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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 "utils/simError.h"
45	<	namespace oopse {
46	<
47	<	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
48	<	: Atom(dAtomType){
45	>	namespace OpenMD {
46	>
47	>	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
48	>	: Atom(dAtomType){
49		objType_= otDAtom;
50		if (dAtomType->isMultipole()) {
51	<	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
51	>	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
52		}
53	<
54	<	//check if one of the diagonal inertia tensor of this directional atom  is zero
53	>
54	>	// Check if one of the diagonal inertia tensor of this directional
55	>	// atom is zero:
56		int nLinearAxis = 0;
57		Mat3x3d inertiaTensor = getI();
58		for (int i = 0; i < 3; i++) {
59	<	if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
60	<	linear_ = true;
61	<	linearAxis_ = i;
62	<	++ nLinearAxis;
63	<	}
59	>	if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
60	>	linear_ = true;
61	>	linearAxis_ = i;
62	>	++ nLinearAxis;
63	>	}
64		}
65
66		if (nLinearAxis > 1) {
67	<	sprintf( painCave.errMsg,
68	<	"Directional Atom error.\n"
69	<	"\tOOPSE found more than one axis in this directional atom with a vanishing \n"
70	<	"\tmoment of inertia.");
71	<	painCave.isFatal = 1;
72	<	simError();
73	<	}
74	<
75	<	}
76	<
75	<	Mat3x3d DirectionalAtom::getI() {
67	>	sprintf( painCave.errMsg,
68	>	"Directional Atom warning.\n"
69	>	"\tOpenMD found more than one axis in this directional atom with a vanishing \n"
70	>	"\tmoment of inertia.");
71	>	painCave.isFatal = 0;
72	>	simError();
73	>	}
74	>	}
75	>
76	>	Mat3x3d DirectionalAtom::getI() {
77		return static_cast<DirectionalAtomType*>(getAtomType())->getI();
78	<	}
79	<
80	<	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
78	>	}
79	>
80	>	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
81		((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
82		if (atomType_->isMultipole()) {
83	<	((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
83	>	((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
84		}
85	<	}
86	<
87	<
88	<	void DirectionalAtom::setA(const RotMat3x3d& a) {
85	>	}
86	>
87	>
88	>	void DirectionalAtom::setA(const RotMat3x3d& a) {
89		((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
90	<
90	>
91		if (atomType_->isMultipole()) {
92	<	((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
92	>	((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
93		}
94	<	}
95	<
96	<	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
94	>	}
95	>
96	>	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
97		((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
98	<
98	>
99		if (atomType_->isMultipole()) {
100	<	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
100	>	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
101		}
102	<	}
103	<
104	<	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
102	>	}
103	>
104	>	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
105		setA(m *getA());
106	<	}
107	<
108	<	std::vector<double> DirectionalAtom::getGrad() {
109	<	std::vector<double> grad(6, 0.0);
106	>	}
107	>
108	>	std::vector<RealType> DirectionalAtom::getGrad() {
109	>	std::vector<RealType> grad(6, 0.0);
110		Vector3d force;
111		Vector3d torque;
112		Vector3d myEuler;
113	<	double phi, theta, psi;
114	<	double cphi, sphi, ctheta, stheta;
113	>	RealType phi, theta, psi;
114	>	RealType cphi, sphi, ctheta, stheta;
115		Vector3d ephi;
116		Vector3d etheta;
117		Vector3d epsi;
118	<
118	>
119		force = getFrc();
120		torque =getTrq();
121		myEuler = getA().toEulerAngles();
122	<
122	>
123		phi = myEuler[0];
124		theta = myEuler[1];
125		psi = myEuler[2];
126	<
126	>
127		cphi = cos(phi);
128		sphi = sin(phi);
129		ctheta = cos(theta);
130		stheta = sin(theta);
131	<
131	>
132		// get unit vectors along the phi, theta and psi rotation axes
133	<
133	>
134		ephi[0] = 0.0;
135		ephi[1] = 0.0;
136		ephi[2] = 1.0;
137	<
137	>
138	>	//etheta[0] = -sphi;
139	>	//etheta[1] =  cphi;
140	>	//etheta[2] =  0.0;
141	>
142		etheta[0] = cphi;
143		etheta[1] = sphi;
144		etheta[2] = 0.0;
145	<
145	>
146		epsi[0] = stheta * cphi;
147		epsi[1] = stheta * sphi;
148		epsi[2] = ctheta;
149	<
149	>
150		//gradient is equal to -force
151		for (int j = 0 ; j<3; j++)
152	<	grad[j] = -force[j];
153	<
154	<	for (int j = 0; j < 3; j++ ) {
155	<
156	<	grad[3] += torque[j]*ephi[j];
157	<	grad[4] += torque[j]*etheta[j];
153	<	grad[5] += torque[j]*epsi[j];
154	<
152	>	grad[j] = -force[j];
153	>
154	>	for (int j = 0; j < 3; j++ ) {
155	>	grad[3] -= torque[j]*ephi[j];
156	>	grad[4] -= torque[j]*etheta[j];
157	>	grad[5] -= torque[j]*epsi[j];
158		}
159
160		return grad;
161	<	}
162	<
163	<	void DirectionalAtom::accept(BaseVisitor* v) {
161	>	}
162	>
163	>	void DirectionalAtom::accept(BaseVisitor* v) {
164		v->visit(this);
165	<	}
163	<
165	>	}
166		}
167

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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

Diff Legend

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