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

Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 281 by tim, Wed Feb 2 23:13:11 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	<	class Context {
65	<	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);
72	>
73	>	bool loadScriptString(const std::string& script);
74	>	bool loadScriptFile(const std::string& filename);
75
76	<	void clear() {
77	<	linenumbers.clear();
61	<	lineIndices.clear();
62	<	aatoken.clear();
63	<	}
76	>	OpenMDBitSet evaluate();
77	>	OpenMDBitSet evaluate(int frame);
78
79	<	std::string filename;
80	<	std::string script;
81	<	std::vector<int> linenumbers;
82	<	std::vector<int> lineIndices;
83	<	std::vector<std::vector<Token> > aatoken;
84	<	int pc;
71	<	};
79	>	/**
80	>	* Tests if the result from evaluation of script is dynamic.
81	>	*/
82	>	bool isDynamic() {
83	>	return isDynamic_;
84	>	}
85
86	<	/**
87	<	* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
88	<	* @brief Evalute the tokens compiled by SelectionCompiler and return a BitSet
76	<	*/
77	<	class SelectionEvaluator{
78	<	public:
86	>	bool hadRuntimeError() const{
87	>	return error;
88	>	}
89
90	<	SelectionEvaluator(SimInfo* info, const std::string& script);
90	>	std::string getErrorMessage() const {
91	>	return errorMessage;
92	>	}
93
94
95	<	BitSet evaluate();
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	<	BitSet evaluate(int frameNo);
127	>	bool loadScript(const std::string& filename, const std::string& script);
128
129	<	/**
88	<	* Tests if the result from evaluation of script is static.
89	<	* @return true if the result keeps the same even the frame change, otherwise return false
90	<	*/
91	<	bool isStatic();
129	>	bool loadScriptFileInternal(const std::string& filename);
130
93	–	bool hadRuntimeError() const{
94	–	return error;
95	–	}
131
132	<	std::string getErrorMessage() const {
133	<	return errorMessage;
134	<	}
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	+	void instructionDispatchLoop(OpenMDBitSet& bs);
140	+	void instructionDispatchLoop(OpenMDBitSet& bs, int frame);
141
142	<	int getLinenumber() {
143	<	return linenumbers[pc];
144	<	}
142	>	void withinInstruction(const Token& instruction, OpenMDBitSet& bs);
143	>	void withinInstruction(const Token& instruction, OpenMDBitSet& bs, int frame);
144	>	OpenMDBitSet allInstruction();
145	>
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::string getLine() {
107	<	int ichBegin = lineIndices[pc];
108	<	int ichEnd;
109	<	if ((ichEnd = script.find('\r', ichBegin)) == std::string::npos &&
110	<	(ichEnd = script.find('\n', ichBegin)) == std::string::npos) {
111	<	ichEnd = script.size();
112	<	}
113	<	return script.substr(ichBegin, ichEnd);
114	<	}
115	<
116	<	private:
155	>	OpenMDBitSet lookupValue(const std::string& variable);
156
157	<	void clearState();
157	>	OpenMDBitSet hull();
158	>	OpenMDBitSet hull(int frame);
159
160	<	bool loadScript(const std::string& filename, const std::string& script);
161	<	bool loadScriptString(const std::string& script);
162	<	bool loadScriptFileInternal(const std::string& filename);
163	<	bool loadScriptFile(const std::string& filename);
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 clearDefinitionsAndLoadPredefined();
169	<
170	<	void define();
128	<
129	<	void predefine();
168	>	void unrecognizedCommand(const Token& token) {
169	>	evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
170	>	}
171
172	<	void instructionDispatchLoop();
172	>	void unrecognizedExpression() {
173	>	evalError("unrecognized expression");
174	>	}
175
176	<	void withinInstruction(const Token& instruction, BitSet& , BitSet&);
176	>	void unrecognizedAtomProperty(int property){
177	>	evalError("unrecognized atom property");
178	>	}
179
180	<	BitSet expression(std::vector<Token>& tokens, int pc);
180	>	void unrecognizedIdentifier(const std::string& identifier) {
181	>	evalError("unrecognized identifier:" + identifier);
182	>	}
183
184	<	SelectionCompiler compiler;
184	>	void invalidIndexRange(std::pair<int, int> range) {
185	>	evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
186	>	}
187
188	<	const static int scriptLevelMax = 10;
189	<	int scriptLevel;
188	>	void invalidIndex(int index) {
189	>	evalError("invalid index : " + toString(index) );
190	>	}
191
192	<	Context stack[scriptLevelMax];
192	>
193	>	bool containDynamicToken(const std::vector<Token>& tokens);
194
195	<	std::string filename;
196	<	std::string script;
197	<	std::vector<int> linenumbers;
198	<	std::vector<int> lineIndices;
148	<	std::vector<std::vector<Token> > aatoken;
149	<	int pc; // program counter
195	>	RealType getCharge(Atom* atom);
196	>	RealType getCharge(Atom* atom, int frame);
197	>
198	>	SelectionCompiler compiler;
199
200	<	bool error;
201	<	std::string errorMessage;
200	>	//const static int scriptLevelMax = 10;
201	>	//int scriptLevel;
202
203	<	std::vector<Token> statement;
155	<	int statementLength;
203	>	//Context stack[scriptLevelMax];
204
205	<	SimInfo* info;
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	<	std::map<std::string, std::vector<Token> > variables;
213	<	};
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 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

#	Line 0 | Line 1
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