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root/OpenMD/branches/development/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.
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 {
46	>	namespace OpenMD {
47
48		Shape* ShapeBuilder::createShape(StuntDouble* sd) {
49		Shape* currShape = NULL;
#	Line 66 | Line 67 | namespace oopse {
67
68		if (ljData != NULL) {
69		LJParam ljParam = ljData->getData();
70	<	currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
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;
74	>	painCave.severity = OPENMD_ERROR;
75		painCave.isFatal = 1;
76		simError();
77		}
78		}
79	<	} else if (atomType->isEAM()) {
80	<	GenericData* data = atomType->getPropertyByName("EAM");
81	<	if (data != NULL) {
82	<	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
83	<
84	<	if (eamData != NULL) {
85	<	EAMParam eamParam = eamData->getData();
86	<	currShape = new Spheric(atom->getPos(), eamParam.rcut);
87	<	} else {
88	<	sprintf( painCave.errMsg,
88	<	"Can not cast GenericData to EAMParam\n");
89	<	painCave.severity = OOPSE_ERROR;
90	<	painCave.isFatal = 1;
91	<	simError();
92	<	}
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	<	}
90	>	}
91		return currShape;
92		}
93
#	Line 107 | Line 103 | namespace oopse {
103
104		if (gayBerneData != NULL) {
105		GayBerneParam gayBerneParam = gayBerneData->getData();
106	<	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
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,
110		"Can not cast GenericData to GayBerneParam\n");
111	<	painCave.severity = OOPSE_ERROR;
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 = OOPSE_ERROR;
117	>	painCave.severity = OPENMD_ERROR;
118		painCave.isFatal = 1;
119		simError();
120		}
#	Line 128 | Line 125 | namespace oopse {
125
126		if (ljData != NULL) {
127		LJParam ljParam = ljData->getData();
128	<	currShape = new Spheric(datom->getPos(), ljParam.sigma/2.0);
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 = OOPSE_ERROR;
132	>	painCave.severity = OPENMD_ERROR;
133		painCave.isFatal = 1;
134		simError();
135		}
136	<	} else if (atomType->isEAM()) {
137	<	GenericData* data = atomType->getPropertyByName("EAM");
138	<	if (data != NULL) {
139	<	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
140	<	if (eamData != NULL) {
141	<	EAMParam eamParam = eamData->getData();
142	<	currShape = new Spheric(datom->getPos(), eamParam.rcut);
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"Can not cast GenericData to EAMParam\n");
149	<	painCave.severity = OOPSE_ERROR;
150	<	painCave.isFatal = 1;
151	<	simError();
152	<	}
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	<	}
147	>	}
148		}
149		return currShape;
150		}

Comparing:
trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (property svn:keywords), Revision 944 by gezelter, Tue Apr 25 02:06:12 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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