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Comparing trunk/src/brains/SimCreator.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 50 | Line 50
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 "types/MakeStamps.hpp"
56   #include "io/Globals.hpp"
57   #include "UseTheForce/ForceField.hpp"
58  
59 < // this routine is defined in BASS_interface.cpp
61 < //another OOPS
62 < extern void set_interface_stamps( MakeStamps* ms, Globals* g );
59 > namespace OpenMD {
60  
64 – namespace oopse {
65 –
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
# Line 85 | Line 80 | namespace oopse {
80      /**
81       * Parses the meta-data file
82       * @param mdfile
83 <     * @param stamps
89 <     * @param simParams
83 >     * @return simParams
84       */
85 <    void parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams);
85 >    Globals*  parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine);
86  
87  
88      /** create the molecules belong to current processor*/
# Line 103 | Line 97 | namespace oopse {
97      void setGlobalIndex(SimInfo* info);
98  
99      void gatherParameters(SimInfo *info, const std::string& mdfile);            
106 –
100          
108 –    /** Extracts the molecules stamps and adds them into SimInfo class */
109 –    void compList(MakeStamps* stamps,  Globals* simParams,
110 –                  std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ;
111 –
101      /**
102       * Divide the molecules among the processors
103       */
# Line 116 | Line 105 | namespace oopse {
105      void divideMolecules(SimInfo* info);
106  
107      /** Load initial coordinates */
108 <    void loadCoordinates(SimInfo* info);    
108 >    void loadCoordinates(SimInfo* info, const std::string& mdFileName);    
109  
110      std::string mdFileName_;  //save the meta-data file name which may be used later
111    };
112  
113 < } //end namespace oopse
113 > } //end namespace OpenMD
114   #endif //BRAINS_SIMCREATOR_HPP
115  

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