src/visitors/OtherVisitor.cpp

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

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

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

    for( i = frame.begin(); i != frame.end(); ++i )
        outStream << *i << 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:	1818
Committed:	Wed Dec 1 20:05:49 2004 UTC (19 years, 7 months ago) by tim
File size:	14422 byte(s)
Log Message:	visitors get built
#	User	Rev	Content
1	tim	1492	#include "visitors/OtherVisitor.hpp"
2			#include "primitives/DirectionalAtom.hpp"
3			#include "primitives/RigidBody.hpp"
4			#include "primitives/Molecule.hpp"
5			#include "brains/SimInfo.hpp"
6	tim	1625	namespace oopse {
7
8	gezelter	1490	//----------------------------------------------------------------------------//
9	tim	1818	void IgnoreVisitor::visit(Atom *atom) {
10			if (isIgnoreType(atom->getType()))
11			internalVisit(atom);
12	gezelter	1490	}
13
14	tim	1818	void IgnoreVisitor::visit(DirectionalAtom *datom) {
15			if (isIgnoreType(datom->getType()))
16			internalVisit(datom);
17	gezelter	1490	}
18
19	tim	1818	void IgnoreVisitor::visit(RigidBody *rb) {
20			std::vector<Atom *> myAtoms;
21			std::vector<Atom *>::iterator atomIter;
22			AtomInfo * atomInfo;
23	gezelter	1490
24	tim	1818	if (isIgnoreType(rb->getType())) {
25			internalVisit(rb);
26	gezelter	1490
27	tim	1818	myAtoms = rb->getAtoms();
28
29			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
30			internalVisit(*atomIter);
31			}
32	gezelter	1490	}
33
34	tim	1818	bool IgnoreVisitor::isIgnoreType(const std::string&name) {
35			return itList.find(name) != itList.end() ? true : false;
36	gezelter	1490	}
37
38	tim	1818	void IgnoreVisitor::internalVisit(StuntDouble *sd) {
39			GenericData *data;
40			data = sd->getPropertyByName("IGNORE");
41	gezelter	1490
42	tim	1818	//if this stuntdoulbe is already marked as ignore just skip it
43			if (data == NULL) {
44			data = new GenericData;
45			data->setID("IGNORE");
46			sd->addProperty(data);
47			}
48	gezelter	1490	}
49
50	tim	1818	const std::string IgnoreVisitor::toString() {
51			char buffer[65535];
52			std::string result;
53			std::set<std::string>::iterator i;
54	gezelter	1490
55	tim	1818	sprintf(buffer,
56			"------------------------------------------------------------------\n");
57			result += buffer;
58	gezelter	1490
59	tim	1818	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
60			result += buffer;
61	gezelter	1490
62	tim	1818	sprintf(buffer, "Visitor Description: ignore stuntdoubles\n");
63			result += buffer;
64	gezelter	1490
65	tim	1818	//print the ignore type list
66			sprintf(buffer, "Ignore type list contains below types:\n");
67	gezelter	1490	result += buffer;
68
69	tim	1818	for( i = itList.begin(); i != itList.end(); ++i ) {
70			sprintf(buffer, "%s\t", i->c_str());
71			result += buffer;
72			}
73	gezelter	1490
74	tim	1818	sprintf(buffer, "\n");
75			result += buffer;
76	gezelter	1490
77	tim	1818	sprintf(buffer,
78			"------------------------------------------------------------------\n");
79			result += buffer;
80
81			return result;
82	gezelter	1490	}
83
84			//----------------------------------------------------------------------------//
85
86	tim	1818	void WrappingVisitor::visit(Atom *atom) {
87			internalVisit(atom);
88	gezelter	1490	}
89	tim	1818
90			void WrappingVisitor::visit(DirectionalAtom *datom) {
91			internalVisit(datom);
92	gezelter	1490	}
93
94	tim	1818	void WrappingVisitor::visit(RigidBody *rb) {
95			internalVisit(rb);
96	gezelter	1490	}
97
98	tim	1818	void WrappingVisitor::internalVisit(StuntDouble *sd) {
99			GenericData * data;
100			AtomData * atomData;
101			AtomInfo * atomInfo;
102			std::vector<AtomInfo *>::iterator i;
103	gezelter	1490
104	tim	1818	data = sd->getPropertyByName("ATOMDATA");
105	gezelter	1490
106	tim	1818	if (data != NULL) {
107			atomData = dynamic_cast<AtomData *>(data);
108	gezelter	1490
109	tim	1818	if (atomData == NULL)
110			return;
111			} else
112			return;
113
114			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
115
116			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
117			currSnapshot->wrapVector(atomInfo->pos);
