ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/UseTheForce/DUFF.cpp (file contents), Revision 1269 by gezelter, Tue Jul 1 13:28:23 2008 UTC vs.
branches/development/src/UseTheForce/DUFF.cpp (file contents), Revision 1483 by gezelter, Tue Jul 27 21:17:31 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"
46	–	#include "UseTheForce/DarkSide/gb_interface.h"
45		#include "UseTheForce/ForceFieldFactory.hpp"
46		#include "io/BaseAtomTypesSectionParser.hpp"
47		#include "io/DirectionalAtomTypesSectionParser.hpp"
48		#include "io/AtomTypesSectionParser.hpp"
49	+	#include "io/BaseAtomTypesSectionParser.hpp"
50		#include "io/LennardJonesAtomTypesSectionParser.hpp"
51		#include "io/ChargeAtomTypesSectionParser.hpp"
52		#include "io/MultipoleAtomTypesSectionParser.hpp"
#	Line 60 | Line 59
59		#include "io/OptionSectionParser.hpp"
60		#include "UseTheForce/ForceFieldCreator.hpp"
61
62	<	namespace oopse {
62	>	namespace OpenMD {
63
64		DUFF::DUFF(){
65
66		//set default force field filename
67		setForceFieldFileName("DUFF2.frc");
68
70	–	//The order of adding section parsers is important.
71	–	//OptionSectionParser must come first to set options for other parsers
72	–	//DirectionalAtomTypesSectionParser should be added before
73	–	//AtomTypesSectionParser, and these two section parsers will actually
74	–	//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
75	–	//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
76	–	//is a subclass of AtomType and should come first). Other AtomTypes Section
77	–	//Parser will not create the "real" AtomType, they only add and set some
78	–	//attribute of the AtomType. Thus their order are not important.
79	–	//AtomTypesSectionParser should be added before other atom type section
80	–	//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
81	–	//and AtomTypesSectionParser. The order of BondTypesSectionParser,
82	–	//BendTypesSectionParser and TorsionTypesSectionParser are not important.
69		spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
84	–	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
70		spMan_.push_back(new BaseAtomTypesSectionParser());
71		spMan_.push_back(new AtomTypesSectionParser());
72	+	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
73		spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
74		spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
75		spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
#	Line 98 | Line 84 | namespace oopse {
84
85		void DUFF::parse(const std::string& filename) {
86		ifstrstream* ffStream;
101	–	bool hasGBtypes;
87
88		ffStream = openForceFieldFile(filename);
89
#	Line 109 | Line 94 | namespace oopse {
94
95		for (at = atomTypeCont_.beginType(i); at != NULL;
96		at = atomTypeCont_.nextType(i)) {
97	+	// useBase sets the responsibilities, and these have to be done
98	+	// after the atomTypes and Base types have all been scanned:
99	+
100	+	std::vector<AtomType*> ayb = at->allYourBase();
101	+	if (ayb.size() > 1) {
102	+	for (int j = ayb.size()-1; j > 0; j--) {
103	+
104	+	ayb[j-1]->useBase(ayb[j]);
105	+
106	+	}
107	+	}
108		at->makeFortranAtomType();
109		}
110
#	Line 117 | Line 113 | namespace oopse {
113		at->complete();
114		}
115
120	–	hasGBtypes = false;
121	–	for (at = atomTypeCont_.beginType(i); at != NULL;
122	–	at = atomTypeCont_.nextType(i)) {
123	–	if (at->isGayBerne())
124	–	hasGBtypes = true;
125	–	}
126	–
116		int isError = 0;
117
129	–	if (hasGBtypes) {
130	–	completeGBFF(&isError);
131	–	}
132	–
118		delete ffStream;
134	–
119		}
120
121		DUFF::~DUFF(){
138	–	destroyLJTypes();
122		destroyStickyTypes();
140	–	destroyGayBerneTypes();
123		}
124	<	} //end namespace oopse
124	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/DUFF.cpp (property svn:keywords), Revision 1269 by gezelter, Tue Jul 1 13:28:23 2008 UTC vs.
branches/development/src/UseTheForce/DUFF.cpp (property svn:keywords), Revision 1483 by gezelter, Tue Jul 27 21:17:31 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines