src/UseTheForce/DUFF.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).                        
 */


#include "UseTheForce/DUFF.hpp"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/DarkSide/gb_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/DirectionalAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/MultipoleAtomTypesSectionParser.hpp"
#include "io/StickyAtomTypesSectionParser.hpp"
#include "io/StickyPowerAtomTypesSectionParser.hpp"
#include "io/GayBerneAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"

namespace OpenMD {
    
  DUFF::DUFF(){

    //set default force field filename
    setForceFieldFileName("DUFF2.frc");

    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
    
  }

  void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    bool hasGBtypes;

    ffStream = openForceFieldFile(filename);

    spMan_.parse(*ffStream, *this);

    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    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();
    }

    hasGBtypes = false;
    for (at = atomTypeCont_.beginType(i); at != NULL; 
         at = atomTypeCont_.nextType(i)) {
      if (at->isGayBerne()) 
        hasGBtypes = true;
    }
    
    int isError = 0;

    if (hasGBtypes) {
      completeGBFF(&isError);
    }

    delete ffStream;
    
  }

  DUFF::~DUFF(){
    destroyStickyTypes();
    destroyGayBerneTypes();
  }
} //end namespace OpenMD
Revision:	1467
Committed:	Sat Jul 17 15:33:03 2010 UTC (14 years, 9 months ago) by gezelter
File size:	5323 byte(s)
Log Message:	well, it compiles, but still segfaults
#	User	Rev	Content
1	gezelter	246	/*
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	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
41	gezelter	2
42
43	gezelter	246	#include "UseTheForce/DUFF.hpp"
44	chuckv	124	#include "UseTheForce/DarkSide/sticky_interface.h"
45	kdaily	668	#include "UseTheForce/DarkSide/gb_interface.h"
46	gezelter	246	#include "UseTheForce/ForceFieldFactory.hpp"
47	gezelter	1269	#include "io/BaseAtomTypesSectionParser.hpp"
48	gezelter	246	#include "io/DirectionalAtomTypesSectionParser.hpp"
49			#include "io/AtomTypesSectionParser.hpp"
50	cli2	1275	#include "io/BaseAtomTypesSectionParser.hpp"
51	gezelter	246	#include "io/LennardJonesAtomTypesSectionParser.hpp"
52	tim	413	#include "io/ChargeAtomTypesSectionParser.hpp"
53			#include "io/MultipoleAtomTypesSectionParser.hpp"
54	gezelter	246	#include "io/StickyAtomTypesSectionParser.hpp"
55	chrisfen	523	#include "io/StickyPowerAtomTypesSectionParser.hpp"
56	chrisfen	532	#include "io/GayBerneAtomTypesSectionParser.hpp"
57	gezelter	246	#include "io/BondTypesSectionParser.hpp"
58			#include "io/BendTypesSectionParser.hpp"
59			#include "io/TorsionTypesSectionParser.hpp"
60	tim	749	#include "io/OptionSectionParser.hpp"
61	gezelter	246	#include "UseTheForce/ForceFieldCreator.hpp"
62	gezelter	2
63	gezelter	1390	namespace OpenMD {
64	gezelter	2
65	gezelter	507	DUFF::DUFF(){
66	gezelter	2
67	gezelter	246	//set default force field filename
68			setForceFieldFileName("DUFF2.frc");
69	gezelter	2
70	tim	749	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
71	gezelter	1269	spMan_.push_back(new BaseAtomTypesSectionParser());
72	gezelter	246	spMan_.push_back(new AtomTypesSectionParser());
73	gezelter	1282	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
74	chuckv	801	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
75	chuckv	802	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
76			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
77			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
78			spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
79			spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
80			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
81			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
82			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
83	gezelter	2
84	gezelter	507	}
85	gezelter	2
86	gezelter	507	void DUFF::parse(const std::string& filename) {
87	gezelter	246	ifstrstream* ffStream;
88	gezelter	981	bool hasGBtypes;
89
90	gezelter	246	ffStream = openForceFieldFile(filename);
91	gezelter	2
92	gezelter	246	spMan_.parse(ffStream, this);
93	gezelter	2
94	gezelter	246	ForceField::AtomTypeContainer::MapTypeIterator i;
95			AtomType* at;
96	gezelter	2
97	chrisfen	523	for (at = atomTypeCont_.beginType(i); at != NULL;
98			at = atomTypeCont_.nextType(i)) {
99	gezelter	1280	// useBase sets the responsibilities, and these have to be done
100			// after the atomTypes and Base types have all been scanned:
101
102			std::vector<AtomType*> ayb = at->allYourBase();
103			if (ayb.size() > 1) {
104			for (int j = ayb.size()-1; j > 0; j--) {
105
106			ayb[j-1]->useBase(ayb[j]);
107
108			}
109			}
110	gezelter	507	at->makeFortranAtomType();
111	gezelter	2	}
112
113	chrisfen	523	for (at = atomTypeCont_.beginType(i); at != NULL;
114			at = atomTypeCont_.nextType(i)) {
115	gezelter	507	at->complete();
116	gezelter	2	}
117	tim	425
118	gezelter	981	hasGBtypes = false;
119			for (at = atomTypeCont_.beginType(i); at != NULL;
120			at = atomTypeCont_.nextType(i)) {
121			if (at->isGayBerne())
122			hasGBtypes = true;
123			}
124
125	kdaily	668	int isError = 0;
126
127	gezelter	981	if (hasGBtypes) {
128			completeGBFF(&isError);
129			}
130
131	tim	425	delete ffStream;
132	gezelter	2
133	gezelter	507	}
134	gezelter	2
135	gezelter	507	DUFF::~DUFF(){
136			destroyStickyTypes();
137	kdaily	668	destroyGayBerneTypes();
138	gezelter	507	}
139	gezelter	1390	} //end namespace OpenMD