applications/hydrodynamics/MoleculeShape.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/MoleculeShape.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.first = 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.first = origin_ + r;
    return boundary;
}


MoleculeShape::MoleculeShape(Molecule* mol) {
    std::vector<Atom*>::iterator ai; 
    Atom* atom;
    for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        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();          
                }       
            }

        }

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

    }

}

MoleculeShape::~MoleculeShape() {
    MemoryUtils::deletePointers(shapes_);
}
bool MoleculeShape::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;
}

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> MoleculeShape::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:	2596
Committed:	Wed Feb 22 20:35:16 2006 UTC (19 years, 8 months ago) by tim
File size:	6866 byte(s)
Log Message:	Adding Hydrodynamics Module
#	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/MoleculeShape.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.first = 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.first = origin_ + r;
99	return boundary;
100	}
101
102
103	MoleculeShape::MoleculeShape(Molecule* mol) {
104	std::vector<Atom*>::iterator ai;
105	Atom* atom;
106	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
107	AtomType* atomType = atom->getAtomType();
108	Shape* currShape = NULL;
109	if (atomType->isGayBerne()) {
110	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
111
112	GenericData* data = dAtomType->getPropertyByName("GayBerne");
113	if (data != NULL) {
114	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
115
116	if (gayBerneData != NULL) {
117	GayBerneParam gayBerneParam = gayBerneData->getData();
118	currShape = new Ellipsoid(atom->getPos(), gayBerneParam.GB_sigma, gayBerneParam.GB_l2b_ratio, atom->getA());
119	} else {
120	sprintf( painCave.errMsg,
121	"Can not cast GenericData to GayBerneParam\n");
122	painCave.severity = OOPSE_ERROR;
123	painCave.isFatal = 1;
124	simError();
125	}
126	} else {
127	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
128	painCave.severity = OOPSE_ERROR;
129	painCave.isFatal = 1;
130	simError();
131	}
132	} else if (atomType->isLennardJones()){
133	GenericData* data = atomType->getPropertyByName("LennardJones");
134	if (data != NULL) {
135	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
136
137	if (ljData != NULL) {
138	LJParam ljParam = ljData->getData();
139	currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
140	} else {
141	sprintf( painCave.errMsg,
142	"Can not cast GenericData to LJParam\n");
143	painCave.severity = OOPSE_ERROR;
144	painCave.isFatal = 1;
145	simError();
146	}
147	}
148
149	}
150
151	if (currShape != NULL)
152	shapes_.push_back(currShape);
153
154	}
155
156	}
157
158	MoleculeShape::~MoleculeShape() {
159	MemoryUtils::deletePointers(shapes_);
160	}
161	bool MoleculeShape::isInterior(Vector3d pos) {
162	bool result = false;
163	std::vector<Shape*>::iterator iter;
164	for (iter = shapes_.begin(); iter != shapes_.end(); ++ iter) {
165	if ((*iter)->isInterior(pos)) {
166	result = true;
167	break;
168	}
169	}
170
171	return result;
172	}
173
174	template<class Cont, class Predict>
175	void swap_if(Cont& b1, Cont& b2, Predict predict) {
176	unsigned int size = b1.size();
177	assert(size == b2.size());
178	for (unsigned int i = 0 ; i < size; ++i) {
179	if (predict(b1[i], b2[i]))
180	std::swap(b1[i], b2[i]);
181	}
182
183	}
184
185	std::pair<Vector3d, Vector3d> MoleculeShape::getBox() {
186	std::vector<Shape*>::iterator iter = shapes_.begin();
187	std::pair<Vector3d, Vector3d> boundary = (*iter)->getBox();
188	for (++iter; iter != shapes_.end(); ++iter) {
189	std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBox();
190	swap_if(boundary.first, currBoundary.first, std::less<double>());
191	swap_if(boundary.second, currBoundary.second, std::greater<double>());
192	}
193
194	return boundary;
195	}
196
197
198	}