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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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:	1456
Committed:	Fri Jun 25 17:40:24 2010 UTC (14 years, 10 months ago) by gezelter
File size:	5516 byte(s)
Log Message:	more changes to make Dump2XYZ do velocities & forces
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "visitors/LipidTransVisitor.hpp"
43	#include "utils/simError.h"
44
45	namespace OpenMD {
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	currSnapshot->wrapVector(tmp);
129	atomInfo->pos = rotMat_ * tmp;;
130	atomInfo->vec = rotMat_ * atomInfo->vec;
131	}
132	}
133
134	const std::string LipidTransVisitor::toString() {
135	char buffer[65535];
136	std::string result;
137
138	sprintf(buffer,
139	"------------------------------------------------------------------\n");
140	result += buffer;
141
142	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
143	result += buffer;
144
145	sprintf(buffer,
146	"Visitor Description: rotate the whole system\n");
147	result += buffer;
148
149	sprintf(buffer,
150	"------------------------------------------------------------------\n");
151	result += buffer;
152
153	return result;
154	}
155
156	}