applications/hydrodynamics/StuntDoubleShape.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/StuntDoubleShape.hpp" 
#include "utils/MemoryUtils.hpp"

namespace oopse {

Spheric::Spheric(Vector3d origin, double radius) : origin_(origin), radius_(radius){

}

bool Spheric::isInterior(Vector3d pos) {
    Vector3d r = pos - origin_;

    bool result;
    if (r.length() < radius_)
        result = true;
    else
        result = false;
    
    return result;
}

std::pair<Vector3d, Vector3d> Spheric::getBox() {
    std::pair<Vector3d, Vector3d>  boundary;
    Vector3d r(radius_, radius_, radius_);
    boundary.first = origin_ - r;
    boundary.second = origin_ + r;
    return boundary;
}
Ellipsoid::Ellipsoid(Vector3d origin, double radius, double ratio, Mat3x3d rotMat) 
    : origin_(origin), a_(radius), b_(radius*ratio), rotMat_(rotMat) {

}
bool Ellipsoid::isInterior(Vector3d pos) {
    Vector3d r = pos - origin_;
    Vector3d rbody = rotMat_ * r;
    double xovera = rbody[0]/a_;
    double yovera = rbody[1]/a_;
    double zoverb = rbody[2]/b_;

    bool result;
    if (xovera*xovera + yovera*yovera + zoverb*zoverb < 1)
        result = true;
    else
        result = false;

    return result;
        
}

std::pair<Vector3d, Vector3d> Ellipsoid::getBox() {

    std::pair<Vector3d, Vector3d>  boundary;
    //make a cubic box
    double rad  = a_ > b_ ? a_ : b_; 
    Vector3d r(rad, rad, rad);
    boundary.first = origin_ - r;
    boundary.second = origin_ + r;
    return boundary;
}


StuntDoubleShape::StuntDoubleShape(StuntDouble* sd) {
    if (sd->isAtom()) {
      Shape* currShape = createShape(static_cast<Atom*>(sd));

        if (currShape != NULL)
            shapes_.push_back(currShape);

    } else if (sd->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(sd);
        std::vector<Atom*>::iterator ai; 
        Atom* atom;
        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
            Shape* currShape = createShape(static_cast<Atom*>(sd));

            if (currShape != NULL)
                shapes_.push_back(currShape);
        }
    }

}

StuntDoubleShape::~StuntDoubleShape() {
    MemoryUtils::deletePointers(shapes_);
}
bool StuntDoubleShape::isInterior(Vector3d pos) {
    bool result = false;
    std::vector<Shape*>::iterator iter;
    for (iter = shapes_.begin(); iter != shapes_.end(); ++ iter) {
        if ((*iter)->isInterior(pos)) {
            result = true;
            break;
        }
    }

    return result;
}

Shape* StuntDoubleShape::createShape(Atom* atom) {
        AtomType* atomType = atom->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(atom->getPos(), gayBerneParam.GB_sigma, gayBerneParam.GB_l2b_ratio, atom->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();    
            }            
        } else 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;
  }

template<class Cont, class Predict>
void swap_if(Cont& b1, Cont& b2, Predict predict) {
    unsigned int size = b1.size();
    assert(size == b2.size());
    for (unsigned int i = 0 ; i < size; ++i) {
        if (predict(b1[i], b2[i]))
            std::swap(b1[i], b2[i]);
    }

}

std::pair<Vector3d, Vector3d> StuntDoubleShape::getBox() {
    std::vector<Shape*>::iterator iter = shapes_.begin();
    std::pair<Vector3d, Vector3d>  boundary = (*iter)->getBox();
    for (++iter; iter != shapes_.end(); ++iter) {
        std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBox();
            swap_if(boundary.first, currBoundary.first, std::less<double>());
            swap_if(boundary.second, currBoundary.second, std::greater<double>());        
    }

