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Comparing trunk/src/UseTheForce/EAM_FF.cpp (file contents):
Revision 409 by gezelter, Wed Mar 9 14:25:51 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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		#include "UseTheForce/EAM_FF.hpp"
43	+	#include "UseTheForce/DarkSide/eam_interface.h"
44		#include "UseTheForce/DarkSide/lj_interface.h"
45		#include "UseTheForce/DarkSide/sticky_interface.h"
46		#include "UseTheForce/ForceFieldFactory.hpp"
47	<	#include "io/DirectionalAtomTypesSectionParser.hpp"
47	>	#include "io/BaseAtomTypesSectionParser.hpp"
48		#include "io/AtomTypesSectionParser.hpp"
48	–	#include "io/LennardJonesAtomTypesSectionParser.hpp"
49	–	#include "io/ElectrostaticAtomTypesSectionParser.hpp"
49		#include "io/EAMAtomTypesSectionParser.hpp"
50	<	#include "io/StickyAtomTypesSectionParser.hpp"
52	<	#include "io/BondTypesSectionParser.hpp"
53	<	#include "io/BendTypesSectionParser.hpp"
54	<	#include "io/TorsionTypesSectionParser.hpp"
50	>	#include "io/OptionSectionParser.hpp"
51		#include "UseTheForce/ForceFieldCreator.hpp"
52		#include "utils/simError.h"
53	<	namespace oopse {
53	>	namespace OpenMD {
54
55	<	EAM_FF::EAM_FF(){
55	>	EAM_FF::EAM_FF(){
56
57		//set default force field filename
58		setForceFieldFileName("EAM.frc");
59
60		//the order of adding section parsers are important
61	<	//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
62	<	//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
63	<	//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
68	<	//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
69	<	//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
70	<	//important. AtomTypesSectionParser should be added before other atom type section parsers.
71	<	//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
72	<	//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
73	<	//not important.
74	<	spMan_.push_back(new DirectionalAtomTypesSectionParser());
61	>	//OptionSectionParser must come first to set options for other parsers
62	>	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
63	>	spMan_.push_back(new BaseAtomTypesSectionParser());
64		spMan_.push_back(new AtomTypesSectionParser());
65	<	spMan_.push_back(new LennardJonesAtomTypesSectionParser());
66	<	spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
78	<	spMan_.push_back(new EAMAtomTypesSectionParser());
79	<	spMan_.push_back(new StickyAtomTypesSectionParser());
80	<	spMan_.push_back(new BondTypesSectionParser());
81	<	spMan_.push_back(new BendTypesSectionParser());
82	<	spMan_.push_back(new TorsionTypesSectionParser());
83	<
84	<	}
65	>	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
66	>	}
67
68	<	void EAM_FF::parse(const std::string& filename) {
68	>	void EAM_FF::parse(const std::string& filename) {
69		ifstrstream* ffStream;
70		ffStream = openForceFieldFile(filename);
71
#	Line 93 | Line 75 | void EAM_FF::parse(const std::string& filename) {
75		AtomType* at;
76
77		for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
78	<	at->makeFortranAtomType();
78	>	// useBase sets the responsibilities, and these have to be done
79	>	// after the atomTypes and Base types have all been scanned:
80	>
81	>	std::vector<AtomType*> ayb = at->allYourBase();
82	>	if (ayb.size() > 1) {
83	>	for (int j = ayb.size()-1; j > 0; j--) {
84	>
85	>	ayb[j-1]->useBase(ayb[j]);
86	>
87	>	}
88	>	}
89	>	at->makeFortranAtomType();
90		}
91
92		for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
93	<	at->complete();
93	>	at->complete();
94		}
102	–
103	–	}
95
96	+	delete ffStream;
97	+	}
98
99	<	double EAM_FF::getRcutFromAtomType(AtomType* at){
100	<	double rcut = 0.0;
99	>
100	>	RealType EAM_FF::getRcutFromAtomType(AtomType* at){
101	>	RealType rcut = 0.0;
102		if (at->isEAM()) {
103	<	GenericData* data = at->getPropertyByName("EAM");
104	<	if (data != NULL) {
105	<	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
103	>	GenericData* data = at->getPropertyByName("EAM");
104	>	if (data != NULL) {
105	>	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
106
107	<	if (eamData != NULL) {
107	>	if (eamData != NULL) {
108
109	<	EAMParam& eamParam = eamData->getData();
110	<	rcut =  eamParam.rcut;
111	<	} else {
112	<	sprintf( painCave.errMsg,
113	<	"Can not cast GenericData to EAMParam\n");
114	<	painCave.severity = OOPSE_ERROR;
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
118	<	} else {
119	<	sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
120	<	painCave.severity = OOPSE_ERROR;
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
109	>	EAMParam& eamParam = eamData->getData();
110	>	rcut =  eamParam.rcut;
111	>	} else {
112	>	sprintf( painCave.errMsg,
113	>	"Can not cast GenericData to EAMParam\n");
114	>	painCave.severity = OPENMD_ERROR;
115	>	painCave.isFatal = 1;
116	>	simError();
117	>	}
118	>	} else {
119	>	sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
120	>	painCave.severity = OPENMD_ERROR;
121	>	painCave.isFatal = 1;
122	>	simError();
123	>	}
124		}    else {
125	<	rcut = ForceField::getRcutFromAtomType(at);
125	>	rcut = ForceField::getRcutFromAtomType(at);
126		}
127
128		return rcut;
129	<	}
129	>	}
130
131	<	} //end namespace oopse
131	>	EAM_FF::~EAM_FF(){
132	>	// We need to clean up the fortran side so we don't have bad things happen if
133	>	// we try to create a second EAM force field.
134	>	destroyEAMTypes();
135	>	}
136	>	} //end namespace OpenMD

Comparing trunk/src/UseTheForce/EAM_FF.cpp (property svn:keywords):
Revision 409 by gezelter, Wed Mar 9 14:25:51 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
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