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root/OpenMD/branches/development/src/visitors/LipidTransVisitor.cpp

Comparing:
trunk/src/visitors/LipidTransVisitor.cpp (file contents), Revision 449 by tim, Mon Mar 28 22:30:06 2005 UTC vs.
branches/development/src/visitors/LipidTransVisitor.cpp (file contents), Revision 1787 by gezelter, Wed Aug 29 18:13:11 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 "visitors/LipidTransVisitor.hpp"
44	+	#include "types/MultipoleAdapter.hpp"
45		#include "utils/simError.h"
46
47	<	namespace oopse {
48	<	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
47	>	namespace OpenMD {
48	>	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
49		: BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) {
50
51
52	<	visitorName = "LipidTransVisitor";
52	>	visitorName = "LipidTransVisitor";
53
54	<	originEvaluator_.loadScriptString(originSeleScript);
55	<	if (!originEvaluator_.isDynamic()) {
54	>	originEvaluator_.loadScriptString(originSeleScript);
55	>	if (!originEvaluator_.isDynamic()) {
56		originSeleMan_.setSelectionSet(originEvaluator_.evaluate());
57		if (originSeleMan_.getSelectionCount() == 1) {
58	<	int i;
59	<	originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
60	<	if (originDatom_ ==  NULL) {
61	<	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
62	<	painCave.isFatal = 1;
63	<	simError();
64	<	}
58	>	int i;
59	>	originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
60	>	if (originDatom_ ==  NULL) {
61	>	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
62	>	painCave.isFatal = 1;
63	>	simError();
64	>	}
65		} else {
66	<	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
67	<	painCave.isFatal = 1;
68	<	simError();
66	>	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
67	>	painCave.isFatal = 1;
68	>	simError();
69
70		}
71	<	}
71	>	}
72
73	<	refEvaluator_.loadScriptString(refSeleScript);
74	<	if (!refEvaluator_.isDynamic()) {
73	>	refEvaluator_.loadScriptString(refSeleScript);
74	>	if (!refEvaluator_.isDynamic()) {
75		refSeleMan_.setSelectionSet(refEvaluator_.evaluate());
76		if (refSeleMan_.getSelectionCount() == 1) {
77	<	int i;
78	<	refSd_ = refSeleMan_.beginSelected(i);
77	>	int i;
78	>	refSd_ = refSeleMan_.beginSelected(i);
79
80		} else {
81	<	//error
81	>	//error
82
83		}
84	<	}
84	>	}
85
86	<	}
86	>	}
87
88	<	void LipidTransVisitor::update() {
88	>	void LipidTransVisitor::update() {
89
90	<	Vector3d ref = refSd_->getPos();
91	<	origin_ = originDatom_->getPos();
92	<	Vector3d v1 =  ref - origin_;
93	<	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
92	<	Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
93	<	Vector3d xaxis = cross(v1, zaxis);
94	<	Vector3d yaxis = cross(zaxis, xaxis);
90	>	Vector3d ref = refSd_->getPos();
91	>	origin_ = originDatom_->getPos();
92	>	Vector3d v1 =  ref - origin_;
93	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
94
95	<	xaxis.normalize();
96	<	yaxis.normalize();
97	<	zaxis.normalize();
95	>	MultipoleAdapter ma = MultipoleAdapter(originDatom_->getAtomType());
96	>	Vector3d zaxis;
97	>	if (ma.isDipole() ) {
98	>	zaxis = originDatom_->getDipole();
99	>	} else {
100	>	zaxis = originDatom_->getA().transpose()*V3Z;
101	>	}
102	>
103	>	Vector3d xaxis = cross(v1, zaxis);
104	>	Vector3d yaxis = cross(zaxis, xaxis);
105	>
106	>	xaxis.normalize();
107	>	yaxis.normalize();
108	>	zaxis.normalize();
109
110	<	rotMat_.setRow(0, xaxis);
111	<	rotMat_.setRow(1, yaxis);
112	<	rotMat_.setRow(2, zaxis);
110	>	rotMat_.setRow(0, xaxis);
111	>	rotMat_.setRow(1, yaxis);
112	>	rotMat_.setRow(2, zaxis);
113
114
115	<	}
115	>	}
116
117	<	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
117	>	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
118		GenericData *                     data;
119		AtomData *                        atomData;
120		AtomInfo *                        atomInfo;
#	Line 113 | Line 123 | void LipidTransVisitor::internalVisit(StuntDouble *sd)
123		data = sd->getPropertyByName("ATOMDATA");
124
125		if (data != NULL) {
126	<	atomData = dynamic_cast<AtomData *>(data);
126	>	atomData = dynamic_cast<AtomData *>(data);
127
128	<	if (atomData == NULL)
129	<	return;
128	>	if (atomData == NULL)
129	>	return;
130		} else
131	<	return;
131	>	return;
132
133		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
134
135		for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
136
137	<	Vector3d tmp= atomInfo->pos - origin_;
138	<	atomInfo->pos = rotMat_ * tmp - origin_;;
139	<	atomInfo->dipole = rotMat_ * atomInfo->dipole;
137	>	Vector3d tmp= atomInfo->pos - origin_;
138	>	currSnapshot->wrapVector(tmp);
139	>	atomInfo->pos = rotMat_ * tmp;;
140	>	atomInfo->vec = rotMat_ * atomInfo->vec;
141		}
142	<	}
142	>	}
143
144	<	const std::string LipidTransVisitor::toString() {
144	>	const std::string LipidTransVisitor::toString() {
145		char        buffer[65535];
146		std::string result;
147
#	Line 150 | Line 161 | const std::string LipidTransVisitor::toString() {
161		result += buffer;
162
163		return result;
164	<	}
164	>	}
165
166		}

Comparing:
trunk/src/visitors/LipidTransVisitor.cpp (property svn:keywords), Revision 449 by tim, Mon Mar 28 22:30:06 2005 UTC vs.
branches/development/src/visitors/LipidTransVisitor.cpp (property svn:keywords), Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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