    return boundary;
}


}
Revision:	2611
Committed:	Mon Mar 13 22:42:40 2006 UTC (18 years, 3 months ago) by tim
File size:	7314 byte(s)
Log Message:	LangevinDynamics in progress
#	Content
1	/*
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
42	#include "applications/hydrodynamics/StuntDoubleShape.hpp"
43	#include "utils/MemoryUtils.hpp"
44
45	namespace oopse {
46
47	Spheric::Spheric(Vector3d origin, double radius) : origin_(origin), radius_(radius){
48
49	}
50
51	bool Spheric::isInterior(Vector3d pos) {
52	Vector3d r = pos - origin_;
53
54	bool result;
55	if (r.length() < radius_)
56	result = true;
57	else
58	result = false;
59
60	return result;
61	}
62
63	std::pair<Vector3d, Vector3d> Spheric::getBox() {
64	std::pair<Vector3d, Vector3d> boundary;
65	Vector3d r(radius_, radius_, radius_);
66	boundary.first = origin_ - r;
67	boundary.second = origin_ + r;
68	return boundary;
69	}
70	Ellipsoid::Ellipsoid(Vector3d origin, double radius, double ratio, Mat3x3d rotMat)
71	: origin_(origin), a_(radius), b_(radius*ratio), rotMat_(rotMat) {
72
73	}
74	bool Ellipsoid::isInterior(Vector3d pos) {
75	Vector3d r = pos - origin_;
76	Vector3d rbody = rotMat_ * r;
77	double xovera = rbody[0]/a_;
78	double yovera = rbody[1]/a_;
79	double zoverb = rbody[2]/b_;
80
81	bool result;
82	if (xoveraxovera + yoverayovera + zoverb*zoverb < 1)
83	result = true;
84	else
85	result = false;
86
87	return result;
88
89	}
90
91	std::pair<Vector3d, Vector3d> Ellipsoid::getBox() {
92
93	std::pair<Vector3d, Vector3d> boundary;
94	//make a cubic box
95	double rad = a_ > b_ ? a_ : b_;
96	Vector3d r(rad, rad, rad);
97	boundary.first = origin_ - r;
98	boundary.second = origin_ + r;
99	return boundary;
100	}
101
102
103	StuntDoubleShape::StuntDoubleShape(StuntDouble* sd) {
104	if (sd->isAtom()) {
105	Shape* currShape = createShape(static_cast<Atom*>(sd));
106
107	if (currShape != NULL)
108	shapes_.push_back(currShape);
109
110	} else if (sd->isRigidBody()) {
111	RigidBody* rb = static_cast<RigidBody*>(sd);
112	std::vector<Atom*>::iterator ai;
113	Atom* atom;
114	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115	Shape* currShape = createShape(static_cast<Atom*>(sd));
116
117	if (currShape != NULL)
118	shapes_.push_back(currShape);
119	}
120	}
121
122	}
123
124	StuntDoubleShape::~StuntDoubleShape() {
125	MemoryUtils::deletePointers(shapes_);
126	}
127	bool StuntDoubleShape::isInterior(Vector3d pos) {
128	bool result = false;
129	std::vector<Shape*>::iterator iter;
130	for (iter = shapes_.begin(); iter != shapes_.end(); ++ iter) {
131	if ((*iter)->isInterior(pos)) {
132	result = true;
133	break;
134	}
135	}
136
137	return result;
138	}
139
140	Shape* StuntDoubleShape::createShape(Atom* atom) {
141	AtomType* atomType = atom->getAtomType();
142	Shape* currShape = NULL;
143	if (atomType->isGayBerne()) {
144	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
145
146	GenericData* data = dAtomType->getPropertyByName("GayBerne");
147	if (data != NULL) {
148	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
149
150	if (gayBerneData != NULL) {
151	GayBerneParam gayBerneParam = gayBerneData->getData();
152	currShape = new Ellipsoid(atom->getPos(), gayBerneParam.GB_sigma, gayBerneParam.GB_l2b_ratio, atom->getA());
153	} else {
154	sprintf( painCave.errMsg,
155	"Can not cast GenericData to GayBerneParam\n");
156	painCave.severity = OOPSE_ERROR;
157	painCave.isFatal = 1;
158	simError();
159	}
160	} else {
161	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
162	painCave.severity = OOPSE_ERROR;
163	painCave.isFatal = 1;
164	simError();
165	}
166	} else if (atomType->isLennardJones()){
167	GenericData* data = atomType->getPropertyByName("LennardJones");
168	if (data != NULL) {
169	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
170
171	if (ljData != NULL) {
172	LJParam ljParam = ljData->getData();
173	currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
174	} else {
175	sprintf( painCave.errMsg,
176	"Can not cast GenericData to LJParam\n");
177	painCave.severity = OOPSE_ERROR;
178	painCave.isFatal = 1;
179	simError();
180	}
181	}
182
183	}
184
185	return currShape;
186	}
187
188	template<class Cont, class Predict>
189	void swap_if(Cont& b1, Cont& b2, Predict predict) {
190	unsigned int size = b1.size();
191	assert(size == b2.size());
192	for (unsigned int i = 0 ; i < size; ++i) {
193	if (predict(b1[i], b2[i]))
194	std::swap(b1[i], b2[i]);
195	}
196
197	}
198
199	std::pair<Vector3d, Vector3d> StuntDoubleShape::getBox() {
200	std::vector<Shape*>::iterator iter = shapes_.begin();
201	std::pair<Vector3d, Vector3d> boundary = (*iter)->getBox();
202	for (++iter; iter != shapes_.end(); ++iter) {
203	std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBox();
204	swap_if(boundary.first, currBoundary.first, std::less<double>());
205	swap_if(boundary.second, currBoundary.second, std::greater<double>());
206	}
207
208	return boundary;
209	}
210
211
212	}