118			}
119	gezelter	1490	}
120
121	tim	1818	const std::string WrappingVisitor::toString() {
122			char buffer[65535];
123			std::string result;
124	gezelter	1490
125	tim	1818	sprintf(buffer,
126			"------------------------------------------------------------------\n");
127			result += buffer;
128	gezelter	1490
129	tim	1818	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
130			result += buffer;
131	gezelter	1490
132	tim	1818	sprintf(buffer,
133			"Visitor Description: wrapping atoms back to periodic box\n");
134			result += buffer;
135
136			sprintf(buffer,
137			"------------------------------------------------------------------\n");
138			result += buffer;
139
140			return result;
141	gezelter	1490	}
142
143			//----------------------------------------------------------------------------//
144
145	tim	1818	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
146			BaseVisitor() {
147			this->info = info;
148			visitorName = "ReplicateVisitor";
149			this->replicateOpt = opt;
150
151			//generate the replicate directions
152			for( int i = 0; i <= replicateOpt[0]; i++ ) {
153			for( int j = 0; j <= replicateOpt[1]; j++ ) {
154			for( int k = 0; k <= replicateOpt[2]; k++ ) {
155			//skip original frame
156			if (i == 0 && j == 0 && k == 0) {
157			continue;
158			} else {
159			dir.push_back(Vector3i(i, j, k));
160			}
161			}
162			}
163			}
164
165	gezelter	1490	}
166	tim	1818
167			void ReplicateVisitor::visit(Atom *atom) {
168			internalVisit(atom);
169	gezelter	1490	}
170	tim	1818
171			void ReplicateVisitor::visit(DirectionalAtom *datom) {
172			internalVisit(datom);
173	gezelter	1490	}
174
175	tim	1818	void ReplicateVisitor::visit(RigidBody *rb) {
176			internalVisit(rb);
177	gezelter	1490	}
178
179	tim	1818	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
180			GenericData * data;
181			AtomData * atomData;
182	gezelter	1490
183	tim	1818	//if there is not atom data, just skip it
184			data = sd->getPropertyByName("ATOMDATA");
185	gezelter	1490
186	tim	1818	if (data != NULL) {
187			atomData = dynamic_cast<AtomData *>(data);
188	gezelter	1490
189	tim	1818	if (atomData == NULL) {
190			return;
191			}
192			} else {
193			return;
194			}
195
196			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
197			Mat3x3d box = currSnapshot->getHmat();
198
199			std::vector<AtomInfo *> atomInfoList = atomData->getData();
200
201			replicate(atomInfoList, atomData, box);
202	gezelter	1490	}
203
204	tim	1818	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
205			AtomInfo* newAtomInfo;
206			std::vector<Vector3i>::iterator dirIter;
207			std::vector<AtomInfo *>::iterator i;
208	gezelter	1490
209	tim	1818	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
210			for( i = infoList.begin(); i != infoList.end(); i++ ) {
211			newAtomInfo = new AtomInfo();
212			newAtomInfo = (*i);
213	gezelter	1490
214	tim	1818	for( int j = 0; j < 3; j++ )
215			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
216
217			data->addAtomInfo(newAtomInfo);
218			}
219			} // end for(dirIter)
220	gezelter	1490	}
221
222	tim	1818	const std::string ReplicateVisitor::toString() {
223			char buffer[65535];
224			std::string result;
225			std::set<std::string>::iterator i;
226	gezelter	1490
227	tim	1818	sprintf(buffer,
228			"------------------------------------------------------------------\n");
229			result += buffer;
230	gezelter	1490
231	tim	1818	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
232			result += buffer;
233	gezelter	1490
234	tim	1818	sprintf(buffer,
235			"Visitor Description: replicate the atoms in different direction\n");
236			result += buffer;
237	gezelter	1490
238	tim	1818	//print the replicate direction
239			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
240			result += buffer;
241	gezelter	1490
242	tim	1818	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
243			result += buffer;
244	gezelter	1490
245	tim	1818	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
246			result += buffer;
247	gezelter	1490
248	tim	1818	sprintf(buffer,
249			"------------------------------------------------------------------\n");
250			result += buffer;
251
