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 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) {
    info->getSelectionManager()->clearSelection(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 (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::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) ) {
      printf("SD type is %s\n", sd->getType().c_str());
      printf("XYZVisitor thinks %s\n", atomInfo->atomTypeName.c_str());
      if (printDipole) {
        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]); 
      } else {
        sprintf(buffer,                     "%s%15.8f%15.8f%15.8f",
                atomInfo->atomTypeName.c_str(), atomInfo->pos[0],
                atomInfo->pos[1],           atomInfo->pos[2]);
      }
        
        frame.push_back(buffer);
    }
}

bool XYZVisitor::isSelected(StuntDouble *sd) {
    return info->getSelectionManager()->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:	2091
Committed:	Tue Mar 8 21:07:49 2005 UTC (19 years, 4 months ago) by gezelter
File size:	16792 byte(s)
Log Message:	fixing a strange icc8 bug (we think).
#	User	Rev	Content
1	gezelter	2091	/*
2	gezelter	1930	* 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	2008	#include "selection/SelectionManager.hpp"
42	tim	1492	#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	1625	namespace oopse {
48
49	gezelter	1490	//----------------------------------------------------------------------------//
50	gezelter	1930	void IgnoreVisitor::visit(Atom *atom) {
51			if (isIgnoreType(atom->getType()))
52			internalVisit(atom);
53	gezelter	1490	}
54
55	gezelter	1930	void IgnoreVisitor::visit(DirectionalAtom *datom) {
56			if (isIgnoreType(datom->getType()))
57			internalVisit(datom);
58	gezelter	1490	}
59
60	gezelter	1930	void IgnoreVisitor::visit(RigidBody *rb) {
61			std::vector<Atom *> myAtoms;
62			std::vector<Atom *>::iterator atomIter;
63			AtomInfo * atomInfo;
64	gezelter	1490
65	gezelter	1930	if (isIgnoreType(rb->getType())) {
66			internalVisit(rb);
67	gezelter	1490
68	gezelter	1930	myAtoms = rb->getAtoms();
69
70			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
71			internalVisit(*atomIter);
72			}
73	gezelter	1490	}
74
75	gezelter	1930	bool IgnoreVisitor::isIgnoreType(const std::string&name) {
76			return itList.find(name) != itList.end() ? true : false;
77	gezelter	1490	}
78
79	gezelter	1930	void IgnoreVisitor::internalVisit(StuntDouble *sd) {
80	tim	1977	info->getSelectionManager()->clearSelection(sd);
81			//GenericData *data;
82			//data = sd->getPropertyByName("IGNORE");
83			//
84			////if this stuntdoulbe is already marked as ignore just skip it
85			//if (data == NULL) {
86			// data = new GenericData;
87			// data->setID("IGNORE");
88			// sd->addProperty(data);
89			//}
90	gezelter	1490	}
91
92	gezelter	1930	const std::string IgnoreVisitor::toString() {
93			char buffer[65535];
94			std::string result;
95			std::set<std::string>::iterator i;
96	gezelter	1490
97	gezelter	1930	sprintf(buffer,
98			"------------------------------------------------------------------\n");
99			result += buffer;
100	gezelter	1490
101	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
102			result += buffer;
103	gezelter	1490
104	gezelter	1930	sprintf(buffer, "Visitor Description: ignore stuntdoubles\n");
105			result += buffer;
106	gezelter	1490
107	gezelter	1930	//print the ignore type list
108			sprintf(buffer, "Ignore type list contains below types:\n");
109	gezelter	1490	result += buffer;
110
111	gezelter	1930	for( i = itList.begin(); i != itList.end(); ++i ) {
112			sprintf(buffer, "%s\t", i->c_str());
113			result += buffer;
114			}
115	gezelter	1490
116	gezelter	1930	sprintf(buffer, "\n");
117			result += buffer;
118	gezelter	1490
119	gezelter	1930	sprintf(buffer,
120			"------------------------------------------------------------------\n");
121			result += buffer;
122
123			return result;
124	gezelter	1490	}
125
126			//----------------------------------------------------------------------------//
127
128	gezelter	1930	void WrappingVisitor::visit(Atom *atom) {
129			internalVisit(atom);
130	gezelter	1490	}
131	gezelter	1930
132			void WrappingVisitor::visit(DirectionalAtom *datom) {
133			internalVisit(datom);
134	gezelter	1490	}
135
136	gezelter	1930	void WrappingVisitor::visit(RigidBody *rb) {
137			internalVisit(rb);
138	gezelter	1490	}
139
140	gezelter	1930	void WrappingVisitor::internalVisit(StuntDouble *sd) {
141			GenericData * data;
142			AtomData * atomData;
