ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/src/primitives/DirectionalAtom.cpp

Comparing:
trunk/src/primitives/DirectionalAtom.cpp (file contents), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/primitives/DirectionalAtom.cpp (file contents), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "primitives/DirectionalAtom.hpp"
44	+	#include "types/DirectionalAdapter.hpp"
45	+	#include "types/MultipoleAdapter.hpp"
46		#include "utils/simError.h"
47	<	namespace oopse {
48	<
49	<	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
50	<	: Atom(dAtomType){
47	>	namespace OpenMD {
48	>
49	>	DirectionalAtom::DirectionalAtom(AtomType* dAtomType)
50	>	: Atom(dAtomType) {
51		objType_= otDAtom;
52	<	if (dAtomType->isMultipole()) {
53	<	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
52	>
53	>	DirectionalAdapter da = DirectionalAdapter(dAtomType);
54	>	I_ = da.getI();
55	>
56	>	MultipoleAdapter ma = MultipoleAdapter(dAtomType);
57	>	if (ma.isDipole()) {
58	>	dipole_ = ma.getDipole();
59		}
60	+	if (ma.isQuadrupole()) {
61	+	quadrupole_ = ma.getQuadrupole();
62	+	}
63
64	<	//check if one of the diagonal inertia tensor of this directional atom  is zero
64	>	// Check if one of the diagonal inertia tensor of this directional
65	>	// atom is zero:
66		int nLinearAxis = 0;
67		Mat3x3d inertiaTensor = getI();
68		for (int i = 0; i < 3; i++) {
69	<	if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
70	<	linear_ = true;
71	<	linearAxis_ = i;
72	<	++ nLinearAxis;
73	<	}
69	>	if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
70	>	linear_ = true;
71	>	linearAxis_ = i;
72	>	++ nLinearAxis;
73	>	}
74		}
75
76		if (nLinearAxis > 1) {
77	<	sprintf( painCave.errMsg,
78	<	"Directional Atom error.\n"
79	<	"\tOOPSE found more than one axis in this directional atom with a vanishing \n"
80	<	"\tmoment of inertia.");
81	<	painCave.isFatal = 1;
82	<	simError();
83	<	}
84	<
85	<	}
86	<
87	<	Mat3x3d DirectionalAtom::getI() {
88	<	return static_cast<DirectionalAtomType*>(getAtomType())->getI();
89	<	}
90	<
79	<	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
77	>	sprintf( painCave.errMsg,
78	>	"Directional Atom warning.\n"
79	>	"\tOpenMD found more than one axis in this directional atom with a vanishing \n"
80	>	"\tmoment of inertia.");
81	>	painCave.isFatal = 0;
82	>	simError();
83	>	}
84	>	}
85	>
86	>	Mat3x3d DirectionalAtom::getI() {
87	>	return I_;
88	>	}
89	>
90	>	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
91		((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
81	–	if (atomType_->isMultipole()) {
82	–	((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
83	–	}
84	–	}
92
93	+	if (atomType_->isMultipole()) {
94	+	RotMat3x3d atrans = a.transpose();
95
96	<	void DirectionalAtom::setA(const RotMat3x3d& a) {
97	<	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
96	>	if (atomType_->isDipole()) {
97	>	((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
98	>	}
99
100	+	if (atomType_->isQuadrupole()) {
101	+	((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
102	+	}
103	+	}
104	+	}
105	+
106	+
107	+	void DirectionalAtom::setA(const RotMat3x3d& a) {
108	+	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
109	+
110		if (atomType_->isMultipole()) {
111	<	((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
111	>	RotMat3x3d atrans = a.transpose();
112	>
113	>	if (atomType_->isDipole()) {
114	>	((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
115	>	}
116	>
117	>	if (atomType_->isQuadrupole()) {
118	>	((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
119	>	}
120		}
121	<	}
122	<
123	<	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
121	>
122	>	}
123	>
124	>	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
125		((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
126
127		if (atomType_->isMultipole()) {
128	<	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
128	>	RotMat3x3d atrans = a.transpose();
129	>
130	>	if (atomType_->isDipole()) {
131	>	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_;
132	>	}
133	>
134	>	if (atomType_->isQuadrupole()) {
135	>	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
136	>	}
137		}
101	–	}
138
139	<	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
139	>	}
140	>
141	>	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
142		setA(m *getA());
143	<	}
144	<
145	<	std::vector<double> DirectionalAtom::getGrad() {
146	<	std::vector<double> grad(6, 0.0);
143	>	}
144	>
145	>	std::vector<RealType> DirectionalAtom::getGrad() {
146	>	std::vector<RealType> grad(6, 0.0);
147		Vector3d force;
148		Vector3d torque;
149		Vector3d myEuler;
150	<	double phi, theta, psi;
151	<	double cphi, sphi, ctheta, stheta;
150	>	RealType phi, theta;
151	>	// RealType psi;
152	>	RealType cphi, sphi, ctheta, stheta;
153		Vector3d ephi;
154		Vector3d etheta;
155		Vector3d epsi;
156	<
156	>
157		force = getFrc();
158		torque =getTrq();
159		myEuler = getA().toEulerAngles();
160	<
160	>
161		phi = myEuler[0];
162		theta = myEuler[1];
163	<	psi = myEuler[2];
164	<
163	>	// psi = myEuler[2];
164	>
165		cphi = cos(phi);
166		sphi = sin(phi);
167		ctheta = cos(theta);
168		stheta = sin(theta);
169	<
169	>
170		// get unit vectors along the phi, theta and psi rotation axes
171	<
171	>
172		ephi[0] = 0.0;
173		ephi[1] = 0.0;
174		ephi[2] = 1.0;
175	<
175	>
176	>	//etheta[0] = -sphi;
177	>	//etheta[1] =  cphi;
178	>	//etheta[2] =  0.0;
179	>
180		etheta[0] = cphi;
181		etheta[1] = sphi;
182		etheta[2] = 0.0;
183	<
183	>
184		epsi[0] = stheta * cphi;
185		epsi[1] = stheta * sphi;
186		epsi[2] = ctheta;
187	<
187	>
188		//gradient is equal to -force
189		for (int j = 0 ; j<3; j++)
190	<	grad[j] = -force[j];
191	<
192	<	for (int j = 0; j < 3; j++ ) {
193	<
194	<	grad[3] += torque[j]*ephi[j];
195	<	grad[4] += torque[j]*etheta[j];
153	<	grad[5] += torque[j]*epsi[j];
154	<
190	>	grad[j] = -force[j];
191	>
192	>	for (int j = 0; j < 3; j++ ) {
193	>	grad[3] -= torque[j]*ephi[j];
194	>	grad[4] -= torque[j]*etheta[j];
195	>	grad[5] -= torque[j]*epsi[j];
196		}
197
198		return grad;
199	<	}
200	<
201	<	void DirectionalAtom::accept(BaseVisitor* v) {
199	>	}
200	>
201	>	void DirectionalAtom::accept(BaseVisitor* v) {
202		v->visit(this);
203	<	}
163	<
203	>	}
204		}
205

Comparing:
trunk/src/primitives/DirectionalAtom.cpp (property svn:keywords), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/primitives/DirectionalAtom.cpp (property svn:keywords), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines