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Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC

# Line 6 | Line 6
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_SELECTIONEVALUATOR_HPP
# Line 45 | Line 45
45   #include <map>
46   #include <string>
47   #include <vector>
48 + #include <fstream>
49  
50   #include "brains/SimInfo.hpp"
51 < #include "selection/Token.hpp"
51 > #include "selection/SelectionToken.hpp"
52   #include "selection/SelectionCompiler.hpp"
53 < #include "utils/BitSet.hpp"
53 > #include "selection/NameFinder.hpp"
54 > #include "selection/DistanceFinder.hpp"
55 > #include "selection/HullFinder.hpp"
56 > #include "selection/IndexFinder.hpp"
57 > #include "utils/OpenMDBitSet.hpp"
58 > #include "primitives/StuntDouble.hpp"
59 > #include "utils/StringUtils.hpp"
60 > namespace OpenMD {
61  
54 – namespace oopse {
62  
63 < /**
64 < * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
65 < * @brief Evalute the tokens compiled by SelectionCompiler and return a BitSet
66 < */
67 < class SelectionEvaluator{
68 <    public:
63 >  /**
64 >   * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
65 >   * @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
66 >   */
67 >  class SelectionEvaluator{
68 >  public:
69  
70 <        SelectionEvaluator(SimInfo* info, const std::string& script);
70 >    SelectionEvaluator(SimInfo* info);
71  
72 <        BitSet evaluate();
72 >    bool loadScriptString(const std::string& script);
73 >    bool loadScriptFile(const std::string& filename);
74          
75 <        BitSet evaluate(int frameNo);
75 >    OpenMDBitSet evaluate();
76 >        
77 >    /**
78 >     * Tests if the result from evaluation of script is dynamic.
79 >     */        
80 >    bool isDynamic() {
81 >      return isDynamic_;
82 >    }
83  
84 <        /**
85 <         * Tests if the result from evaluation of script is static.
86 <         * @return true if the result keeps the same even the frame change, otherwise return false
87 <         */        
88 <        bool isStatic();
84 >    bool hadRuntimeError() const{
85 >      return error;
86 >    }
87 >
88 >    std::string getErrorMessage() const {
89 >      return errorMessage;
90 >    }
91 >
92 >
93 >    int getLinenumber() {
94 >      return linenumbers[pc];
95 >    }
96 >
97 >    std::string getLine() {
98 >      int ichBegin = lineIndices[pc];
99 >      int ichEnd;
100 >      if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
101 >          (ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
102 >        ichEnd = script.size();
103 >      }            
104 >      return script.substr(ichBegin, ichEnd);
105 >    }
106 >  
107 >  private:
108 >
109 >    void clearState();
110          
111 <    private:
111 >    bool loadScript(const std::string& filename, const std::string& script);
112  
113 <        /** */
78 <        void define();
113 >    bool loadScriptFileInternal(const std::string& filename);
114  
80 –        /** */
81 –        void predefine();
115  
116 <        withinInstruction(Token instruction, BitSet , BitSet);
116 >    void clearDefinitionsAndLoadPredefined();
117 >        
118 >    void define();
119 >    void select(OpenMDBitSet& bs);
120 >    void predefine(const std::string& script);
121  
122 <        BitSet expression(std::vector<Token>& tokens, int pc);
122 >    void instructionDispatchLoop(OpenMDBitSet& bs);
123 >
124 >    void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
125          
126 <        SimInfo* info_;
126 >    OpenMDBitSet comparatorInstruction(const Token& instruction);
127 >    void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue);
128 >    OpenMDBitSet nameInstruction(const std::string& name);
129 >    OpenMDBitSet indexInstruction(const boost::any& value);
130 >    OpenMDBitSet expression(const std::vector<Token>& tokens, int pc);
131  
132 <        std::map<std::string, std::vector<Token> > variables_;
90 <        std::string script_;
91 < };
132 >    OpenMDBitSet lookupValue(const std::string& variable);
133  
134 +    OpenMDBitSet hull();
135 +        
136 +    void evalError(const std::string& message) {
137 +      sprintf( painCave.errMsg,
138 +               "SelectionEvaluator Error: %s\n", message.c_str());
139 +      painCave.severity = OPENMD_ERROR;
140 +      painCave.isFatal = 1;
141 +      simError();
142 +    }
143 +
144 +    void unrecognizedCommand(const Token& token) {
145 +      evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
146 +    }        
147 +
148 +    void unrecognizedExpression() {
149 +      evalError("unrecognized expression");
150 +    }
151 +
152 +    void unrecognizedAtomProperty(int property){
153 +      evalError("unrecognized atom property");
154 +    }
155 +
156 +    void unrecognizedIdentifier(const std::string& identifier) {
157 +      evalError("unrecognized identifier:" + identifier);
158 +    }    
159 +
160 +    void invalidIndexRange(std::pair<int, int> range) {
161 +      evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
162 +    }
163 +
164 +    void invalidIndex(int index) {
165 +      evalError("invalid index : " + toString(index) );
166 +    }
167 +
168 +        
169 +    bool containDynamicToken(const std::vector<Token>& tokens);
170 +
171 +    RealType getCharge(Atom* atom);
172 +        
173 +    SelectionCompiler compiler;
174 +
175 +    //const static int scriptLevelMax = 10;
176 +    //int scriptLevel;
177 +
178 +    //Context stack[scriptLevelMax];
179 +
180 +    std::string filename;
181 +    std::string script;
182 +    std::vector<int> linenumbers;
183 +    std::vector<int> lineIndices;
184 +    std::vector<std::vector<Token> > aatoken;
185 +    int pc; // program counter
186 +
187 +    bool error;
188 +    std::string errorMessage;
189 +
190 +    std::vector<Token> statement;
191 +    int statementLength;
192 +
193 +    SimInfo* info;
194 +    NameFinder nameFinder;
195 +    DistanceFinder distanceFinder;
196 +    HullFinder hullFinder;
197 +    IndexFinder indexFinder;
198 +    int nStuntDouble;   //nGLOBALatoms + nGLOBALrigidbodies
199 +
200 +    typedef std::map<std::string, boost::any > VariablesType;
201 +    VariablesType variables;
202 +
203 +    bool isDynamic_;
204 +    bool isLoaded_;
205 +        
206 +  };
207 +
208   }
209   #endif

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