src/visitors/OtherVisitor.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
#include "selection/SelectionManager.hpp" 
#include "visitors/OtherVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Molecule.hpp"
#include "brains/SimInfo.hpp"
namespace oopse {

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

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

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

  void WrappingVisitor::internalVisit(StuntDouble *sd) {
    GenericData *                     data;
    AtomData *                        atomData;
    AtomInfo *                        atomInfo;
    std::vector<AtomInfo *>::iterator i;

    data = sd->getPropertyByName("ATOMDATA");

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

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

    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
    
    for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
      Vector3d newPos = atomInfo->pos - origin_;
      currSnapshot->wrapVector(newPos);
      atomInfo->pos = newPos;
    }
  }

  void WrappingVisitor::update() {
    if (useCom_){
      origin_ = info->getCom();
    }
  }
  
  const std::string WrappingVisitor::toString() {
    char        buffer[65535];
    std::string result;

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

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

    sprintf(buffer,
            "Visitor Description: wrapping atoms back to periodic box\n");
    result += buffer;

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

    return result;
  }

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

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

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

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

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

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

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

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

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

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

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

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

    replicate(atomInfoList, atomData, box);
  }

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

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

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

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

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

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

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

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

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

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

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

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

    return result;
  }

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

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

      evaluator.loadScriptString("select all");

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

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

      evaluator.loadScriptString(script);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    outStream << buffer << std::endl;

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

  const std::string XYZVisitor::toString() {
    char        buffer[65535];
    std::string result;

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

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

    sprintf(buffer,
            "Visitor Description: assemble the atom data and output xyz file\n");
    result += buffer;

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

    return result;
  }

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

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

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

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

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

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

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

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

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

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

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

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

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

    myAtoms = rb->getAtoms();

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

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

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

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

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

    rbName = rb->getType();

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

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

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

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

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

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

  const std::string WaterTypeVisitor::toString() {
    char buffer[65535];
    std::string result;

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

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

    sprintf(buffer,
            "Visitor Description: Replace the atom type in water model\n");
    result += buffer;

