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

# 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 2097 SelectionEvaluator::SelectionEvaluator(SimInfo* si)
53     : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54    
55 tim 1979 nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56 tim 1967 }
57    
58 tim 1962 bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
59 tim 1972 clearDefinitionsAndLoadPredefined();
60 tim 1962 this->filename = filename;
61     this->script = script;
62     if (! compiler.compile(filename, script)) {
63     error = true;
64     errorMessage = compiler.getErrorMessage();
65 tim 1972 std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
66 tim 1962 return false;
67     }
68    
69     pc = 0;
70     aatoken = compiler.getAatokenCompiled();
71     linenumbers = compiler.getLineNumbers();
72     lineIndices = compiler.getLineIndices();
73 tim 1972
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 tim 1962 return true;
86 tim 1961 }
87 tim 1962
88     void SelectionEvaluator::clearState() {
89 tim 1972 //for (int i = scriptLevelMax; --i >= 0; )
90     // stack[i].clear();
91     //scriptLevel = 0;
92 tim 1962 error = false;
93 tim 1965 errorMessage = "";
94 tim 1962 }
95    
96     bool SelectionEvaluator::loadScriptString(const std::string& script) {
97     clearState();
98 tim 1965 return loadScript("", script);
99 tim 1962 }
100    
101     bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
102     clearState();
103     return loadScriptFileInternal(filename);
104     }
105    
106 tim 1967 bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
107 chrisfen 1985 std::ifstream ifs(filename.c_str());
108 tim 1972 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 tim 1966 }
120    
121 tim 1972 void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
122    
123 tim 1965 while ( pc < aatoken.size()) {
124 tim 1962 statement = aatoken[pc++];
125 tim 1965 statementLength = statement.size();
126 tim 1962 Token token = statement[0];
127     switch (token.tok) {
128 tim 1965 case Token::define:
129 tim 1962 define();
130     break;
131 tim 1965 case Token::select:
132 tim 1972 select(bs);
133 tim 1962 break;
134     default:
135     unrecognizedCommand(token);
136     return;
137     }
138     }
139 tim 1972
140 tim 1962 }
141    
142 tim 1967 BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143 tim 1962 BitSet bs;
144 tim 1967 std::stack<BitSet> stack;
145    
146 tim 1972 for (int pc = pcStart; pc < code.size(); ++pc) {
147 tim 1962 Token instruction = code[pc];
148 tim 1966
149 tim 1962 switch (instruction.tok) {
150 tim 1965 case Token::expressionBegin:
151 tim 1962 break;
152 tim 1965 case Token::expressionEnd:
153 tim 1966 break;
154 tim 1965 case Token::all:
155 tim 1967 bs = BitSet(nStuntDouble);
156     bs.setAll();
157     stack.push(bs);
158 tim 1962 break;
159 tim 1965 case Token::none:
160 tim 1967 bs = BitSet(nStuntDouble);
161     stack.push(bs);
162 tim 1962 break;
163 tim 1965 case Token::opOr:
164 tim 1967 bs = stack.top();
165     stack.pop();
166     stack.top() |= bs;
167 tim 1962 break;
168 tim 1965 case Token::opAnd:
169 tim 1967 bs = stack.top();
170     stack.pop();
171     stack.top() &= bs;
172 tim 1962 break;
173 tim 1965 case Token::opNot:
174 tim 1967 stack.top().flip();
175 tim 1962 break;
176 tim 1965 case Token::within:
177 tim 1967
178     withinInstruction(instruction, stack.top());
179 tim 1962 break;
180 tim 1967 //case Token::selected:
181     // stack.push(getSelectionSet());
182     // break;
183 tim 1965 case Token::name:
184 tim 1967 stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
185 tim 1962 break;
186 tim 1979 case Token::index:
187     stack.push(indexInstruction(instruction.value));
188 tim 1965 break;
189     case Token::identifier:
190 tim 1967 stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
191 tim 1965 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 tim 1967 stack.push(comparatorInstruction(instruction));
199 tim 1962 break;
200     default:
201     unrecognizedExpression();
202     }
203     }
204 tim 1967 if (stack.size() != 1)
205 tim 1962 evalError("atom expression compiler error - stack over/underflow");
206 tim 1967
207     return stack.top();
208 tim 1962 }
209    
210    
211    
212 tim 1967 BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
213 tim 1962 int comparator = instruction.tok;
214     int property = instruction.intValue;
215 tim 1967 float comparisonValue = boost::any_cast<float>(instruction.value);
216     float propertyValue;
217     BitSet bs(nStuntDouble);
218 tim 1979 bs.clearAll();
219 tim 1967
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 tim 1965
229 tim 1967 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 tim 1962 }
238    
239 tim 1967 return bs;
240     }
241 tim 1962
242 tim 1967 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 tim 1979
286 tim 1965 boost::any withinSpec = instruction.value;
287 tim 1979 float distance;
288 tim 1966 if (withinSpec.type() == typeid(float)){
289 tim 1979 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 tim 1962 }
296 tim 1966
297 tim 1979 bs = distanceFinder.find(bs, distance);
298 tim 1962 }
299    
300 tim 1967 void SelectionEvaluator::define() {
301 tim 1966 assert(statement.size() >= 3);
302    
303     std::string variable = boost::any_cast<std::string>(statement[1].value);
304 tim 1967
305 tim 2035 variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
306 tim 1962 }
307    
308 tim 1967
309 tim 1966 /** @todo */
310     void SelectionEvaluator::predefine(const std::string& script) {
311 tim 1962
312 tim 1966 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 tim 1967 std::string variable = boost::any_cast<std::string>(statement[1].value);
324 tim 2034 variables.insert(VariablesType::value_type(variable, statement));
325 tim 1966
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 tim 1972 void SelectionEvaluator::select(BitSet& bs){
342     bs = expression(statement, 1);
343 tim 1966 }
344    
345     BitSet SelectionEvaluator::lookupValue(const std::string& variable){
346    
347 tim 1979 BitSet bs(nStuntDouble);
348 tim 1966 std::map<std::string, boost::any>::iterator i = variables.find(variable);
349 tim 1979
350 tim 1966 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 tim 1979 bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
355 tim 1966 i->second = bs; /**@todo fixme */
356     return bs;
357     }
358 tim 1967 } else {
359     unrecognizedIdentifier(variable);
360 tim 1966 }
361 tim 1979
362     return bs;
363 tim 1966 }
364    
365 tim 1967 BitSet SelectionEvaluator::nameInstruction(const std::string& name){
366    
367 tim 1979 return nameFinder.match(name);
368 tim 1972
369 tim 1967 }
370    
371 tim 1972 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 tim 1967
379 tim 1972 return false;
380     }
381    
382     void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
383     variables.clear();
384     //load predefine
385     //predefine();
386 tim 1966 }
387 tim 1972
388     BitSet SelectionEvaluator::evaluate() {
389     BitSet bs(nStuntDouble);
390     if (isLoaded_) {
391 tim 1982 pc = 0;
392 tim 1972 instructionDispatchLoop(bs);
393     }
394    
395     return bs;
396     }
397 tim 1979
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 tim 2099 bs = indexFinder.find(index);
407 tim 1979 }
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 tim 2099 bs = indexFinder.find(indexRange.first, indexRange.second);
415 tim 1979 }
416     }
417    
418     return bs;
419     }
420    
421 tim 1972 }