }
83
84 isLoaded_ = true;
85 return true;
86 }
87
88 void SelectionEvaluator::clearState() {
89 //for (int i = scriptLevelMax; --i >= 0; )
90 // stack[i].clear();
91 //scriptLevel = 0;
92 error = false;
93 errorMessage = "";
94 }
95
96 bool SelectionEvaluator::loadScriptString(const std::string& script) {
97 clearState();
98 return loadScript("", script);
99 }
100
101 bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
102 clearState();
103 return loadScriptFileInternal(filename);
104 }
105
106 bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
107 std::ifstream ifs(filename.c_str());
108 if (!ifs.is_open()) {
109 return false;
110 }
111
112 const int bufferSize = 65535;
113 char buffer[bufferSize];
114 std::string script;
115 while(ifs.getline(buffer, bufferSize)) {
116 script += buffer;
117 }
118 return loadScript(filename, script);
119 }
120
121 void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
122
123 while ( pc < aatoken.size()) {
124 statement = aatoken[pc++];
125 statementLength = statement.size();
126 Token token = statement[0];
127 switch (token.tok) {
128 case Token::define:
129 define();
130 break;
131 case Token::select:
132 select(bs);
133 break;
134 default:
135 unrecognizedCommand(token);
136 return;
137 }
138 }
139
140 }
141
142 BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143 BitSet bs;
144 std::stack<BitSet> stack;
145
146 for (int pc = pcStart; pc < code.size(); ++pc) {
147 Token instruction = code[pc];
148
149 switch (instruction.tok) {
150 case Token::expressionBegin:
151 break;
152 case Token::expressionEnd:
153 break;
154 case Token::all:
155 bs = BitSet(nStuntDouble);
156 bs.setAll();
157 stack.push(bs);
158 break;
159 case Token::none:
160 bs = BitSet(nStuntDouble);
161 stack.push(bs);
162 break;
163 case Token::opOr:
164 bs = stack.top();
165 stack.pop();
166 stack.top() |= bs;
167 break;
168 case Token::opAnd:
169 bs = stack.top();
170 stack.pop();
171 stack.top() &= bs;
172 break;
173 case Token::opNot:
174 stack.top().flip();
175 break;
176 case Token::within:
177
178 withinInstruction(instruction, stack.top());
179 break;
180 //case Token::selected:
181 // stack.push(getSelectionSet());
182 // break;
183 case Token::name:
184 stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
185 break;
186 case Token::index:
187 stack.push(indexInstruction(instruction.value));
188 break;
189 case Token::identifier:
190 stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
191 break;
192 case Token::opLT:
193 case Token::opLE:
194 case Token::opGE:
195 case Token::opGT:
196 case Token::opEQ:
197 case Token::opNE:
198 stack.push(comparatorInstruction(instruction));
199 break;
200 default:
201 unrecognizedExpression();
202 }
203 }
204 if (stack.size() != 1)
205 evalError("atom expression compiler error - stack over/underflow");
206
207 return stack.top();
208 }
209
210
211
212 BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
213 int comparator = instruction.tok;
214 int property = instruction.intValue;
215 float comparisonValue = boost::any_cast<float>(instruction.value);
216 float propertyValue;
217 BitSet bs(nStuntDouble);
218 bs.clearAll();
219
220 SimInfo::MoleculeIterator mi;
221 Molecule* mol;
222 Molecule::AtomIterator ai;
223 Atom* atom;
224 Molecule::RigidBodyIterator rbIter;
225 RigidBody* rb;
226
227 for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
228
229 for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
230 compareProperty(atom, bs, property, comparator, comparisonValue);
231 }
232
233 //change the positions of atoms which belong to the rigidbodies
234 for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
235 compareProperty(rb, bs, property, comparator, comparisonValue);
236 }
237 }
238
239 return bs;
240 }
241
242 void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
243 double propertyValue;
244 switch (property) {
245 case Token::mass:
246 propertyValue = sd->getMass();
247 break;
248 case Token::charge:
249 return;
250 //break;
251 case Token::dipole:
252 return;
253 //break;
254 default:
255 unrecognizedAtomProperty(property);
256 }
257
258 bool match = false;
259 switch (comparator) {
260 case Token::opLT:
261 match = propertyValue < comparisonValue;