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

    return result;
  }

} //namespace oopse
Revision:	1118
Committed:	Tue Jan 16 22:18:04 2007 UTC (18 years, 3 months ago) by chuckv
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	14915 byte(s)
Log Message:	Support for printPosOnly in Dump2XYZ.
#	User	Rev	Content
1	gezelter	407	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41	tim	324	#include "selection/SelectionManager.hpp"
42	tim	3	#include "visitors/OtherVisitor.hpp"
43			#include "primitives/DirectionalAtom.hpp"
44			#include "primitives/RigidBody.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "brains/SimInfo.hpp"
47	tim	132	namespace oopse {
48
49	gezelter	507	void WrappingVisitor::visit(Atom *atom) {
50			internalVisit(atom);
51			}
52	gezelter	246
53	gezelter	507	void WrappingVisitor::visit(DirectionalAtom *datom) {
54			internalVisit(datom);
55			}
56	gezelter	2
57	gezelter	507	void WrappingVisitor::visit(RigidBody *rb) {
58			internalVisit(rb);
59			}
60	gezelter	2
61	gezelter	507	void WrappingVisitor::internalVisit(StuntDouble *sd) {
62	gezelter	246	GenericData * data;
63			AtomData * atomData;
64			AtomInfo * atomInfo;
65			std::vector<AtomInfo *>::iterator i;
66	gezelter	2
67	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
68	gezelter	2
69	gezelter	246	if (data != NULL) {
70	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
71	gezelter	2
72	gezelter	507	if (atomData == NULL)
73			return;
74	gezelter	246	} else
75	gezelter	507	return;
76	gezelter	246
77			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78
79			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80	tim	543	Vector3d newPos = atomInfo->pos - origin_;
81			currSnapshot->wrapVector(newPos);
82			atomInfo->pos = newPos;
83	gezelter	246	}
84	gezelter	507	}
85	gezelter	2
86	tim	543	void WrappingVisitor::update() {
87			if (useCom_){
88			origin_ = info->getCom();
89			}
90			}
91
92	gezelter	507	const std::string WrappingVisitor::toString() {
93	gezelter	246	char buffer[65535];
94			std::string result;
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,
104			"Visitor Description: wrapping atoms back to periodic box\n");
105			result += buffer;
106
107			sprintf(buffer,
108			"------------------------------------------------------------------\n");
109			result += buffer;
110
111			return result;
112	gezelter	507	}
113	gezelter	2
114	gezelter	507	//----------------------------------------------------------------------------//
115	gezelter	2
116	gezelter	507	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
117	gezelter	246	BaseVisitor() {
118	gezelter	507	this->info = info;
119			visitorName = "ReplicateVisitor";
120			this->replicateOpt = opt;
121	gezelter	246
122	gezelter	507	//generate the replicate directions
123			for( int i = 0; i <= replicateOpt[0]; i++ ) {
124	gezelter	246	for( int j = 0; j <= replicateOpt[1]; j++ ) {
125	gezelter	507	for( int k = 0; k <= replicateOpt[2]; k++ ) {
126			//skip original frame
127			if (i == 0 && j == 0 && k == 0) {
128			continue;
129			} else {
130			dir.push_back(Vector3i(i, j, k));
131			}
132			}
133	gezelter	246	}
134	gezelter	507	}
135
136	gezelter	246	}
137
138	gezelter	507	void ReplicateVisitor::visit(Atom *atom) {
139			internalVisit(atom);
140			}
141	gezelter	246
142	gezelter	507	void ReplicateVisitor::visit(DirectionalAtom *datom) {
143			internalVisit(datom);
144			}
145	gezelter	2
146	gezelter	507	void ReplicateVisitor::visit(RigidBody *rb) {
147			internalVisit(rb);
148			}
149	gezelter	2
150	gezelter	507	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
151	gezelter	246	GenericData * data;
152			AtomData * atomData;
153	gezelter	2
154	gezelter	246	//if there is not atom data, just skip it
155			data = sd->getPropertyByName("ATOMDATA");
156	gezelter	2
157	gezelter	246	if (data != NULL) {
158	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
159	gezelter	2
160	gezelter	507	if (atomData == NULL) {
161			return;
162			}
163	gezelter	246	} else {
164	gezelter	507	return;
165	gezelter	246	}
166
167			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
168			Mat3x3d box = currSnapshot->getHmat();
169
170			std::vector<AtomInfo *> atomInfoList = atomData->getData();
171
172			replicate(atomInfoList, atomData, box);
173	gezelter	507	}
174	gezelter	2
175	gezelter	507	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
176	gezelter	246	AtomInfo* newAtomInfo;
177			std::vector<Vector3i>::iterator dirIter;
178			std::vector<AtomInfo *>::iterator i;
179	gezelter	2
180	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
181	gezelter	507	for( i = infoList.begin(); i != infoList.end(); i++ ) {
182			newAtomInfo = new AtomInfo();
183			newAtomInfo = (*i);
184	gezelter	2
185	gezelter	507	for( int j = 0; j < 3; j++ )
186			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
187	gezelter	246
188	gezelter	507	data->addAtomInfo(newAtomInfo);
189			}
190	gezelter	246	} // end for(dirIter)
191	gezelter	507	}
192	gezelter	2
193	gezelter	507	const std::string ReplicateVisitor::toString() {
194	gezelter	246	char buffer[65535];
195			std::string result;
196			std::set<std::string>::iterator i;
197	gezelter	2
198	gezelter	246	sprintf(buffer,
199			"------------------------------------------------------------------\n");
200			result += buffer;
