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 1.10 2008-07-16 02:07:09 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");
    
    //the order of adding section parsers are important
    //OptionSectionParser must come first to set options for other parsers
    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
    //AtomType and DirectionalAtomTypesSectionParser will creat 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 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 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:	3435
Committed:	Wed Jul 16 02:07:09 2008 UTC (16 years, 9 months ago) by gezelter
File size:	5255 byte(s)
Log Message:	All your base are belong to us!
#	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. 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	* @version $Id: SC_FF.cpp,v 1.10 2008-07-16 02:07:09 gezelter Exp $
48	*
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	#include "io/OptionSectionParser.hpp"
58	#include "io/BaseAtomTypesSectionParser.hpp"
59	#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	setForceFieldFileName("SuttonChen.frc");
69
70	//the order of adding section parsers are important
71	//OptionSectionParser must come first to set options for other parsers
72	//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
73	//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
74	//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
75	//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
76	//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
77	//important. AtomTypesSectionParser should be added before other atom type section parsers.
78	//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
79	//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
80	//not important.
81	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
82	spMan_.push_back(new BaseAtomTypesSectionParser());
83	spMan_.push_back(new AtomTypesSectionParser());
84	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
85
86	}
87
88	void SC_FF::parse(const std::string& filename) {
89	ifstrstream* ffStream;
90	ffStream = openForceFieldFile(filename);
91
92	spMan_.parse(ffStream, this);
93
94	ForceField::AtomTypeContainer::MapTypeIterator i;
95	AtomType* at;
96
97	// Set forcefield options
98
99	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
100	// useBase sets the responsibilities, and these have to be done
101	// after the atomTypes and Base types have all been scanned:
102
103	std::vector<AtomType*> ayb = at->allYourBase();
104	if (ayb.size() > 1) {
105	for (int j = ayb.size()-1; j > 0; j--) {
106
107	ayb[j-1]->useBase(ayb[j]);
108
109	}
110	}
111	at->makeFortranAtomType();
112	}
113
114
115	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
116	at->complete();
117	}
118
119	delete ffStream;
120	}
121
122
123	SC_FF::~SC_FF(){
124	// We need to clean up the fortran side so we don't have bad things happen if
125	// we try to create a second SC force field.
126	destroySCTypes();
127	}
128	} //end namespace oopse
129