src/UseTheForce/SHAPES_FF.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/OptionSectionParser.hpp"
#include "io/DirectionalAtomTypesSectionParser.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/MultipoleAtomTypesSectionParser.hpp"
#include "io/ShapeAtomTypesSectionParser.hpp"
#include "io/StickyAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"
#include "UseTheForce/SHAPES_FF.hpp"
#include "utils/simError.h"
namespace OpenMD {
    
  SHAPES_FF::SHAPES_FF(){
    
    //set default force field filename
    setForceFieldFileName("Shapes.frc");
    
    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
    spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
    
  }
  
  void SHAPES_FF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFieldFile(filename);
    
    spMan_.parse(*ffStream, *this);
    
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;
    
    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
      // useBase sets the responsibilities, and these have to be done 
      // after the atomTypes and Base types have all been scanned:

      std::vector<AtomType*> ayb = at->allYourBase();      
      if (ayb.size() > 1) {
        for (int j = ayb.size()-1; j > 0; j--) {
          
          ayb[j-1]->useBase(ayb[j]);

        }
      } 
    }
    
    delete ffStream;
  }
} //end namespace OpenMD 
  
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	4640 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	chrisfen	512	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chrisfen	512	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chrisfen	512	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chrisfen	512	*/
42
43			#include "UseTheForce/ForceFieldFactory.hpp"
44	chuckv	801	#include "io/OptionSectionParser.hpp"
45	chrisfen	512	#include "io/DirectionalAtomTypesSectionParser.hpp"
46	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
47	chrisfen	512	#include "io/AtomTypesSectionParser.hpp"
48			#include "io/LennardJonesAtomTypesSectionParser.hpp"
49			#include "io/ChargeAtomTypesSectionParser.hpp"
50			#include "io/MultipoleAtomTypesSectionParser.hpp"
51			#include "io/ShapeAtomTypesSectionParser.hpp"
52			#include "io/StickyAtomTypesSectionParser.hpp"
53			#include "io/BondTypesSectionParser.hpp"
54			#include "io/BendTypesSectionParser.hpp"
55			#include "io/TorsionTypesSectionParser.hpp"
56			#include "UseTheForce/ForceFieldCreator.hpp"
57	chrisfen	514	#include "UseTheForce/SHAPES_FF.hpp"
58	chrisfen	512	#include "utils/simError.h"
59	gezelter	1390	namespace OpenMD {
60	chrisfen	512
61			SHAPES_FF::SHAPES_FF(){
62
63			//set default force field filename
64	chrisfen	514	setForceFieldFileName("Shapes.frc");
65	chrisfen	512
66	chuckv	801	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
67	chuckv	802	spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
68	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
69	chrisfen	512	spMan_.push_back(new AtomTypesSectionParser());
70	gezelter	1282	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
71	chuckv	801	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
72	chuckv	802	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
73			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
74			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
75			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
76			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
77			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
78	chrisfen	512
79	chrisfen	514	}
80
81			void SHAPES_FF::parse(const std::string& filename) {
82	chrisfen	512	ifstrstream* ffStream;
83			ffStream = openForceFieldFile(filename);
84	chrisfen	514
85	chrisfen	512	spMan_.parse(ffStream, this);
86	chrisfen	514
87	chrisfen	512	ForceField::AtomTypeContainer::MapTypeIterator i;
88			AtomType* at;
89	chrisfen	514
90	chrisfen	512	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
91	gezelter	1280	// useBase sets the responsibilities, and these have to be done
92			// after the atomTypes and Base types have all been scanned:
93
94			std::vector<AtomType*> ayb = at->allYourBase();
95			if (ayb.size() > 1) {
96			for (int j = ayb.size()-1; j > 0; j--) {
97
98			ayb[j-1]->useBase(ayb[j]);
99
100			}
101			}
102	chrisfen	512	}
103	chrisfen	514
104	chrisfen	512	delete ffStream;
105	chrisfen	514	}
106	gezelter	1390	} //end namespace OpenMD
107	chrisfen	514