src/primitives/DirectionalAtom.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 "primitives/DirectionalAtom.hpp"

namespace oopse {

DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) 
                         : Atom(dAtomType){
    objType_= otDAtom;
    if (dAtomType->isMultipole()) {
        electroBodyFrame_ = dAtomType->getElectroBodyFrame();
    }
}

Mat3x3d DirectionalAtom::getI() {
    return static_cast<DirectionalAtomType*>(getAtomType())->getI();
}    

void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
    ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
    if (atomType_->isMultipole()) {
        ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
    }
}

      
void DirectionalAtom::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;

    if (atomType_->isMultipole()) {
        ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
    }
}    
    
void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
    ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;

    if (atomType_->isMultipole()) {
        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;    
    }
}    

void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
    setA(m *getA());
}

std::vector<double> DirectionalAtom::getGrad() {
    std::vector<double> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    double phi, theta, psi;
    double cphi, sphi, ctheta, stheta;
    Vector3d ephi;
    Vector3d etheta;
    Vector3d epsi;

    force = getFrc();
    torque =getTrq();
    myEuler = getA().toEulerAngles();

    phi = myEuler[0];
    theta = myEuler[1];
    psi = myEuler[2];

    cphi = cos(phi);
    sphi = sin(phi);
    ctheta = cos(theta);
    stheta = sin(theta);

    // get unit vectors along the phi, theta and psi rotation axes

    ephi[0] = 0.0;
    ephi[1] = 0.0;
    ephi[2] = 1.0;

    etheta[0] = cphi;
    etheta[1] = sphi;
    etheta[2] = 0.0;

    epsi[0] = stheta * cphi;
    epsi[1] = stheta * sphi;
    epsi[2] = ctheta;

    //gradient is equal to -force
    for (int j = 0 ; j<3; j++)
        grad[j] = -force[j];

    for (int j = 0; j < 3; j++ ) {

        grad[3] += torque[j]*ephi[j];
        grad[4] += torque[j]*etheta[j];
        grad[5] += torque[j]*epsi[j];

    }
    
    return grad;
}    

void DirectionalAtom::accept(BaseVisitor* v) {
    v->visit(this);
}    

}

Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 7 months ago) by tim
File size:	4646 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1692	*
4	tim	1927	* 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	tim	1692	*/
41	tim	1927
42	tim	1492	#include "primitives/DirectionalAtom.hpp"
43	gezelter	1490
44	tim	1692	namespace oopse {
45	gezelter	1490
46	tim	1692	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
47			: Atom(dAtomType){
48			objType_= otDAtom;
49	tim	1813	if (dAtomType->isMultipole()) {
50	tim	1815	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
51	tim	1813	}
52	gezelter	1490	}
53
54	tim	1692	Mat3x3d DirectionalAtom::getI() {
55			return static_cast<DirectionalAtomType*>(getAtomType())->getI();
56			}
57	gezelter	1490
58	tim	1692	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
59			((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
60	tim	1813	if (atomType_->isMultipole()) {
61			((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
62			}
63	gezelter	1490	}
64
65	tim	1692
66			void DirectionalAtom::setA(const RotMat3x3d& a) {
67			((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
68	tim	1813
69			if (atomType_->isMultipole()) {
70			((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
71			}
72	tim	1692	}
73	gezelter	1490
74	tim	1692	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
75			((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
76	tim	1813
77			if (atomType_->isMultipole()) {
78			((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
79			}
80	tim	1692	}
81	gezelter	1490
82	tim	1692	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
83			setA(m *getA());
84	gezelter	1490	}
85
86	tim	1692	std::vector<double> DirectionalAtom::getGrad() {
87	tim	1816	std::vector<double> grad(6, 0.0);
88	tim	1692	Vector3d force;
89			Vector3d torque;
90			Vector3d myEuler;
91			double phi, theta, psi;
92			double cphi, sphi, ctheta, stheta;
93			Vector3d ephi;
94			Vector3d etheta;
95			Vector3d epsi;
96	gezelter	1490
97	tim	1692	force = getFrc();
98			torque =getTrq();
99			myEuler = getA().toEulerAngles();
100	gezelter	1490
101	tim	1692	phi = myEuler[0];
102			theta = myEuler[1];
103			psi = myEuler[2];
104	gezelter	1490
105	tim	1692	cphi = cos(phi);
106			sphi = sin(phi);
107			ctheta = cos(theta);
108			stheta = sin(theta);
109	gezelter	1490
110	tim	1692	// get unit vectors along the phi, theta and psi rotation axes
111	gezelter	1490
112	tim	1692	ephi[0] = 0.0;
113			ephi[1] = 0.0;
114			ephi[2] = 1.0;
115	gezelter	1490
116	tim	1692	etheta[0] = cphi;
117			etheta[1] = sphi;
118			etheta[2] = 0.0;
119	gezelter	1490
120	tim	1692	epsi[0] = stheta * cphi;
121			epsi[1] = stheta * sphi;
122			epsi[2] = ctheta;
123	gezelter	1490
124	tim	1692	//gradient is equal to -force
125			for (int j = 0 ; j<3; j++)
126			grad[j] = -force[j];
127	gezelter	1490
128	tim	1692	for (int j = 0; j < 3; j++ ) {
129	gezelter	1490
130	tim	1692	grad[3] += torque[j]*ephi[j];
131			grad[4] += torque[j]*etheta[j];
132			grad[5] += torque[j]*epsi[j];
133	gezelter	1490
134			}
135
136	tim	1692	return grad;
137			}
138	gezelter	1490
139	tim	1692	void DirectionalAtom::accept(BaseVisitor* v) {
140			v->visit(this);
141			}
142	gezelter	1490
143			}
144