143			AtomInfo * atomInfo;
144			std::vector<AtomInfo *>::iterator i;
145	gezelter	1490
146	gezelter	1930	data = sd->getPropertyByName("ATOMDATA");
147	gezelter	1490
148	gezelter	1930	if (data != NULL) {
149			atomData = dynamic_cast<AtomData *>(data);
150	gezelter	1490
151	gezelter	1930	if (atomData == NULL)
152			return;
153			} else
154			return;
155
156			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
157
158			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
159			currSnapshot->wrapVector(atomInfo->pos);
160			}
161	gezelter	1490	}
162
163	gezelter	1930	const std::string WrappingVisitor::toString() {
164			char buffer[65535];
165			std::string result;
166	gezelter	1490
167	gezelter	1930	sprintf(buffer,
168			"------------------------------------------------------------------\n");
169			result += buffer;
170	gezelter	1490
171	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
172			result += buffer;
173	gezelter	1490
174	gezelter	1930	sprintf(buffer,
175			"Visitor Description: wrapping atoms back to periodic box\n");
176			result += buffer;
177
178			sprintf(buffer,
179			"------------------------------------------------------------------\n");
180			result += buffer;
181
182			return result;
183	gezelter	1490	}
184
185			//----------------------------------------------------------------------------//
186
187	gezelter	1930	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
188			BaseVisitor() {
189			this->info = info;
190			visitorName = "ReplicateVisitor";
191			this->replicateOpt = opt;
192
193			//generate the replicate directions
194			for( int i = 0; i <= replicateOpt[0]; i++ ) {
195			for( int j = 0; j <= replicateOpt[1]; j++ ) {
196			for( int k = 0; k <= replicateOpt[2]; k++ ) {
197			//skip original frame
198			if (i == 0 && j == 0 && k == 0) {
199			continue;
200			} else {
201			dir.push_back(Vector3i(i, j, k));
202			}
203			}
204			}
205			}
206
207	gezelter	1490	}
208	gezelter	1930
209			void ReplicateVisitor::visit(Atom *atom) {
210			internalVisit(atom);
211	gezelter	1490	}
212	gezelter	1930
213			void ReplicateVisitor::visit(DirectionalAtom *datom) {
214			internalVisit(datom);
215	gezelter	1490	}
216
217	gezelter	1930	void ReplicateVisitor::visit(RigidBody *rb) {
218			internalVisit(rb);
219	gezelter	1490	}
220
221	gezelter	1930	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
222			GenericData * data;
223			AtomData * atomData;
224	gezelter	1490
225	gezelter	1930	//if there is not atom data, just skip it
226			data = sd->getPropertyByName("ATOMDATA");
227	gezelter	1490
228	gezelter	1930	if (data != NULL) {
229			atomData = dynamic_cast<AtomData *>(data);
230	gezelter	1490
231	gezelter	1930	if (atomData == NULL) {
232			return;
233			}
234			} else {
235			return;
236			}
237
238			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
239			Mat3x3d box = currSnapshot->getHmat();
240
241			std::vector<AtomInfo *> atomInfoList = atomData->getData();
242
243			replicate(atomInfoList, atomData, box);
244	gezelter	1490	}
245
246	gezelter	1930	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
247			AtomInfo* newAtomInfo;
248			std::vector<Vector3i>::iterator dirIter;
249			std::vector<AtomInfo *>::iterator i;
250	gezelter	1490
251	gezelter	1930	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
252			for( i = infoList.begin(); i != infoList.end(); i++ ) {
253			newAtomInfo = new AtomInfo();
254			newAtomInfo = (*i);
255	gezelter	1490
256	gezelter	1930	for( int j = 0; j < 3; j++ )
257			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
258
259			data->addAtomInfo(newAtomInfo);
260			}
261			} // end for(dirIter)
262	gezelter	1490	}
263
264	gezelter	1930	const std::string ReplicateVisitor::toString() {
265			char buffer[65535];
266			std::string result;
267			std::set<std::string>::iterator i;
268	gezelter	1490
269	gezelter	1930	sprintf(buffer,
270			"------------------------------------------------------------------\n");
271			result += buffer;
272	gezelter	1490
273	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
274			result += buffer;
275	gezelter	1490
276	gezelter	1930	sprintf(buffer,
277			"Visitor Description: replicate the atoms in different direction\n");
278			result += buffer;
279	gezelter	1490
280	gezelter	1930	//print the replicate direction
281			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
282			result += buffer;
283	gezelter	1490
284	gezelter	1930	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
285			result += buffer;
