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. 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).                        
 *
 *  Created by Charles F. Vardeman II on 11/9/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id$
 *
 */

#include "UseTheForce/SC_FF.hpp"
#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 OpenMD {
  
  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;
  }
} //end namespace OpenMD

Revision:	1489
Committed:	Tue Aug 10 18:34:59 2010 UTC (14 years, 8 months ago) by gezelter
File size:	3861 byte(s)
Log Message:	Migrating Sutton-Chen from Fortran over to C++
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	728	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	728	* 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			*
32	gezelter	1390	* 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	chuckv	728	*
41			* Created by Charles F. Vardeman II on 11/9/05.
42			* @author Charles F. Vardeman II
43	gezelter	1442	* @version $Id$
44	chuckv	728	*
45			*/
46
47			#include "UseTheForce/SC_FF.hpp"
48			#include "UseTheForce/ForceFieldFactory.hpp"
49	gezelter	1280	#include "io/OptionSectionParser.hpp"
50			#include "io/BaseAtomTypesSectionParser.hpp"
51	chuckv	728	#include "io/AtomTypesSectionParser.hpp"
52			#include "io/SCAtomTypesSectionParser.hpp"
53			#include "UseTheForce/ForceFieldCreator.hpp"
54			#include "utils/simError.h"
55	gezelter	1390	namespace OpenMD {
56	chuckv	728
57			SC_FF::SC_FF(){
58
59			//set default force field filename
60	chuckv	867	setForceFieldFileName("SuttonChen.frc");
61	tim	837	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
62	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
63	chuckv	728	spMan_.push_back(new AtomTypesSectionParser());
64	tim	837	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
65	chuckv	728	}
66
67			void SC_FF::parse(const std::string& filename) {
68			ifstrstream* ffStream;
69			ffStream = openForceFieldFile(filename);
70
71			spMan_.parse(ffStream, this);
72
73			ForceField::AtomTypeContainer::MapTypeIterator i;
74			AtomType* at;
75
76	chuckv	793	// Set forcefield options
77
78	chuckv	728	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
79	gezelter	1280	// useBase sets the responsibilities, and these have to be done
80			// after the atomTypes and Base types have all been scanned:
81
82			std::vector<AtomType*> ayb = at->allYourBase();
83			if (ayb.size() > 1) {
84			for (int j = ayb.size()-1; j > 0; j--) {
85
86			ayb[j-1]->useBase(ayb[j]);
87
88			}
89			}
90	chuckv	728	at->makeFortranAtomType();
91			}
92
93	chuckv	793
94	chuckv	728	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
95			at->complete();
96			}
97
98			delete ffStream;
99			}
100	gezelter	1390	} //end namespace OpenMD
101	chuckv	728