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Comparing branches/development/src/brains/SimCreator.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
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).                        
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   /**
# Line 60 | Line 61 | namespace OpenMD {
61  
62    /**
63     * @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
64 <   * The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
65 <   * instance based on the information returned by parser.
64 >   *
65 >   * The only responsibility of SimCreator is to parse the meta-data
66 >   * file and create a SimInfo instance based on the information
67 >   * returned by parser.
68     */
69    class SimCreator {
70    public:
# Line 82 | Line 85 | namespace OpenMD {
85       * @param mdfile
86       * @return simParams
87       */
88 <    Globals*  parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine);
88 >    Globals*  parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine);
89  
90  
91      /** create the molecules belong to current processor*/
92      virtual void createMolecules(SimInfo* info);
93 <
93 >    
94      /**
95 <     * Sets the global index for atoms, rigidbodies and cutoff groups and fill up
96 <     * globalGroupMembership and globalMolMembership arrays which map atoms'
97 <     * global index to the global index of the groups (or molecules) they belong to.
98 <     * These array are never changed during the simulation.
95 >     * Sets the global index for atoms, rigidbodies and cutoff groups
96 >     * and fill up globalGroupMembership and globalMolMembership
97 >     * arrays which map atoms' global index to the global index of the
98 >     * groups (or molecules) they belong to.  These array are never
99 >     * changed during the simulation.
100       */
101      void setGlobalIndex(SimInfo* info);
102  
# Line 108 | Line 112 | namespace OpenMD {
112      void loadCoordinates(SimInfo* info, const std::string& mdFileName);    
113  
114      std::string mdFileName_;  //save the meta-data file name which may be used later
115 +
116    };
117  
118   } //end namespace OpenMD

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