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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "visitors/LipidTransVisitor.hpp"
#include "utils/simError.h"

namespace OpenMD {
  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_;
      currSnapshot->wrapVector(tmp);
      atomInfo->pos = rotMat_ * tmp;;
      atomInfo->vec = rotMat_ * atomInfo->vec;
    }
  }

  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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5582 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	tim	369	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	369	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	369	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	369	*/
42
43			#include "visitors/LipidTransVisitor.hpp"
44	tim	373	#include "utils/simError.h"
45	tim	369
46	gezelter	1390	namespace OpenMD {
47	gezelter	507	LipidTransVisitor::LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript)
48	tim	373	: BaseVisitor(), info_(info), originEvaluator_(info), originSeleMan_(info), refEvaluator_(info), refSeleMan_(info), refSd_(NULL) {
49
50
51	gezelter	507	visitorName = "LipidTransVisitor";
52	tim	373
53	gezelter	507	originEvaluator_.loadScriptString(originSeleScript);
54			if (!originEvaluator_.isDynamic()) {
55	tim	373	originSeleMan_.setSelectionSet(originEvaluator_.evaluate());
56			if (originSeleMan_.getSelectionCount() == 1) {
57	gezelter	507	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	tim	373	} else {
65	gezelter	507	sprintf(painCave.errMsg, "LipidTransVisitor: origin selection must select an directional atom");
66			painCave.isFatal = 1;
67			simError();
68	tim	373
69			}
70	gezelter	507	}
71	tim	373
72	gezelter	507	refEvaluator_.loadScriptString(refSeleScript);
73			if (!refEvaluator_.isDynamic()) {
74	tim	373	refSeleMan_.setSelectionSet(refEvaluator_.evaluate());
75			if (refSeleMan_.getSelectionCount() == 1) {
76	gezelter	507	int i;
77			refSd_ = refSeleMan_.beginSelected(i);
78	tim	373
79			} else {
80	gezelter	507	//error
81	tim	373
82			}
83	gezelter	507	}
84
85	tim	373	}
86
87	gezelter	507	void LipidTransVisitor::update() {
88	tim	369
89	gezelter	507	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	tim	369
97	gezelter	507	xaxis.normalize();
98			yaxis.normalize();
99			zaxis.normalize();
100	tim	369
101	gezelter	507	rotMat_.setRow(0, xaxis);
102			rotMat_.setRow(1, yaxis);
103			rotMat_.setRow(2, zaxis);
104	tim	369
105
106	gezelter	507	}
107	tim	369
108	gezelter	507	void LipidTransVisitor::internalVisit(StuntDouble *sd) {
109	tim	369	GenericData * data;
110			AtomData * atomData;
111			AtomInfo * atomInfo;
112			std::vector<AtomInfo *>::iterator i;
113
114			data = sd->getPropertyByName("ATOMDATA");
115
116			if (data != NULL) {
117	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
118	tim	369
119	gezelter	507	if (atomData == NULL)
120			return;
121	tim	369	} else
122	gezelter	507	return;
123	tim	369
124			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
125
126			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
127
128	gezelter	507	Vector3d tmp= atomInfo->pos - origin_;
129			currSnapshot->wrapVector(tmp);
130			atomInfo->pos = rotMat_ * tmp;;
131	gezelter	1456	atomInfo->vec = rotMat_ * atomInfo->vec;
132	tim	369	}
133	gezelter	507	}
134	tim	369
135	gezelter	507	const std::string LipidTransVisitor::toString() {
136	tim	369	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	gezelter	507	}
156	tim	369
157			}