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

Comparing trunk/src/selection/SelectionEvaluator.hpp (file contents):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 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 "selection/SelectionSet.hpp"
59	>	#include "primitives/StuntDouble.hpp"
60	>	#include "utils/StringUtils.hpp"
61	>	namespace OpenMD {
62
54	–	namespace oopse {
63
64	<	class Context {
65	<	std::string filename;
66	<	std::tring script;
67	<	std::vector<int> linenumbers;
68	<	std::vector<int> lineIndices;
69	<	std::vector<std::vector<Token> > aatoken;
62	<	int pc;
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	<	/**
66	<	* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator"
67	<	* @brief Evalute the tokens compiled by SelectionCompiler and return a BitSet
68	<	*/
69	<	class SelectionEvaluator{
70	<	public:
71	>	SelectionEvaluator(SimInfo* info);
72
73	<	SelectionEvaluator(SimInfo* info, const std::string& script);
74	<
74	<
75	<	BitSet evaluate();
73	>	bool loadScriptString(const std::string& script);
74	>	bool loadScriptFile(const std::string& filename);
75
76	<	BitSet evaluate(int frameNo);
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	<	/**
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
82	<	*/
83	<	bool isStatic();
86	>	bool hadRuntimeError() const{
87	>	return error;
88	>	}
89
90	<	bool hadRuntimeError() const{
91	<	return error;
92	<	}
90	>	std::string getErrorMessage() const {
91	>	return errorMessage;
92	>	}
93
89	–	std::string getErrorMessage() const {
90	–	return errorMessage;
91	–	}
94
95	+	int getLinenumber() {
96	+	return linenumbers[pc];
97	+	}
98
99	<	int getLinenumber() {
100	<	return linenumbers[pc];
101	<	}
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
98	–	std::string getLine() {
99	–	int ichBegin = lineIndices[pc];
100	–	int ichEnd;
101	–	if ((ichEnd = script.find('\r', ichBegin)) == std::string:npos &&
102	–	(ichEnd = script.find('\n', ichBegin)) == std::string:npos) {
103	–	ichEnd = script.size();
104	–	}
105	–	return script.substr(ichBegin, ichEnd);
106	–	}
122
123	<	private:
123	>	private:
124
125	<	void clearState();
125	>	void clearState();
126
127	<	bool loadScript(const std::string& filename, const std::string& script);
127	>	bool loadScript(const std::string& filename, const std::string& script);
128
129	<	bool loadScriptString(const std::string& script);
129	>	bool loadScriptFileInternal(const std::string& filename);
130
131	<	bool loadScriptFileInternal(const std::string& filename);
132	<
118	<	void clearDefinitionsAndLoadPredefined();
131	>	SelectionSet createSelectionSets();
132	>	void clearDefinitionsAndLoadPredefined();
133
134	<	void define();
135	<
136	<	void predefine();
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();
139	>	void instructionDispatchLoop(SelectionSet& bs);
140	>	void instructionDispatchLoop(SelectionSet& bs, int frame);
141
142	<	withinInstruction(Token instruction, BitSet , BitSet);
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	<	BitSet expression(std::vector<Token>& tokens, int pc);
157	>	SelectionSet lookupValue(const std::string& variable);
158
159	<	SelectionCompiler compiler;
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	<	const static int scriptLevelMax = 10;
171	<	int scriptLevel;
170	>	void unrecognizedCommand(const Token& token) {
171	>	evalError("unrecognized command:" + boost::any_cast<std::string>(token.value));
172	>	}
173
174	<	Context stack[scriptLevelMax];
174	>	void unrecognizedExpression() {
175	>	evalError("unrecognized expression");
176	>	}
177
178	<	std::string filename;
179	<	std::string script;
180	<	std::vector<int> linenumbers;
181	<	std::vector<int> lineIndices;
182	<	std::vector<std::vector<Token> > aatoken;
183	<	int pc; // program counter
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	<	boolean error;
187	<	std::string errorMessage;
186	>	void unrecognizedIdentifier(const std::string& identifier) {
187	>	evalError("unrecognized identifier:" + identifier);
188	>	}
189
190	<	std::vector<Token> statement;
191	<	int statementLength;
190	>	void invalidIndexRange(std::pair<int, int> range) {
191	>	evalError("invalid index range: [" + toString(range.first) + ", " + toString(range.second) + ")");
192	>	}
193
194	<	SimInfo* info_;
194	>	void invalidIndex(int index) {
195	>	evalError("invalid index : " + toString(index) );
196	>	}
197
198	<	std::map<std::string, std::vector<Token> > variables_;
199	<	std::string script_;
198	>
199	>	bool containDynamicToken(const std::vector<Token>& tokens);
200
201	<	Hashtable variables = new Hashtable();
202	<	};
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

Comparing trunk/src/selection/SelectionEvaluator.hpp (property svn:keywords):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

#	Line 0 | Line 1
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