src/visitors/OtherVisitor.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 "selection/SelectionManager.hpp" 
#include "visitors/OtherVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Molecule.hpp"
#include "brains/SimInfo.hpp"
namespace oopse {

void WrappingVisitor::visit(Atom *atom) {
internalVisit(atom);
}

void WrappingVisitor::visit(DirectionalAtom *datom) {
internalVisit(datom);
}

void WrappingVisitor::visit(RigidBody *rb) {
internalVisit(rb);
}

void WrappingVisitor::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) ) {
        currSnapshot->wrapVector(atomInfo->pos);
    }
}

const std::string WrappingVisitor::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: wrapping atoms back to periodic box\n");
    result += buffer;

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

    return result;
}

//----------------------------------------------------------------------------//

ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
    BaseVisitor() {
    this->info = info;
    visitorName = "ReplicateVisitor";
    this->replicateOpt = opt;

    //generate the replicate directions
    for( int i = 0; i <= replicateOpt[0]; i++ ) {
        for( int j = 0; j <= replicateOpt[1]; j++ ) {
            for( int k = 0; k <= replicateOpt[2]; k++ ) {
                //skip original frame
                if (i == 0 && j == 0 && k == 0) {
                    continue; 
                } else {
                    dir.push_back(Vector3i(i, j, k));
                }
            }
        }
    }
    
}

void ReplicateVisitor::visit(Atom *atom) {
internalVisit(atom);
}

void ReplicateVisitor::visit(DirectionalAtom *datom) {
internalVisit(datom);
}

void ReplicateVisitor::visit(RigidBody *rb) {
internalVisit(rb);
}

void ReplicateVisitor::internalVisit(StuntDouble *sd) {
    GenericData *          data;
    AtomData *             atomData;

    //if there is not atom data, just skip it
    data = sd->getPropertyByName("ATOMDATA");

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

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

    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d box = currSnapshot->getHmat();

    std::vector<AtomInfo *> atomInfoList = atomData->getData();

    replicate(atomInfoList, atomData, box);
}

void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) {
    AtomInfo* newAtomInfo;
    std::vector<Vector3i>::iterator dirIter;
    std::vector<AtomInfo *>::iterator i;

    for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
        for( i = infoList.begin(); i != infoList.end(); i++ ) {
            newAtomInfo = new AtomInfo();
            *newAtomInfo = *(*i);

            for( int j = 0; j < 3; j++ )
                newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2);

            data->addAtomInfo(newAtomInfo);
        }
    } // end for(dirIter)  
}

const std::string ReplicateVisitor::toString() {
    char                            buffer[65535];
    std::string                     result;
    std::set<std::string>::iterator i;

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

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

    sprintf(buffer,
            "Visitor Description: replicate the atoms in different direction\n");
    result += buffer;

    //print the replicate direction
    sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
    result += buffer;

    sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
    result += buffer;

    sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
    result += buffer;

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

    return result;
}

//----------------------------------------------------------------------------//

XYZVisitor::XYZVisitor(SimInfo *info) :
    BaseVisitor(), seleMan(info), evaluator(info){
    this->info = info;
    visitorName = "XYZVisitor";

    evaluator.loadScriptString("select all");

    if (!evaluator.isDynamic()) {
        seleMan.setSelectionSet(evaluator.evaluate());
    }

}

XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
    BaseVisitor(), seleMan(info), evaluator(info) {
    this->info = info;
    visitorName = "XYZVisitor";

    evaluator.loadScriptString(script);

    if (!evaluator.isDynamic()) {
        seleMan.setSelectionSet(evaluator.evaluate());
    }
          
}
    
void XYZVisitor::visit(Atom *atom) {
    if (isSelected(atom))
        internalVisit(atom);
}

void XYZVisitor::visit(DirectionalAtom *datom) {
    if (isSelected(datom))
        internalVisit(datom);
}

void XYZVisitor::visit(RigidBody *rb) {
    if (isSelected(rb))
        internalVisit(rb);
}

void XYZVisitor::update() {
    //if dynamic, we need to re-evaluate the selection
    if (evaluator.isDynamic()) {
       seleMan.setSelectionSet(evaluator.evaluate());
    }
}

void XYZVisitor::internalVisit(StuntDouble *sd) {
    GenericData *                     data;
    AtomData *                        atomData;
    AtomInfo *                        atomInfo;
    std::vector<AtomInfo *>::iterator i;
    char                              buffer[1024];

