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Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 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 48 | Line 48
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 "selection/NameFinder.hpp"
54   #include "selection/DistanceFinder.hpp"
55 + #include "selection/HullFinder.hpp"
56   #include "selection/IndexFinder.hpp"
57 < #include "utils/BitSet.hpp"
57 > #include "utils/OpenMDBitSet.hpp"
58   #include "primitives/StuntDouble.hpp"
59   #include "utils/StringUtils.hpp"
60 < namespace oopse {
60 > namespace OpenMD {
61  
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);
70 >    SelectionEvaluator(SimInfo* info);
71  
72 <
73 <        bool loadScriptString(const std::string& script);
73 <        bool loadScriptFile(const std::string& filename);
72 >    bool loadScriptString(const std::string& script);
73 >    bool loadScriptFile(const std::string& filename);
74          
75 <        BitSet evaluate();
75 >    OpenMDBitSet evaluate();
76          
77 <        /**
78 <         * Tests if the result from evaluation of script is dynamic.
79 <         */        
80 <        bool isDynamic() {
81 <            return isDynamic_;
82 <        }
77 >    /**
78 >     * Tests if the result from evaluation of script is dynamic.
79 >     */        
80 >    bool isDynamic() {
81 >      return isDynamic_;
82 >    }
83  
84 <        bool hadRuntimeError() const{
85 <            return error;
86 <        }
84 >    bool hadRuntimeError() const{
85 >      return error;
86 >    }
87  
88 <        std::string getErrorMessage() const {
89 <            return errorMessage;
90 <        }
88 >    std::string getErrorMessage() const {
89 >      return errorMessage;
90 >    }
91  
92  
93 <        int getLinenumber() {
94 <            return linenumbers[pc];
95 <        }
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 <        }
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:
107 >  private:
108  
109 <        void clearState();
109 >    void clearState();
110          
111 <        bool loadScript(const std::string& filename, const std::string& script);
111 >    bool loadScript(const std::string& filename, const std::string& script);
112  
113 <        bool loadScriptFileInternal(const std::string& filename);
113 >    bool loadScriptFileInternal(const std::string& filename);
114  
115  
116 <        void clearDefinitionsAndLoadPredefined();
116 >    void clearDefinitionsAndLoadPredefined();
117          
118 <        void define();
119 <        void select(BitSet& bs);
120 <        void predefine(const std::string& script);
118 >    void define();
119 >    void select(OpenMDBitSet& bs);
120 >    void predefine(const std::string& script);
121  
122 <        void instructionDispatchLoop(BitSet& bs);
122 >    void instructionDispatchLoop(OpenMDBitSet& bs);
123  
124 <        void withinInstruction(const Token& instruction, BitSet& bs);
124 >    void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
125          
126 <        BitSet comparatorInstruction(const Token& instruction);
127 <        void compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue);
128 <        BitSet nameInstruction(const std::string& name);
129 <        BitSet indexInstruction(const boost::any& value);
130 <        BitSet expression(const std::vector<Token>& tokens, int pc);
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 <        BitSet lookupValue(const std::string& variable);
132 >    OpenMDBitSet lookupValue(const std::string& variable);
133 >
134 >    OpenMDBitSet hull();
135          
136 <        void evalError(const std::string& message) {
137 <            std::cerr << "SelectionEvaulator Error: " << message <<  std::endl;
138 <        }
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 <        }        
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 <        }
148 >    void unrecognizedExpression() {
149 >      evalError("unrecognized expression");
150 >    }
151  
152 <        void unrecognizedAtomProperty(int property){
153 <            evalError("unrecognized atom property");
154 <        }
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 <        }    
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 <        }
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 <        }
164 >    void invalidIndex(int index) {
165 >      evalError("invalid index : " + toString(index) );
166 >    }
167  
168          
169 <        bool containDynamicToken(const std::vector<Token>& tokens);
169 >    bool containDynamicToken(const std::vector<Token>& tokens);
170 >
171 >    RealType getCharge(Atom* atom);
172          
173 <        SelectionCompiler compiler;
173 >    SelectionCompiler compiler;
174  
175 <        //const static int scriptLevelMax = 10;
176 <        //int scriptLevel;
175 >    //const static int scriptLevelMax = 10;
176 >    //int scriptLevel;
177  
178 <        //Context stack[scriptLevelMax];
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
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;
187 >    bool error;
188 >    std::string errorMessage;
189  
190 <        std::vector<Token> statement;
191 <        int statementLength;
190 >    std::vector<Token> statement;
191 >    int statementLength;
192  
193 <        SimInfo* info;
194 <        NameFinder nameFinder;
195 <        DistanceFinder distanceFinder;
196 <        IndexFinder indexFinder;
197 <        int nStuntDouble;   //natoms + nrigidbodies
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;
200 >    typedef std::map<std::string, boost::any > VariablesType;
201 >    VariablesType variables;
202  
203 <        bool isDynamic_;
204 <        bool isLoaded_;
203 >    bool isDynamic_;
204 >    bool isLoaded_;
205          
206 < };
206 >  };
207  
208   }
209   #endif

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