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 "utils/OpenMDBitSet.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);
        
    OpenMDBitSet evaluate();
    OpenMDBitSet 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);


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

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

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

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

    OpenMDBitSet hull();
    OpenMDBitSet 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 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;
    int nStuntDouble;   //nGLOBALatoms + nGLOBALrigidbodies

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

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

}
#endif
Revision:	1903
Committed:	Tue Jul 16 18:58:08 2013 UTC (11 years, 9 months ago) by gezelter
File size:	7750 byte(s)
Log Message:	Test to see if we can eliminate a bug in MPI runs involving RNEMD.
#	User	Rev	Content
1	tim	277	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	277	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	277	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	277	*/
42
43			#ifndef SELECTION_SELECTIONEVALUATOR_HPP
44			#define SELECTION_SELECTIONEVALUATOR_HPP
45
46			#include <map>
47			#include <string>
48			#include <vector>
49	chrisfen	301	#include <fstream>
50	tim	277
51			#include "brains/SimInfo.hpp"
52	tim	770	#include "selection/SelectionToken.hpp"
53	tim	277	#include "selection/SelectionCompiler.hpp"
54	tim	283	#include "selection/NameFinder.hpp"
55	tim	295	#include "selection/DistanceFinder.hpp"
56	gezelter	1412	#include "selection/HullFinder.hpp"
57	tim	413	#include "selection/IndexFinder.hpp"
58	gezelter	1390	#include "utils/OpenMDBitSet.hpp"
59	tim	283	#include "primitives/StuntDouble.hpp"
60	tim	295	#include "utils/StringUtils.hpp"
61	gezelter	1390	namespace OpenMD {
62	tim	277
63	tim	283
64	gezelter	507	/**
65			* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
66	gezelter	1390	* @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet
67	gezelter	507	*/
68			class SelectionEvaluator{
69			public:
70	tim	277
71	gezelter	507	SelectionEvaluator(SimInfo* info);
72	tim	277
73	gezelter	507	bool loadScriptString(const std::string& script);
74			bool loadScriptFile(const std::string& filename);
75	tim	288
76	gezelter	1390	OpenMDBitSet evaluate();
77	gezelter	1816	OpenMDBitSet evaluate(int frame);
78	tim	277
79	gezelter	507	/**
80			* Tests if the result from evaluation of script is dynamic.
81			*/
82			bool isDynamic() {
83			return isDynamic_;
84			}
85	tim	278
86	gezelter	507	bool hadRuntimeError() const{
87			return error;
88			}
89	tim	278
90	gezelter	507	std::string getErrorMessage() const {
91			return errorMessage;
92			}
93	tim	278
94
95	gezelter	507	int getLinenumber() {
96			return linenumbers[pc];
97			}
98	tim	278
99	gezelter	507	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	gezelter	1903	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	tim	278
123	gezelter	507	private:
124	tim	277
125	gezelter	507	void clearState();
126	tim	278
127	gezelter	507	bool loadScript(const std::string& filename, const std::string& script);
128	tim	288
129	gezelter	507	bool loadScriptFileInternal(const std::string& filename);
130	tim	278
131	tim	288
132	gezelter	507	void clearDefinitionsAndLoadPredefined();
133	tim	278
134	gezelter	507	void define();
135	gezelter	1390	void select(OpenMDBitSet& bs);
136	gezelter	1816	void select(OpenMDBitSet& bs, int frame);
137	gezelter	507	void predefine(const std::string& script);
138	tim	277
139	gezelter	1390	void instructionDispatchLoop(OpenMDBitSet& bs);
140	gezelter	1816	void instructionDispatchLoop(OpenMDBitSet& bs, int frame);
141	tim	278
142	gezelter	1390	void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
143	gezelter	1816	void withinInstruction(const Token& instruction, OpenMDBitSet& bs, int frame);
144	gezelter	1801	OpenMDBitSet allInstruction();
145	tim	283
146	gezelter	1390	OpenMDBitSet comparatorInstruction(const Token& instruction);
147	gezelter	1816	OpenMDBitSet comparatorInstruction(const Token& instruction, int frame);
148	gezelter	1390	void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue);
149	gezelter	1816	void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue, int frame);
150	gezelter	1390	OpenMDBitSet nameInstruction(const std::string& name);
151			OpenMDBitSet indexInstruction(const boost::any& value);
152			OpenMDBitSet expression(const std::vector<Token>& tokens, int pc);
153	gezelter	1816	OpenMDBitSet expression(const std::vector<Token>& tokens, int pc, int frame);
154	tim	278
155	gezelter	1390	OpenMDBitSet lookupValue(const std::string& variable);
156	gezelter	1412
157			OpenMDBitSet hull();
158	gezelter	1816	OpenMDBitSet hull(int frame);
159	tim	283
160	gezelter	507	void evalError(const std::string& message) {
161	cli2	1364	sprintf( painCave.errMsg,
162			"SelectionEvaluator Error: %s\n", message.c_str());
163	gezelter	1390	painCave.severity = OPENMD_ERROR;
164	cli2	1364	painCave.isFatal = 1;
165			simError();
166	gezelter	507	}
167	tim	282
168	gezelter	507	void unrecognizedCommand(const Token& token) {
169			evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
170			}
171	tim	283
172	gezelter	507	void unrecognizedExpression() {
173			evalError("unrecognized expression");
174			}
175	tim	283
176	gezelter	507	void unrecognizedAtomProperty(int property){
177			evalError("unrecognized atom property");
178			}
179	tim	283
180	gezelter	507	void unrecognizedIdentifier(const std::string& identifier) {
181			evalError("unrecognized identifier:" + identifier);
182			}
183	tim	288
184	gezelter	507	void invalidIndexRange(std::pair<int, int> range) {
185			evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
186			}
187	tim	295
188	gezelter	507	void invalidIndex(int index) {
189			evalError("invalid index : " + toString(index) );
190			}
191	tim	295
192
193	gezelter	507	bool containDynamicToken(const std::vector<Token>& tokens);
194	tim	432
195	tim	963	RealType getCharge(Atom* atom);
196	gezelter	1816	RealType getCharge(Atom* atom, int frame);
197	tim	288
198	gezelter	507	SelectionCompiler compiler;
199	tim	278
200	gezelter	507	//const static int scriptLevelMax = 10;
201			//int scriptLevel;
202	tim	278
203	gezelter	507	//Context stack[scriptLevelMax];
204	tim	278
205	gezelter	507	std::string filename;
206			std::string script;
207			std::vector<int> linenumbers;
208			std::vector<int> lineIndices;
209			std::vector<std::vector<Token> > aatoken;
210	gezelter	1782	unsigned int pc; // program counter
211	tim	278
212	gezelter	507	bool error;
213			std::string errorMessage;
214	tim	278
215	gezelter	507	std::vector<Token> statement;
216			int statementLength;
217	tim	278
218	gezelter	507	SimInfo* info;
219			NameFinder nameFinder;
220			DistanceFinder distanceFinder;
221	gezelter	1412	HullFinder hullFinder;
222	gezelter	507	IndexFinder indexFinder;
223	cli2	1364	int nStuntDouble; //nGLOBALatoms + nGLOBALrigidbodies
224	tim	288
225	gezelter	507	typedef std::map<std::string, boost::any > VariablesType;
226			VariablesType variables;
227	tim	350
228	gezelter	507	bool isDynamic_;
229			bool isLoaded_;
230	gezelter	1903	bool hasSurfaceArea_;
231			RealType surfaceArea_;
232	tim	288
233	gezelter	507	};
234	tim	277
235			}
236			#endif