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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 1390 by gezelter, Wed Nov 25 20:02:06 2009 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/IndexFinder.hpp"
56 < #include "utils/BitSet.hpp"
56 > #include "utils/OpenMDBitSet.hpp"
57   #include "primitives/StuntDouble.hpp"
58   #include "utils/StringUtils.hpp"
59 < namespace oopse {
59 > namespace OpenMD {
60  
61  
62 < /**
63 < * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
64 < * @brief Evalute the tokens compiled by SelectionCompiler and return a BitSet
65 < */
66 < class SelectionEvaluator{
67 <    public:
62 >  /**
63 >   * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
64 >   * @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
65 >   */
66 >  class SelectionEvaluator{
67 >  public:
68  
69 <        SelectionEvaluator(SimInfo* info);
69 >    SelectionEvaluator(SimInfo* info);
70  
71 <
72 <        bool loadScriptString(const std::string& script);
73 <        bool loadScriptFile(const std::string& filename);
71 >    bool loadScriptString(const std::string& script);
72 >    bool loadScriptFile(const std::string& filename);
73          
74 <        BitSet evaluate();
74 >    OpenMDBitSet evaluate();
75          
76 <        /**
77 <         * Tests if the result from evaluation of script is dynamic.
78 <         */        
79 <        bool isDynamic() {
80 <            return isDynamic_;
81 <        }
76 >    /**
77 >     * Tests if the result from evaluation of script is dynamic.
78 >     */        
79 >    bool isDynamic() {
80 >      return isDynamic_;
81 >    }
82  
83 <        bool hadRuntimeError() const{
84 <            return error;
85 <        }
83 >    bool hadRuntimeError() const{
84 >      return error;
85 >    }
86  
87 <        std::string getErrorMessage() const {
88 <            return errorMessage;
89 <        }
87 >    std::string getErrorMessage() const {
88 >      return errorMessage;
89 >    }
90  
91  
92 <        int getLinenumber() {
93 <            return linenumbers[pc];
94 <        }
92 >    int getLinenumber() {
93 >      return linenumbers[pc];
94 >    }
95  
96 <        std::string getLine() {
97 <            int ichBegin = lineIndices[pc];
98 <            int ichEnd;
99 <            if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
100 <                (ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
101 <                ichEnd = script.size();
102 <            }            
103 <            return script.substr(ichBegin, ichEnd);
104 <        }
96 >    std::string getLine() {
97 >      int ichBegin = lineIndices[pc];
98 >      int ichEnd;
99 >      if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
100 >          (ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
101 >        ichEnd = script.size();
102 >      }            
103 >      return script.substr(ichBegin, ichEnd);
104 >    }
105    
106 <    private:
106 >  private:
107  
108 <        void clearState();
108 >    void clearState();
109          
110 <        bool loadScript(const std::string& filename, const std::string& script);
110 >    bool loadScript(const std::string& filename, const std::string& script);
111  
112 <        bool loadScriptFileInternal(const std::string& filename);
112 >    bool loadScriptFileInternal(const std::string& filename);
113  
114  
115 <        void clearDefinitionsAndLoadPredefined();
115 >    void clearDefinitionsAndLoadPredefined();
116          
117 <        void define();
118 <        void select(BitSet& bs);
119 <        void predefine(const std::string& script);
117 >    void define();
118 >    void select(OpenMDBitSet& bs);
119 >    void predefine(const std::string& script);
120  
121 <        void instructionDispatchLoop(BitSet& bs);
121 >    void instructionDispatchLoop(OpenMDBitSet& bs);
122  
123 <        void withinInstruction(const Token& instruction, BitSet& bs);
123 >    void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
124          
125 <        BitSet comparatorInstruction(const Token& instruction);
126 <        void compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue);
127 <        BitSet nameInstruction(const std::string& name);
128 <        BitSet indexInstruction(const boost::any& value);
129 <        BitSet expression(const std::vector<Token>& tokens, int pc);
125 >    OpenMDBitSet comparatorInstruction(const Token& instruction);
126 >    void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue);
127 >    OpenMDBitSet nameInstruction(const std::string& name);
