src/selection/SelectionEvaluator.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifndef SELECTION_SELECTIONEVALUATOR_HPP
#define SELECTION_SELECTIONEVALUATOR_HPP

#include <map>
#include <string>
#include <vector>
#include <fstream>

#include "brains/SimInfo.hpp"
#include "selection/SelectionToken.hpp"
#include "selection/SelectionCompiler.hpp"
#include "selection/NameFinder.hpp"
#include "selection/DistanceFinder.hpp"
#include "selection/HullFinder.hpp"
#include "selection/IndexFinder.hpp"
#include "selection/SelectionSet.hpp"
#include "primitives/StuntDouble.hpp"
#include "utils/StringUtils.hpp"
namespace OpenMD {


  /**
   * @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
   * @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
   */
  class SelectionEvaluator{
  public:

    SelectionEvaluator(SimInfo* info);

    bool loadScriptString(const std::string& script);
    bool loadScriptFile(const std::string& filename);
        
    SelectionSet evaluate();
    SelectionSet evaluate(int frame);
        
    /**
     * Tests if the result from evaluation of script is dynamic.
     */         
    bool isDynamic() {
      return isDynamic_;
    }

    bool hadRuntimeError() const{
      return error;
    }

    std::string getErrorMessage() const {
      return errorMessage;
    }


    int getLinenumber() {
      return linenumbers[pc];
    }

    std::string getLine() {
      int ichBegin = lineIndices[pc];
      int ichEnd;
      if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
          (ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
        ichEnd = script.size();
      }            
      return script.substr(ichBegin, ichEnd);
    }
    bool hasSurfaceArea() { return hasSurfaceArea_; }
    RealType getSurfaceArea() { 
      if (hasSurfaceArea_) {
        return surfaceArea_;
      } else {
        sprintf( painCave.errMsg,
                 "SelectionEvaluator Error: %s\n", "No Surface Area For You!");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
        return 0.0;
      }
    }

  
  private:

    void clearState();
        
    bool loadScript(const std::string& filename, const std::string& script); 

    bool loadScriptFileInternal(const std::string& filename);

    SelectionSet createSelectionSets();
    void clearDefinitionsAndLoadPredefined();
         
    void define();
    void select(SelectionSet& bs);
    void select(SelectionSet& bs, int frame);
    void predefine(const std::string& script);

    void instructionDispatchLoop(SelectionSet& bs);
    void instructionDispatchLoop(SelectionSet& bs, int frame);

    void withinInstruction(const Token& instruction, SelectionSet& bs);
    void withinInstruction(const Token& instruction, SelectionSet& bs, int frame);
    SelectionSet allInstruction();
        
    SelectionSet comparatorInstruction(const Token& instruction); 
    SelectionSet comparatorInstruction(const Token& instruction, int frame); 
    void compareProperty(StuntDouble* sd, SelectionSet& bs, int property, int comparator, float comparisonValue);
    void compareProperty(StuntDouble* sd, SelectionSet& bs, int property, int comparator, float comparisonValue, int frame);
    void compareProperty(Molecule* mol, SelectionSet& bs, int property, int comparator, float comparisonValue);
    void compareProperty(Molecule* mol, SelectionSet& bs, int property, int comparator, float comparisonValue, int frame);
    SelectionSet nameInstruction(const std::string& name);
    SelectionSet indexInstruction(const boost::any& value);
    SelectionSet expression(const std::vector<Token>& tokens, int pc);
    SelectionSet expression(const std::vector<Token>& tokens, int pc, int frame);

    SelectionSet lookupValue(const std::string& variable);

    SelectionSet hull();
    SelectionSet hull(int frame);
        
    void evalError(const std::string& message) {
      sprintf( painCave.errMsg,
               "SelectionEvaluator Error: %s\n", message.c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }

    void unrecognizedCommand(const Token& token) {
      evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
    }        

    void unrecognizedExpression() {
      evalError("unrecognized expression");
    }

    void unrecognizedAtomProperty(int property){
      evalError("unrecognized atom property");
    }
    
    void unrecognizedMoleculeProperty(int property){
      evalError("unrecognized molecule property");
    }

    void unrecognizedIdentifier(const std::string& identifier) {
      evalError("unrecognized identifier:" + identifier);
    }    

    void invalidIndexRange(std::pair<int, int> range) {
      evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
    }

    void invalidIndex(int index) {
      evalError("invalid index : " + toString(index) );
    }

        
    bool containDynamicToken(const std::vector<Token>& tokens);

    RealType getCharge(Atom* atom);
    RealType getCharge(Atom* atom, int frame);
        
