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

//----------------------------------------------------------------------------//
void IgnoreVisitor::visit(Atom *atom) {
    if (isIgnoreType(atom->getType()))
        internalVisit(atom);
}

void IgnoreVisitor::visit(DirectionalAtom *datom) {
    if (isIgnoreType(datom->getType()))
        internalVisit(datom);
}

void IgnoreVisitor::visit(RigidBody *rb) {
    std::vector<Atom *>           myAtoms;
    std::vector<Atom *>::iterator atomIter;
    AtomInfo *                    atomInfo;

    if (isIgnoreType(rb->getType())) {
        internalVisit(rb);

        myAtoms = rb->getAtoms();

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

bool IgnoreVisitor::isIgnoreType(const std::string&name) {
return itList.find(name) != itList.end() ? true : false;
}

void IgnoreVisitor::internalVisit(StuntDouble *sd) {
    GenericData *data;
    data = sd->getPropertyByName("IGNORE");

    //if this stuntdoulbe is already marked as ignore just skip it
    if (data == NULL) {
        data = new GenericData;
        data->setID("IGNORE");
        sd->addProperty(data);
    }
}

const std::string IgnoreVisitor::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: ignore  stuntdoubles\n");
    result += buffer;

    //print the ignore type list
    sprintf(buffer, "Ignore type list contains below types:\n");
    result += buffer;

    for( i = itList.begin(); i != itList.end(); ++i ) {
        sprintf(buffer, "%s\t", i->c_str());
        result += buffer;
    }

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

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

    return result;
}

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

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, bool printDipole) :
    BaseVisitor() {
    this->info = info;
    visitorName = "XYZVisitor";
    this->printDipole = printDipole;
}

void XYZVisitor::visit(Atom *atom) {
    if (!isIgnore(atom))
        internalVisit(atom);
}

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

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

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) ) {
        if (printDipole)
            sprintf(buffer,
                    "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
                    atomInfo->AtomType.c_str(),
                    atomInfo->pos[0],
                    atomInfo->pos[1],
                    atomInfo->pos[2],
                    atomInfo->dipole[0],
                    atomInfo->dipole[1],
                    atomInfo->dipole[2]); else
            sprintf(buffer,                     "%s%15.8f%15.8f%15.8f",
                    atomInfo->AtomType.c_str(), atomInfo->pos[0],
                    atomInfo->pos[1],           atomInfo->pos[2]);

        frame.push_back(buffer);
    }
}

bool XYZVisitor::isIgnore(StuntDouble *sd) {
    GenericData *data;

    data = sd->getPropertyByName("IGNORE");
    return data == NULL ? false : true;
}

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) ) {
            replaceType(atomInfo->AtomType);
            } //end for(atomInfo)
        }     //end for(atomIter)
    }         //end if (waterTypeList.find(rbName) != waterTypeList.end())
}

