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"
#include "brains/Thermo.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_){
      Thermo thermo(info);
      origin_ = thermo.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:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (13 years, 4 months ago) by gezelter
File size:	16278 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	1764	#include "brains/Thermo.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	tim	132
52	gezelter	507	void WrappingVisitor::visit(Atom *atom) {
53			internalVisit(atom);
54			}
55	gezelter	246
56	gezelter	507	void WrappingVisitor::visit(DirectionalAtom *datom) {
57			internalVisit(datom);
58			}
59	gezelter	2
60	gezelter	507	void WrappingVisitor::visit(RigidBody *rb) {
61			internalVisit(rb);
62			}
63	gezelter	2
64	gezelter	507	void WrappingVisitor::internalVisit(StuntDouble *sd) {
65	gezelter	246	GenericData * data;
66			AtomData * atomData;
67			AtomInfo * atomInfo;
68			std::vector<AtomInfo *>::iterator i;
69	gezelter	2
70	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
71	gezelter	2
72	gezelter	246	if (data != NULL) {
73	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
74	gezelter	2
75	gezelter	507	if (atomData == NULL)
76			return;
77	gezelter	246	} else
78	gezelter	507	return;
79	gezelter	246
80			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
81
82	gezelter	1764	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
83			atomInfo = atomData->nextAtomInfo(i) ) {
84
85	tim	543	Vector3d newPos = atomInfo->pos - origin_;
86			currSnapshot->wrapVector(newPos);
87			atomInfo->pos = newPos;
88	gezelter	1764
89	gezelter	246	}
90	gezelter	507	}
91	gezelter	2
92	tim	543	void WrappingVisitor::update() {
93			if (useCom_){
94	gezelter	1764	Thermo thermo(info);
95			origin_ = thermo.getCom();
96	tim	543	}
97			}
98
99	gezelter	507	const std::string WrappingVisitor::toString() {
100	gezelter	246	char buffer[65535];
101			std::string result;
102	gezelter	2
103	gezelter	246	sprintf(buffer,
104			"------------------------------------------------------------------\n");
105			result += buffer;
106	gezelter	2
107	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
108			result += buffer;
109	gezelter	2
110	gezelter	246	sprintf(buffer,
111			"Visitor Description: wrapping atoms back to periodic box\n");
112			result += buffer;
113
114			sprintf(buffer,
115			"------------------------------------------------------------------\n");
116			result += buffer;
117
118			return result;
119	gezelter	507	}
120	gezelter	2
121	gezelter	507	//----------------------------------------------------------------------------//
122	gezelter	2
123	gezelter	507	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
124	gezelter	246	BaseVisitor() {
125	gezelter	507	this->info = info;
126			visitorName = "ReplicateVisitor";
127			this->replicateOpt = opt;
128	gezelter	246
129	gezelter	507	//generate the replicate directions
130			for( int i = 0; i <= replicateOpt[0]; i++ ) {
131	gezelter	246	for( int j = 0; j <= replicateOpt[1]; j++ ) {
132	gezelter	507	for( int k = 0; k <= replicateOpt[2]; k++ ) {
133			//skip original frame
134			if (i == 0 && j == 0 && k == 0) {
135			continue;
136			} else {
137			dir.push_back(Vector3i(i, j, k));
138			}
139			}
140	gezelter	246	}
141	gezelter	507	}
142
143	gezelter	246	}
144
145	gezelter	507	void ReplicateVisitor::visit(Atom *atom) {
146			internalVisit(atom);
147			}
148	gezelter	246
149	gezelter	507	void ReplicateVisitor::visit(DirectionalAtom *datom) {
150			internalVisit(datom);
151			}
152	gezelter	2
153	gezelter	507	void ReplicateVisitor::visit(RigidBody *rb) {
154			internalVisit(rb);
155			}
156	gezelter	2
157	gezelter	507	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
158	gezelter	246	GenericData * data;
159			AtomData * atomData;
160	gezelter	2
161	gezelter	246	//if there is not atom data, just skip it
162			data = sd->getPropertyByName("ATOMDATA");
163	gezelter	2
164	gezelter	246	if (data != NULL) {
165	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
166	gezelter	2
167	gezelter	507	if (atomData == NULL) {
168			return;
169			}
170	gezelter	246	} else {
171	gezelter	507	return;
172	gezelter	246	}
173
