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

Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents):
Revision 944 by gezelter, Tue Apr 25 02:06:12 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	>	namespace OpenMD {
50
51		Shape* ShapeBuilder::createShape(StuntDouble* sd) {
52		Shape* currShape = NULL;
#	Line 59 | Line 63 | namespace oopse {
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;
75	<	simError();
76	<	}
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	<	} else if (atomType->isEAM()) {
79	<	GenericData* data = atomType->getPropertyByName("EAM");
80	<	if (data != NULL) {
81	<	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
82	<
83	<	if (eamData != NULL) {
84	<	EAMParam eamParam = eamData->getData();
85	<	currShape = new Spheric(atom->getPos(), eamParam.rcut);
86	<	} else {
87	<	sprintf( painCave.errMsg,
88	<	"Can not cast GenericData to EAMParam\n");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
93	<	}
94	<	}
80	>	}
81		return currShape;
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);
89	<
90	<	GenericData* data = dAtomType->getPropertyByName("GayBerne");
91	<	if (data != NULL) {
92	<	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
93	<
94	<	if (gayBerneData != NULL) {
95	<	GayBerneParam gayBerneParam = gayBerneData->getData();
96	<	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
97	<	} else {
112	<	sprintf( painCave.errMsg,
113	<	"Can not cast GenericData to GayBerneParam\n");
114	<	painCave.severity = OOPSE_ERROR;
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
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, "Can not find Parameters for GayBerne\n");
100	<	painCave.severity = OOPSE_ERROR;
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();
123	<	}
124	<	} else if (atomType->isLennardJones()) {
125	<	GenericData* data = atomType->getPropertyByName("LennardJones");
126	<	if (data != NULL) {
127	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
128	<
129	<	if (ljData != NULL) {
130	<	LJParam ljParam = ljData->getData();
131	<	currShape = new Spheric(datom->getPos(), ljParam.sigma/2.0);
132	<	} else {
133	<	sprintf( painCave.errMsg,
134	<	"Can not cast GenericData to LJParam\n");
135	<	painCave.severity = OOPSE_ERROR;
136	<	painCave.isFatal = 1;
137	<	simError();
138	<	}
139	<	} else if (atomType->isEAM()) {
140	<	GenericData* data = atomType->getPropertyByName("EAM");
141	<	if (data != NULL) {
142	<	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
143	<	if (eamData != NULL) {
144	<	EAMParam eamParam = eamData->getData();
145	<	currShape = new Spheric(datom->getPos(), eamParam.rcut);
146	<	} else {
147	<	sprintf( painCave.errMsg,
148	<	"Can not cast GenericData to EAMParam\n");
149	<	painCave.severity = OOPSE_ERROR;
150	<	painCave.isFatal = 1;
151	<	simError();
152	<	}
153	<	}
103	>	simError();
104		}
105	<	}
105	>	}
106		return currShape;
107		}
108

Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (property svn:keywords):
Revision 944 by gezelter, Tue Apr 25 02:06:12 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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