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:	891
Committed:	Wed Feb 22 20:35:16 2006 UTC (19 years, 2 months ago) by tim
File size:	6866 byte(s)
Log Message:	Adding Hydrodynamics Module
#	User	Rev	Content
1	tim	891	/*
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			}