# | Line 6 | Line 6 | |
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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 |
9 | > | * 1. Redistributions of source code must retain the above copyright |
10 | * notice, this list of conditions and the following disclaimer. | |
11 | * | |
12 | < | * 3. Redistributions in binary form must reproduce the above copyright |
12 | > | * 2. Redistributions in binary form must reproduce the above copyright |
13 | * notice, this list of conditions and the following disclaimer in the | |
14 | * documentation and/or other materials provided with the | |
15 | * distribution. | |
# | Line 37 | Line 28 | |
28 | * arising out of the use of or inability to use software, even if the | |
29 | * University of Notre Dame has been advised of the possibility of | |
30 | * such damages. | |
31 | + | * |
32 | + | * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 | + | * research, please cite the appropriate papers when you publish your |
34 | + | * work. Good starting points are: |
35 | + | * |
36 | + | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
37 | + | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
38 | + | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
39 | + | * [4] Vardeman & Gezelter, in progress (2009). |
40 | */ | |
41 | ||
42 | #ifndef SELECTION_SELECTIONCOMPILER_HPP | |
43 | #define SELECTION_SELECTIONCOMPILER_HPP | |
44 | < | |
44 | > | #include <iostream> |
45 | > | #include <string> |
46 | #include <vector> | |
46 | – | namespace oopse { |
47 | ||
48 | + | #include "selection/SelectionToken.hpp" |
49 | + | #include "selection/TokenMap.hpp" |
50 | + | #include "brains/SimInfo.hpp" |
51 | ||
52 | < | /** |
50 | < | * @class SelectionCompiler SelectionCompiler.hpp "selection/SelectionCompiler.hpp" |
51 | < | * @brief compile a selection script to tokens |
52 | < | * <pre> |
52 | > | namespace OpenMD { |
53 | ||
54 | – | expression :: = clauseOr |
54 | ||
55 | < | clauseOr ::= clauseAnd {OR clauseAnd}* |
55 | > | /** |
56 | > | * @class SelectionCompiler SelectionCompiler.hpp "selection/SelectionCompiler.hpp" |
57 | > | * @brief compile a selection script to tokens |
58 | > | * @todo document |
59 | > | * <pre> |
60 | ||
61 | < | clauseAnd ::= clauseNot {AND clauseNot}* |
61 | > | expression :: = clauseOr |
62 | ||
63 | < | clauseNot ::= NOT clauseNot | clausePrimitive |
63 | > | clauseOr ::= clauseAnd {OR clauseAnd}* |
64 | ||
65 | < | clausePrimitive ::= clauseComparator | |
63 | < | clauseWithin | |
64 | < | clauseResidueSpec | |
65 | < | none | all | |
66 | < | ( clauseOr ) |
65 | > | clauseAnd ::= clauseNot {AND clauseNot}* |
66 | ||
67 | < | clauseComparator ::= atomproperty comparatorop integer |
67 | > | clauseNot ::= NOT clauseNot | clausePrimitive |
68 | ||
69 | < | clauseWithin ::= WITHIN ( clauseDistance , expression ) |
69 | > | clausePrimitive ::= clauseComparator | |
70 | > | clauseWithin | |
71 | > | clauseName | |
72 | > | none | all | |
73 | > | ( clauseOr ) |
74 | ||
75 | < | clauseDistance ::= integer | decimal |
75 | > | clauseComparator ::= atomproperty comparatorop integer |
76 | ||
77 | < | |
77 | > | clauseWithin ::= WITHIN ( clauseDistance , expression ) |
78 | ||
79 | + | clauseDistance ::= integer | decimal |
80 | + | |
81 | + | clauseName::= *|string{.string{.string}} |
82 | ||
77 | – | clauseResidueSpec::= { clauseResNameSpec } |
