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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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), doPositions_(true),
                                          doVelocities_(false), 
                                          doForces_(false), doVectors_(false),
                                          doCharges_(false) {
    this->info = info;
    visitorName = "XYZVisitor";
    
    evaluator.loadScriptString("select all");
    
    if (!evaluator.isDynamic()) {
      seleMan.setSelectionSet(evaluator.evaluate());
    }
  }
  
  XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
    BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
    doVelocities_(false), doForces_(false), doVectors_(false),
    doCharges_(false) {
    
    this->info = info;
    visitorName = "XYZVisitor";
    
    evaluator.loadScriptString(script);
    
    if (!evaluator.isDynamic()) {
      seleMan.setSelectionSet(evaluator.evaluate());
    }
  }
    
  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;

    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
         atomInfo = atomData->nextAtomInfo(i) ) {
     
      std::string line;
      sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
      line += buffer;
      
      if (doPositions_){
        sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0], 
                atomInfo->pos[1], atomInfo->pos[2]);
        line += buffer;
      }      
      if (doCharges_ && atomInfo->hasCharge) {
        sprintf(buffer, "%15.8f", atomInfo->charge);
        line += buffer;
      }
      if (doVectors_ && atomInfo->hasVector) {
        sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0], 
                atomInfo->vec[1], atomInfo->vec[2]);
        line += buffer;
      }
      if (doVelocities_ && atomInfo->hasVelocity) {
        sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0], 
                atomInfo->vel[1], atomInfo->vel[2]);
        line += buffer;
      }
      if (doForces_ && atomInfo->hasForce) {
        sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0], 
                atomInfo->frc[1], atomInfo->frc[2]);
        line += buffer;
      }      
      frame.push_back(line);
    }    
  }