252			return result;
253	gezelter	1490	}
254
255			//----------------------------------------------------------------------------//
256
257	tim	1818	XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) :
258			BaseVisitor() {
259			this->info = info;
260			visitorName = "XYZVisitor";
261			this->printDipole = printDipole;
262	gezelter	1490	}
263
264	tim	1818	void XYZVisitor::visit(Atom *atom) {
265			if (!isIgnore(atom))
266			internalVisit(atom);
267	gezelter	1490	}
268
269	tim	1818	void XYZVisitor::visit(DirectionalAtom *datom) {
270			if (!isIgnore(datom))
271			internalVisit(datom);
272	gezelter	1490	}
273
274	tim	1818	void XYZVisitor::visit(RigidBody *rb) {
275			if (!isIgnore(rb))
276			internalVisit(rb);
277	gezelter	1490	}
278
279	tim	1818	void XYZVisitor::internalVisit(StuntDouble *sd) {
280			GenericData * data;
281			AtomData * atomData;
282			AtomInfo * atomInfo;
283			std::vector<AtomInfo *>::iterator i;
284			char buffer[1024];
285	gezelter	1490
286	tim	1818	//if there is not atom data, just skip it
287			data = sd->getPropertyByName("ATOMDATA");
288	gezelter	1490
289	tim	1818	if (data != NULL) {
290			atomData = dynamic_cast<AtomData *>(data);
291	gezelter	1490
292	tim	1818	if (atomData == NULL)
293			return;
294			} else
295			return;
296	gezelter	1490
297	tim	1818	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
298			atomInfo = atomData->nextAtomInfo(i) ) {
299			if (printDipole)
300			sprintf(buffer,
301			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
302			atomInfo->AtomType.c_str(),
303			atomInfo->pos[0],
304			atomInfo->pos[1],
305			atomInfo->pos[2],
306			atomInfo->dipole[0],
307			atomInfo->dipole[1],
308			atomInfo->dipole[2]); else
309			sprintf(buffer, "%s%15.8f%15.8f%15.8f",
310			atomInfo->AtomType.c_str(), atomInfo->pos[0],
311			atomInfo->pos[1], atomInfo->pos[2]);
312
313			frame.push_back(buffer);
314			}
315	gezelter	1490	}
316
317	tim	1818	bool XYZVisitor::isIgnore(StuntDouble *sd) {
318			GenericData *data;
319
320			data = sd->getPropertyByName("IGNORE");
321			return data == NULL ? false : true;
322	gezelter	1490	}
323
324	tim	1818	void XYZVisitor::writeFrame(ostream &outStream) {
325			std::vector<std::string>::iterator i;
326			char buffer[1024];
327	gezelter	1490
328	tim	1818	if (frame.size() == 0)
329			cerr << "Current Frame does not contain any atoms" << endl;
330	gezelter	1490
331	tim	1818	//total number of atoms
332			outStream << frame.size() << endl;
333	gezelter	1490
334	tim	1818	//write comment line
335			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
336			Mat3x3d box = currSnapshot->getHmat();
337
338			sprintf(buffer,
339			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
340			currSnapshot->getTime(),
341			box(0, 0), box(0, 1), box(0, 2),
342			box(1, 0), box(1, 1), box(1, 2),
343			box(2, 0), box(2, 1), box(2, 2));
344	gezelter	1490
345	tim	1818	outStream << buffer << endl;
346	gezelter	1490
347	tim	1818	for( i = frame.begin(); i != frame.end(); ++i )
348			outStream << *i << endl;
349	gezelter	1490	}
350
351	tim	1818	const std::string XYZVisitor::toString() {
352			char buffer[65535];
353			std::string result;
354	gezelter	1490
355	tim	1818	sprintf(buffer,
356			"------------------------------------------------------------------\n");
357			result += buffer;
358	gezelter	1490
359	tim	1818	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
360			result += buffer;
361	gezelter	1490
362	tim	1818	sprintf(buffer,
363			"Visitor Description: assemble the atom data and output xyz file\n");
364			result += buffer;
365
366			sprintf(buffer,
367			"------------------------------------------------------------------\n");
368			result += buffer;
369
370			return result;
371	gezelter	1490	}
372
373			//----------------------------------------------------------------------------//
374
375	tim	1818	void PrepareVisitor::internalVisit(Atom *atom) {
376			GenericData *data;
377			AtomData * atomData;
378	gezelter	1490
379	tim	1818	//if visited property is existed, remove it
380			data = atom->getPropertyByName("VISITED");
381	gezelter	1490
382	tim	1818	if (data != NULL) {
383			atom->removeProperty("VISITED");
384			}
385
