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root/OpenMD/trunk/src/selection/SelectionEvaluator.hpp
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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 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 53 | Line 53
53   #include "selection/NameFinder.hpp"
54   #include "selection/DistanceFinder.hpp"
55   #include "selection/IndexFinder.hpp"
56 < #include "utils/OOPSEBitSet.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 OOPSEBitSet
64 >   * @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
65     */
66    class SelectionEvaluator{
67    public:
68  
69      SelectionEvaluator(SimInfo* info);
70  
71 –
71      bool loadScriptString(const std::string& script);
72      bool loadScriptFile(const std::string& filename);
73          
74 <    OOPSEBitSet evaluate();
74 >    OpenMDBitSet evaluate();
75          
76      /**
77       * Tests if the result from evaluation of script is dynamic.
# Line 116 | Line 115 | namespace oopse {
115      void clearDefinitionsAndLoadPredefined();
116          
117      void define();
118 <    void select(OOPSEBitSet& bs);
118 >    void select(OpenMDBitSet& bs);
119      void predefine(const std::string& script);
120  
121 <    void instructionDispatchLoop(OOPSEBitSet& bs);
121 >    void instructionDispatchLoop(OpenMDBitSet& bs);
122  
123 <    void withinInstruction(const Token& instruction, OOPSEBitSet& bs);
123 >    void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
124          
125 <    OOPSEBitSet comparatorInstruction(const Token& instruction);
126 <    void compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue);
127 <    OOPSEBitSet nameInstruction(const std::string& name);
128 <    OOPSEBitSet indexInstruction(const boost::any& value);
129 <    OOPSEBitSet 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 <    OOPSEBitSet 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;
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) {
# Line 162 | Line 165 | namespace oopse {
165          
166      bool containDynamicToken(const std::vector<Token>& tokens);
167  
168 <    double getCharge(Atom* atom);
168 >    RealType getCharge(Atom* atom);
169          
170      SelectionCompiler compiler;
171  
# Line 188 | Line 191 | namespace oopse {
191      NameFinder nameFinder;
192      DistanceFinder distanceFinder;
193      IndexFinder indexFinder;
194 <    int nStuntDouble;   //natoms + nrigidbodies
194 >    int nStuntDouble;   //nGLOBALatoms + nGLOBALrigidbodies
195  
196      typedef std::map<std::string, boost::any > VariablesType;
197      VariablesType variables;

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