    //if there is not atom data, just skip it
    data = sd->getPropertyByName("ATOMDATA");

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

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

    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
        atomInfo = atomData->nextAtomInfo(i) ) {
        sprintf(buffer,
                "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
                atomInfo->atomTypeName.c_str(),
                atomInfo->pos[0],
                atomInfo->pos[1],
                atomInfo->pos[2],
                atomInfo->dipole[0],
                atomInfo->dipole[1],
                atomInfo->dipole[2]); 
        frame.push_back(buffer);
    }
}

bool XYZVisitor::isSelected(StuntDouble *sd) {
    return seleMan.isSelected(sd);
}

void XYZVisitor::writeFrame(std::ostream &outStream) {
    std::vector<std::string>::iterator i;
    char buffer[1024];

    if (frame.size() == 0)
        std::cerr << "Current Frame does not contain any atoms" << std::endl;

    //total number of atoms  
    outStream << frame.size() << std::endl;

    //write comment line
    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d box = currSnapshot->getHmat();
    
    sprintf(buffer,
            "%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
            currSnapshot->getTime(),
            box(0, 0), box(0, 1), box(0, 2),
            box(1, 0), box(1, 1), box(1, 2),
            box(2, 0), box(2, 1), box(2, 2));

    outStream << buffer << std::endl;

    for( i = frame.begin(); i != frame.end(); ++i )
        outStream << *i << std::endl;
}

const std::string XYZVisitor::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: assemble the atom data and output xyz file\n");
    result += buffer;

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

    return result;
}

//----------------------------------------------------------------------------//

void PrepareVisitor::internalVisit(Atom *atom) {
    GenericData *data;
    AtomData *   atomData;

    //if visited property is  existed, remove it
    data = atom->getPropertyByName("VISITED");

    if (data != NULL) {
    atom->removeProperty("VISITED");
    }

    //remove atomdata
    data = atom->getPropertyByName("ATOMDATA");

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

        if (atomData != NULL)
            atom->removeProperty("ATOMDATA");
    }
}

void PrepareVisitor::internalVisit(RigidBody *rb) {
    GenericData* data;
    AtomData* atomData;
    std::vector<Atom *> myAtoms;
    std::vector<Atom *>::iterator atomIter;

    //if visited property is  existed, remove it
    data = rb->getPropertyByName("VISITED");

    if (data != NULL) {
    rb->removeProperty("VISITED");
    }

    //remove atomdata
    data = rb->getPropertyByName("ATOMDATA");

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

        if (atomData != NULL)
            rb->removeProperty("ATOMDATA");
    }

    myAtoms = rb->getAtoms();

    for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
        internalVisit(*atomIter);
}

const std::string PrepareVisitor::toString() {
     char buffer[65535];
     std::string result;
 
     sprintf(buffer,
             "------------------------------------------------------------------\n");
     result += buffer;
 
     sprintf(buffer, "Visitor name: %s", visitorName.c_str());
     result += buffer;
 
     sprintf(buffer,
             "Visitor Description: prepare for operation of other vistors\n");
     result += buffer;
 
     sprintf(buffer,
             "------------------------------------------------------------------\n");
     result += buffer;
 
     return result;
}

//----------------------------------------------------------------------------//

WaterTypeVisitor::WaterTypeVisitor() {
    visitorName = "WaterTypeVisitor";
    waterTypeList.insert("TIP3P_RB_0");
    waterTypeList.insert("TIP4P_RB_0");
    waterTypeList.insert("TIP5P_RB_0");
    waterTypeList.insert("SPCE_RB_0");
}

void WaterTypeVisitor::visit(RigidBody *rb) {
    std::string rbName;
    std::vector<Atom *> myAtoms;
    std::vector<Atom *>::iterator atomIter;
    GenericData* data;
    AtomData* atomData;
    AtomInfo* atomInfo;
    std::vector<AtomInfo *>::iterator i;

    rbName = rb->getType();

    if (waterTypeList.find(rbName) != waterTypeList.end()) {
        myAtoms = rb->getAtoms();

        for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
            ++atomIter ) {
            data = (*atomIter)->getPropertyByName("ATOMDATA");