78 | – | { clauseResNumSpec } |
79 | – | { chainSpec } |
80 | – | { clauseAtomSpec } |
81 | – | { modelSpec } |
83 | ||
84 | < | clauseResNameSpec::= * | [ resNamePattern ] | resNamePattern |
84 | > | * </pre> |
85 | > | */ |
86 | > | class SelectionCompiler{ |
87 | > | public: |
88 | > | bool compile(const std::string& filename, const std::string& script ); |
89 | > | |
90 | ||
91 | < | // question marks are part of identifiers |
92 | < | // they get split up and dealt with as wildcards at runtime |
93 | < | // and the integers which are residue number chains get bundled |
88 | < | // in with the identifier and also split out at runtime |
89 | < | // iff a variable of that name does not exist |
91 | > | std::vector<int> getLineNumbers() { |
92 | > | return lineNumbers; |
93 | > | } |
94 | ||
95 | < | resNamePattern ::= up to 3 alphanumeric chars with * and ? |
95 | > | std::vector<int> getLineIndices() { |
96 | > | return lineIndices; |
97 | > | } |
98 | ||
99 | < | clauseResNumSpec ::= * | clauseSequenceRange |
99 | > | std::vector<std::vector<Token> > getAatokenCompiled() { |
100 | > | return aatokenCompiled; |
101 | > | } |
102 | ||
103 | < | clauseSequenceRange ::= clauseSequenceCode { - clauseSequenceCode } |
103 | > | std::string getErrorMessage() { |
104 | > | std::string strError = errorMessage; |
105 | > | strError += " : " + errorLine + "\n"; |
106 | ||
107 | < | clauseSequenceCode ::= seqcode | {-} integer |
107 | > | if (!filename.empty()) { |
108 | > | strError += filename; |
109 | > | } |
110 | ||
111 | < | clauseChainSpec ::= {:} * | identifier | integer |
111 | > | return strError; |
112 | > | } |
113 | ||
114 | < | clauseAtomSpec ::= . * | . identifier {*} // note that this * is *not* a wildcard |
114 | > | |
115 | > | private: |
116 | ||
117 | < | clauseModelSpec ::= {:|/} * | integer |
104 | < | |
105 | < | * </pre> |
106 | < | */ |
107 | < | class SelectionCompiler{ |
108 | < | public: |
109 | < | bool compile(); |
117 | > | bool internalCompile(); |
118 | ||
111 | – | std::vector<Token> getCompiledTokens(); |
112 | – | private: |
119 | ||
120 | < | bool clauseOr(); |
121 | < | bool clauseAnd(); |
122 | < | bool clauseNot(); |
123 | < | bool clausePrimitive(); |
124 | < | bool clauseWithin(); |
125 | < | bool clauseComparator(); |
120 | > | bool lookingAtLeadingWhitespace(); |
121 | > | //bool lookingAtComment(); |
122 | > | bool lookingAtEndOfLine(); |
123 | > | bool lookingAtEndOfStatement(); |
124 | > | bool lookingAtString(); |
125 | > | bool lookingAtDecimal(bool allowNegative); |
126 | > | bool lookingAtInteger(bool allowNegative); |
127 | > | bool lookingAtLookupToken(); |
128 | > | bool lookingAtSpecialString(); |
129 | > | |
130 | > | std::string getUnescapedStringLiteral(); |
131 | > | int getHexitValue(char ch); |
132 | > | |
133 | > | bool compileCommand(const std::vector<Token>& ltoken); |
134 | > | bool compileExpression(); |
135 | > | bool compileExpression(int itoken); |
136 | ||
137 | < | internalCompile(); |
137 | > | bool clauseOr(); |
138 | > | bool clauseAnd(); |
139 | > | bool clauseNot(); |
140 | > | bool clausePrimitive(); |
141 | > | bool clauseWithin(); |
142 | > | bool clauseComparator(); |
143 | > | bool clauseChemObjName(); |
144 | > | bool clauseIndex(); |
145 | > | Token tokenNext(); |
146 | > | boost::any valuePeek(); |