128 >    OpenMDBitSet indexInstruction(const boost::any& value);
129 >    OpenMDBitSet expression(const std::vector<Token>& tokens, int pc);
130  
131 <        BitSet lookupValue(const std::string& variable);
131 >    OpenMDBitSet lookupValue(const std::string& variable);
132          
133 <        void evalError(const std::string& message) {
134 <            std::cerr << "SelectionEvaulator Error: " << message <<  std::endl;
135 <        }
133 >    void evalError(const std::string& message) {
134 >      sprintf( painCave.errMsg,
135 >               "SelectionEvaluator Error: %s\n", message.c_str());
136 >      painCave.severity = OPENMD_ERROR;
137 >      painCave.isFatal = 1;
138 >      simError();
139 >    }
140  
141 <        void unrecognizedCommand(const Token& token) {
142 <            evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
143 <        }        
141 >    void unrecognizedCommand(const Token& token) {
142 >      evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
143 >    }        
144  
145 <        void unrecognizedExpression() {
146 <            evalError("unrecognized expression");
147 <        }
145 >    void unrecognizedExpression() {
146 >      evalError("unrecognized expression");
147 >    }
148  
149 <        void unrecognizedAtomProperty(int property){
150 <            evalError("unrecognized atom property");
151 <        }
149 >    void unrecognizedAtomProperty(int property){
150 >      evalError("unrecognized atom property");
151 >    }
152  
153 <        void unrecognizedIdentifier(const std::string& identifier) {
154 <            evalError("unrecognized identifier:" + identifier);
155 <        }    
153 >    void unrecognizedIdentifier(const std::string& identifier) {
154 >      evalError("unrecognized identifier:" + identifier);
155 >    }    
156  
157 <        void invalidIndexRange(std::pair<int, int> range) {
158 <            evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
159 <        }
157 >    void invalidIndexRange(std::pair<int, int> range) {
158 >      evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
159 >    }
160  
161 <        void invalidIndex(int index) {
162 <            evalError("invalid index : " + toString(index) );
163 <        }
161 >    void invalidIndex(int index) {
162 >      evalError("invalid index : " + toString(index) );
163 >    }
164  
165          
166 <        bool containDynamicToken(const std::vector<Token>& tokens);
166 >    bool containDynamicToken(const std::vector<Token>& tokens);
167 >
168 >    RealType getCharge(Atom* atom);
169          
170 <        SelectionCompiler compiler;
170 >    SelectionCompiler compiler;
171  
172 <        //const static int scriptLevelMax = 10;
173 <        //int scriptLevel;
172 >    //const static int scriptLevelMax = 10;
173 >    //int scriptLevel;
174  
175 <        //Context stack[scriptLevelMax];
175 >    //Context stack[scriptLevelMax];
176  
177 <        std::string filename;
178 <        std::string script;
179 <        std::vector<int> linenumbers;
180 <        std::vector<int> lineIndices;
181 <        std::vector<std::vector<Token> > aatoken;
182 <        int pc; // program counter
177 >    std::string filename;
178 >    std::string script;
179 >    std::vector<int> linenumbers;
180 >    std::vector<int> lineIndices;
181 >    std::vector<std::vector<Token> > aatoken;
182 >    int pc; // program counter
183  
184 <        bool error;
185 <        std::string errorMessage;
184 >    bool error;
185 >    std::string errorMessage;
186  
187 <        std::vector<Token> statement;
188 <        int statementLength;
187 >    std::vector<Token> statement;
188 >    int statementLength;
189  
190 <        SimInfo* info;
191 <        NameFinder nameFinder;
192 <        DistanceFinder distanceFinder;
193 <        IndexFinder indexFinder;
194 <        int nStuntDouble;   //natoms + nrigidbodies
190 >    SimInfo* info;
191 >    NameFinder nameFinder;
192 >    DistanceFinder distanceFinder;
193 >    IndexFinder indexFinder;
194 >    int nStuntDouble;   //nGLOBALatoms + nGLOBALrigidbodies
195  
196 <        typedef std::map<std::string, boost::any > VariablesType;
197 <        VariablesType variables;
196 >    typedef std::map<std::string, boost::any > VariablesType;
197 >    VariablesType variables;
198  
199 <        bool isDynamic_;
200 <        bool isLoaded_;
199 >    bool isDynamic_;
200 >    bool isLoaded_;
201          
202 < };
202 >  };
203  
204   }
205   #endif

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