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. 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/DarkSide/shapes_interface.h"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/DirectionalAtomTypesSectionParser.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 oopse {
    
  SHAPES_FF::SHAPES_FF(){
    
    //set default force field filename
    setForceFieldFileName("Shapes.frc");
    
    //The ordering of section parsers is important
    //DirectionalAtomTypesSectionParser should be before 
    //AtomTypesSectionParser since these two section parsers will actually 
    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType 
    //and DirectionalAtomTypesSectionParser will create DirectionalAtomType 
    //which is a subclass of AtomType, therefore it should come first). Other 
    //AtomTypes Section Parser will not create the "real" AtomType, they only 
    //add and set some attribute of the AtomType. Thus the ordering of these
    //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 ShapeAtomTypesSectionParser());
    spMan_.push_back(new DirectionalAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
    spMan_.push_back(new ChargeAtomTypesSectionParser());
    spMan_.push_back(new MultipoleAtomTypesSectionParser());
    spMan_.push_back(new StickyAtomTypesSectionParser());
    spMan_.push_back(new BondTypesSectionParser());
    spMan_.push_back(new BendTypesSectionParser());
    spMan_.push_back(new TorsionTypesSectionParser());
    
  }
  
  SHAPES_FF::~SHAPES_FF(){
    // We need to clean up the fortran side so we don't have bad things happen if
    // we try to create a second EAM force field.
    destroyShapeTypes();
  }
  
  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)) {
      at->makeFortranAtomType();
    }
    
    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
      at->complete();
    }

    int isError = 0;
    completeShapeFF(&isError);
    
    delete ffStream;
  }
  
  
//  double SHAPES_FF::getRcutFromAtomType(AtomType* at){
//  }
} //end namespace oopse 
  
Revision:	2211
Committed:	Thu Apr 21 14:12:19 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	5343 byte(s)
Log Message:	Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
#	User	Rev	Content
1	chrisfen	2209	/*
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
42			#include "UseTheForce/DarkSide/shapes_interface.h"
43			#include "UseTheForce/DarkSide/lj_interface.h"
44			#include "UseTheForce/DarkSide/sticky_interface.h"
45			#include "UseTheForce/ForceFieldFactory.hpp"
46			#include "io/DirectionalAtomTypesSectionParser.hpp"
47			#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	2211	#include "UseTheForce/SHAPES_FF.hpp"
58	chrisfen	2209	#include "utils/simError.h"
59			namespace oopse {
60
61			SHAPES_FF::SHAPES_FF(){
62
63			//set default force field filename
64	chrisfen	2211	setForceFieldFileName("Shapes.frc");
65	chrisfen	2209
66	chrisfen	2211	//The ordering of section parsers is important
67			//DirectionalAtomTypesSectionParser should be before
68	chrisfen	2209	//AtomTypesSectionParser since these two section parsers will actually
69			//create "real" AtomTypes (AtomTypesSectionParser will create AtomType
70	chrisfen	2211	//and DirectionalAtomTypesSectionParser will create DirectionalAtomType
71	chrisfen	2209	//which is a subclass of AtomType, therefore it should come first). Other
72			//AtomTypes Section Parser will not create the "real" AtomType, they only
73	chrisfen	2211	//add and set some attribute of the AtomType. Thus the ordering of these
74			//are not important. AtomTypesSectionParser should be added before other atom
75	chrisfen	2209	//type section parsers. Make sure they are added after
76			//DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order
77			//of BondTypesSectionParser, BendTypesSectionParser and
78			//TorsionTypesSectionParser are not important.
79
80			spMan_.push_back(new ShapeAtomTypesSectionParser());
81			spMan_.push_back(new DirectionalAtomTypesSectionParser());
82			spMan_.push_back(new AtomTypesSectionParser());
83			spMan_.push_back(new LennardJonesAtomTypesSectionParser());
84			spMan_.push_back(new ChargeAtomTypesSectionParser());
85			spMan_.push_back(new MultipoleAtomTypesSectionParser());
86			spMan_.push_back(new StickyAtomTypesSectionParser());
87			spMan_.push_back(new BondTypesSectionParser());
88			spMan_.push_back(new BendTypesSectionParser());
89			spMan_.push_back(new TorsionTypesSectionParser());
90
91	chrisfen	2211	}
92
93	chrisfen	2209	SHAPES_FF::~SHAPES_FF(){
94			// We need to clean up the fortran side so we don't have bad things happen if
95			// we try to create a second EAM force field.
96	chrisfen	2211	destroyShapeTypes();
97	chrisfen	2209	}
98	chrisfen	2211
99			void SHAPES_FF::parse(const std::string& filename) {
100	chrisfen	2209	ifstrstream* ffStream;
101			ffStream = openForceFieldFile(filename);
102	chrisfen	2211
103	chrisfen	2209	spMan_.parse(ffStream, this);
104	chrisfen	2211
105	chrisfen	2209	ForceField::AtomTypeContainer::MapTypeIterator i;
106			AtomType* at;
107	chrisfen	2211
108	chrisfen	2209	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
109	chrisfen	2211	at->makeFortranAtomType();
110	chrisfen	2209	}
111	chrisfen	2211
112	chrisfen	2209	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
113	chrisfen	2211	at->complete();
114	chrisfen	2209	}
115
116	chrisfen	2211	int isError = 0;
117			completeShapeFF(&isError);
118
119	chrisfen	2209	delete ffStream;
120	chrisfen	2211	}
121
122
123			// double SHAPES_FF::getRcutFromAtomType(AtomType* at){
124			// }
125			} //end namespace oopse
126