src/UseTheForce/Amber_FF.cpp

/*
 * Copyright (c) 2008 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]  Vardeman & Gezelter, in progress (2009).                        
 */


#include "UseTheForce/Amber_FF.hpp"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "io/InversionTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"

namespace OpenMD {
    
  Amber_FF::Amber_FF(){

    //set default force field filename
    setForceFieldFileName("Amber.frc");

    //The order of adding section parsers is important.

    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
  }

  void Amber_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]);

        }
      }
      at->makeFortranAtomType();      
    }

    for (at = atomTypeCont_.beginType(i); at != NULL; 
         at = atomTypeCont_.nextType(i)) {
      at->complete();
    }    
    
    delete ffStream;
    
  }

  Amber_FF::~Amber_FF(){
    destroyLJTypes();
  }
} //end namespace OpenMD
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	4474 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	gezelter	1271	/*
2			* Copyright (c) 2008 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	gezelter	1271	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	1271	* 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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	1271	*/
41
42
43			#include "UseTheForce/Amber_FF.hpp"
44			#include "UseTheForce/DarkSide/lj_interface.h"
45			#include "UseTheForce/ForceFieldFactory.hpp"
46			#include "io/BaseAtomTypesSectionParser.hpp"
47			#include "io/AtomTypesSectionParser.hpp"
48			#include "io/LennardJonesAtomTypesSectionParser.hpp"
49			#include "io/ChargeAtomTypesSectionParser.hpp"
50			#include "io/BondTypesSectionParser.hpp"
51			#include "io/BendTypesSectionParser.hpp"
52			#include "io/TorsionTypesSectionParser.hpp"
53	cli2	1275	#include "io/InversionTypesSectionParser.hpp"
54	gezelter	1271	#include "io/OptionSectionParser.hpp"
55			#include "UseTheForce/ForceFieldCreator.hpp"
56
57	gezelter	1390	namespace OpenMD {
58	gezelter	1271
59			Amber_FF::Amber_FF(){
60
61			//set default force field filename
62			setForceFieldFileName("Amber.frc");
63
64			//The order of adding section parsers is important.
65
66			spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
67			spMan_.push_back(new BaseAtomTypesSectionParser());
68			spMan_.push_back(new AtomTypesSectionParser());
69			spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
70			spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
71			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
72			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
73			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
74	cli2	1275	spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
75	gezelter	1271	}
76
77			void Amber_FF::parse(const std::string& filename) {
78			ifstrstream* ffStream;
79
80			ffStream = openForceFieldFile(filename);
81			spMan_.parse(ffStream, this);
82
83			ForceField::AtomTypeContainer::MapTypeIterator i;
84			AtomType* at;
85
86			for (at = atomTypeCont_.beginType(i); at != NULL;
87			at = atomTypeCont_.nextType(i)) {
88	gezelter	1277
89			// useBase sets the responsibilities, and these have to be done
90			// after the atomTypes and Base types have all been scanned:
91
92			std::vector<AtomType*> ayb = at->allYourBase();
93			if (ayb.size() > 1) {
94			for (int j = ayb.size()-1; j > 0; j--) {
95
96			ayb[j-1]->useBase(ayb[j]);
97
98			}
99			}
100			at->makeFortranAtomType();
101	gezelter	1271	}
102
103			for (at = atomTypeCont_.beginType(i); at != NULL;
104			at = atomTypeCont_.nextType(i)) {
105			at->complete();
106			}
107	gezelter	1277
108	gezelter	1271	delete ffStream;
109
110			}
111
112			Amber_FF::~Amber_FF(){
113			destroyLJTypes();
114			}
115	gezelter	1390	} //end namespace OpenMD