286	gezelter	1490
287	gezelter	1930	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
288			result += buffer;
289	gezelter	1490
290	gezelter	1930	sprintf(buffer,
291			"------------------------------------------------------------------\n");
292			result += buffer;
293
294			return result;
295	gezelter	1490	}
296
297			//----------------------------------------------------------------------------//
298
299	gezelter	1930	XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) :
300			BaseVisitor() {
301			this->info = info;
302			visitorName = "XYZVisitor";
303			this->printDipole = printDipole;
304	gezelter	1490	}
305
306	gezelter	1930	void XYZVisitor::visit(Atom *atom) {
307	tim	1977	if (isSelected(atom))
308	gezelter	1930	internalVisit(atom);
309	gezelter	1490	}
310
311	gezelter	1930	void XYZVisitor::visit(DirectionalAtom *datom) {
312	tim	1977	if (isSelected(datom))
313	gezelter	1930	internalVisit(datom);
314	gezelter	1490	}
315
316	gezelter	1930	void XYZVisitor::visit(RigidBody *rb) {
317	tim	1977	if (isSelected(rb))
318	gezelter	1930	internalVisit(rb);
319	gezelter	1490	}
320
321	gezelter	1930	void XYZVisitor::internalVisit(StuntDouble *sd) {
322			GenericData * data;
323			AtomData * atomData;
324			AtomInfo * atomInfo;
325			std::vector<AtomInfo *>::iterator i;
326			char buffer[1024];
327	gezelter	1490
328	gezelter	1930	//if there is not atom data, just skip it
329			data = sd->getPropertyByName("ATOMDATA");
330	gezelter	1490
331	gezelter	1930	if (data != NULL) {
332			atomData = dynamic_cast<AtomData *>(data);
333	gezelter	1490
334	gezelter	1930	if (atomData == NULL)
335			return;
336			} else
337			return;
338	gezelter	1490
339	gezelter	1930	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
340			atomInfo = atomData->nextAtomInfo(i) ) {
341	gezelter	2091	printf("SD type is %s\n", sd->getType().c_str());
342			printf("XYZVisitor thinks %s\n", atomInfo->atomTypeName.c_str());
343			if (printDipole) {
344			sprintf(buffer,
345			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
346			atomInfo->atomTypeName.c_str(),
347			atomInfo->pos[0],
348			atomInfo->pos[1],
349			atomInfo->pos[2],
350			atomInfo->dipole[0],
351			atomInfo->dipole[1],
352			atomInfo->dipole[2]);
353			} else {
354			sprintf(buffer, "%s%15.8f%15.8f%15.8f",
355			atomInfo->atomTypeName.c_str(), atomInfo->pos[0],
356			atomInfo->pos[1], atomInfo->pos[2]);
357			}
358
359	gezelter	1930	frame.push_back(buffer);
360			}
361	gezelter	1490	}
362
363	tim	1977	bool XYZVisitor::isSelected(StuntDouble *sd) {
364			return info->getSelectionManager()->isSelected(sd);
365	gezelter	1490	}
366
367	gezelter	1930	void XYZVisitor::writeFrame(std::ostream &outStream) {
368			std::vector<std::string>::iterator i;
369			char buffer[1024];
370	gezelter	1490
371	gezelter	1930	if (frame.size() == 0)
372			std::cerr << "Current Frame does not contain any atoms" << std::endl;
373	gezelter	1490
374	gezelter	1930	//total number of atoms
375			outStream << frame.size() << std::endl;
376	gezelter	1490
377	gezelter	1930	//write comment line
378			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
379			Mat3x3d box = currSnapshot->getHmat();
380
381			sprintf(buffer,
382			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
383			currSnapshot->getTime(),
384			box(0, 0), box(0, 1), box(0, 2),
385			box(1, 0), box(1, 1), box(1, 2),
386			box(2, 0), box(2, 1), box(2, 2));
387	gezelter	1490
388	gezelter	1930	outStream << buffer << std::endl;
389	gezelter	1490
390	gezelter	1930	for( i = frame.begin(); i != frame.end(); ++i )
391			outStream << *i << std::endl;
392	gezelter	1490	}
393
394	gezelter	1930	const std::string XYZVisitor::toString() {
395			char buffer[65535];
396			std::string result;
397	gezelter	1490
398	gezelter	1930	sprintf(buffer,
399			"------------------------------------------------------------------\n");
400			result += buffer;
401	gezelter	1490
402	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
403			result += buffer;
404	gezelter	1490
405	gezelter	1930	sprintf(buffer,
406			"Visitor Description: assemble the atom data and output xyz file\n");
407			result += buffer;
408
409			sprintf(buffer,
410			"------------------------------------------------------------------\n");
411			result += buffer;
412
413			return result;
414	gezelter	1490	}
415
416			//----------------------------------------------------------------------------//
417
418	gezelter	1930	void PrepareVisitor::internalVisit(Atom *atom) {
419			GenericData *data;