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

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

            for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
                 atomInfo = atomData->nextAtomInfo(i) ) {
              atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
            } //end for(atomInfo)
        }     //end for(atomIter)
    }         //end if (waterTypeList.find(rbName) != waterTypeList.end())
}

  std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
    return atomTypeName.substr(0, atomTypeName.find('_'));
  }

const std::string WaterTypeVisitor::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: Replace the atom type in water model\n");
    result += buffer;

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

    return result;
}

} //namespace oopse
Revision:	413
Committed:	Wed Mar 9 17:30:29 2005 UTC (20 years, 1 month ago) by tim
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	14762 byte(s)
Log Message:	adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
#	User	Rev	Content
1	gezelter	407	/*
2	gezelter	246	* 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	tim	324	#include "selection/SelectionManager.hpp"
42	tim	3	#include "visitors/OtherVisitor.hpp"
43			#include "primitives/DirectionalAtom.hpp"
44			#include "primitives/RigidBody.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "brains/SimInfo.hpp"
47	tim	132	namespace oopse {
48
49	gezelter	246	void WrappingVisitor::visit(Atom *atom) {
50			internalVisit(atom);
51	gezelter	2	}
52	gezelter	246
53			void WrappingVisitor::visit(DirectionalAtom *datom) {
54			internalVisit(datom);
55	gezelter	2	}
56
57	gezelter	246	void WrappingVisitor::visit(RigidBody *rb) {
58			internalVisit(rb);
59	gezelter	2	}
60
61	gezelter	246	void WrappingVisitor::internalVisit(StuntDouble *sd) {
62			GenericData * data;
63			AtomData * atomData;
64			AtomInfo * atomInfo;
65			std::vector<AtomInfo *>::iterator i;
66	gezelter	2
67	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
68	gezelter	2
69	gezelter	246	if (data != NULL) {
70			atomData = dynamic_cast<AtomData *>(data);
71	gezelter	2
72	gezelter	246	if (atomData == NULL)
73			return;
74			} else
75			return;
76
77			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78
79			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80			currSnapshot->wrapVector(atomInfo->pos);
81			}
82	gezelter	2	}
83
84	gezelter	246	const std::string WrappingVisitor::toString() {
85			char buffer[65535];
86			std::string result;
87	gezelter	2
88	gezelter	246	sprintf(buffer,
89			"------------------------------------------------------------------\n");
90			result += buffer;
91	gezelter	2
92	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
93			result += buffer;
94	gezelter	2
95	gezelter	246	sprintf(buffer,
96			"Visitor Description: wrapping atoms back to periodic box\n");
97			result += buffer;
98
99			sprintf(buffer,
100			"------------------------------------------------------------------\n");
101			result += buffer;
102
103			return result;
104	gezelter	2	}
105
106			//----------------------------------------------------------------------------//
107
108	gezelter	246	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
109			BaseVisitor() {
110			this->info = info;
111			visitorName = "ReplicateVisitor";
112			this->replicateOpt = opt;
113
114			//generate the replicate directions
115			for( int i = 0; i <= replicateOpt[0]; i++ ) {
116			for( int j = 0; j <= replicateOpt[1]; j++ ) {
117			for( int k = 0; k <= replicateOpt[2]; k++ ) {
118			//skip original frame
119			if (i == 0 && j == 0 && k == 0) {
120			continue;
121			} else {
122			dir.push_back(Vector3i(i, j, k));
123			}
124			}
125			}
126			}
127
128	gezelter	2	}
129	gezelter	246
130			void ReplicateVisitor::visit(Atom *atom) {