147 | > | int tokPeek(); |
148 | ||
149 | < | std::vector<Token> compiledTokens_; |
150 | < | }; |
149 | > | bool addTokenToPostfix(const Token& token); |
150 | > | bool isNameValid(const std::string& name); |
151 | ||
152 | + | bool compileError(const std::string& errorMsg) { |
153 | + | |
154 | + | sprintf( painCave.errMsg, |
155 | + | "SelectionCompiler Error: %s\n", errorMsg.c_str()); |
156 | + | painCave.severity = OPENMD_ERROR; |
157 | + | painCave.isFatal = 1; |
158 | + | simError(); |
159 | + | |
160 | + | error = true; |
161 | + | this->errorMessage = errorMsg; |
162 | + | return false; |
163 | + | } |
164 | + | |
165 | + | bool commandExpected() { |
166 | + | return compileError("command expected"); |
167 | + | } |
168 | + | |
169 | + | bool invalidExpressionToken(const std::string& ident) { |
170 | + | return compileError("invalid expression token:" + ident); |
171 | + | } |
172 | + | |
173 | + | bool unrecognizedToken() { |
174 | + | return compileError("unrecognized token"); |
175 | + | } |
176 | + | |
177 | + | bool badArgumentCount() { |
178 | + | return compileError("bad argument count"); |
179 | + | } |
180 | + | |
181 | + | bool endOfExpressionExpected() { |
182 | + | return compileError("end of expression expected"); |
183 | + | } |
184 | + | |
185 | + | bool leftParenthesisExpected() { |
186 | + | return compileError("left parenthesis expected"); |
187 | + | } |
188 | + | |
189 | + | bool rightParenthesisExpected() { |
190 | + | return compileError("right parenthesis expected"); |
191 | + | } |
192 | + | |
193 | + | bool commaExpected() { |
194 | + | return compileError("comma expected"); |
195 | + | } |
196 | + | |
197 | + | bool unrecognizedExpressionToken() { |
198 | + | boost::any tmp = valuePeek(); |
199 | + | std::string tokenStr; |
200 | + | |
201 | + | try { |
202 | + | tokenStr = boost::any_cast<std::string>(tmp); |
203 | + | } catch(const boost::bad_any_cast &) { |
204 | + | return compileError("any_cast error"); |
205 | + | } |
206 | + | |
207 | + | return compileError("unrecognized expression token:" + tokenStr); |
208 | + | } |
209 | + | |
210 | + | bool comparisonOperatorExpected() { |
211 | + | return compileError("comparison operator expected"); |
212 | + | } |
213 | + | |
214 | + | bool numberExpected() { |
215 | + | return compileError("number expected"); |
216 | + | } |
217 | + | |
218 | + | bool numberOrKeywordExpected() { |
219 | + | return compileError("number or keyword expected"); |
220 | + | } |
221 | + | |
222 | + | std::string filename; |
223 | + | std::string script; |
224 | + | |
225 | + | std::vector<int> lineNumbers; |
226 | + | std::vector<int> lineIndices; |
227 | + | std::vector<std::vector<Token> >aatokenCompiled; |
228 | + | |
229 | + | bool error; |
230 | + | std::string errorMessage; |
231 | + | std::string errorLine; |
232 | + | |
233 | + | int cchScript; |
234 | + | short lineCurrent; |
235 | + | |
236 | + | int ichToken; |
237 | + | int cchToken; |
238 | + | std::vector<Token> atokenCommand; |
239 | + | |
240 | + | int ichCurrentCommand; |
241 | + | |
242 | + | std::vector<Token> ltokenPostfix; |
243 | + | std::vector<Token> atokenInfix; |
244 | + | int itokenInfix; |
245 | + | |
246 | + | //std::vector<Token> compiledTokens_; |
247 | + | }; |
248 | + | |
249 | } | |
250 | #endif | |
251 | + |
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