174			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
175			Mat3x3d box = currSnapshot->getHmat();
176
177			std::vector<AtomInfo *> atomInfoList = atomData->getData();
178
179			replicate(atomInfoList, atomData, box);
180	gezelter	507	}
181	gezelter	2
182	gezelter	507	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
183	gezelter	246	AtomInfo* newAtomInfo;
184			std::vector<Vector3i>::iterator dirIter;
185			std::vector<AtomInfo *>::iterator i;
186	gezelter	2
187	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
188	gezelter	507	for( i = infoList.begin(); i != infoList.end(); i++ ) {
189			newAtomInfo = new AtomInfo();
190			newAtomInfo = (*i);
191	gezelter	2
192	gezelter	507	for( int j = 0; j < 3; j++ )
193			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
194	gezelter	246
195	gezelter	507	data->addAtomInfo(newAtomInfo);
196			}
197	gezelter	246	} // end for(dirIter)
198	gezelter	507	}
199	gezelter	2
200	gezelter	507	const std::string ReplicateVisitor::toString() {
201	gezelter	246	char buffer[65535];
202			std::string result;
203			std::set<std::string>::iterator i;
204	gezelter	2
205	gezelter	246	sprintf(buffer,
206			"------------------------------------------------------------------\n");
207			result += buffer;
208	gezelter	2
209	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
210			result += buffer;
211	gezelter	2
212	gezelter	246	sprintf(buffer,
213			"Visitor Description: replicate the atoms in different direction\n");
214			result += buffer;
215	gezelter	2
216	gezelter	246	//print the replicate direction
217			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
218			result += buffer;
219	gezelter	2
220	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
221			result += buffer;
222	gezelter	2
223	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
224			result += buffer;
225	gezelter	2
226	gezelter	246	sprintf(buffer,
227			"------------------------------------------------------------------\n");
228			result += buffer;
229
230			return result;
231	gezelter	507	}
232	gezelter	2
233	gezelter	1456	//------------------------------------------------------------------------//
234	gezelter	2
235	gezelter	1456	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
236			evaluator(info), doPositions_(true),
237			doVelocities_(false),
238			doForces_(false), doVectors_(false),
239			doCharges_(false) {
240			this->info = info;
241			visitorName = "XYZVisitor";
242
243			evaluator.loadScriptString("select all");
244
245			if (!evaluator.isDynamic()) {
246			seleMan.setSelectionSet(evaluator.evaluate());
247	tim	413	}
248	gezelter	1456	}
249
250	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
251	gezelter	1456	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
252			doVelocities_(false), doForces_(false), doVectors_(false),
253			doCharges_(false) {
254
255			this->info = info;
256			visitorName = "XYZVisitor";
257
258			evaluator.loadScriptString(script);
259
260			if (!evaluator.isDynamic()) {
261			seleMan.setSelectionSet(evaluator.evaluate());
262	tim	413	}
263	gezelter	1456	}
264	tim	413
265	gezelter	507	void XYZVisitor::visit(Atom *atom) {
266	tim	293	if (isSelected(atom))
267	gezelter	507	internalVisit(atom);
268			}
269	gezelter	2
270	gezelter	507	void XYZVisitor::visit(DirectionalAtom *datom) {
271	tim	293	if (isSelected(datom))
272	gezelter	507	internalVisit(datom);
273			}
274	gezelter	1456
275	gezelter	507	void XYZVisitor::visit(RigidBody *rb) {
276	tim	293	if (isSelected(rb))
277	gezelter	507	internalVisit(rb);
278			}
279	gezelter	1456
280	gezelter	507	void XYZVisitor::update() {
281	tim	413	//if dynamic, we need to re-evaluate the selection
282			if (evaluator.isDynamic()) {
283	gezelter	507	seleMan.setSelectionSet(evaluator.evaluate());
284	tim	413	}
285	gezelter	507	}
286	gezelter	1456
287	gezelter	507	void XYZVisitor::internalVisit(StuntDouble *sd) {
288	gezelter	246	GenericData * data;
289			AtomData * atomData;
290			AtomInfo * atomInfo;
291			std::vector<AtomInfo *>::iterator i;
292			char buffer[1024];
293	gezelter	1456
294	gezelter	246	//if there is not atom data, just skip it
295			data = sd->getPropertyByName("ATOMDATA");
296	gezelter	1456
297	gezelter	246	if (data != NULL) {
