src/UseTheForce/SC_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.
 *
 *
 *  SC_FF.cpp
 *  OOPSE-2.0
 *
 *  Created by Charles F. Vardeman II on 11/9/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id: SC_FF.cpp,v 1.11 2008-07-30 18:11:18 gezelter Exp $
 *
 */

#include "UseTheForce/SC_FF.hpp"
#include "UseTheForce/DarkSide/eam_interface.h"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/DarkSide/suttonchen_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/OptionSectionParser.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/SCAtomTypesSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"
#include "utils/simError.h"
namespace oopse {
  
  SC_FF::SC_FF(){
    
    //set default force field filename
    setForceFieldFileName("SuttonChen.frc");
    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
  }
  
  void SC_FF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFieldFile(filename);
    
    spMan_.parse(*ffStream, *this);
    
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;
    
    // Set forcefield options
    
    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;
  }
  
    
  SC_FF::~SC_FF(){
    // We need to clean up the fortran side so we don't have bad things happen if
    // we try to create a second SC force field.
    destroySCTypes();
  }
} //end namespace oopse

Revision:	1282
Committed:	Wed Jul 30 18:11:19 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/SC_FF.cpp*
File size:	4289 byte(s)
Log Message:	Many fixes
#	User	Rev	Content
1	chuckv	728	/*
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			* SC_FF.cpp
43			* OOPSE-2.0
44			*
45			* Created by Charles F. Vardeman II on 11/9/05.
46			* @author Charles F. Vardeman II
47	gezelter	1282	* @version $Id: SC_FF.cpp,v 1.11 2008-07-30 18:11:18 gezelter Exp $
48	chuckv	728	*
49			*/
50
51			#include "UseTheForce/SC_FF.hpp"
52			#include "UseTheForce/DarkSide/eam_interface.h"
53			#include "UseTheForce/DarkSide/lj_interface.h"
54			#include "UseTheForce/DarkSide/sticky_interface.h"
55			#include "UseTheForce/DarkSide/suttonchen_interface.h"
56			#include "UseTheForce/ForceFieldFactory.hpp"
57	gezelter	1280	#include "io/OptionSectionParser.hpp"
58			#include "io/BaseAtomTypesSectionParser.hpp"
59	chuckv	728	#include "io/AtomTypesSectionParser.hpp"
60			#include "io/SCAtomTypesSectionParser.hpp"
61			#include "UseTheForce/ForceFieldCreator.hpp"
62			#include "utils/simError.h"
63			namespace oopse {
64
65			SC_FF::SC_FF(){
66
67			//set default force field filename
68	chuckv	867	setForceFieldFileName("SuttonChen.frc");
69	tim	837	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
70	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
71	chuckv	728	spMan_.push_back(new AtomTypesSectionParser());
72	tim	837	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
73	chuckv	728	}
74
75			void SC_FF::parse(const std::string& filename) {
76			ifstrstream* ffStream;
77			ffStream = openForceFieldFile(filename);
78
79			spMan_.parse(ffStream, this);
80
81			ForceField::AtomTypeContainer::MapTypeIterator i;
82			AtomType* at;
83
84	chuckv	793	// Set forcefield options
85
86	chuckv	728	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
87	gezelter	1280	// useBase sets the responsibilities, and these have to be done
88			// after the atomTypes and Base types have all been scanned:
89
90			std::vector<AtomType*> ayb = at->allYourBase();
91			if (ayb.size() > 1) {
92			for (int j = ayb.size()-1; j > 0; j--) {
93
94			ayb[j-1]->useBase(ayb[j]);
95
96			}
97			}
98	chuckv	728	at->makeFortranAtomType();
99			}
100
101	chuckv	793
102	chuckv	728	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
103			at->complete();
104			}
105
106			delete ffStream;
107			}
108
109
110			SC_FF::~SC_FF(){
111			// We need to clean up the fortran side so we don't have bad things happen if
112	chuckv	735	// we try to create a second SC force field.
113	chuckv	728	destroySCTypes();
114			}
115			} //end namespace oopse
116