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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#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 OpenMD {

  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;

    AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
    std::string bn = baseTypeName(at);

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

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

  std::string XYZVisitor::baseTypeName(AtomType* at) {
    std::vector<AtomType*> ayb = at->allYourBase();
    return ayb[ayb.size()-1]->getName();
  }

  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 OpenMD
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	15850 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
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	gezelter	1390	namespace OpenMD {
48	tim	132
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	cli2	1290	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
295			std::string bn = baseTypeName(at);
296
297	chuckv	1118	if (posOnly_){
298			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
299			atomInfo = atomData->nextAtomInfo(i) ) {
300	xsun	1219	if (atomInfo->hasCharge) {
301			sprintf(buffer,
302	cli2	1290	"%s%15.8f%15.8f%15.8f%15.8f",
303			bn.c_str(),
304			atomInfo->pos[0],
305			atomInfo->pos[1],
306			atomInfo->pos[2],
307			atomInfo->charge);
308	xsun	1219	} else {
309			sprintf(buffer,
310	chuckv	1118	"%s%15.8f%15.8f%15.8f",
311	cli2	1290	bn.c_str(),
312			atomInfo->pos[0],
313			atomInfo->pos[1],
314			atomInfo->pos[2]);
315	xsun	1219	}
316	chuckv	1118	frame.push_back(buffer);
317			}
318			}else{
319			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
320			atomInfo = atomData->nextAtomInfo(i) ) {
321	xsun	1219	if (atomInfo->hasCharge) {
322	chuckv	1118	sprintf(buffer,
323	xsun	1219	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
324	cli2	1290	bn.c_str(),
325	xsun	1219	atomInfo->pos[0],
326			atomInfo->pos[1],
327			atomInfo->pos[2],
328			atomInfo->charge,
329			atomInfo->dipole[0],
330			atomInfo->dipole[1],
331			atomInfo->dipole[2]);
332			} else {
333			sprintf(buffer,
334	chuckv	1118	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
335	cli2	1290	bn.c_str(),
336	chuckv	1118	atomInfo->pos[0],
337			atomInfo->pos[1],
338			atomInfo->pos[2],
339			atomInfo->dipole[0],
340			atomInfo->dipole[1],
341			atomInfo->dipole[2]);
342	xsun	1219	}
343	chuckv	1118	frame.push_back(buffer);
344			}
345	gezelter	246	}
346	gezelter	507	}
347	gezelter	2
348	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
349	tim	413	return seleMan.isSelected(sd);
350	gezelter	507	}
351	gezelter	2
352	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
353	gezelter	246	std::vector<std::string>::iterator i;
354			char buffer[1024];
355	gezelter	2
356	gezelter	246	if (frame.size() == 0)
357	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
358	gezelter	2
359	gezelter	246	//total number of atoms
360			outStream << frame.size() << std::endl;
361	gezelter	2
362	gezelter	246	//write comment line
363			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
364			Mat3x3d box = currSnapshot->getHmat();
365
366			sprintf(buffer,
367			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
368			currSnapshot->getTime(),
369			box(0, 0), box(0, 1), box(0, 2),
370			box(1, 0), box(1, 1), box(1, 2),
371			box(2, 0), box(2, 1), box(2, 2));
372	gezelter	2
373	gezelter	246	outStream << buffer << std::endl;
374	gezelter	2
375	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
376	gezelter	507	outStream << *i << std::endl;
377			}
378	gezelter	2
379	cli2	1290	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
380			return atomTypeName.substr(0, atomTypeName.find('-'));
381			}
382
383			std::string XYZVisitor::baseTypeName(AtomType* at) {
384			std::vector<AtomType*> ayb = at->allYourBase();
385			return ayb[ayb.size()-1]->getName();
386			}
387
388	gezelter	507	const std::string XYZVisitor::toString() {
389	gezelter	246	char buffer[65535];
390			std::string result;
391	gezelter	2
392	gezelter	246	sprintf(buffer,
393			"------------------------------------------------------------------\n");
394			result += buffer;
395	gezelter	2
396	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
397			result += buffer;
398	gezelter	2
399	gezelter	246	sprintf(buffer,
400			"Visitor Description: assemble the atom data and output xyz file\n");
401			result += buffer;
402
403			sprintf(buffer,
404			"------------------------------------------------------------------\n");
405			result += buffer;
406
407			return result;
408	gezelter	507	}
409	gezelter	2
410	gezelter	507	//----------------------------------------------------------------------------//
411	gezelter	2
