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 |
} |