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root/OpenMD/trunk/src/applications/hydrodynamics/ShapeBuilder.cpp

Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents):
Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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 {
46	>	#include "types/LennardJonesAdapter.hpp"
47	>	#include "types/GayBerneAdapter.hpp"
48
49	<	Shape* ShapeBuilder::createShape(StuntDouble* sd) {
49	>	namespace OpenMD {
50	>
51	>	Shape* ShapeBuilder::createShape(StuntDouble* sd) {
52		Shape* currShape = NULL;
53	<	if (sd->isDirectionalAtom()) {
54	<	currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
55	<	} else if (sd->isAtom()) {
56	<	currShape = internalCreateShape(static_cast<Atom*>(sd));
57	<	} else if (sd->isRigidBody()) {
58	<	currShape = internalCreateShape(static_cast<RigidBody*>(sd));
59	<	}
60	<
61	<
62	<
63	<	return currShape;
60	<
61	<	}
62	<
63	<	Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
53	>	if (sd->isDirectionalAtom()) {
54	>	currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
55	>	} else if (sd->isAtom()) {
56	>	currShape = internalCreateShape(static_cast<Atom*>(sd));
57	>	} else if (sd->isRigidBody()) {
58	>	currShape = internalCreateShape(static_cast<RigidBody*>(sd));
59	>	}
60	>	return currShape;
61	>	}
62	>
63	>	Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
64		AtomType* atomType = atom->getAtomType();
65		Shape* currShape = NULL;
66	<	if (atomType->isLennardJones()){
67	<	GenericData* data = atomType->getPropertyByName("LennardJones");
68	<	if (data != NULL) {
69	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
70	<
71	<	if (ljData != NULL) {
72	<	LJParam ljParam = ljData->getData();
73	<	currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
74	<	} else {
75	<	sprintf( painCave.errMsg,
76	<	"Can not cast GenericData to LJParam\n");
77	<	painCave.severity = OOPSE_ERROR;
78	<	painCave.isFatal = 1;
79	<	simError();
80	<	}
81	<	}
82	<
66	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
67	>	if (lja.isLennardJones()){
68	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
69	>	} else {
70	>	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
71	>	if (obanum != 0) {
72	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
73	>	} else {
74	>	sprintf( painCave.errMsg,
75	>	"Could not find atom type in default element.txt\n");
76	>	painCave.severity = OPENMD_ERROR;
77	>	painCave.isFatal = 1;
78	>	simError();
79	>	}
80		}
84	–
81		return currShape;
82	<	}
83	<
84	<	Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
82	>	}
83	>
84	>	Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
85		AtomType* atomType = datom->getAtomType();
86		Shape* currShape = NULL;
87	<	if (atomType->isGayBerne()) {
88	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
87	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
88	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
89	>	if (gba.isGayBerne()) {
90	>	currShape = new Ellipsoid(datom->getPos(), gba.getL()/2.0,
91	>	gba.getD()/2.0, datom->getA());
92	>	} else if (lja.isLennardJones()) {
93	>	currShape = new Sphere(datom->getPos(), lja.getSigma()/2.0);
94	>	} else {
95	>	int obanum = etab.GetAtomicNum((datom->getType()).c_str());
96	>	if (obanum != 0) {
97	>	currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
98	>	} else {
99	>	sprintf( painCave.errMsg,
100	>	"Could not find atom type in default element.txt\n");
101	>	painCave.severity = OPENMD_ERROR;
102	>	painCave.isFatal = 1;
103	>	simError();
104	>	}
105	>	}
106	>	return currShape;
107	>	}
108
109	<	GenericData* data = dAtomType->getPropertyByName("GayBerne");
110	<	if (data != NULL) {
111	<	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
112	<
113	<	if (gayBerneData != NULL) {
114	<	GayBerneParam gayBerneParam = gayBerneData->getData();
115	<	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
116	<	} else {
117	<	sprintf( painCave.errMsg,
118	<	"Can not cast GenericData to GayBerneParam\n");
119	<	painCave.severity = OOPSE_ERROR;
120	<	painCave.isFatal = 1;
121	<	simError();
122	<	}
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	>	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
110	>
111	>	std::vector<Atom*>::iterator ai;
112	>	CompositeShape* compositeShape = new CompositeShape;
113	>	Atom* atom;
114	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115	>	Shape* currShape = NULL;
116	>	if (atom->isDirectionalAtom()){
117	>	currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
118	>	}else if (atom->isAtom()){
119	>	currShape =  internalCreateShape(static_cast<Atom*>(atom));
120	>	}
121	>	if (currShape != NULL)
122	>	compositeShape->addShape(currShape);
123		}
124	<	return currShape;
124	>
125	>	return compositeShape;
126	>	}
127		}
117	–	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
118	–
119	–	std::vector<Atom*>::iterator ai;
120	–	CompositeShape* compositeShape = new CompositeShape;
121	–	Atom* atom;
122	–	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
123	–	Shape* currShape = NULL;
124	–	if (atom->isDirectionalAtom()){
125	–	currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
126	–	}else if (atom->isAtom()){
127	–	currShape =  internalCreateShape(static_cast<Atom*>(atom));
128	–	}
129	–	if (currShape != NULL)
130	–	compositeShape->addShape(currShape);
131	–	}
132	–
133	–	return compositeShape;
134	–	}
135	–
136	–	}

Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (property svn:keywords):
Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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