386			//remove atomdata
387			data = atom->getPropertyByName("ATOMDATA");
388
389			if (data != NULL) {
390			atomData = dynamic_cast<AtomData *>(data);
391
392			if (atomData != NULL)
393			atom->removeProperty("ATOMDATA");
394			}
395	gezelter	1490	}
396
397	tim	1818	void PrepareVisitor::internalVisit(RigidBody *rb) {
398			GenericData* data;
399			AtomData* atomData;
400			std::vector<Atom *> myAtoms;
401			std::vector<Atom *>::iterator atomIter;
402	gezelter	1490
403	tim	1818	//if visited property is existed, remove it
404			data = rb->getPropertyByName("VISITED");
405	gezelter	1490
406	tim	1818	if (data != NULL) {
407			rb->removeProperty("VISITED");
408			}
409
410			//remove atomdata
411			data = rb->getPropertyByName("ATOMDATA");
412
413			if (data != NULL) {
414			atomData = dynamic_cast<AtomData *>(data);
415
416			if (atomData != NULL)
417			rb->removeProperty("ATOMDATA");
418			}
419
420			myAtoms = rb->getAtoms();
421
422			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
423			internalVisit(*atomIter);
424	gezelter	1490	}
425
426	tim	1818	const std::string PrepareVisitor::toString() {
427			char buffer[65535];
428			std::string result;
429	gezelter	1490
430	tim	1818	sprintf(buffer,
431			"------------------------------------------------------------------\n");
432			result += buffer;
433	gezelter	1490
434	tim	1818	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
435			result += buffer;
436	gezelter	1490
437	tim	1818	sprintf(buffer,
438			"Visitor Description: prepare for operation of other vistors\n");
439			result += buffer;
440	gezelter	1490
441	tim	1818	sprintf(buffer,
442			"------------------------------------------------------------------\n");
443			result += buffer;
444
445			return result;
446	gezelter	1490	}
447
448			//----------------------------------------------------------------------------//
449
450	tim	1818	WaterTypeVisitor::WaterTypeVisitor() {
451			visitorName = "WaterTypeVisitor";
452			waterTypeList.insert("TIP3P_RB_0");
453			waterTypeList.insert("TIP4P_RB_0");
454			waterTypeList.insert("TIP5P_RB_0");
455			waterTypeList.insert("SPCE_RB_0");
456	gezelter	1490	}
457
458	tim	1818	void WaterTypeVisitor::visit(RigidBody *rb) {
459			std::string rbName;
460			std::vector<Atom *> myAtoms;
461			std::vector<Atom *>::iterator atomIter;
462			GenericData* data;
463			AtomData* atomData;
464			AtomInfo* atomInfo;
465			std::vector<AtomInfo *>::iterator i;
466	gezelter	1490
467	tim	1818	rbName = rb->getType();
468	gezelter	1490
469	tim	1818	if (waterTypeList.find(rbName) != waterTypeList.end()) {
470			myAtoms = rb->getAtoms();
471	gezelter	1490
472	tim	1818	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
473			++atomIter ) {
474			data = (*atomIter)->getPropertyByName("ATOMDATA");
475	gezelter	1490
476	tim	1818	if (data != NULL) {
477			atomData = dynamic_cast<AtomData *>(data);
478	gezelter	1490
479	tim	1818	if (atomData == NULL)
480			continue;
481			} else
482			continue;
483
484			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
485			atomInfo = atomData->nextAtomInfo(i) ) {
486			replaceType(atomInfo->AtomType);
487			} //end for(atomInfo)
488			} //end for(atomIter)
489			} //end if (waterTypeList.find(rbName) != waterTypeList.end())
490	gezelter	1490	}
491
492	tim	1818	void WaterTypeVisitor::replaceType(std::string&atomType) {
493			atomType = atomType.substr(0, atomType.find('_'));
494	gezelter	1490	}
495
496	tim	1818	const std::string WaterTypeVisitor::toString() {
497			char buffer[65535];
498			std::string result;
499	gezelter	1490
500	tim	1818	sprintf(buffer,
501			"------------------------------------------------------------------\n");
502			result += buffer;
503	gezelter	1490
504	tim	1818	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
505			result += buffer;
506	gezelter	1490
507	tim	1818	sprintf(buffer,
508			"Visitor Description: Replace the atom type in water model\n");
509			result += buffer;
510	gezelter	1490
511	tim	1818	sprintf(buffer,
512			"------------------------------------------------------------------\n");
513			result += buffer;
514
515			return result;
516	gezelter	1490	}
517
518	tim	1818	} //namespace oopse