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"
#include "utils/simError.h"

namespace oopse {
LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript) 
    : BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) {

 
    visitorName = "LipidTransVisitor";
    
    originEvaluator_.loadScriptString(originSeleScript);            
    if (!originEvaluator_.isDynamic()) {  
        originSeleMan_.setSelectionSet(originEvaluator_.evaluate());
        if (originSeleMan_.getSelectionCount() == 1) {
            int i;
            originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
            if (originDatom_ ==  NULL) {
                sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
                painCave.isFatal = 1;
                simError();                  
            }
        } else {
            sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
            painCave.isFatal = 1;
            simError();                  
            
        }
    }

    refEvaluator_.loadScriptString(refSeleScript);
    if (!refEvaluator_.isDynamic()) {  
        refSeleMan_.setSelectionSet(refEvaluator_.evaluate());
        if (refSeleMan_.getSelectionCount() == 1) {
            int i;
            refSd_ = refSeleMan_.beginSelected(i);
            
        } else {
            //error
            
        }
    }
    
}

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:	2057
Committed:	Mon Feb 21 16:57:22 2005 UTC (19 years, 4 months ago) by tim
File size:	5754 byte(s)
Log Message:	Fix a bug in GofRAngle
#	Content
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. 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	#include "utils/simError.h"
44
45	namespace oopse {
46	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
47	: BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) {
48
49
50	visitorName = "LipidTransVisitor";
51
52	originEvaluator_.loadScriptString(originSeleScript);
53	if (!originEvaluator_.isDynamic()) {
54	originSeleMan_.setSelectionSet(originEvaluator_.evaluate());
55	if (originSeleMan_.getSelectionCount() == 1) {
56	int i;
57	originDatom_ = dynamic_cast<DirectionalAtom*>(originSeleMan_.beginSelected(i));
58	if (originDatom_ == NULL) {
59	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
60	painCave.isFatal = 1;
61	simError();
62	}
63	} else {
64	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
65	painCave.isFatal = 1;
66	simError();
67
68	}
69	}
70
71	refEvaluator_.loadScriptString(refSeleScript);
72	if (!refEvaluator_.isDynamic()) {
73	refSeleMan_.setSelectionSet(refEvaluator_.evaluate());
74	if (refSeleMan_.getSelectionCount() == 1) {
75	int i;
76	refSd_ = refSeleMan_.beginSelected(i);
77
78	} else {
79	//error
80
81	}
82	}
83
84	}
85
86	void LipidTransVisitor::update() {
87
88	Vector3d ref = refSd_->getPos();
89	origin_ = originDatom_->getPos();
90	Vector3d v1 = ref - origin_;
91	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
92	Vector3d zaxis = originDatom_->getElectroFrame().getColumn(2);
93	Vector3d xaxis = cross(v1, zaxis);
94	Vector3d yaxis = cross(zaxis, xaxis);
95
96	xaxis.normalize();
97	yaxis.normalize();
98	zaxis.normalize();
99
100	rotMat_.setRow(0, xaxis);
101	rotMat_.setRow(1, yaxis);
102	rotMat_.setRow(2, zaxis);
103
104
105	}
106
107	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
108	GenericData * data;
109	AtomData * atomData;
110	AtomInfo * atomInfo;
111	std::vector<AtomInfo *>::iterator i;
112
113	data = sd->getPropertyByName("ATOMDATA");
114
115	if (data != NULL) {
116	atomData = dynamic_cast<AtomData *>(data);
117
118	if (atomData == NULL)
119	return;
120	} else
121	return;
122
123	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
124
125	for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
126
127	Vector3d tmp= atomInfo->pos - origin_;
128	//we don't need to do the wrapping anymore, since LipidTransVisitor will be execute after
129	//WrappingVistor and ReplicateVisitor
130	atomInfo->pos = rotMat_ * tmp;
131	atomInfo->dipole = rotMat_ * atomInfo->dipole;
132	}
133	}
134
135	const std::string LipidTransVisitor::toString() {
136	char buffer[65535];
137	std::string result;
138
139	sprintf(buffer,
140	"------------------------------------------------------------------\n");
141	result += buffer;
142
143	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
144	result += buffer;
145
146	sprintf(buffer,
147	"Visitor Description: rotate the whole system\n");
148	result += buffer;
149
150	sprintf(buffer,
151	"------------------------------------------------------------------\n");
152	result += buffer;
153
154	return result;
155	}
156
157	}