void WaterTypeVisitor::replaceType(std::string&atomType) {
atomType = atomType.substr(0, atomType.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:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 3 months ago) by gezelter
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	16529 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
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	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	2	//----------------------------------------------------------------------------//
50	gezelter	246	void IgnoreVisitor::visit(Atom *atom) {
51			if (isIgnoreType(atom->getType()))
52			internalVisit(atom);
53	gezelter	2	}
54
55	gezelter	246	void IgnoreVisitor::visit(DirectionalAtom *datom) {
56			if (isIgnoreType(datom->getType()))
57			internalVisit(datom);
58	gezelter	2	}
59
60	gezelter	246	void IgnoreVisitor::visit(RigidBody *rb) {
61			std::vector<Atom *> myAtoms;
62			std::vector<Atom *>::iterator atomIter;
63			AtomInfo * atomInfo;
64	gezelter	2
65	gezelter	246	if (isIgnoreType(rb->getType())) {
66			internalVisit(rb);
67	gezelter	2
68	gezelter	246	myAtoms = rb->getAtoms();
69
70			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
71			internalVisit(*atomIter);
72			}
73	gezelter	2	}
74
75	gezelter	246	bool IgnoreVisitor::isIgnoreType(const std::string&name) {
76			return itList.find(name) != itList.end() ? true : false;
77	gezelter	2	}
78
79	gezelter	246	void IgnoreVisitor::internalVisit(StuntDouble *sd) {
80			GenericData *data;
81			data = sd->getPropertyByName("IGNORE");
82	gezelter	2
83	gezelter	246	//if this stuntdoulbe is already marked as ignore just skip it
84			if (data == NULL) {
85			data = new GenericData;
86			data->setID("IGNORE");
87			sd->addProperty(data);
88			}
89	gezelter	2	}
90
91	gezelter	246	const std::string IgnoreVisitor::toString() {
92			char buffer[65535];
93			std::string result;
94			std::set<std::string>::iterator i;
95	gezelter	2
96	gezelter	246	sprintf(buffer,
97			"------------------------------------------------------------------\n");
98			result += buffer;
99	gezelter	2
100	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
101			result += buffer;
102	gezelter	2
103	gezelter	246	sprintf(buffer, "Visitor Description: ignore stuntdoubles\n");
104			result += buffer;
105	gezelter	2
106	gezelter	246	//print the ignore type list
107			sprintf(buffer, "Ignore type list contains below types:\n");
108	gezelter	2	result += buffer;
109
110	gezelter	246	for( i = itList.begin(); i != itList.end(); ++i ) {
111			sprintf(buffer, "%s\t", i->c_str());
112			result += buffer;
113			}
114	gezelter	2
115	gezelter	246	sprintf(buffer, "\n");
116			result += buffer;
117	gezelter	2
118	gezelter	246	sprintf(buffer,
119			"------------------------------------------------------------------\n");
120			result += buffer;
121
122			return result;
123	gezelter	2	}
124
125			//----------------------------------------------------------------------------//
126
127	gezelter	246	void WrappingVisitor::visit(Atom *atom) {
128			internalVisit(atom);
129	gezelter	2	}
130	gezelter	246
131			void WrappingVisitor::visit(DirectionalAtom *datom) {
132			internalVisit(datom);
133	gezelter	2	}
134
135	gezelter	246	void WrappingVisitor::visit(RigidBody *rb) {
136			internalVisit(rb);
137	gezelter	2	}
138
139	gezelter	246	void WrappingVisitor::internalVisit(StuntDouble *sd) {
140			GenericData * data;
141			AtomData * atomData;
142			AtomInfo * atomInfo;
143			std::vector<AtomInfo *>::iterator i;
144	gezelter	2
145	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
146	gezelter	2
147	gezelter	246	if (data != NULL) {
148			atomData = dynamic_cast<AtomData *>(data);
149	gezelter	2
150	gezelter	246	if (atomData == NULL)
151			return;
152			} else
153			return;
154
155			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
156
157			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
158			currSnapshot->wrapVector(atomInfo->pos);
159			}
160	gezelter	2	}
161
162	gezelter	246	const std::string WrappingVisitor::toString() {
163			char buffer[65535];
164			std::string result;