201	gezelter	2
202	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
203			result += buffer;
204	gezelter	2
205	gezelter	246	sprintf(buffer,
206			"Visitor Description: replicate the atoms in different direction\n");
207			result += buffer;
208	gezelter	2
209	gezelter	246	//print the replicate direction
210			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
211			result += buffer;
212	gezelter	2
213	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
214			result += buffer;
215	gezelter	2
216	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
217			result += buffer;
218	gezelter	2
219	gezelter	246	sprintf(buffer,
220			"------------------------------------------------------------------\n");
221			result += buffer;
222
223			return result;
224	gezelter	507	}
225	gezelter	2
226	gezelter	507	//----------------------------------------------------------------------------//
227	gezelter	2
228	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info) :
229	tim	413	BaseVisitor(), seleMan(info), evaluator(info){
230	gezelter	507	this->info = info;
231			visitorName = "XYZVisitor";
232	tim	413
233	gezelter	507	evaluator.loadScriptString("select all");
234	tim	413
235	gezelter	507	if (!evaluator.isDynamic()) {
236	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
237	gezelter	507	}
238	chuckv	1118	posOnly_ = false;
239	tim	413	}
240
241	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
242	tim	413	BaseVisitor(), seleMan(info), evaluator(info) {
243	gezelter	507	this->info = info;
244			visitorName = "XYZVisitor";
245	tim	413
246	gezelter	507	evaluator.loadScriptString(script);
247	tim	413
248	gezelter	507	if (!evaluator.isDynamic()) {
249	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
250	gezelter	507	}
251	chuckv	1118	posOnly_ = false;
252	tim	413	}
253
254	gezelter	507	void XYZVisitor::visit(Atom *atom) {
255	tim	293	if (isSelected(atom))
256	gezelter	507	internalVisit(atom);
257			}
258	gezelter	2
259	gezelter	507	void XYZVisitor::visit(DirectionalAtom *datom) {
260	tim	293	if (isSelected(datom))
261	gezelter	507	internalVisit(datom);
262			}
263	gezelter	2
264	gezelter	507	void XYZVisitor::visit(RigidBody *rb) {
265	tim	293	if (isSelected(rb))
266	gezelter	507	internalVisit(rb);
267			}
268	gezelter	2
269	gezelter	507	void XYZVisitor::update() {
270	tim	413	//if dynamic, we need to re-evaluate the selection
271			if (evaluator.isDynamic()) {
272	gezelter	507	seleMan.setSelectionSet(evaluator.evaluate());
273	tim	413	}
274	gezelter	507	}
275	tim	413
276	gezelter	507	void XYZVisitor::internalVisit(StuntDouble *sd) {
277	gezelter	246	GenericData * data;
278			AtomData * atomData;
279			AtomInfo * atomInfo;
280			std::vector<AtomInfo *>::iterator i;
281			char buffer[1024];
282	gezelter	2
283	gezelter	246	//if there is not atom data, just skip it
284			data = sd->getPropertyByName("ATOMDATA");
285	gezelter	2
286	gezelter	246	if (data != NULL) {
287	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
288	gezelter	2
289	gezelter	507	if (atomData == NULL)
290			return;
291	gezelter	246	} else
292	gezelter	507	return;
293	gezelter	2
294	chuckv	1118	if (posOnly_){
295			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
296			atomInfo = atomData->nextAtomInfo(i) ) {
297			sprintf(buffer,
298			"%s%15.8f%15.8f%15.8f",
299			atomInfo->atomTypeName.c_str(),
300			atomInfo->pos[0],
301			atomInfo->pos[1],
302			atomInfo->pos[2]);
303			frame.push_back(buffer);
304			}
305			}else{
306			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
307			atomInfo = atomData->nextAtomInfo(i) ) {
308			sprintf(buffer,
309			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
310			atomInfo->atomTypeName.c_str(),
311			atomInfo->pos[0],
312			atomInfo->pos[1],
313			atomInfo->pos[2],
314			atomInfo->dipole[0],
315			atomInfo->dipole[1],
316			atomInfo->dipole[2]);
317			frame.push_back(buffer);
318			}
319	gezelter	246	}
320	gezelter	507	}
321	gezelter	2
322	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
323	tim	413	return seleMan.isSelected(sd);
324	gezelter	507	}
325	gezelter	2
326	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
327	gezelter	246	std::vector<std::string>::iterator i;
328			char buffer[1024];
329	gezelter	2
330	gezelter	246	if (frame.size() == 0)
331	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
332	gezelter	2
333	gezelter	246	//total number of atoms
334			outStream << frame.size() << std::endl;
335	gezelter	2
336	gezelter	246	//write comment line
337			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
338			Mat3x3d box = currSnapshot->getHmat();
339
340			sprintf(buffer,
341			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
342			currSnapshot->getTime(),
343			box(0, 0), box(0, 1), box(0, 2),
344			box(1, 0), box(1, 1), box(1, 2),
345			box(2, 0), box(2, 1), box(2, 2));
346	gezelter	2
347	gezelter	246	outStream << buffer << std::endl;
348	gezelter	2
349	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
350	gezelter	507	outStream << *i << std::endl;
351			}
352	gezelter	2
353	gezelter	507	const std::string XYZVisitor::toString() {
354	gezelter	246	char buffer[65535];
355			std::string result;
356	gezelter	2
357	gezelter	246	sprintf(buffer,
358			"------------------------------------------------------------------\n");
359			result += buffer;