412	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
413	gezelter	246	GenericData *data;
414			AtomData * atomData;
415	gezelter	2
416	gezelter	246	//if visited property is existed, remove it
417			data = atom->getPropertyByName("VISITED");
418	gezelter	2
419	gezelter	246	if (data != NULL) {
420	gezelter	507	atom->removeProperty("VISITED");
421	gezelter	246	}
422
423			//remove atomdata
424			data = atom->getPropertyByName("ATOMDATA");
425
426			if (data != NULL) {
427	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
428	gezelter	246
429	gezelter	507	if (atomData != NULL)
430			atom->removeProperty("ATOMDATA");
431	gezelter	246	}
432	gezelter	507	}
433	gezelter	2
434	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
435	gezelter	246	GenericData* data;
436			AtomData* atomData;
437			std::vector<Atom *> myAtoms;
438			std::vector<Atom *>::iterator atomIter;
439	gezelter	2
440	gezelter	246	//if visited property is existed, remove it
441			data = rb->getPropertyByName("VISITED");
442	gezelter	2
443	gezelter	246	if (data != NULL) {
444	gezelter	507	rb->removeProperty("VISITED");
445	gezelter	246	}
446
447			//remove atomdata
448			data = rb->getPropertyByName("ATOMDATA");
449
450			if (data != NULL) {
451	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
452	gezelter	246
453	gezelter	507	if (atomData != NULL)
454			rb->removeProperty("ATOMDATA");
455	gezelter	246	}
456
457			myAtoms = rb->getAtoms();
458
459			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
460	gezelter	507	internalVisit(*atomIter);
461			}
462	gezelter	2
463	gezelter	507	const std::string PrepareVisitor::toString() {
464			char buffer[65535];
465			std::string result;
466	tim	293
467	gezelter	507	sprintf(buffer,
468			"------------------------------------------------------------------\n");
469			result += buffer;
470	tim	293
471	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
472			result += buffer;
473	tim	293
474	gezelter	507	sprintf(buffer,
475			"Visitor Description: prepare for operation of other vistors\n");
476			result += buffer;
477	tim	293
478	gezelter	507	sprintf(buffer,
479			"------------------------------------------------------------------\n");
480			result += buffer;
481	tim	293
482	gezelter	507	return result;
483			}
484	gezelter	2
485	gezelter	507	//----------------------------------------------------------------------------//
486	gezelter	2
487	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
488	gezelter	246	visitorName = "WaterTypeVisitor";
489			waterTypeList.insert("TIP3P_RB_0");
490			waterTypeList.insert("TIP4P_RB_0");
491			waterTypeList.insert("TIP5P_RB_0");
492			waterTypeList.insert("SPCE_RB_0");
493	gezelter	507	}
494	gezelter	2
495	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
496	gezelter	246	std::string rbName;
497			std::vector<Atom *> myAtoms;
498			std::vector<Atom *>::iterator atomIter;
499			GenericData* data;
500			AtomData* atomData;
501			AtomInfo* atomInfo;
502			std::vector<AtomInfo *>::iterator i;
503	gezelter	2
504	gezelter	246	rbName = rb->getType();
505	gezelter	2
506	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
507	gezelter	507	myAtoms = rb->getAtoms();
508	gezelter	2
509	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
510			++atomIter ) {
511			data = (*atomIter)->getPropertyByName("ATOMDATA");
512	gezelter	2
513	gezelter	507	if (data != NULL) {
514			atomData = dynamic_cast<AtomData *>(data);
515	gezelter	2
516	gezelter	507	if (atomData == NULL)
517			continue;
518			} else
519			continue;
520	gezelter	246
521	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
522			atomInfo = atomData->nextAtomInfo(i) ) {
523			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
524			} //end for(atomInfo)
525			} //end for(atomIter)
526	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
527	gezelter	507	}
528	gezelter	2
529	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
530			return atomTypeName.substr(0, atomTypeName.find('_'));
531			}
532	gezelter	2
533	gezelter	507	const std::string WaterTypeVisitor::toString() {
534	gezelter	246	char buffer[65535];
535			std::string result;
536	gezelter	2
537	gezelter	246	sprintf(buffer,
538			"------------------------------------------------------------------\n");
539			result += buffer;
540	gezelter	2
541	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
542			result += buffer;
543	gezelter	2
544	gezelter	246	sprintf(buffer,
545			"Visitor Description: Replace the atom type in water model\n");
546			result += buffer;
547	gezelter	2
548	gezelter	246	sprintf(buffer,
549			"------------------------------------------------------------------\n");
550			result += buffer;
551
552			return result;
553	gezelter	507	}
554	gezelter	2
555	gezelter	1390	} //namespace OpenMD