165	gezelter	2
166	gezelter	246	sprintf(buffer,
167			"------------------------------------------------------------------\n");
168			result += buffer;
169	gezelter	2
170	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
171			result += buffer;
172	gezelter	2
173	gezelter	246	sprintf(buffer,
174			"Visitor Description: wrapping atoms back to periodic box\n");
175			result += buffer;
176
177			sprintf(buffer,
178			"------------------------------------------------------------------\n");
179			result += buffer;
180
181			return result;
182	gezelter	2	}
183
184			//----------------------------------------------------------------------------//
185
186	gezelter	246	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
187			BaseVisitor() {
188			this->info = info;
189			visitorName = "ReplicateVisitor";
190			this->replicateOpt = opt;
191
192			//generate the replicate directions
193			for( int i = 0; i <= replicateOpt[0]; i++ ) {
194			for( int j = 0; j <= replicateOpt[1]; j++ ) {
195			for( int k = 0; k <= replicateOpt[2]; k++ ) {
196			//skip original frame
197			if (i == 0 && j == 0 && k == 0) {
198			continue;
199			} else {
200			dir.push_back(Vector3i(i, j, k));
201			}
202			}
203			}
204			}
205
206	gezelter	2	}
207	gezelter	246
208			void ReplicateVisitor::visit(Atom *atom) {
209			internalVisit(atom);
210	gezelter	2	}
211	gezelter	246
212			void ReplicateVisitor::visit(DirectionalAtom *datom) {
213			internalVisit(datom);
214	gezelter	2	}
215
216	gezelter	246	void ReplicateVisitor::visit(RigidBody *rb) {
217			internalVisit(rb);
218	gezelter	2	}
219
220	gezelter	246	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
221			GenericData * data;
222			AtomData * atomData;
223	gezelter	2
224	gezelter	246	//if there is not atom data, just skip it
225			data = sd->getPropertyByName("ATOMDATA");
226	gezelter	2
227	gezelter	246	if (data != NULL) {
228			atomData = dynamic_cast<AtomData *>(data);
229	gezelter	2
230	gezelter	246	if (atomData == NULL) {
231			return;
232			}
233			} else {
234			return;
235			}
236
237			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
238			Mat3x3d box = currSnapshot->getHmat();
239
240			std::vector<AtomInfo *> atomInfoList = atomData->getData();
241
242			replicate(atomInfoList, atomData, box);
243	gezelter	2	}
244
245	gezelter	246	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
246			AtomInfo* newAtomInfo;
247			std::vector<Vector3i>::iterator dirIter;
248			std::vector<AtomInfo *>::iterator i;
249	gezelter	2
250	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
251			for( i = infoList.begin(); i != infoList.end(); i++ ) {
252			newAtomInfo = new AtomInfo();
253			newAtomInfo = (*i);
254	gezelter	2
255	gezelter	246	for( int j = 0; j < 3; j++ )
256			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
257
258			data->addAtomInfo(newAtomInfo);
259			}
260			} // end for(dirIter)
261	gezelter	2	}
262
263	gezelter	246	const std::string ReplicateVisitor::toString() {
264			char buffer[65535];
265			std::string result;
266			std::set<std::string>::iterator i;
267	gezelter	2
268	gezelter	246	sprintf(buffer,
269			"------------------------------------------------------------------\n");
270			result += buffer;
271	gezelter	2
272	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
273			result += buffer;
274	gezelter	2
275	gezelter	246	sprintf(buffer,
276			"Visitor Description: replicate the atoms in different direction\n");
277			result += buffer;
278	gezelter	2
279	gezelter	246	//print the replicate direction
280			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
281			result += buffer;
282	gezelter	2
283	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
284			result += buffer;
285	gezelter	2
286	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
287			result += buffer;
288	gezelter	2
289	gezelter	246	sprintf(buffer,
290			"------------------------------------------------------------------\n");
291			result += buffer;
292
293			return result;
294	gezelter	2	}
295
296			//----------------------------------------------------------------------------//
297