  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('-'));
  }
  
  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("TIP4P-Ew_RB_0");
    waterTypeList.insert("TIP5P_RB_0");
    waterTypeList.insert("TIP5P-E_RB_0");
    waterTypeList.insert("SPCE_RB_0");
    waterTypeList.insert("SPC_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:	1702
Committed:	Thu Apr 5 19:49:59 2012 UTC (13 years, 1 month ago) by kstocke1
File size:	16208 byte(s)
Log Message:	Un-did some changes that weren't ready to be committed.
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42	tim	324	#include "selection/SelectionManager.hpp"
43	tim	3	#include "visitors/OtherVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "primitives/RigidBody.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "brains/SimInfo.hpp"
48	gezelter	1390	namespace OpenMD {
49	tim	132
50	gezelter	507	void WrappingVisitor::visit(Atom *atom) {
51			internalVisit(atom);
52			}
53	gezelter	246
54	gezelter	507	void WrappingVisitor::visit(DirectionalAtom *datom) {
55			internalVisit(datom);
56			}
57	gezelter	2
58	gezelter	507	void WrappingVisitor::visit(RigidBody *rb) {
59			internalVisit(rb);
60			}
61	gezelter	2
62	gezelter	507	void WrappingVisitor::internalVisit(StuntDouble *sd) {
63	gezelter	246	GenericData * data;
64			AtomData * atomData;
65			AtomInfo * atomInfo;
66			std::vector<AtomInfo *>::iterator i;
67	gezelter	2
68	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
69	gezelter	2
70	gezelter	246	if (data != NULL) {
71	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
72	gezelter	2
73	gezelter	507	if (atomData == NULL)
74			return;
75	gezelter	246	} else
76	gezelter	507	return;
77	gezelter	246
78			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
79
80			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
81	tim	543	Vector3d newPos = atomInfo->pos - origin_;
82			currSnapshot->wrapVector(newPos);
83			atomInfo->pos = newPos;
84	gezelter	246	}
85	gezelter	507	}
86	gezelter	2
87	tim	543	void WrappingVisitor::update() {
88			if (useCom_){
89			origin_ = info->getCom();
90			}
91			}
92
93	gezelter	507	const std::string WrappingVisitor::toString() {
94	gezelter	246	char buffer[65535];
95			std::string result;
96	gezelter	2
97	gezelter	246	sprintf(buffer,
98			"------------------------------------------------------------------\n");
99			result += buffer;
100	gezelter	2
101	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
102			result += buffer;
103	gezelter	2
104	gezelter	246	sprintf(buffer,
105			"Visitor Description: wrapping atoms back to periodic box\n");
106			result += buffer;
107
108			sprintf(buffer,
109			"------------------------------------------------------------------\n");
110			result += buffer;
111
112			return result;
113	gezelter	507	}
114	gezelter	2
115	gezelter	507	//----------------------------------------------------------------------------//
116	gezelter	2
117	gezelter	507	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
118	gezelter	246	BaseVisitor() {
119	gezelter	507	this->info = info;
120			visitorName = "ReplicateVisitor";
121			this->replicateOpt = opt;
122	gezelter	246
123	gezelter	507	//generate the replicate directions
124			for( int i = 0; i <= replicateOpt[0]; i++ ) {
125	gezelter	246	for( int j = 0; j <= replicateOpt[1]; j++ ) {
126	gezelter	507	for( int k = 0; k <= replicateOpt[2]; k++ ) {
127			//skip original frame
128			if (i == 0 && j == 0 && k == 0) {
129			continue;
130			} else {
131			dir.push_back(Vector3i(i, j, k));
132			}
133			}
134	gezelter	246	}
135	gezelter	507	}
136
137	gezelter	246	}
138
139	gezelter	507	void ReplicateVisitor::visit(Atom *atom) {
140			internalVisit(atom);
141			}
142	gezelter	246
143	gezelter	507	void ReplicateVisitor::visit(DirectionalAtom *datom) {
144			internalVisit(datom);
145			}
146	gezelter	2
147	gezelter	507	void ReplicateVisitor::visit(RigidBody *rb) {
148			internalVisit(rb);
149			}
150	gezelter	2
151	gezelter	507	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
152	gezelter	246	GenericData * data;
153			AtomData * atomData;
154	gezelter	2
155	gezelter	246	//if there is not atom data, just skip it
156			data = sd->getPropertyByName("ATOMDATA");
157	gezelter	2
158	gezelter	246	if (data != NULL) {
159	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
160	gezelter	2
161	gezelter	507	if (atomData == NULL) {
162			return;
163			}
164	gezelter	246	} else {
165	gezelter	507	return;
166	gezelter	246	}
167
168			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
169			Mat3x3d box = currSnapshot->getHmat();
170
171			std::vector<AtomInfo *> atomInfoList = atomData->getData();
172
173			replicate(atomInfoList, atomData, box);
174	gezelter	507	}
175	gezelter	2
176	gezelter	507	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
177	gezelter	246	AtomInfo* newAtomInfo;
178			std::vector<Vector3i>::iterator dirIter;
179			std::vector<AtomInfo *>::iterator i;
180	gezelter	2
181	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
182	gezelter	507	for( i = infoList.begin(); i != infoList.end(); i++ ) {
183			newAtomInfo = new AtomInfo();
184			newAtomInfo = (*i);
185	gezelter	2
186	gezelter	507	for( int j = 0; j < 3; j++ )
187			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
188	gezelter	246
189	gezelter	507	data->addAtomInfo(newAtomInfo);
190			}
191	gezelter	246	} // end for(dirIter)
192	gezelter	507	}
193	gezelter	2
194	gezelter	507	const std::string ReplicateVisitor::toString() {
195	gezelter	246	char buffer[65535];
196			std::string result;
197			std::set<std::string>::iterator i;
198	gezelter	2
199	gezelter	246	sprintf(buffer,
200			"------------------------------------------------------------------\n");
201			result += buffer;
