applications/hydrodynamics/ShapeBuilder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
#include "applications/hydrodynamics/ShapeBuilder.hpp"
#include "applications/hydrodynamics/Spheric.hpp"
#include "applications/hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"
namespace oopse {

Shape* ShapeBuilder::createShape(StuntDouble* sd) {
    Shape* currShape = NULL;
            if (sd->isDirectionalAtom()) {
              currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
            } else if (sd->isAtom()) {
                currShape = internalCreateShape(static_cast<Atom*>(sd));
            } else if (sd->isRigidBody()) {
                currShape = internalCreateShape(static_cast<RigidBody*>(sd));
            }
            

        
        return currShape;

}

Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
    AtomType* atomType = atom->getAtomType();
    Shape* currShape = NULL;
    if (atomType->isLennardJones()){
        GenericData* data = atomType->getPropertyByName("LennardJones");
        if (data != NULL) {
            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);

            if (ljData != NULL) {
                LJParam ljParam = ljData->getData();
                currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
        } else {
            sprintf( painCave.errMsg,
            "Can not cast GenericData to LJParam\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
            }       
        }

    }

    return currShape;
}

Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
    AtomType* atomType = datom->getAtomType();
    Shape* currShape = NULL;
    if (atomType->isGayBerne()) {
        DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);

        GenericData* data = dAtomType->getPropertyByName("GayBerne");
        if (data != NULL) {
            GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);

            if (gayBerneData != NULL) {  
                GayBerneParam gayBerneParam = gayBerneData->getData();
                currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
            } else {
                sprintf( painCave.errMsg,
                       "Can not cast GenericData to GayBerneParam\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();   
            }
        } else {
          sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();    
        }            
    }
    return currShape;
}
Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {

        std::vector<Atom*>::iterator ai; 
        CompositeShape* compositeShape = new CompositeShape;
        Atom* atom;
        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
            Shape* currShape = NULL;
            if (atom->isDirectionalAtom()){
                currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
            }else if (atom->isAtom()){
                currShape =  internalCreateShape(static_cast<Atom*>(atom));
            }
            if (currShape != NULL)
                compositeShape->addShape(currShape);
        }

        return compositeShape;
}

}
Revision:	2644
Committed:	Mon Mar 20 19:12:14 2006 UTC (18 years, 5 months ago) by tim
File size:	5531 byte(s)
Log Message:	Verify the correctness of Ellipsoid's hydrodynamics properties
#	User	Rev	Content
1	tim	2634	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include "applications/hydrodynamics/ShapeBuilder.hpp"
42			#include "applications/hydrodynamics/Spheric.hpp"
43			#include "applications/hydrodynamics/Ellipsoid.hpp"
44			#include "applications/hydrodynamics/CompositeShape.hpp"
45			namespace oopse {
46
47			Shape* ShapeBuilder::createShape(StuntDouble* sd) {
48			Shape* currShape = NULL;
49			if (sd->isDirectionalAtom()) {
50	tim	2635	currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
51	tim	2634	} else if (sd->isAtom()) {
52	tim	2635	currShape = internalCreateShape(static_cast<Atom*>(sd));
53	tim	2634	} else if (sd->isRigidBody()) {
54			currShape = internalCreateShape(static_cast<RigidBody*>(sd));
55			}
56
57
58
59			return currShape;
60
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
83			}
84
85			return currShape;
86			}
87
88			Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
89			AtomType* atomType = datom->getAtomType();
90			Shape* currShape = NULL;
91			if (atomType->isGayBerne()) {
92			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
93
94			GenericData* data = dAtomType->getPropertyByName("GayBerne");
95			if (data != NULL) {
96			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
97
98			if (gayBerneData != NULL) {
99			GayBerneParam gayBerneParam = gayBerneData->getData();
100	tim	2644	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
101	tim	2634	} 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			}
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			}
114			}
115			return currShape;
116			}
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	tim	2635	currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
126	tim	2634	}else if (atom->isAtom()){
127	tim	2635	currShape = internalCreateShape(static_cast<Atom*>(atom));
128	tim	2634	}
129			if (currShape != NULL)
130			compositeShape->addShape(currShape);
131			}
132
133			return compositeShape;
134			}
135
136			}