360	gezelter	2
361	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
362			result += buffer;
363	gezelter	2
364	gezelter	246	sprintf(buffer,
365			"Visitor Description: assemble the atom data and output xyz file\n");
366			result += buffer;
367
368			sprintf(buffer,
369			"------------------------------------------------------------------\n");
370			result += buffer;
371
372			return result;
373	gezelter	507	}
374	gezelter	2
375	gezelter	507	//----------------------------------------------------------------------------//
376	gezelter	2
377	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
378	gezelter	246	GenericData *data;
379			AtomData * atomData;
380	gezelter	2
381	gezelter	246	//if visited property is existed, remove it
382			data = atom->getPropertyByName("VISITED");
383	gezelter	2
384	gezelter	246	if (data != NULL) {
385	gezelter	507	atom->removeProperty("VISITED");
386	gezelter	246	}
387
388			//remove atomdata
389			data = atom->getPropertyByName("ATOMDATA");
390
391			if (data != NULL) {
392	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
393	gezelter	246
394	gezelter	507	if (atomData != NULL)
395			atom->removeProperty("ATOMDATA");
396	gezelter	246	}
397	gezelter	507	}
398	gezelter	2
399	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
400	gezelter	246	GenericData* data;
401			AtomData* atomData;
402			std::vector<Atom *> myAtoms;
403			std::vector<Atom *>::iterator atomIter;
404	gezelter	2
405	gezelter	246	//if visited property is existed, remove it
406			data = rb->getPropertyByName("VISITED");
407	gezelter	2
408	gezelter	246	if (data != NULL) {
409	gezelter	507	rb->removeProperty("VISITED");
410	gezelter	246	}
411
412			//remove atomdata
413			data = rb->getPropertyByName("ATOMDATA");
414
415			if (data != NULL) {
416	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
417	gezelter	246
418	gezelter	507	if (atomData != NULL)
419			rb->removeProperty("ATOMDATA");
420	gezelter	246	}
421
422			myAtoms = rb->getAtoms();
423
424			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
425	gezelter	507	internalVisit(*atomIter);
426			}
427	gezelter	2
428	gezelter	507	const std::string PrepareVisitor::toString() {
429			char buffer[65535];
430			std::string result;
431	tim	293
432	gezelter	507	sprintf(buffer,
433			"------------------------------------------------------------------\n");
434			result += buffer;
435	tim	293
436	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
437			result += buffer;
438	tim	293
439	gezelter	507	sprintf(buffer,
440			"Visitor Description: prepare for operation of other vistors\n");
441			result += buffer;
442	tim	293
443	gezelter	507	sprintf(buffer,
444			"------------------------------------------------------------------\n");
445			result += buffer;
446	tim	293
447	gezelter	507	return result;
448			}
449	gezelter	2
450	gezelter	507	//----------------------------------------------------------------------------//
451	gezelter	2
452	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
453	gezelter	246	visitorName = "WaterTypeVisitor";
454			waterTypeList.insert("TIP3P_RB_0");
455			waterTypeList.insert("TIP4P_RB_0");
456			waterTypeList.insert("TIP5P_RB_0");
457			waterTypeList.insert("SPCE_RB_0");
458	gezelter	507	}
459	gezelter	2
460	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
461	gezelter	246	std::string rbName;
462			std::vector<Atom *> myAtoms;
463			std::vector<Atom *>::iterator atomIter;
464			GenericData* data;
465			AtomData* atomData;
466			AtomInfo* atomInfo;
467			std::vector<AtomInfo *>::iterator i;
468	gezelter	2
469	gezelter	246	rbName = rb->getType();
470	gezelter	2
471	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
472	gezelter	507	myAtoms = rb->getAtoms();
473	gezelter	2
474	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
475			++atomIter ) {
476			data = (*atomIter)->getPropertyByName("ATOMDATA");
477	gezelter	2
478	gezelter	507	if (data != NULL) {
479			atomData = dynamic_cast<AtomData *>(data);
480	gezelter	2
481	gezelter	507	if (atomData == NULL)
482			continue;
483			} else
484			continue;
485	gezelter	246
486	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
487			atomInfo = atomData->nextAtomInfo(i) ) {
488			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
489			} //end for(atomInfo)
490			} //end for(atomIter)
491	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
492	gezelter	507	}
493	gezelter	2
494	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
495			return atomTypeName.substr(0, atomTypeName.find('_'));
496			}
497	gezelter	2
498	gezelter	507	const std::string WaterTypeVisitor::toString() {
499	gezelter	246	char buffer[65535];
500			std::string result;
501	gezelter	2
502	gezelter	246	sprintf(buffer,
503			"------------------------------------------------------------------\n");
504			result += buffer;
505	gezelter	2
506	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
507			result += buffer;
508	gezelter	2
509	gezelter	246	sprintf(buffer,
510			"Visitor Description: Replace the atom type in water model\n");
511			result += buffer;
512	gezelter	2
513	gezelter	246	sprintf(buffer,
514			"------------------------------------------------------------------\n");
515			result += buffer;
516
517			return result;
518	gezelter	507	}
519	gezelter	2
520	gezelter	246	} //namespace oopse