298	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
299	gezelter	1456
300	gezelter	507	if (atomData == NULL)
301			return;
302	gezelter	246	} else
303	gezelter	507	return;
304	gezelter	2
305	gezelter	1456	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
306			atomInfo = atomData->nextAtomInfo(i) ) {
307
308			std::string line;
309			sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
310			line += buffer;
311
312			if (doPositions_){
313			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
314			atomInfo->pos[1], atomInfo->pos[2]);
315			line += buffer;
316			}
317			if (doCharges_ && atomInfo->hasCharge) {
318			sprintf(buffer, "%15.8f", atomInfo->charge);
319			line += buffer;
320	chuckv	1118	}
321	gezelter	1456	if (doVectors_ && atomInfo->hasVector) {
322			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
323			atomInfo->vec[1], atomInfo->vec[2]);
324			line += buffer;
325	chuckv	1118	}
326	gezelter	1456	if (doVelocities_ && atomInfo->hasVelocity) {
327			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
328			atomInfo->vel[1], atomInfo->vel[2]);
329			line += buffer;
330			}
331			if (doForces_ && atomInfo->hasForce) {
332			sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
333			atomInfo->frc[1], atomInfo->frc[2]);
334			line += buffer;
335			}
336			frame.push_back(line);
337			}
338	gezelter	507	}
339	gezelter	2
340	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
341	tim	413	return seleMan.isSelected(sd);
342	gezelter	507	}
343	gezelter	2
344	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
345	gezelter	246	std::vector<std::string>::iterator i;
346			char buffer[1024];
347	gezelter	1456
348	gezelter	246	if (frame.size() == 0)
349	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
350	gezelter	1456
351	gezelter	246	//total number of atoms
352			outStream << frame.size() << std::endl;
353	gezelter	1456
354	gezelter	246	//write comment line
355			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
356			Mat3x3d box = currSnapshot->getHmat();
357
358			sprintf(buffer,
359			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
360			currSnapshot->getTime(),
361			box(0, 0), box(0, 1), box(0, 2),
362			box(1, 0), box(1, 1), box(1, 2),
363			box(2, 0), box(2, 1), box(2, 2));
364	gezelter	1456
365	gezelter	246	outStream << buffer << std::endl;
366	gezelter	1456
367	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
368	gezelter	507	outStream << *i << std::endl;
369			}
370	gezelter	1456
371	cli2	1290	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
372			return atomTypeName.substr(0, atomTypeName.find('-'));
373			}
374	gezelter	1456
375	gezelter	507	const std::string XYZVisitor::toString() {
376	gezelter	246	char buffer[65535];
377			std::string result;
378	gezelter	1456
379	gezelter	246	sprintf(buffer,
380			"------------------------------------------------------------------\n");
381			result += buffer;
382	gezelter	1456
383	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
384			result += buffer;
385	gezelter	1456
386	gezelter	246	sprintf(buffer,
387			"Visitor Description: assemble the atom data and output xyz file\n");
388			result += buffer;
389
390			sprintf(buffer,
391			"------------------------------------------------------------------\n");
392			result += buffer;
393	gezelter	1456
394	gezelter	246	return result;
395	gezelter	507	}
396	gezelter	1456
397	gezelter	507	//----------------------------------------------------------------------------//
398	gezelter	1456
399	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
400	gezelter	246	GenericData *data;
401			AtomData * atomData;
402	gezelter	1456
403	gezelter	246	//if visited property is existed, remove it
404			data = atom->getPropertyByName("VISITED");
405	gezelter	1456
406	gezelter	246	if (data != NULL) {
407	gezelter	507	atom->removeProperty("VISITED");
408	gezelter	246	}
409	gezelter	1456
410	gezelter	246	//remove atomdata
411			data = atom->getPropertyByName("ATOMDATA");
412
413			if (data != NULL) {
414	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
415	gezelter	246
416	gezelter	507	if (atomData != NULL)
417			atom->removeProperty("ATOMDATA");
418	gezelter	246	}
419	gezelter	507	}
420	gezelter	2
421	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