202	gezelter	2
203	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204			result += buffer;
205	gezelter	2
206	gezelter	246	sprintf(buffer,
207			"Visitor Description: replicate the atoms in different direction\n");
208			result += buffer;
209	gezelter	2
210	gezelter	246	//print the replicate direction
211			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
212			result += buffer;
213	gezelter	2
214	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
215			result += buffer;
216	gezelter	2
217	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
218			result += buffer;
219	gezelter	2
220	gezelter	246	sprintf(buffer,
221			"------------------------------------------------------------------\n");
222			result += buffer;
223
224			return result;
225	gezelter	507	}
226	gezelter	2
227	gezelter	1456	//------------------------------------------------------------------------//
228	gezelter	2
229	gezelter	1456	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
230			evaluator(info), doPositions_(true),
231			doVelocities_(false),
232			doForces_(false), doVectors_(false),
233			doCharges_(false) {
234			this->info = info;
235			visitorName = "XYZVisitor";
236
237			evaluator.loadScriptString("select all");
238
239			if (!evaluator.isDynamic()) {
240			seleMan.setSelectionSet(evaluator.evaluate());
241	tim	413	}
242	gezelter	1456	}
243
244	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
245	gezelter	1456	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
246			doVelocities_(false), doForces_(false), doVectors_(false),
247			doCharges_(false) {
248
249			this->info = info;
250			visitorName = "XYZVisitor";
251
252			evaluator.loadScriptString(script);
253
254			if (!evaluator.isDynamic()) {
255			seleMan.setSelectionSet(evaluator.evaluate());
256	tim	413	}
257	gezelter	1456	}
258	tim	413
259	gezelter	507	void XYZVisitor::visit(Atom *atom) {
260	tim	293	if (isSelected(atom))
261	gezelter	507	internalVisit(atom);
262			}
263	gezelter	2
264	gezelter	507	void XYZVisitor::visit(DirectionalAtom *datom) {
265	tim	293	if (isSelected(datom))
266	gezelter	507	internalVisit(datom);
267			}
268	gezelter	1456
269	gezelter	507	void XYZVisitor::visit(RigidBody *rb) {
270	tim	293	if (isSelected(rb))
271	gezelter	507	internalVisit(rb);
272			}
273	gezelter	1456
274	gezelter	507	void XYZVisitor::update() {
275	tim	413	//if dynamic, we need to re-evaluate the selection
276			if (evaluator.isDynamic()) {
277	gezelter	507	seleMan.setSelectionSet(evaluator.evaluate());
278	tim	413	}
279	gezelter	507	}
280	gezelter	1456
281	gezelter	507	void XYZVisitor::internalVisit(StuntDouble *sd) {
282	gezelter	246	GenericData * data;
283			AtomData * atomData;
284			AtomInfo * atomInfo;
285			std::vector<AtomInfo *>::iterator i;
286			char buffer[1024];
287	gezelter	1456
288	gezelter	246	//if there is not atom data, just skip it
289			data = sd->getPropertyByName("ATOMDATA");
290	gezelter	1456
291	gezelter	246	if (data != NULL) {
292	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
293	gezelter	1456
294	gezelter	507	if (atomData == NULL)
295			return;
296	gezelter	246	} else
297	gezelter	507	return;
298	gezelter	2
299	gezelter	1456	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
300			atomInfo = atomData->nextAtomInfo(i) ) {
301
302			std::string line;
303			sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
304			line += buffer;
305
306			if (doPositions_){
307			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
308			atomInfo->pos[1], atomInfo->pos[2]);
309			line += buffer;
310			}
311			if (doCharges_ && atomInfo->hasCharge) {
312			sprintf(buffer, "%15.8f", atomInfo->charge);
313			line += buffer;
314	chuckv	1118	}
315	gezelter	1456	if (doVectors_ && atomInfo->hasVector) {
316			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
317			atomInfo->vec[1], atomInfo->vec[2]);
318			line += buffer;
319	chuckv	1118	}
320	gezelter	1456	if (doVelocities_ && atomInfo->hasVelocity) {
321			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
322			atomInfo->vel[1], atomInfo->vel[2]);
323			line += buffer;
324			}
325			if (doForces_ && atomInfo->hasForce) {
326			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
327			atomInfo->frc[1], atomInfo->frc[2]);
328			line += buffer;
329			}
330			frame.push_back(line);
331			}
332	gezelter	507	}
333	gezelter	2
334	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
335	tim	413	return seleMan.isSelected(sd);
336	gezelter	507	}
337	gezelter	2
338	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
339	gezelter	246	std::vector<std::string>::iterator i;
340			char buffer[1024];
341	gezelter	1456
342	gezelter	246	if (frame.size() == 0)
343	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
344	gezelter	1456
345	gezelter	246	//total number of atoms
346			outStream << frame.size() << std::endl;
347	gezelter	1456
348	gezelter	246	//write comment line
349			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
350			Mat3x3d box = currSnapshot->getHmat();
351
352			sprintf(buffer,
353			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
354			currSnapshot->getTime(),
355			box(0, 0), box(0, 1), box(0, 2),
356			box(1, 0), box(1, 1), box(1, 2),
357			box(2, 0), box(2, 1), box(2, 2));
358	gezelter	1456
359	gezelter	246	outStream << buffer << std::endl;
360	gezelter	1456
361	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
362	gezelter	507	outStream << *i << std::endl;
363			}
364	gezelter	1456
365	cli2	1290	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
366			return atomTypeName.substr(0, atomTypeName.find('-'));
367			}
368	gezelter	1456
369	gezelter	507	const std::string XYZVisitor::toString() {
370	gezelter	246	char buffer[65535];
371			std::string result;
