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Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2067 by gezelter, Thu Mar 5 15:35:37 2015 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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef SELECTION_SELECTIONEVALUATOR_HPP
# Line 52 | Line 53
53   #include "selection/SelectionCompiler.hpp"
54   #include "selection/NameFinder.hpp"
55   #include "selection/DistanceFinder.hpp"
56 + #include "selection/HullFinder.hpp"
57   #include "selection/IndexFinder.hpp"
58 < #include "utils/OOPSEBitSet.hpp"
58 > #include "selection/SelectionSet.hpp"
59   #include "primitives/StuntDouble.hpp"
60   #include "utils/StringUtils.hpp"
61 < namespace oopse {
61 > namespace OpenMD {
62  
63  
64    /**
65     * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
66 <   * @brief Evalute the tokens compiled by SelectionCompiler and return a OOPSEBitSet
66 >   * @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
67     */
68    class SelectionEvaluator{
69    public:
70  
71      SelectionEvaluator(SimInfo* info);
72  
71 –
73      bool loadScriptString(const std::string& script);
74      bool loadScriptFile(const std::string& filename);
75          
76 <    OOPSEBitSet evaluate();
76 >    SelectionSet evaluate();
77 >    SelectionSet evaluate(int frame);
78          
79      /**
80       * Tests if the result from evaluation of script is dynamic.
# Line 95 | Line 97 | namespace oopse {
97      }
98  
99      std::string getLine() {
100 <      int ichBegin = lineIndices[pc];
101 <      int ichEnd;
100 >      std::size_t ichBegin = lineIndices[pc];
101 >      std::size_t ichEnd;
102        if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
103            (ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
104          ichEnd = script.size();
105        }            
106        return script.substr(ichBegin, ichEnd);
107      }
108 +    bool hasSurfaceArea() { return hasSurfaceArea_; }
109 +    RealType getSurfaceArea() {
110 +      if (hasSurfaceArea_) {
111 +        return surfaceArea_;
112 +      } else {
113 +        sprintf( painCave.errMsg,
114 +                 "SelectionEvaluator Error: %s\n", "No Surface Area For You!");
115 +        painCave.severity = OPENMD_ERROR;
116 +        painCave.isFatal = 1;
117 +        simError();
118 +        return 0.0;
119 +      }
120 +    }
121 +
122    
123    private:
124  
# Line 112 | Line 128 | namespace oopse {
128  
129      bool loadScriptFileInternal(const std::string& filename);
130  
131 <
131 >    SelectionSet createSelectionSets();
132      void clearDefinitionsAndLoadPredefined();
133          
134      void define();
135 <    void select(OOPSEBitSet& bs);
135 >    void select(SelectionSet& bs);
136 >    void select(SelectionSet& bs, int frame);
137      void predefine(const std::string& script);
138  
139 <    void instructionDispatchLoop(OOPSEBitSet& bs);
139 >    void instructionDispatchLoop(SelectionSet& bs);
140 >    void instructionDispatchLoop(SelectionSet& bs, int frame);
141  
142 <    void withinInstruction(const Token& instruction, OOPSEBitSet& bs);
142 >    void withinInstruction(const Token& instruction, SelectionSet& bs);
143 >    void withinInstruction(const Token& instruction, SelectionSet& bs, int frame);
144 >    SelectionSet allInstruction();
145          
146 <    OOPSEBitSet comparatorInstruction(const Token& instruction);
147 <    void compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue);
148 <    OOPSEBitSet nameInstruction(const std::string& name);
149 <    OOPSEBitSet indexInstruction(const boost::any& value);
150 <    OOPSEBitSet expression(const std::vector<Token>& tokens, int pc);
146 >    SelectionSet comparatorInstruction(const Token& instruction);
147 >    SelectionSet comparatorInstruction(const Token& instruction, int frame);
148 >    void compareProperty(StuntDouble* sd, SelectionSet& bs, int property, int comparator, float comparisonValue);
149 >    void compareProperty(StuntDouble* sd, SelectionSet& bs, int property, int comparator, float comparisonValue, int frame);
150 >    void compareProperty(Molecule* mol, SelectionSet& bs, int property, int comparator, float comparisonValue);
151 >    void compareProperty(Molecule* mol, SelectionSet& bs, int property, int comparator, float comparisonValue, int frame);
152 >    SelectionSet nameInstruction(const std::string& name);
153 >    SelectionSet indexInstruction(const boost::any& value);
154 >    SelectionSet expression(const std::vector<Token>& tokens, int pc);
155 >    SelectionSet expression(const std::vector<Token>& tokens, int pc, int frame);
156  
157 <    OOPSEBitSet lookupValue(const std::string& variable);
157 >    SelectionSet lookupValue(const std::string& variable);
158 >
159 >    SelectionSet hull();
160 >    SelectionSet hull(int frame);
161          
162      void evalError(const std::string& message) {
163 <      std::cerr << "SelectionEvaulator Error: " << message <<  std::endl;
163 >      sprintf( painCave.errMsg,
164 >               "SelectionEvaluator Error: %s\n", message.c_str());
165 >      painCave.severity = OPENMD_ERROR;
166 >      painCave.isFatal = 1;
167 >      simError();
168      }
169  
170      void unrecognizedCommand(const Token& token) {
# Line 146 | Line 178 | namespace oopse {
178      void unrecognizedAtomProperty(int property){
179        evalError("unrecognized atom property");
180      }
181 +    
182 +    void unrecognizedMoleculeProperty(int property){
183 +      evalError("unrecognized molecule property");
184 +    }
185  
186      void unrecognizedIdentifier(const std::string& identifier) {
187        evalError("unrecognized identifier:" + identifier);
# Line 162 | Line 198 | namespace oopse {
198          
199      bool containDynamicToken(const std::vector<Token>& tokens);
200  
201 <    double getCharge(Atom* atom);
201 >    RealType getCharge(Atom* atom);
202 >    RealType getCharge(Atom* atom, int frame);
203          
204      SelectionCompiler compiler;
205  
# Line 176 | Line 213 | namespace oopse {
213      std::vector<int> linenumbers;
214      std::vector<int> lineIndices;
215      std::vector<std::vector<Token> > aatoken;
216 <    int pc; // program counter
216 >    unsigned int pc; // program counter
217  
218      bool error;
219      std::string errorMessage;
# Line 187 | Line 224 | namespace oopse {
224      SimInfo* info;
225      NameFinder nameFinder;
226      DistanceFinder distanceFinder;
227 +    HullFinder hullFinder;
228      IndexFinder indexFinder;
229 <    int nStuntDouble;   //natoms + nrigidbodies
229 >    vector<int> nObjects;
230  
231      typedef std::map<std::string, boost::any > VariablesType;
232      VariablesType variables;
233  
234      bool isDynamic_;
235      bool isLoaded_;
236 +    bool hasSurfaceArea_;
237 +    RealType surfaceArea_;
238          
239    };
240  

Comparing trunk/src/selection/SelectionEvaluator.hpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2067 by gezelter, Thu Mar 5 15:35:37 2015 UTC

# Line 0 | Line 1
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