422	gezelter	246	GenericData* data;
423			AtomData* atomData;
424			std::vector<Atom *> myAtoms;
425			std::vector<Atom *>::iterator atomIter;
426	gezelter	2
427	gezelter	246	//if visited property is existed, remove it
428			data = rb->getPropertyByName("VISITED");
429	gezelter	2
430	gezelter	246	if (data != NULL) {
431	gezelter	507	rb->removeProperty("VISITED");
432	gezelter	246	}
433
434			//remove atomdata
435			data = rb->getPropertyByName("ATOMDATA");
436
437			if (data != NULL) {
438	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
439	gezelter	246
440	gezelter	507	if (atomData != NULL)
441			rb->removeProperty("ATOMDATA");
442	gezelter	246	}
443
444			myAtoms = rb->getAtoms();
445
446			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
447	gezelter	507	internalVisit(*atomIter);
448			}
449	gezelter	2
450	gezelter	507	const std::string PrepareVisitor::toString() {
451			char buffer[65535];
452			std::string result;
453	tim	293
454	gezelter	507	sprintf(buffer,
455			"------------------------------------------------------------------\n");
456			result += buffer;
457	tim	293
458	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
459			result += buffer;
460	tim	293
461	gezelter	507	sprintf(buffer,
462			"Visitor Description: prepare for operation of other vistors\n");
463			result += buffer;
464	tim	293
465	gezelter	507	sprintf(buffer,
466			"------------------------------------------------------------------\n");
467			result += buffer;
468	tim	293
469	gezelter	507	return result;
470			}
471	gezelter	2
472	gezelter	507	//----------------------------------------------------------------------------//
473	gezelter	2
474	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
475	gezelter	246	visitorName = "WaterTypeVisitor";
476			waterTypeList.insert("TIP3P_RB_0");
477			waterTypeList.insert("TIP4P_RB_0");
478	gezelter	1456	waterTypeList.insert("TIP4P-Ew_RB_0");
479	gezelter	246	waterTypeList.insert("TIP5P_RB_0");
480	gezelter	1456	waterTypeList.insert("TIP5P-E_RB_0");
481	gezelter	246	waterTypeList.insert("SPCE_RB_0");
482	gezelter	1456	waterTypeList.insert("SPC_RB_0");
483	gezelter	507	}
484	gezelter	2
485	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
486	gezelter	246	std::string rbName;
487			std::vector<Atom *> myAtoms;
488			std::vector<Atom *>::iterator atomIter;
489			GenericData* data;
490			AtomData* atomData;
491			AtomInfo* atomInfo;
492			std::vector<AtomInfo *>::iterator i;
493	gezelter	2
494	gezelter	246	rbName = rb->getType();
495	gezelter	1456
496	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
497	gezelter	507	myAtoms = rb->getAtoms();
498	gezelter	2
499	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
500			++atomIter ) {
501			data = (*atomIter)->getPropertyByName("ATOMDATA");
502	gezelter	1456
503	gezelter	507	if (data != NULL) {
504			atomData = dynamic_cast<AtomData *>(data);
505	gezelter	1456
506	gezelter	507	if (atomData == NULL)
507			continue;
508			} else
509			continue;
510	gezelter	1456
511	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
512			atomInfo = atomData->nextAtomInfo(i) ) {
513			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
514			} //end for(atomInfo)
515			} //end for(atomIter)
516	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
517	gezelter	507	}
518	gezelter	2
519	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
520			return atomTypeName.substr(0, atomTypeName.find('_'));
521			}
522	gezelter	2
523	gezelter	507	const std::string WaterTypeVisitor::toString() {
524	gezelter	246	char buffer[65535];
525			std::string result;
526	gezelter	2
527	gezelter	246	sprintf(buffer,
528			"------------------------------------------------------------------\n");
529			result += buffer;
530	gezelter	2
531	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
532			result += buffer;
533	gezelter	2
534	gezelter	246	sprintf(buffer,
535			"Visitor Description: Replace the atom type in water model\n");
536			result += buffer;
537	gezelter	2
538	gezelter	246	sprintf(buffer,
539			"------------------------------------------------------------------\n");
540			result += buffer;
541
542			return result;
543	gezelter	507	}
544	gezelter	2
545	gezelter	1390	} //namespace OpenMD