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++
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	* 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	*
41	* Created by Charles F. Vardeman II on 11/9/05.
42	* @author Charles F. Vardeman II
43	* @version $Id$
44	*
45	*/
46
47	#include "UseTheForce/SC_FF.hpp"
48	#include "UseTheForce/ForceFieldFactory.hpp"
49	#include "io/OptionSectionParser.hpp"
50	#include "io/BaseAtomTypesSectionParser.hpp"
51	#include "io/AtomTypesSectionParser.hpp"
52	#include "io/SCAtomTypesSectionParser.hpp"
53	#include "UseTheForce/ForceFieldCreator.hpp"
54	#include "utils/simError.h"
55	namespace OpenMD {
56
57	SC_FF::SC_FF(){
58
59	//set default force field filename
60	setForceFieldFileName("SuttonChen.frc");
61	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
62	spMan_.push_back(new BaseAtomTypesSectionParser());
63	spMan_.push_back(new AtomTypesSectionParser());
64	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
65	}
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	// Set forcefield options
77
78	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
79	// 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	at->makeFortranAtomType();
91	}
92
93
94	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
95	at->complete();
96	}
97
98	delete ffStream;
99	}
100	} //end namespace OpenMD
101