131			internalVisit(atom);
132	gezelter	2	}
133	gezelter	246
134			void ReplicateVisitor::visit(DirectionalAtom *datom) {
135			internalVisit(datom);
136	gezelter	2	}
137
138	gezelter	246	void ReplicateVisitor::visit(RigidBody *rb) {
139			internalVisit(rb);
140	gezelter	2	}
141
142	gezelter	246	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
143			GenericData * data;
144			AtomData * atomData;
145	gezelter	2
146	gezelter	246	//if there is not atom data, just skip it
147			data = sd->getPropertyByName("ATOMDATA");
148	gezelter	2
149	gezelter	246	if (data != NULL) {
150			atomData = dynamic_cast<AtomData *>(data);
151	gezelter	2
152	gezelter	246	if (atomData == NULL) {
153			return;
154			}
155			} else {
156			return;
157			}
158
159			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
160			Mat3x3d box = currSnapshot->getHmat();
161
162			std::vector<AtomInfo *> atomInfoList = atomData->getData();
163
164			replicate(atomInfoList, atomData, box);
165	gezelter	2	}
166
167	gezelter	246	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
168			AtomInfo* newAtomInfo;
169			std::vector<Vector3i>::iterator dirIter;
170			std::vector<AtomInfo *>::iterator i;
171	gezelter	2
172	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
173			for( i = infoList.begin(); i != infoList.end(); i++ ) {
174			newAtomInfo = new AtomInfo();
175			newAtomInfo = (*i);
176	gezelter	2
177	gezelter	246	for( int j = 0; j < 3; j++ )
178			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
179
180			data->addAtomInfo(newAtomInfo);
181			}
182			} // end for(dirIter)
183	gezelter	2	}
184
185	gezelter	246	const std::string ReplicateVisitor::toString() {
186			char buffer[65535];
187			std::string result;
188			std::set<std::string>::iterator i;
189	gezelter	2
190	gezelter	246	sprintf(buffer,
191			"------------------------------------------------------------------\n");
192			result += buffer;
193	gezelter	2
194	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
195			result += buffer;
196	gezelter	2
197	gezelter	246	sprintf(buffer,
198			"Visitor Description: replicate the atoms in different direction\n");
199			result += buffer;
200	gezelter	2
201	gezelter	246	//print the replicate direction
202			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
203			result += buffer;
204	gezelter	2
205	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
206			result += buffer;
207	gezelter	2
208	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
209			result += buffer;
210	gezelter	2
211	gezelter	246	sprintf(buffer,
212			"------------------------------------------------------------------\n");
213			result += buffer;
214
215			return result;
216	gezelter	2	}
217
218			//----------------------------------------------------------------------------//
219
220	tim	413	XYZVisitor::XYZVisitor(SimInfo *info) :
221			BaseVisitor(), seleMan(info), evaluator(info){
222	gezelter	246	this->info = info;
223			visitorName = "XYZVisitor";
224	tim	413
225			evaluator.loadScriptString("select all");
226
227			if (!evaluator.isDynamic()) {
228			seleMan.setSelectionSet(evaluator.evaluate());
229			}
230
231	gezelter	2	}
232
233	tim	413	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
234			BaseVisitor(), seleMan(info), evaluator(info) {
235			this->info = info;
236			visitorName = "XYZVisitor";
237
238			evaluator.loadScriptString(script);
239
240			if (!evaluator.isDynamic()) {
241			seleMan.setSelectionSet(evaluator.evaluate());
242			}
243
244			}
245
246	gezelter	246	void XYZVisitor::visit(Atom *atom) {
247	tim	293	if (isSelected(atom))
248	gezelter	246	internalVisit(atom);
249	gezelter	2	}
250
251	gezelter	246	void XYZVisitor::visit(DirectionalAtom *datom) {
252	tim	293	if (isSelected(datom))
253	gezelter	246	internalVisit(datom);
254	gezelter	2	}
255
256	gezelter	246	void XYZVisitor::visit(RigidBody *rb) {
