src/UseTheForce/DUFF.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */


#include "UseTheForce/DUFF.hpp"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/DarkSide/gb_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/DirectionalAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/MultipoleAtomTypesSectionParser.hpp"
#include "io/StickyAtomTypesSectionParser.hpp"
#include "io/StickyPowerAtomTypesSectionParser.hpp"
#include "io/GayBerneAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"

namespace oopse {
    
  DUFF::DUFF(){

    //set default force field filename
    setForceFieldFileName("DUFF2.frc");

    //The order of adding section parsers is important.
    //OptionSectionParser must come first to set options for other parsers
    //DirectionalAtomTypesSectionParser should be added before 
    //AtomTypesSectionParser, and these two section parsers will actually 
    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and 
    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which 
    //is a subclass of AtomType and should come first). Other AtomTypes Section 
    //Parser will not create the "real" AtomType, they only add and set some 
    //attribute of the AtomType. Thus their order are not important. 
    //AtomTypesSectionParser should be added before other atom type section 
    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser 
    //and AtomTypesSectionParser. The order of BondTypesSectionParser, 
    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
    spMan_.push_back(new DirectionalAtomTypesSectionParser(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 MultipoleAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
    
  }

  void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    bool hasGBtypes;

    ffStream = openForceFieldFile(filename);

    spMan_.parse(*ffStream, *this);

    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

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

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

    hasGBtypes = false;
    for (at = atomTypeCont_.beginType(i); at != NULL; 
         at = atomTypeCont_.nextType(i)) {
      if (at->isGayBerne()) 
        hasGBtypes = true;
    }
    
    int isError = 0;

    if (hasGBtypes) {
      completeGBFF(&isError);
    }

    delete ffStream;
    
  }

  DUFF::~DUFF(){
    destroyLJTypes();
    destroyStickyTypes();
    destroyGayBerneTypes();
  }
} //end namespace oopse
Revision:	1269
Committed:	Tue Jul 1 13:28:23 2008 UTC (16 years, 10 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/DUFF.cpp*
File size:	5928 byte(s)
Log Message:	Adding infrastructure for Amber force field.
#	User	Rev	Content
1	gezelter	246	/*
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			* 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41	gezelter	2
42
43	gezelter	246	#include "UseTheForce/DUFF.hpp"
44	gezelter	141	#include "UseTheForce/DarkSide/lj_interface.h"
45	chuckv	124	#include "UseTheForce/DarkSide/sticky_interface.h"
46	kdaily	668	#include "UseTheForce/DarkSide/gb_interface.h"
47	gezelter	246	#include "UseTheForce/ForceFieldFactory.hpp"
48	gezelter	1269	#include "io/BaseAtomTypesSectionParser.hpp"
49	gezelter	246	#include "io/DirectionalAtomTypesSectionParser.hpp"
50			#include "io/AtomTypesSectionParser.hpp"
51			#include "io/LennardJonesAtomTypesSectionParser.hpp"
52	tim	413	#include "io/ChargeAtomTypesSectionParser.hpp"
53			#include "io/MultipoleAtomTypesSectionParser.hpp"
54	gezelter	246	#include "io/StickyAtomTypesSectionParser.hpp"
55	chrisfen	523	#include "io/StickyPowerAtomTypesSectionParser.hpp"
56	chrisfen	532	#include "io/GayBerneAtomTypesSectionParser.hpp"
57	gezelter	246	#include "io/BondTypesSectionParser.hpp"
58			#include "io/BendTypesSectionParser.hpp"
59			#include "io/TorsionTypesSectionParser.hpp"
60	tim	749	#include "io/OptionSectionParser.hpp"
61	gezelter	246	#include "UseTheForce/ForceFieldCreator.hpp"
62	gezelter	2
63	gezelter	246	namespace oopse {
64	gezelter	2
65	gezelter	507	DUFF::DUFF(){
66	gezelter	2
67	gezelter	246	//set default force field filename
68			setForceFieldFileName("DUFF2.frc");
69	gezelter	2
70	chrisfen	523	//The order of adding section parsers is important.
71	chuckv	802	//OptionSectionParser must come first to set options for other parsers
72	chrisfen	523	//DirectionalAtomTypesSectionParser should be added before
73			//AtomTypesSectionParser, and these two section parsers will actually
74			//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
75			//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
76			//is a subclass of AtomType and should come first). Other AtomTypes Section
77			//Parser will not create the "real" AtomType, they only add and set some
78			//attribute of the AtomType. Thus their order are not important.
79			//AtomTypesSectionParser should be added before other atom type section
80			//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
81			//and AtomTypesSectionParser. The order of BondTypesSectionParser,
82			//BendTypesSectionParser and TorsionTypesSectionParser are not important.
83	tim	749	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
84	chuckv	802	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
85	gezelter	1269	spMan_.push_back(new BaseAtomTypesSectionParser());
86	gezelter	246	spMan_.push_back(new AtomTypesSectionParser());
87	chuckv	801	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
88	chuckv	802	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
89			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
90			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
91			spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
92			spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
93			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
94			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
95			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
96	gezelter	2
97	gezelter	507	}
98	gezelter	2
99	gezelter	507	void DUFF::parse(const std::string& filename) {
100	gezelter	246	ifstrstream* ffStream;
101	gezelter	981	bool hasGBtypes;
102
103	gezelter	246	ffStream = openForceFieldFile(filename);
104	gezelter	2
105	gezelter	246	spMan_.parse(ffStream, this);
106	gezelter	2
107	gezelter	246	ForceField::AtomTypeContainer::MapTypeIterator i;
108			AtomType* at;
109	gezelter	2
110	chrisfen	523	for (at = atomTypeCont_.beginType(i); at != NULL;
111			at = atomTypeCont_.nextType(i)) {
112	gezelter	507	at->makeFortranAtomType();
113	gezelter	2	}
114
115	chrisfen	523	for (at = atomTypeCont_.beginType(i); at != NULL;
116			at = atomTypeCont_.nextType(i)) {
117	gezelter	507	at->complete();
118	gezelter	2	}
119	tim	425
120	gezelter	981	hasGBtypes = false;
121			for (at = atomTypeCont_.beginType(i); at != NULL;
122			at = atomTypeCont_.nextType(i)) {
123			if (at->isGayBerne())
124			hasGBtypes = true;
125			}
126
127	kdaily	668	int isError = 0;
128
129	gezelter	981	if (hasGBtypes) {
130			completeGBFF(&isError);
131			}
132
133	tim	425	delete ffStream;
134	gezelter	2
135	gezelter	507	}
136	gezelter	2
137	gezelter	507	DUFF::~DUFF(){
138			destroyLJTypes();
139			destroyStickyTypes();
140	kdaily	668	destroyGayBerneTypes();
141	gezelter	507	}
142	gezelter	246	} //end namespace oopse