src/visitors/LipidTransVisitor.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include "visitors/LipidTransVisitor.hpp"

namespace oopse {
void LipidTransVisitor::update() {

        Vector3d ref = refSd_->getPos();
        origin_ = originDatom_->getPos();
        Vector3d v1 =  ref - origin_;
        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
        Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
        Vector3d xaxis = cross(v1, zaxis);
        Vector3d yaxis = cross(zaxis, xaxis);

        xaxis.normalize();
        yaxis.normalize();
        zaxis.normalize();
        
        rotMat_.setRow(0, xaxis);
        rotMat_.setRow(1, yaxis);
        rotMat_.setRow(2, zaxis);


}

void LipidTransVisitor::internalVisit(StuntDouble *sd) {
    GenericData *                     data;
    AtomData *                        atomData;
    AtomInfo *                        atomInfo;
    std::vector<AtomInfo *>::iterator i;

    data = sd->getPropertyByName("ATOMDATA");

    if (data != NULL) {
        atomData = dynamic_cast<AtomData *>(data);

        if (atomData == NULL)
            return;
    } else
        return;

    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    
    for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {

        Vector3d tmp= atomInfo->pos - origin_;
        //we don't need to do the wrapping anymore, since LipidTransVisitor will be execute after 
        //WrappingVistor and ReplicateVisitor
        atomInfo->pos = rotMat_ * tmp;
        atomInfo->dipole = rotMat_ * atomInfo->dipole;
    }
}

const std::string LipidTransVisitor::toString() {
    char        buffer[65535];
    std::string result;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer,
            "Visitor Description: rotate the whole system\n");
    result += buffer;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    return result;
}

}
Revision:	2053
Committed:	Fri Feb 18 23:07:32 2005 UTC (19 years, 4 months ago) by tim
File size:	4226 byte(s)
Log Message:	adding LipidTransVisitor, GofXyz is working now
#	User	Rev	Content
1	tim	2053	/*
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. 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "visitors/LipidTransVisitor.hpp"
43
44			namespace oopse {
45			void LipidTransVisitor::update() {
46
47			Vector3d ref = refSd_->getPos();
48			origin_ = originDatom_->getPos();
49			Vector3d v1 = ref - origin_;
50			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
51			Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
52			Vector3d xaxis = cross(v1, zaxis);
53			Vector3d yaxis = cross(zaxis, xaxis);
54
55			xaxis.normalize();
56			yaxis.normalize();
57			zaxis.normalize();
58
59			rotMat_.setRow(0, xaxis);
60			rotMat_.setRow(1, yaxis);
61			rotMat_.setRow(2, zaxis);
62
63
64			}
65
66			void LipidTransVisitor::internalVisit(StuntDouble *sd) {
67			GenericData * data;
68			AtomData * atomData;
69			AtomInfo * atomInfo;
70			std::vector<AtomInfo *>::iterator i;
71
72			data = sd->getPropertyByName("ATOMDATA");
73
74			if (data != NULL) {
75			atomData = dynamic_cast<AtomData *>(data);
76
77			if (atomData == NULL)
78			return;
79			} else
80			return;
81
82			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
83
84			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
85
86			Vector3d tmp= atomInfo->pos - origin_;
87			//we don't need to do the wrapping anymore, since LipidTransVisitor will be execute after
88			//WrappingVistor and ReplicateVisitor
89			atomInfo->pos = rotMat_ * tmp;
90			atomInfo->dipole = rotMat_ * atomInfo->dipole;
91			}
92			}
93
94			const std::string LipidTransVisitor::toString() {
95			char buffer[65535];
96			std::string result;
97
98			sprintf(buffer,
99			"------------------------------------------------------------------\n");
100			result += buffer;
101
102			sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
103			result += buffer;
104
105			sprintf(buffer,
106			"Visitor Description: rotate the whole system\n");
107			result += buffer;
108
109			sprintf(buffer,
110			"------------------------------------------------------------------\n");
111			result += buffer;
112
113			return result;
114			}
115
116			}