257	tim	293	if (isSelected(rb))
258	gezelter	246	internalVisit(rb);
259	gezelter	2	}
260
261	tim	413	void XYZVisitor::update() {
262			//if dynamic, we need to re-evaluate the selection
263			if (evaluator.isDynamic()) {
264			seleMan.setSelectionSet(evaluator.evaluate());
265			}
266			}
267
268	gezelter	246	void XYZVisitor::internalVisit(StuntDouble *sd) {
269			GenericData * data;
270			AtomData * atomData;
271			AtomInfo * atomInfo;
272			std::vector<AtomInfo *>::iterator i;
273			char buffer[1024];
274	gezelter	2
275	gezelter	246	//if there is not atom data, just skip it
276			data = sd->getPropertyByName("ATOMDATA");
277	gezelter	2
278	gezelter	246	if (data != NULL) {
279			atomData = dynamic_cast<AtomData *>(data);
280	gezelter	2
281	gezelter	246	if (atomData == NULL)
282			return;
283			} else
284			return;
285	gezelter	2
286	gezelter	246	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
287			atomInfo = atomData->nextAtomInfo(i) ) {
288	gezelter	407	sprintf(buffer,
289			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
290			atomInfo->atomTypeName.c_str(),
291			atomInfo->pos[0],
292			atomInfo->pos[1],
293			atomInfo->pos[2],
294			atomInfo->dipole[0],
295			atomInfo->dipole[1],
296			atomInfo->dipole[2]);
297	gezelter	246	frame.push_back(buffer);
298			}
299	gezelter	2	}
300
301	tim	293	bool XYZVisitor::isSelected(StuntDouble *sd) {
302	tim	413	return seleMan.isSelected(sd);
303	gezelter	2	}
304
305	gezelter	246	void XYZVisitor::writeFrame(std::ostream &outStream) {
306			std::vector<std::string>::iterator i;
307			char buffer[1024];
308	gezelter	2
309	gezelter	246	if (frame.size() == 0)
310			std::cerr << "Current Frame does not contain any atoms" << std::endl;
311	gezelter	2
312	gezelter	246	//total number of atoms
313			outStream << frame.size() << std::endl;
314	gezelter	2
315	gezelter	246	//write comment line
316			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
317			Mat3x3d box = currSnapshot->getHmat();
318
319			sprintf(buffer,
320			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
321			currSnapshot->getTime(),
322			box(0, 0), box(0, 1), box(0, 2),
323			box(1, 0), box(1, 1), box(1, 2),
324			box(2, 0), box(2, 1), box(2, 2));
325	gezelter	2
326	gezelter	246	outStream << buffer << std::endl;
327	gezelter	2
328	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
329			outStream << *i << std::endl;
330	gezelter	2	}
331
332	gezelter	246	const std::string XYZVisitor::toString() {
333			char buffer[65535];
334			std::string result;
335	gezelter	2
336	gezelter	246	sprintf(buffer,
337			"------------------------------------------------------------------\n");
338			result += buffer;
339	gezelter	2
340	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
341			result += buffer;
342	gezelter	2
343	gezelter	246	sprintf(buffer,
344			"Visitor Description: assemble the atom data and output xyz file\n");
345			result += buffer;
346
347			sprintf(buffer,
348			"------------------------------------------------------------------\n");
349			result += buffer;
350
351			return result;
352	gezelter	2	}
353
354			//----------------------------------------------------------------------------//
355
356	gezelter	246	void PrepareVisitor::internalVisit(Atom *atom) {
357			GenericData *data;
358			AtomData * atomData;
359	gezelter	2
360	gezelter	246	//if visited property is existed, remove it
361			data = atom->getPropertyByName("VISITED");
362	gezelter	2
363	gezelter	246	if (data != NULL) {
364			atom->removeProperty("VISITED");
365			}
366
367			//remove atomdata
368			data = atom->getPropertyByName("ATOMDATA");
369
370			if (data != NULL) {
371			atomData = dynamic_cast<AtomData *>(data);
372
373			if (atomData != NULL)
374			atom->removeProperty("ATOMDATA");
375			}
376	gezelter	2	}
377