298	gezelter	246	XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) :
299			BaseVisitor() {
300			this->info = info;
301			visitorName = "XYZVisitor";
302			this->printDipole = printDipole;
303	gezelter	2	}
304
305	gezelter	246	void XYZVisitor::visit(Atom *atom) {
306			if (!isIgnore(atom))
307			internalVisit(atom);
308	gezelter	2	}
309
310	gezelter	246	void XYZVisitor::visit(DirectionalAtom *datom) {
311			if (!isIgnore(datom))
312			internalVisit(datom);
313	gezelter	2	}
314
315	gezelter	246	void XYZVisitor::visit(RigidBody *rb) {
316			if (!isIgnore(rb))
317			internalVisit(rb);
318	gezelter	2	}
319
320	gezelter	246	void XYZVisitor::internalVisit(StuntDouble *sd) {
321			GenericData * data;
322			AtomData * atomData;
323			AtomInfo * atomInfo;
324			std::vector<AtomInfo *>::iterator i;
325			char buffer[1024];
326	gezelter	2
327	gezelter	246	//if there is not atom data, just skip it
328			data = sd->getPropertyByName("ATOMDATA");
329	gezelter	2
330	gezelter	246	if (data != NULL) {
331			atomData = dynamic_cast<AtomData *>(data);
332	gezelter	2
333	gezelter	246	if (atomData == NULL)
334			return;
335			} else
336			return;
337	gezelter	2
338	gezelter	246	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
339			atomInfo = atomData->nextAtomInfo(i) ) {
340			if (printDipole)
341			sprintf(buffer,
342			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
343			atomInfo->AtomType.c_str(),
344			atomInfo->pos[0],
345			atomInfo->pos[1],
346			atomInfo->pos[2],
347			atomInfo->dipole[0],
348			atomInfo->dipole[1],
349			atomInfo->dipole[2]); else
350			sprintf(buffer, "%s%15.8f%15.8f%15.8f",
351			atomInfo->AtomType.c_str(), atomInfo->pos[0],
352			atomInfo->pos[1], atomInfo->pos[2]);
353
354			frame.push_back(buffer);
355			}
356	gezelter	2	}
357
358	gezelter	246	bool XYZVisitor::isIgnore(StuntDouble *sd) {
359			GenericData *data;
360
361			data = sd->getPropertyByName("IGNORE");
362			return data == NULL ? false : true;
363	gezelter	2	}
364
365	gezelter	246	void XYZVisitor::writeFrame(std::ostream &outStream) {
366			std::vector<std::string>::iterator i;
367			char buffer[1024];
368	gezelter	2
369	gezelter	246	if (frame.size() == 0)
370			std::cerr << "Current Frame does not contain any atoms" << std::endl;
371	gezelter	2
372	gezelter	246	//total number of atoms
373			outStream << frame.size() << std::endl;
374	gezelter	2
375	gezelter	246	//write comment line
376			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
377			Mat3x3d box = currSnapshot->getHmat();
378
379			sprintf(buffer,
380			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
381			currSnapshot->getTime(),
382			box(0, 0), box(0, 1), box(0, 2),
383			box(1, 0), box(1, 1), box(1, 2),
384			box(2, 0), box(2, 1), box(2, 2));
385	gezelter	2
386	gezelter	246	outStream << buffer << std::endl;
387	gezelter	2
388	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
389			outStream << *i << std::endl;
390	gezelter	2	}
391
392	gezelter	246	const std::string XYZVisitor::toString() {
393			char buffer[65535];
394			std::string result;
395	gezelter	2
396	gezelter	246	sprintf(buffer,
397			"------------------------------------------------------------------\n");
398			result += buffer;
399	gezelter	2
400	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
401			result += buffer;
402	gezelter	2
403	gezelter	246	sprintf(buffer,
404			"Visitor Description: assemble the atom data and output xyz file\n");
405			result += buffer;
406
407			sprintf(buffer,
408			"------------------------------------------------------------------\n");
409			result += buffer;
410
411			return result;
412	gezelter	2	}
413
414			//----------------------------------------------------------------------------//
415
416	gezelter	246	void PrepareVisitor::internalVisit(Atom *atom) {
417			GenericData *data;
418			AtomData * atomData;
419	gezelter	2
420	gezelter	246	//if visited property is existed, remove it
421			data = atom->getPropertyByName("VISITED");
422	gezelter	2
423	gezelter	246	if (data != NULL) {
424			atom->removeProperty("VISITED");
425			}
426
427			//remove atomdata
428			data = atom->getPropertyByName("ATOMDATA");