420			AtomData * atomData;
421	gezelter	1490
422	gezelter	1930	//if visited property is existed, remove it
423			data = atom->getPropertyByName("VISITED");
424	gezelter	1490
425	gezelter	1930	if (data != NULL) {
426			atom->removeProperty("VISITED");
427			}
428
429			//remove atomdata
430			data = atom->getPropertyByName("ATOMDATA");
431
432			if (data != NULL) {
433			atomData = dynamic_cast<AtomData *>(data);
434
435			if (atomData != NULL)
436			atom->removeProperty("ATOMDATA");
437			}
438	gezelter	1490	}
439
440	gezelter	1930	void PrepareVisitor::internalVisit(RigidBody *rb) {
441			GenericData* data;
442			AtomData* atomData;
443			std::vector<Atom *> myAtoms;
444			std::vector<Atom *>::iterator atomIter;
445	gezelter	1490
446	gezelter	1930	//if visited property is existed, remove it
447			data = rb->getPropertyByName("VISITED");
448	gezelter	1490
449	gezelter	1930	if (data != NULL) {
450			rb->removeProperty("VISITED");
451			}
452
453			//remove atomdata
454			data = rb->getPropertyByName("ATOMDATA");
455
456			if (data != NULL) {
457			atomData = dynamic_cast<AtomData *>(data);
458
459			if (atomData != NULL)
460			rb->removeProperty("ATOMDATA");
461			}
462
463			myAtoms = rb->getAtoms();
464
465			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
466			internalVisit(*atomIter);
467	gezelter	1490	}
468
469	gezelter	1930	const std::string PrepareVisitor::toString() {
470	tim	1977	char buffer[65535];
471			std::string result;
472
473			sprintf(buffer,
474			"------------------------------------------------------------------\n");
475			result += buffer;
476
477			sprintf(buffer, "Visitor name: %s", visitorName.c_str());
478			result += buffer;
479
480			sprintf(buffer,
481			"Visitor Description: prepare for operation of other vistors\n");
482			result += buffer;
483
484			sprintf(buffer,
485			"------------------------------------------------------------------\n");
486			result += buffer;
487
488			return result;
489	gezelter	1490	}
490
491			//----------------------------------------------------------------------------//
492
493	gezelter	1930	WaterTypeVisitor::WaterTypeVisitor() {
494			visitorName = "WaterTypeVisitor";
495			waterTypeList.insert("TIP3P_RB_0");
496			waterTypeList.insert("TIP4P_RB_0");
497			waterTypeList.insert("TIP5P_RB_0");
498			waterTypeList.insert("SPCE_RB_0");
499	gezelter	1490	}
500
501	gezelter	1930	void WaterTypeVisitor::visit(RigidBody *rb) {
502			std::string rbName;
503			std::vector<Atom *> myAtoms;
504			std::vector<Atom *>::iterator atomIter;
505			GenericData* data;
506			AtomData* atomData;
507			AtomInfo* atomInfo;
508			std::vector<AtomInfo *>::iterator i;
509	gezelter	1490
510	gezelter	1930	rbName = rb->getType();
511	gezelter	1490
512	gezelter	1930	if (waterTypeList.find(rbName) != waterTypeList.end()) {
513			myAtoms = rb->getAtoms();
514	gezelter	1490
515	gezelter	1930	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
516			++atomIter ) {
517			data = (*atomIter)->getPropertyByName("ATOMDATA");
518	gezelter	1490
519	gezelter	1930	if (data != NULL) {
520			atomData = dynamic_cast<AtomData *>(data);
521	gezelter	1490
522	gezelter	1930	if (atomData == NULL)
523			continue;
524			} else
525			continue;
526
527			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
528	gezelter	2091	atomInfo = atomData->nextAtomInfo(i) ) {
529			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
530	gezelter	1930	} //end for(atomInfo)
531			} //end for(atomIter)
532			} //end if (waterTypeList.find(rbName) != waterTypeList.end())
533	gezelter	1490	}
534
535	gezelter	2091	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
536			return atomTypeName.substr(0, atomTypeName.find('_'));
537			}
538	gezelter	1490
539	gezelter	1930	const std::string WaterTypeVisitor::toString() {
540			char buffer[65535];
541			std::string result;
542	gezelter	1490
543	gezelter	1930	sprintf(buffer,
544			"------------------------------------------------------------------\n");
545			result += buffer;
546	gezelter	1490
547	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
548			result += buffer;
549	gezelter	1490
550	gezelter	1930	sprintf(buffer,
551			"Visitor Description: Replace the atom type in water model\n");
552			result += buffer;
553	gezelter	1490
554	gezelter	1930	sprintf(buffer,
555			"------------------------------------------------------------------\n");
556			result += buffer;
557
558			return result;
559	gezelter	1490	}
560
561	gezelter	1930	} //namespace oopse