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root/OpenMD/trunk/src/brains/SimCreator.hpp

Comparing trunk/src/brains/SimCreator.hpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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		/**
44	<	* @file SimCreatorr.hpp
44	>	* @file SimCreator.hpp
45		* @author tlin
46		* @date 11/02/2004
46	–	* @time 12:126am
47		* @version 1.0
48		*/
49
50		#ifndef BRAINS_SIMCREATOR_HPP
51		#define BRAINS_SIMCREATOR_HPP
52
53	<
53	>	#include <iostream>
54		#include "primitives/Molecule.hpp"
55		#include "brains/SimInfo.hpp"
56		#include "io/Globals.hpp"
57	<	#include "UseTheForce/ForceField.hpp"
57	>	#include "brains/ForceField.hpp"
58
59	<	namespace oopse {
59	>	namespace OpenMD {
60
61		/**
62		* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
63	<	* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
64	<	* instance based on the information returned by parser.
63	>	*
64	>	* The only responsibility of SimCreator is to parse the meta-data
65	>	* file and create a SimInfo instance based on the information
66	>	* returned by parser.
67		*/
68		class SimCreator {
69		public:
#	Line 71 | Line 73 | namespace oopse {
73		/**
74		* Setup Simulation
75		* @return a pointer to SimInfo
76	<	* @param mdfile the meta-data file name
76	>	* @param mdFileName the meta-data file name
77	>	* @param loadInitCoords should the initial coordinates be loaded from a file?
78		*/
79		SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
80
#	Line 79 | Line 82 | namespace oopse {
82
83		/**
84		* Parses the meta-data file
85	<	* @param mdfile
86	<	* @return simParams
85	>	* @param mdFileName the meta-data file name
86	>	* @param rawMetaData the raw meta-data stream
87	>	* @param mdFileVersion the version of code used to create the meta-data file
88	>	* @param metaDataStartingLine the starting line of the meta-data block
89	>	* @return a pointer to the simulation parameters in a #Globals object
90		*/
91	<	Globals*  parseFile(const std::string mdFileName);
91	>	Globals*  parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine);
92
93
94		/** create the molecules belong to current processor*/
95		virtual void createMolecules(SimInfo* info);
96
97	+	/**
98	+	* Figure out the data storage layout based on what kinds of
99	+	* objects are being simulated
100	+	*/
101	+	int computeStorageLayout(SimInfo* info);
102	+
103		/**
104	<	* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
105	<	* globalGroupMembership and globalMolMembership arrays which map atoms'
106	<	* global index to the global index of the groups (or molecules) they belong to.
107	<	* These array are never changed during the simulation.
104	>	* Sets the global index for atoms, rigidbodies and cutoff groups
105	>	* and fill up globalGroupMembership and globalMolMembership
106	>	* arrays which map atoms' global index to the global index of the
107	>	* groups (or molecules) they belong to.  These array are never
108	>	* changed during the simulation.
109		*/
110		void setGlobalIndex(SimInfo* info);
111
#	Line 105 | Line 118 | namespace oopse {
118		void divideMolecules(SimInfo* info);
119
120		/** Load initial coordinates */
121	<	void loadCoordinates(SimInfo* info);
121	>	void loadCoordinates(SimInfo* info, const std::string& mdFileName);
122
123		std::string mdFileName_;  //save the meta-data file name which may be used later
124	+
125		};
126
127	<	} //end namespace oopse
127	>	} //end namespace OpenMD
128		#endif //BRAINS_SIMCREATOR_HPP
129

Comparing trunk/src/brains/SimCreator.hpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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