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root/OpenMD/branches/devel_omp/src/UseTheForce/DUFF.cpp

Comparing:
trunk/src/UseTheForce/DUFF.cpp (file contents), Revision 802 by chuckv, Thu Dec 8 15:38:49 2005 UTC vs.
branches/development/src/UseTheForce/DUFF.cpp (file contents), Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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
42
43		#include "UseTheForce/DUFF.hpp"
44	–	#include "UseTheForce/DarkSide/lj_interface.h"
44		#include "UseTheForce/DarkSide/sticky_interface.h"
45		#include "UseTheForce/DarkSide/gb_interface.h"
46		#include "UseTheForce/ForceFieldFactory.hpp"
47	+	#include "io/BaseAtomTypesSectionParser.hpp"
48		#include "io/DirectionalAtomTypesSectionParser.hpp"
49		#include "io/AtomTypesSectionParser.hpp"
50	+	#include "io/BaseAtomTypesSectionParser.hpp"
51		#include "io/LennardJonesAtomTypesSectionParser.hpp"
52		#include "io/ChargeAtomTypesSectionParser.hpp"
53		#include "io/MultipoleAtomTypesSectionParser.hpp"
#	Line 59 | Line 60
60		#include "io/OptionSectionParser.hpp"
61		#include "UseTheForce/ForceFieldCreator.hpp"
62
63	<	namespace oopse {
63	>	namespace OpenMD {
64
65		DUFF::DUFF(){
66
67		//set default force field filename
68		setForceFieldFileName("DUFF2.frc");
69
69	–	//The order of adding section parsers is important.
70	–	//OptionSectionParser must come first to set options for other parsers
71	–	//DirectionalAtomTypesSectionParser should be added before
72	–	//AtomTypesSectionParser, and these two section parsers will actually
73	–	//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
74	–	//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
75	–	//is a subclass of AtomType and should come first). Other AtomTypes Section
76	–	//Parser will not create the "real" AtomType, they only add and set some
77	–	//attribute of the AtomType. Thus their order are not important.
78	–	//AtomTypesSectionParser should be added before other atom type section
79	–	//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
80	–	//and AtomTypesSectionParser. The order of BondTypesSectionParser,
81	–	//BendTypesSectionParser and TorsionTypesSectionParser are not important.
70		spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
71	<	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
71	>	spMan_.push_back(new BaseAtomTypesSectionParser());
72		spMan_.push_back(new AtomTypesSectionParser());
73	+	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
74		spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
75		spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
76		spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
#	Line 96 | Line 85 | namespace oopse {
85
86		void DUFF::parse(const std::string& filename) {
87		ifstrstream* ffStream;
88	+	bool hasGBtypes;
89	+
90		ffStream = openForceFieldFile(filename);
91
92		spMan_.parse(*ffStream, *this);
#	Line 105 | Line 96 | namespace oopse {
96
97		for (at = atomTypeCont_.beginType(i); at != NULL;
98		at = atomTypeCont_.nextType(i)) {
99	+	// 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		at->makeFortranAtomType();
111		}
112
#	Line 113 | Line 115 | namespace oopse {
115		at->complete();
116		}
117
118	+	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		int isError = 0;
126
127	+	if (hasGBtypes) {
128	+	completeGBFF(&isError);
129	+	}
130	+
131		delete ffStream;
132
133		}
134
135		DUFF::~DUFF(){
123	–	destroyLJTypes();
136		destroyStickyTypes();
137		destroyGayBerneTypes();
138		}
139	<	} //end namespace oopse
139	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/DUFF.cpp (property svn:keywords), Revision 802 by chuckv, Thu Dec 8 15:38:49 2005 UTC vs.
branches/development/src/UseTheForce/DUFF.cpp (property svn:keywords), Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC

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