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

Comparing:
trunk/src/primitives/Atom.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Atom.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1	<	#include <iostream>
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41
3	–	using namespace std;
4	–
5	–	#include "utils/simError.h"
42		#include "primitives/Atom.hpp"
43	<
8	<	Atom::Atom(int theIndex, SimState* theConfig) {
9	<
10	<	objType = OT_ATOM;
11	<	myConfig = theConfig;
12	<	hasCoords = false;
13	<
14	<	has_dipole = 0;
15	<	has_charge = 0;
43	>	namespace OpenMD {
44
45	<	index = theIndex;
46	<	offset = 0;
47	<	offsetX = offset;
20	<	offsetY = offset+1;
21	<	offsetZ = offset+2;
22	<
23	<	Axx = 0;
24	<	Axy = Axx+1;
25	<	Axz = Axx+2;
26	<
27	<	Ayx = Axx+3;
28	<	Ayy = Axx+4;
29	<	Ayz = Axx+5;
30	<
31	<	Azx = Axx+6;
32	<	Azy = Axx+7;
33	<	Azz = Axx+8;
34	<	}
35	<
36	<	void Atom::setIndex(int theIndex) {
37	<	index = theIndex;
38	<	}
39	<
40	<	void Atom::setCoords(void){
41	<
42	<	if( myConfig->isAllocated() ){
43	<
44	<	myConfig->getAtomPointers( index,
45	<	&pos,
46	<	&vel,
47	<	&frc,
48	<	&trq,
49	<	&Amat,
50	<	&mu,
51	<	&ul);
45	>	Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData),
46	>	atomType_(at) {
47	>	mass_ = at->getMass();
48		}
53	–	else{
54	–	sprintf( painCave.errMsg,
55	–	"Attempted to set Atom %d  coordinates with an unallocated "
56	–	"SimState object.\n", index );
57	–	painCave.isFatal = 1;
58	–	simError();
59	–	}
60	–
61	–	hasCoords = true;
62	–
63	–	}
49
50	<	void Atom::getPos( double theP[3] ){
50	>	Mat3x3d Atom::getI() {
51	>	return Mat3x3d::identity();
52	>	}
53
54	<	if( hasCoords ){
55	<	theP[0] = pos[offsetX];
56	<	theP[1] = pos[offsetY];
70	<	theP[2] = pos[offsetZ];
71	<	}
72	<	else{
73	<
74	<	sprintf( painCave.errMsg,
75	<	"Attempt to get Pos for atom %d before coords set.\n",
76	<	index );
77	<	painCave.isFatal = 1;
78	<	simError();
79	<	}
80	<	}
81	<
82	<	void Atom::setPos( double theP[3] ){
83	<
84	<	if( hasCoords ){
85	<	pos[offsetX] = theP[0];
86	<	pos[offsetY] = theP[1];
87	<	pos[offsetZ] = theP[2];
88	<	}
89	<	else{
90	<
91	<	sprintf( painCave.errMsg,
92	<	"Attempt to set Pos for atom %d before coords set.\n",
93	<	index );
94	<	painCave.isFatal = 1;
95	<	simError();
96	<	}
97	<	}
98	<
99	<	void Atom::getVel( double theV[3] ){
100	<
101	<	if( hasCoords ){
102	<	theV[0] = vel[offsetX];
103	<	theV[1] = vel[offsetY];
104	<	theV[2] = vel[offsetZ];
105	<	}
106	<	else{
54	>	std::vector<RealType> Atom::getGrad() {
55	>	std::vector<RealType> grad(3);
56	>	Vector3d force= getFrc();
57
58	<	sprintf( painCave.errMsg,
59	<	"Attempt to get vel for atom %d before coords set.\n",
60	<	index );
111	<	painCave.isFatal = 1;
112	<	simError();
113	<	}
114	<
115	<	}
116	<
117	<	void Atom::setVel( double theV[3] ){
118	<
119	<	if( hasCoords ){
120	<	vel[offsetX] = theV[0];
121	<	vel[offsetY] = theV[1];
122	<	vel[offsetZ] = theV[2];
123	<	}
124	<	else{
58	>	grad[0] = -force[0];
59	>	grad[1] = -force[1];
60	>	grad[2] = -force[2];
61
62	<	sprintf( painCave.errMsg,
63	<	"Attempt to set vel for atom %d before coords set.\n",
128	<	index );
129	<	painCave.isFatal = 1;
130	<	simError();
131	<	}
132	<	}
133	<
134	<	void Atom::getFrc( double theF[3] ){
62	>	return grad;
63	>	}
64
65	<	if( hasCoords ){
66	<	theF[0] = frc[offsetX];
67	<	theF[1] = frc[offsetY];
139	<	theF[2] = frc[offsetZ];
140	<	}
141	<	else{
142	<
143	<	sprintf( painCave.errMsg,
144	<	"Attempt to get frc for atom %d before coords set.\n",
145	<	index );
146	<	painCave.isFatal = 1;
147	<	simError();
148	<	}
65	>	void Atom::accept(BaseVisitor* v) {
66	>	v->visit(this);
67	>	}
68		}
150	–
151	–	void Atom::addFrc( double theF[3] ){
152	–
153	–	if( hasCoords ){
154	–	frc[offsetX] += theF[0];
155	–	frc[offsetY] += theF[1];
156	–	frc[offsetZ] += theF[2];
157	–	}
158	–	else{
159	–
160	–	sprintf( painCave.errMsg,
161	–	"Attempt to add frc for atom %d before coords set.\n",
162	–	index );
163	–	painCave.isFatal = 1;
164	–	simError();
165	–	}
166	–	}
167	–
168	–
169	–	void Atom::zeroForces( void ){
170	–
171	–	if( hasCoords ){
172	–	frc[offsetX] = 0.0;
173	–	frc[offsetY] = 0.0;
174	–	frc[offsetZ] = 0.0;
175	–	}
176	–	else{
177	–
178	–	sprintf( painCave.errMsg,
179	–	"Attempt to zero frc for atom %d before coords set.\n",
180	–	index );
181	–	painCave.isFatal = 1;
182	–	simError();
183	–	}
184	–	}
185	–

Comparing:
trunk/src/primitives/Atom.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Atom.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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