372	gezelter	1456
373	gezelter	246	sprintf(buffer,
374			"------------------------------------------------------------------\n");
375			result += buffer;
376	gezelter	1456
377	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
378			result += buffer;
379	gezelter	1456
380	gezelter	246	sprintf(buffer,
381			"Visitor Description: assemble the atom data and output xyz file\n");
382			result += buffer;
383
384			sprintf(buffer,
385			"------------------------------------------------------------------\n");
386			result += buffer;
387	gezelter	1456
388	gezelter	246	return result;
389	gezelter	507	}
390	gezelter	1456
391	gezelter	507	//----------------------------------------------------------------------------//
392	gezelter	1456
393	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
394	gezelter	246	GenericData *data;
395			AtomData * atomData;
396	gezelter	1456
397	gezelter	246	//if visited property is existed, remove it
398			data = atom->getPropertyByName("VISITED");
399	gezelter	1456
400	gezelter	246	if (data != NULL) {
401	gezelter	507	atom->removeProperty("VISITED");
402	gezelter	246	}
403	gezelter	1456
404	gezelter	246	//remove atomdata
405			data = atom->getPropertyByName("ATOMDATA");
406
407			if (data != NULL) {
408	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
409	gezelter	246
410	gezelter	507	if (atomData != NULL)
411			atom->removeProperty("ATOMDATA");
412	gezelter	246	}
413	gezelter	507	}
414	gezelter	2
415	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
416	gezelter	246	GenericData* data;
417			AtomData* atomData;
418			std::vector<Atom *> myAtoms;
419			std::vector<Atom *>::iterator atomIter;
420	gezelter	2
421	gezelter	246	//if visited property is existed, remove it
422			data = rb->getPropertyByName("VISITED");
423	gezelter	2
424	gezelter	246	if (data != NULL) {
425	gezelter	507	rb->removeProperty("VISITED");
426	gezelter	246	}
427
428			//remove atomdata
429			data = rb->getPropertyByName("ATOMDATA");
430
431			if (data != NULL) {
432	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
433	gezelter	246
434	gezelter	507	if (atomData != NULL)
435			rb->removeProperty("ATOMDATA");
436	gezelter	246	}
437
438			myAtoms = rb->getAtoms();
439
440			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
441	gezelter	507	internalVisit(*atomIter);
442			}
443	gezelter	2
444	gezelter	507	const std::string PrepareVisitor::toString() {
445			char buffer[65535];
446			std::string result;
447	tim	293
448	gezelter	507	sprintf(buffer,
449			"------------------------------------------------------------------\n");
450			result += buffer;
451	tim	293
452	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
453			result += buffer;
454	tim	293
455	gezelter	507	sprintf(buffer,
456			"Visitor Description: prepare for operation of other vistors\n");
457			result += buffer;
458	tim	293
459	gezelter	507	sprintf(buffer,
460			"------------------------------------------------------------------\n");
461			result += buffer;
462	tim	293
463	gezelter	507	return result;
464			}
465	gezelter	2
466	gezelter	507	//----------------------------------------------------------------------------//
467	gezelter	2
468	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
469	gezelter	246	visitorName = "WaterTypeVisitor";
470			waterTypeList.insert("TIP3P_RB_0");
471			waterTypeList.insert("TIP4P_RB_0");
472	gezelter	1456	waterTypeList.insert("TIP4P-Ew_RB_0");
473	gezelter	246	waterTypeList.insert("TIP5P_RB_0");
474	gezelter	1456	waterTypeList.insert("TIP5P-E_RB_0");
475	gezelter	246	waterTypeList.insert("SPCE_RB_0");
476	gezelter	1456	waterTypeList.insert("SPC_RB_0");
477	gezelter	507	}
478	gezelter	2
479	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
480	gezelter	246	std::string rbName;
481			std::vector<Atom *> myAtoms;
482			std::vector<Atom *>::iterator atomIter;
483			GenericData* data;
484			AtomData* atomData;
485			AtomInfo* atomInfo;
486			std::vector<AtomInfo *>::iterator i;
487	gezelter	2
488	gezelter	246	rbName = rb->getType();
489	gezelter	1456
490	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
491	gezelter	507	myAtoms = rb->getAtoms();
492	gezelter	2
493	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
494			++atomIter ) {
495			data = (*atomIter)->getPropertyByName("ATOMDATA");
496	gezelter	1456
497	gezelter	507	if (data != NULL) {
498			atomData = dynamic_cast<AtomData *>(data);
499	gezelter	1456
500	gezelter	507	if (atomData == NULL)
501			continue;
502			} else
503			continue;
504	gezelter	1456
505	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
506			atomInfo = atomData->nextAtomInfo(i) ) {
507			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
508			} //end for(atomInfo)
509			} //end for(atomIter)
510	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
511	gezelter	507	}
512	gezelter	2
513	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
514			return atomTypeName.substr(0, atomTypeName.find('_'));
515			}
516	gezelter	2
517	gezelter	507	const std::string WaterTypeVisitor::toString() {
518	gezelter	246	char buffer[65535];
519			std::string result;
520	gezelter	2
521	gezelter	246	sprintf(buffer,
522			"------------------------------------------------------------------\n");
523			result += buffer;
524	gezelter	2
525	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
526			result += buffer;
527	gezelter	2
528	gezelter	246	sprintf(buffer,
529			"Visitor Description: Replace the atom type in water model\n");
530			result += buffer;
531	gezelter	2
532	gezelter	246	sprintf(buffer,
533			"------------------------------------------------------------------\n");
534			result += buffer;
535
536			return result;
537	gezelter	507	}
538	gezelter	2
539	gezelter	1390	} //namespace OpenMD