262 break;
263 case Token::opLE:
264 match = propertyValue <= comparisonValue;
265 break;
266 case Token::opGE:
267 match = propertyValue >= comparisonValue;
268 break;
269 case Token::opGT:
270 match = propertyValue > comparisonValue;
271 break;
272 case Token::opEQ:
273 match = propertyValue == comparisonValue;
274 break;
275 case Token::opNE:
276 match = propertyValue != comparisonValue;
277 break;
278 }
279 if (match)
280 bs.setBitOn(sd->getGlobalIndex());
281
282 }
283
284 void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
285
286 boost::any withinSpec = instruction.value;
287 float distance;
288 if (withinSpec.type() == typeid(float)){
289 distance = boost::any_cast<float>(withinSpec);
290 } else if (withinSpec.type() == typeid(int)) {
291 distance = boost::any_cast<int>(withinSpec);
292 } else {
293 evalError("casting error in withinInstruction");
294 bs.clearAll();
295 }
296
297 bs = distanceFinder.find(bs, distance);
298 }
299
300 void SelectionEvaluator::define() {
301 assert(statement.size() >= 3);
302
303 std::string variable = boost::any_cast<std::string>(statement[1].value);
304
305 variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
306 }
307
308
309 /** @todo */
310 void SelectionEvaluator::predefine(const std::string& script) {
311
312 if (compiler.compile("#predefine", script)) {
313 std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
314 if (aatoken.size() != 1) {
315 evalError("predefinition does not have exactly 1 command:"
316 + script);
317 return;
318 }
319 std::vector<Token> statement = aatoken[0];
320 if (statement.size() > 2) {
321 int tok = statement[1].tok;
322 if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
323 std::string variable = boost::any_cast<std::string>(statement[1].value);
324 variables.insert(VariablesType::value_type(variable, statement));
325
326 } else {
327 evalError("invalid variable name:" + script);
328 }
329 }else {
330 evalError("bad predefinition length:" + script);
331 }
332
333
334 } else {
335 evalError("predefined set compile error:" + script +
336 "\ncompile error:" + compiler.getErrorMessage());
337 }
338
339 }
340
341 void SelectionEvaluator::select(BitSet& bs){
342 bs = expression(statement, 1);
343 }
344
345 BitSet SelectionEvaluator::lookupValue(const std::string& variable){
346
347 BitSet bs(nStuntDouble);
348 std::map<std::string, boost::any>::iterator i = variables.find(variable);
349
350 if (i != variables.end()) {
351 if (i->second.type() == typeid(BitSet)) {
352 return boost::any_cast<BitSet>(i->second);
353 } else if (i->second.type() == typeid(std::vector<Token>)){
354 bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
355 i->second = bs; /**@todo fixme */
356 return bs;
357 }
358 } else {
359 unrecognizedIdentifier(variable);
360 }
361
362 return bs;
363 }
364
365 BitSet SelectionEvaluator::nameInstruction(const std::string& name){
366
367 return nameFinder.match(name);
368
369 }
370
371 bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
372 std::vector<Token>::const_iterator i;
373 for (i = tokens.begin(); i != tokens.end(); ++i) {
374 if (i->tok & Token::dynamic) {
375 return true;
376 }
377 }
378
379 return false;
380 }
381
382 void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
383 variables.clear();
384 //load predefine
385 //predefine();
386 }
387
388 BitSet SelectionEvaluator::evaluate() {
389 BitSet bs(nStuntDouble);
390 if (isLoaded_) {
391 pc = 0;
392 instructionDispatchLoop(bs);
393 }
394
395 return bs;
396 }
397
398 BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
399 BitSet bs(nStuntDouble);
400
401 if (value.type() == typeid(int)) {
402 int index = boost::any_cast<int>(value);
403 if (index < 0 || index >= bs.size()) {
404 invalidIndex(index);
405 } else {
406 bs = indexFinder.find(index);
407 }
408 } else if (value.type() == typeid(std::pair<int, int>)) {
409 std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
410 assert(indexRange.first <= indexRange.second);
411 if (indexRange.first < 0 || indexRange.second >= bs.size()) {
412 invalidIndexRange(indexRange);
413 }else {
414 bs = indexFinder.find(indexRange.first, indexRange.second);
415 }
416 }
417
418 return bs;
419 }
420
421 }