    SelectionCompiler compiler;

    //const static int scriptLevelMax = 10;
    //int scriptLevel;

    //Context stack[scriptLevelMax];

    std::string filename;
    std::string script;
    std::vector<int> linenumbers;
    std::vector<int> lineIndices;
    std::vector<std::vector<Token> > aatoken;
    unsigned int pc; // program counter

    bool error;
    std::string errorMessage;

    std::vector<Token> statement;
    int statementLength;

    SimInfo* info;
    NameFinder nameFinder;
    DistanceFinder distanceFinder;
    HullFinder hullFinder;
    IndexFinder indexFinder;
    vector<int> nObjects;

    typedef std::map<std::string, boost::any > VariablesType;
    VariablesType variables;

    bool isDynamic_;
    bool isLoaded_;
    bool hasSurfaceArea_;
    RealType surfaceArea_;
        
  };

}
#endif
Revision:	2055
Committed:	Fri Feb 6 18:49:27 2015 UTC (10 years, 2 months ago) by gezelter
File size:	8109 byte(s)
Log Message:	Modified SelectionEvalutator to handle positional information for molecules based on the center of mass.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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
44	#define SELECTION_SELECTIONEVALUATOR_HPP
45
46	#include <map>
47	#include <string>
48	#include <vector>
49	#include <fstream>
50
51	#include "brains/SimInfo.hpp"
52	#include "selection/SelectionToken.hpp"
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 "selection/SelectionSet.hpp"
59	#include "primitives/StuntDouble.hpp"
60	#include "utils/StringUtils.hpp"
61	namespace OpenMD {
62
63
64	/**
65	* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
66	* @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
67	*/
68	class SelectionEvaluator{
69	public:
70
71	SelectionEvaluator(SimInfo* info);
72
73	bool loadScriptString(const std::string& script);
74	bool loadScriptFile(const std::string& filename);
75
76	SelectionSet evaluate();
77	SelectionSet evaluate(int frame);
78
79	/**
80	* Tests if the result from evaluation of script is dynamic.
81	*/
82	bool isDynamic() {
83	return isDynamic_;
84	}
85
86	bool hadRuntimeError() const{
87	return error;
88	}
89
90	std::string getErrorMessage() const {
91	return errorMessage;
92	}
93
94
95	int getLinenumber() {
96	return linenumbers[pc];
97	}
98
99	std::string getLine() {
100	int ichBegin = lineIndices[pc];
101	int 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
125	void clearState();
126
127	bool loadScript(const std::string& filename, const std::string& script);
128
129	bool loadScriptFileInternal(const std::string& filename);
130
131	SelectionSet createSelectionSets();
132	void clearDefinitionsAndLoadPredefined();
133
134	void define();
135	void select(SelectionSet& bs);
136	void select(SelectionSet& bs, int frame);
137	void predefine(const std::string& script);
138
139	void instructionDispatchLoop(SelectionSet& bs);
140	void instructionDispatchLoop(SelectionSet& bs, int frame);
141
142	void withinInstruction(const Token& instruction, SelectionSet& bs);
143	void withinInstruction(const Token& instruction, SelectionSet& bs, int frame);
144	SelectionSet allInstruction();
145
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	SelectionSet lookupValue(const std::string& variable);
158
159	SelectionSet hull();
160	SelectionSet hull(int frame);
161
162	void evalError(const std::string& message) {
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) {
171	evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
172	}
173
174	void unrecognizedExpression() {
175	evalError("unrecognized expression");
176	}
177
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);
188	}
189
190	void invalidIndexRange(std::pair<int, int> range) {
191	evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
192	}
193
194	void invalidIndex(int index) {
195	evalError("invalid index : " + toString(index) );
196	}
197
198
199	bool containDynamicToken(const std::vector<Token>& tokens);
200
201	RealType getCharge(Atom* atom);
202	RealType getCharge(Atom* atom, int frame);
203
204	SelectionCompiler compiler;
205
206	//const static int scriptLevelMax = 10;
207	//int scriptLevel;
208
209	//Context stack[scriptLevelMax];
210
211	std::string filename;
212	std::string script;
213	std::vector<int> linenumbers;
214	std::vector<int> lineIndices;
215	std::vector<std::vector<Token> > aatoken;
216	unsigned int pc; // program counter
217
218	bool error;
219	std::string errorMessage;
220
221	std::vector<Token> statement;
222	int statementLength;
223
224	SimInfo* info;
225	NameFinder nameFinder;
226	DistanceFinder distanceFinder;
227	HullFinder hullFinder;
228	IndexFinder indexFinder;
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
241	}
242	#endif