378	gezelter	246	void PrepareVisitor::internalVisit(RigidBody *rb) {
379			GenericData* data;
380			AtomData* atomData;
381			std::vector<Atom *> myAtoms;
382			std::vector<Atom *>::iterator atomIter;
383	gezelter	2
384	gezelter	246	//if visited property is existed, remove it
385			data = rb->getPropertyByName("VISITED");
386	gezelter	2
387	gezelter	246	if (data != NULL) {
388			rb->removeProperty("VISITED");
389			}
390
391			//remove atomdata
392			data = rb->getPropertyByName("ATOMDATA");
393
394			if (data != NULL) {
395			atomData = dynamic_cast<AtomData *>(data);
396
397			if (atomData != NULL)
398			rb->removeProperty("ATOMDATA");
399			}
400
401			myAtoms = rb->getAtoms();
402
403			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
404			internalVisit(*atomIter);
405	gezelter	2	}
406
407	gezelter	246	const std::string PrepareVisitor::toString() {
408	tim	293	char buffer[65535];
409			std::string result;
410
411			sprintf(buffer,
412			"------------------------------------------------------------------\n");
413			result += buffer;
414
415			sprintf(buffer, "Visitor name: %s", visitorName.c_str());
416			result += buffer;
417
418			sprintf(buffer,
419			"Visitor Description: prepare for operation of other vistors\n");
420			result += buffer;
421
422			sprintf(buffer,
423			"------------------------------------------------------------------\n");
424			result += buffer;
425
426			return result;
427	gezelter	2	}
428
429			//----------------------------------------------------------------------------//
430
431	gezelter	246	WaterTypeVisitor::WaterTypeVisitor() {
432			visitorName = "WaterTypeVisitor";
433			waterTypeList.insert("TIP3P_RB_0");
434			waterTypeList.insert("TIP4P_RB_0");
435			waterTypeList.insert("TIP5P_RB_0");
436			waterTypeList.insert("SPCE_RB_0");
437	gezelter	2	}
438
439	gezelter	246	void WaterTypeVisitor::visit(RigidBody *rb) {
440			std::string rbName;
441			std::vector<Atom *> myAtoms;
442			std::vector<Atom *>::iterator atomIter;
443			GenericData* data;
444			AtomData* atomData;
445			AtomInfo* atomInfo;
446			std::vector<AtomInfo *>::iterator i;
447	gezelter	2
448	gezelter	246	rbName = rb->getType();
449	gezelter	2
450	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
451			myAtoms = rb->getAtoms();
452	gezelter	2
453	gezelter	246	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
454			++atomIter ) {
455			data = (*atomIter)->getPropertyByName("ATOMDATA");
456	gezelter	2
457	gezelter	246	if (data != NULL) {
458			atomData = dynamic_cast<AtomData *>(data);
459	gezelter	2
460	gezelter	246	if (atomData == NULL)
461			continue;
462			} else
463			continue;
464
465			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
466	gezelter	407	atomInfo = atomData->nextAtomInfo(i) ) {
467			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
468	gezelter	246	} //end for(atomInfo)
469			} //end for(atomIter)
470			} //end if (waterTypeList.find(rbName) != waterTypeList.end())
471	gezelter	2	}
472
473	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
474			return atomTypeName.substr(0, atomTypeName.find('_'));
475			}
476	gezelter	2
477	gezelter	246	const std::string WaterTypeVisitor::toString() {
478			char buffer[65535];
479			std::string result;
480	gezelter	2
481	gezelter	246	sprintf(buffer,
482			"------------------------------------------------------------------\n");
483			result += buffer;
484	gezelter	2
485	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
486			result += buffer;
487	gezelter	2
488	gezelter	246	sprintf(buffer,
489			"Visitor Description: Replace the atom type in water model\n");
490			result += buffer;
491	gezelter	2
492	gezelter	246	sprintf(buffer,
493			"------------------------------------------------------------------\n");
494			result += buffer;
495
496			return result;
497	gezelter	2	}
498
499	gezelter	246	} //namespace oopse