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root/OpenMD/branches/development/src/applications/hydrodynamics/ShapeBuilder.cpp

Comparing:
trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents), Revision 907 by tim, Fri Mar 17 23:51:54 2006 UTC vs.
branches/development/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "applications/hydrodynamics/ShapeBuilder.hpp"
43	<	#include "applications/hydrodynamics/Spheric.hpp"
44	<	#include "applications/hydrodynamics/Ellipsoid.hpp"
43	>	#include "hydrodynamics/Sphere.hpp"
44	>	#include "hydrodynamics/Ellipsoid.hpp"
45		#include "applications/hydrodynamics/CompositeShape.hpp"
46	<	namespace oopse {
47	<
48	<	Shape* ShapeBuilder::createShape(StuntDouble* sd) {
46	>	namespace OpenMD {
47	>
48	>	Shape* ShapeBuilder::createShape(StuntDouble* sd) {
49		Shape* currShape = NULL;
50	<	if (sd->isDirectionalAtom()) {
51	<	currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
52	<	} else if (sd->isAtom()) {
53	<	currShape = internalCreateShape(static_cast<Atom*>(sd));
54	<	} else if (sd->isRigidBody()) {
55	<	currShape = internalCreateShape(static_cast<RigidBody*>(sd));
56	<	}
57	<
58	<
59	<
60	<	return currShape;
60	<
61	<	}
62	<
63	<	Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
50	>	if (sd->isDirectionalAtom()) {
51	>	currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
52	>	} else if (sd->isAtom()) {
53	>	currShape = internalCreateShape(static_cast<Atom*>(sd));
54	>	} else if (sd->isRigidBody()) {
55	>	currShape = internalCreateShape(static_cast<RigidBody*>(sd));
56	>	}
57	>	return currShape;
58	>	}
59	>
60	>	Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
61		AtomType* atomType = atom->getAtomType();
62		Shape* currShape = NULL;
63		if (atomType->isLennardJones()){
64	<	GenericData* data = atomType->getPropertyByName("LennardJones");
65	<	if (data != NULL) {
66	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
67	<
68	<	if (ljData != NULL) {
69	<	LJParam ljParam = ljData->getData();
70	<	currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
64	>	GenericData* data = atomType->getPropertyByName("LennardJones");
65	>	if (data != NULL) {
66	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
67	>
68	>	if (ljData != NULL) {
69	>	LJParam ljParam = ljData->getData();
70	>	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
71		} else {
72	<	sprintf( painCave.errMsg,
73	<	"Can not cast GenericData to LJParam\n");
74	<	painCave.severity = OOPSE_ERROR;
75	<	painCave.isFatal = 1;
76	<	simError();
77	<	}
78	<	}
79	<
72	>	sprintf( painCave.errMsg,
73	>	"Can not cast GenericData to LJParam\n");
74	>	painCave.severity = OPENMD_ERROR;
75	>	painCave.isFatal = 1;
76	>	simError();
77	>	}
78	>	}
79	>	} else {
80	>	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
81	>	if (obanum != 0) {
82	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
83	>	} else {
84	>	sprintf( painCave.errMsg,
85	>	"Could not find atom type in default element.txt\n");
86	>	painCave.severity = OPENMD_ERROR;
87	>	painCave.isFatal = 1;
88	>	simError();
89	>	}
90		}
84	–
91		return currShape;
92	<	}
93	<
94	<	Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
92	>	}
93	>
94	>	Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
95		AtomType* atomType = datom->getAtomType();
96		Shape* currShape = NULL;
97		if (atomType->isGayBerne()) {
98	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
99	<
100	<	GenericData* data = dAtomType->getPropertyByName("GayBerne");
101	<	if (data != NULL) {
102	<	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
103	<
104	<	if (gayBerneData != NULL) {
105	<	GayBerneParam gayBerneParam = gayBerneData->getData();
106	<	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma, gayBerneParam.GB_l2b_ratio, datom->getA());
107	<	} else {
102	<	sprintf( painCave.errMsg,
103	<	"Can not cast GenericData to GayBerneParam\n");
104	<	painCave.severity = OOPSE_ERROR;
105	<	painCave.isFatal = 1;
106	<	simError();
107	<	}
98	>	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
99	>
100	>	GenericData* data = dAtomType->getPropertyByName("GayBerne");
101	>	if (data != NULL) {
102	>	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
103	>
104	>	if (gayBerneData != NULL) {
105	>	GayBerneParam gayBerneParam = gayBerneData->getData();
106	>	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0,
107	>	gayBerneParam.GB_d/2.0, datom->getA());
108		} else {
109	<	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
110	<	painCave.severity = OOPSE_ERROR;
111	<	painCave.isFatal = 1;
112	<	simError();
113	<	}
109	>	sprintf( painCave.errMsg,
110	>	"Can not cast GenericData to GayBerneParam\n");
111	>	painCave.severity = OPENMD_ERROR;
112	>	painCave.isFatal = 1;
113	>	simError();
114	>	}
115	>	} else {
116	>	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
117	>	painCave.severity = OPENMD_ERROR;
118	>	painCave.isFatal = 1;
119	>	simError();
120	>	}
121	>	} else if (atomType->isLennardJones()) {
122	>	GenericData* data = atomType->getPropertyByName("LennardJones");
123	>	if (data != NULL) {
124	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
125	>
126	>	if (ljData != NULL) {
127	>	LJParam ljParam = ljData->getData();
128	>	currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
129	>	} else {
130	>	sprintf( painCave.errMsg,
131	>	"Can not cast GenericData to LJParam\n");
132	>	painCave.severity = OPENMD_ERROR;
133	>	painCave.isFatal = 1;
134	>	simError();
135	>	}
136	>	} else {
137	>	int obanum = etab.GetAtomicNum((datom->getType()).c_str());
138	>	if (obanum != 0) {
139	>	currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
140	>	} else {
141	>	sprintf( painCave.errMsg,
142	>	"Could not find atom type in default element.txt\n");
143	>	painCave.severity = OPENMD_ERROR;
144	>	painCave.isFatal = 1;
145	>	simError();
146	>	}
147	>	}
148		}
149		return currShape;
150	<	}
117	<	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
150	>	}
151
152	<	std::vector<Atom*>::iterator ai;
153	<	CompositeShape* compositeShape = new CompositeShape;
154	<	Atom* atom;
155	<	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
156	<	Shape* currShape = NULL;
157	<	if (atom->isDirectionalAtom()){
158	<	currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
159	<	}else if (atom->isAtom()){
160	<	currShape =  internalCreateShape(static_cast<Atom*>(atom));
161	<	}
162	<	if (currShape != NULL)
163	<	compositeShape->addShape(currShape);
164	<	}
165	<
166	<	return compositeShape;
152	>	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
153	>
154	>	std::vector<Atom*>::iterator ai;
155	>	CompositeShape* compositeShape = new CompositeShape;
156	>	Atom* atom;
157	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
158	>	Shape* currShape = NULL;
159	>	if (atom->isDirectionalAtom()){
160	>	currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
161	>	}else if (atom->isAtom()){
162	>	currShape =  internalCreateShape(static_cast<Atom*>(atom));
163	>	}
164	>	if (currShape != NULL)
165	>	compositeShape->addShape(currShape);
166	>	}
167	>
168	>	return compositeShape;
169	>	}
170		}
135	–
136	–	}

Comparing:
trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (property svn:keywords), Revision 907 by tim, Fri Mar 17 23:51:54 2006 UTC vs.
branches/development/src/applications/hydrodynamics/ShapeBuilder.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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