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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 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 "visitors/LipidTransVisitor.hpp"
44		#include "utils/simError.h"
45
46	<	namespace oopse {
47	<	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
46	>	namespace OpenMD {
47	>	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
48		: BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) {
49
50
51	<	visitorName = "LipidTransVisitor";
51	>	visitorName = "LipidTransVisitor";
52
53	<	originEvaluator_.loadScriptString(originSeleScript);
54	<	if (!originEvaluator_.isDynamic()) {
53	>	originEvaluator_.loadScriptString(originSeleScript);
54	>	if (!originEvaluator_.isDynamic()) {
55		originSeleMan_.setSelectionSet(originEvaluator_.evaluate());
56		if (originSeleMan_.getSelectionCount() == 1) {
57	<	int i;
58	<	originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
59	<	if (originDatom_ ==  NULL) {
60	<	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
61	<	painCave.isFatal = 1;
62	<	simError();
63	<	}
57	>	int i;
58	>	originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
59	>	if (originDatom_ ==  NULL) {
60	>	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
61	>	painCave.isFatal = 1;
62	>	simError();
63	>	}
64		} else {
65	<	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
66	<	painCave.isFatal = 1;
67	<	simError();
65	>	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
66	>	painCave.isFatal = 1;
67	>	simError();
68
69		}
70	<	}
70	>	}
71
72	<	refEvaluator_.loadScriptString(refSeleScript);
73	<	if (!refEvaluator_.isDynamic()) {
72	>	refEvaluator_.loadScriptString(refSeleScript);
73	>	if (!refEvaluator_.isDynamic()) {
74		refSeleMan_.setSelectionSet(refEvaluator_.evaluate());
75		if (refSeleMan_.getSelectionCount() == 1) {
76	<	int i;
77	<	refSd_ = refSeleMan_.beginSelected(i);
76	>	int i;
77	>	refSd_ = refSeleMan_.beginSelected(i);
78
79		} else {
80	<	//error
80	>	//error
81
82		}
83	<	}
83	>	}
84
85	<	}
85	>	}
86
87	<	void LipidTransVisitor::update() {
87	>	void LipidTransVisitor::update() {
88
89	<	Vector3d ref = refSd_->getPos();
90	<	origin_ = originDatom_->getPos();
91	<	Vector3d v1 =  ref - origin_;
92	<	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
93	<	Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
94	<	Vector3d xaxis = cross(v1, zaxis);
95	<	Vector3d yaxis = cross(zaxis, xaxis);
89	>	Vector3d ref = refSd_->getPos();
90	>	origin_ = originDatom_->getPos();
91	>	Vector3d v1 =  ref - origin_;
92	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
93	>	Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
94	>	Vector3d xaxis = cross(v1, zaxis);
95	>	Vector3d yaxis = cross(zaxis, xaxis);
96
97	<	xaxis.normalize();
98	<	yaxis.normalize();
99	<	zaxis.normalize();
97	>	xaxis.normalize();
98	>	yaxis.normalize();
99	>	zaxis.normalize();
100
101	<	rotMat_.setRow(0, xaxis);
102	<	rotMat_.setRow(1, yaxis);
103	<	rotMat_.setRow(2, zaxis);
101	>	rotMat_.setRow(0, xaxis);
102	>	rotMat_.setRow(1, yaxis);
103	>	rotMat_.setRow(2, zaxis);
104
105
106	<	}
106	>	}
107
108	<	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
108	>	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
109		GenericData *                     data;
110		AtomData *                        atomData;
111		AtomInfo *                        atomInfo;
#	Line 113 | Line 114 | void LipidTransVisitor::internalVisit(StuntDouble *sd)
114		data = sd->getPropertyByName("ATOMDATA");
115
116		if (data != NULL) {
117	<	atomData = dynamic_cast<AtomData *>(data);
117	>	atomData = dynamic_cast<AtomData *>(data);
118
119	<	if (atomData == NULL)
120	<	return;
119	>	if (atomData == NULL)
120	>	return;
121		} else
122	<	return;
122	>	return;
123
124		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
125
126		for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
127
128	<	Vector3d tmp= atomInfo->pos - origin_;
129	<	atomInfo->pos = rotMat_ * tmp - origin_;;
130	<	atomInfo->dipole = rotMat_ * atomInfo->dipole;
128	>	Vector3d tmp= atomInfo->pos - origin_;
129	>	currSnapshot->wrapVector(tmp);
130	>	atomInfo->pos = rotMat_ * tmp;;
131	>	atomInfo->vec = rotMat_ * atomInfo->vec;
132		}
133	<	}
133	>	}
134
135	<	const std::string LipidTransVisitor::toString() {
135	>	const std::string LipidTransVisitor::toString() {
136		char        buffer[65535];
137		std::string result;
138
#	Line 150 | Line 152 | const std::string LipidTransVisitor::toString() {
152		result += buffer;
153
154		return result;
155	<	}
155	>	}
156
157		}

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

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