429
430			if (data != NULL) {
431			atomData = dynamic_cast<AtomData *>(data);
432
433			if (atomData != NULL)
434			atom->removeProperty("ATOMDATA");
435			}
436	gezelter	2	}
437
438	gezelter	246	void PrepareVisitor::internalVisit(RigidBody *rb) {
439			GenericData* data;
440			AtomData* atomData;
441			std::vector<Atom *> myAtoms;
442			std::vector<Atom *>::iterator atomIter;
443	gezelter	2
444	gezelter	246	//if visited property is existed, remove it
445			data = rb->getPropertyByName("VISITED");
446	gezelter	2
447	gezelter	246	if (data != NULL) {
448			rb->removeProperty("VISITED");
449			}
450
451			//remove atomdata
452			data = rb->getPropertyByName("ATOMDATA");
453
454			if (data != NULL) {
455			atomData = dynamic_cast<AtomData *>(data);
456
457			if (atomData != NULL)
458			rb->removeProperty("ATOMDATA");
459			}
460
461			myAtoms = rb->getAtoms();
462
463			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
464			internalVisit(*atomIter);
465	gezelter	2	}
466
467	gezelter	246	const std::string PrepareVisitor::toString() {
468			char buffer[65535];
469			std::string result;
470	gezelter	2
471	gezelter	246	sprintf(buffer,
472			"------------------------------------------------------------------\n");
473			result += buffer;
474	gezelter	2
475	gezelter	246	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
476			result += buffer;
477	gezelter	2
478	gezelter	246	sprintf(buffer,
479			"Visitor Description: prepare for operation of other vistors\n");
480			result += buffer;
481	gezelter	2
482	gezelter	246	sprintf(buffer,
483			"------------------------------------------------------------------\n");
484			result += buffer;
485
486			return result;
487	gezelter	2	}
488
489			//----------------------------------------------------------------------------//
490
491	gezelter	246	WaterTypeVisitor::WaterTypeVisitor() {
492			visitorName = "WaterTypeVisitor";
493			waterTypeList.insert("TIP3P_RB_0");
494			waterTypeList.insert("TIP4P_RB_0");
495			waterTypeList.insert("TIP5P_RB_0");
496			waterTypeList.insert("SPCE_RB_0");
497	gezelter	2	}
498
499	gezelter	246	void WaterTypeVisitor::visit(RigidBody *rb) {
500			std::string rbName;
501			std::vector<Atom *> myAtoms;
502			std::vector<Atom *>::iterator atomIter;
503			GenericData* data;
504			AtomData* atomData;
505			AtomInfo* atomInfo;
506			std::vector<AtomInfo *>::iterator i;
507	gezelter	2
508	gezelter	246	rbName = rb->getType();
509	gezelter	2
510	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
511			myAtoms = rb->getAtoms();
512	gezelter	2
513	gezelter	246	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
514			++atomIter ) {
515			data = (*atomIter)->getPropertyByName("ATOMDATA");
516	gezelter	2
517	gezelter	246	if (data != NULL) {
518			atomData = dynamic_cast<AtomData *>(data);
519	gezelter	2
520	gezelter	246	if (atomData == NULL)
521			continue;
522			} else
523			continue;
524
525			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
526			atomInfo = atomData->nextAtomInfo(i) ) {
527			replaceType(atomInfo->AtomType);
528			} //end for(atomInfo)
529			} //end for(atomIter)
530			} //end if (waterTypeList.find(rbName) != waterTypeList.end())
531	gezelter	2	}
532
533	gezelter	246	void WaterTypeVisitor::replaceType(std::string&atomType) {
534			atomType = atomType.substr(0, atomType.find('_'));
535	gezelter	2	}
536
537	gezelter	246	const std::string WaterTypeVisitor::toString() {
538			char buffer[65535];
539			std::string result;
540	gezelter	2
541	gezelter	246	sprintf(buffer,
542			"------------------------------------------------------------------\n");
543			result += buffer;
544	gezelter	2
545	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
546			result += buffer;
547	gezelter	2
548	gezelter	246	sprintf(buffer,
549			"Visitor Description: Replace the atom type in water model\n");
550			result += buffer;
551	gezelter	2
552	gezelter	246	sprintf(buffer,
553			"------------------------------------------------------------------\n");
554			result += buffer;
555
556			return result;
557	gezelter	2	}
558
559	gezelter	246	} //namespace oopse