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root/OpenMD/trunk/src/selection/SelectionEvaluator.hpp

Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 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 45 | Line 46
46		#include <map>
47		#include <string>
48		#include <vector>
49	+	#include <fstream>
50
51		#include "brains/SimInfo.hpp"
52	<	#include "selection/Token.hpp"
52	>	#include "selection/SelectionToken.hpp"
53		#include "selection/SelectionCompiler.hpp"
54	<	#include "utils/BitSet.hpp"
54	>	#include "selection/NameFinder.hpp"
55	>	#include "selection/DistanceFinder.hpp"
56	>	#include "selection/HullFinder.hpp"
57	>	#include "selection/IndexFinder.hpp"
58	>	#include "utils/OpenMDBitSet.hpp"
59	>	#include "primitives/StuntDouble.hpp"
60	>	#include "utils/StringUtils.hpp"
61	>	namespace OpenMD {
62
54	–	namespace oopse {
63
64	<	/**
65	<	* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
66	<	* @brief Evalute the tokens compiled by SelectionCompiler and return a BitSet
67	<	*/
68	<	class SelectionEvaluator{
69	<	public:
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, const std::string& script);
71	>	SelectionEvaluator(SimInfo* info);
72
73	<	BitSet evaluate();
73	>	bool loadScriptString(const std::string& script);
74	>	bool loadScriptFile(const std::string& filename);
75
76	<	BitSet evaluate(int frameNo);
76	>	OpenMDBitSet evaluate();
77	>	OpenMDBitSet 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	<	/**
87	<	* Tests if the result from evaluation of script is static.
88	<	* @return true if the result keeps the same even the frame change, otherwise return false
89	<	*/
90	<	bool isStatic();
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	<	private:
127	>	bool loadScript(const std::string& filename, const std::string& script);
128
129	<	/** */
78	<	void define();
129	>	bool loadScriptFileInternal(const std::string& filename);
130
80	–	/** */
81	–	void predefine();
131
132	<	withinInstruction(Token instruction, BitSet , BitSet);
132	>	void clearDefinitionsAndLoadPredefined();
133	>
134	>	void define();
135	>	void select(OpenMDBitSet& bs);
136	>	void select(OpenMDBitSet& bs, int frame);
137	>	void predefine(const std::string& script);
138
139	<	BitSet expression(std::vector<Token>& tokens, int pc);
139	>	void instructionDispatchLoop(OpenMDBitSet& bs);
140	>	void instructionDispatchLoop(OpenMDBitSet& bs, int frame);
141	>
142	>	void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
143	>	void withinInstruction(const Token& instruction, OpenMDBitSet& bs, int frame);
144	>	OpenMDBitSet allInstruction();
145
146	<	SimInfo* info_;
146	>	OpenMDBitSet comparatorInstruction(const Token& instruction);
147	>	OpenMDBitSet comparatorInstruction(const Token& instruction, int frame);
148	>	void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue);
149	>	void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue, int frame);
150	>	OpenMDBitSet nameInstruction(const std::string& name);
151	>	OpenMDBitSet indexInstruction(const boost::any& value);
152	>	OpenMDBitSet expression(const std::vector<Token>& tokens, int pc);
153	>	OpenMDBitSet expression(const std::vector<Token>& tokens, int pc, int frame);
154
155	<	std::map<std::string, std::vector<Token> > variables_;
90	<	std::string script_;
91	<	};
155	>	OpenMDBitSet lookupValue(const std::string& variable);
156
157	+	OpenMDBitSet hull();
158	+	OpenMDBitSet hull(int frame);
159	+
160	+	void evalError(const std::string& message) {
161	+	sprintf( painCave.errMsg,
162	+	"SelectionEvaluator Error: %s\n", message.c_str());
163	+	painCave.severity = OPENMD_ERROR;
164	+	painCave.isFatal = 1;
165	+	simError();
166	+	}
167	+
168	+	void unrecognizedCommand(const Token& token) {
169	+	evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
170	+	}
171	+
172	+	void unrecognizedExpression() {
173	+	evalError("unrecognized expression");
174	+	}
175	+
176	+	void unrecognizedAtomProperty(int property){
177	+	evalError("unrecognized atom property");
178	+	}
179	+
180	+	void unrecognizedIdentifier(const std::string& identifier) {
181	+	evalError("unrecognized identifier:" + identifier);
182	+	}
183	+
184	+	void invalidIndexRange(std::pair<int, int> range) {
185	+	evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
186	+	}
187	+
188	+	void invalidIndex(int index) {
189	+	evalError("invalid index : " + toString(index) );
190	+	}
191	+
192	+
193	+	bool containDynamicToken(const std::vector<Token>& tokens);
194	+
195	+	RealType getCharge(Atom* atom);
196	+	RealType getCharge(Atom* atom, int frame);
197	+
198	+	SelectionCompiler compiler;
199	+
200	+	//const static int scriptLevelMax = 10;
201	+	//int scriptLevel;
202	+
203	+	//Context stack[scriptLevelMax];
204	+
205	+	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	+	unsigned int pc; // program counter
211	+
212	+	bool error;
213	+	std::string errorMessage;
214	+
215	+	std::vector<Token> statement;
216	+	int statementLength;
217	+
218	+	SimInfo* info;
219	+	NameFinder nameFinder;
220	+	DistanceFinder distanceFinder;
221	+	HullFinder hullFinder;
222	+	IndexFinder indexFinder;
223	+	int nStuntDouble;   //nGLOBALatoms + nGLOBALrigidbodies
224	+
225	+	typedef std::map<std::string, boost::any > VariablesType;
226	+	VariablesType variables;
227	+
228	+	bool isDynamic_;
229	+	bool isLoaded_;
230	+	bool hasSurfaceArea_;
231	+	RealType surfaceArea_;
232	+
233	+	};
234	+
235		}
236		#endif

Comparing trunk/src/selection/SelectionEvaluator.hpp (property svn:keywords):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

#	Line 0 | Line 1
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