src/visitors/OtherVisitor.cpp

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    return result;
  }

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

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

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

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

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

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

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

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

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

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

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

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

    replicate(atomInfoList, atomData, box);
  }

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

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

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

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

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

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

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

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

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

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

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

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

    return result;
  }

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

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

      evaluator.loadScriptString("select all");

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

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

      evaluator.loadScriptString(script);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    outStream << buffer << std::endl;

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

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

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

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

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

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

    return result;
  }

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

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

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

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

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

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

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

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

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

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

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

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

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

    myAtoms = rb->getAtoms();

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

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

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

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

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

    rbName = rb->getType();

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

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

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

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

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

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

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

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

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

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

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

    return result;
  }

} //namespace oopse
Revision:	3328
Committed:	Wed Jan 23 21:23:32 2008 UTC (17 years, 6 months ago) by xsun
File size:	15488 byte(s)
Log Message:	new visitors for some odd molecules
#	User	Rev	Content
1	gezelter	2091	/*
2	gezelter	1930	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41	tim	2008	#include "selection/SelectionManager.hpp"
42	tim	1492	#include "visitors/OtherVisitor.hpp"
43			#include "primitives/DirectionalAtom.hpp"
44			#include "primitives/RigidBody.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "brains/SimInfo.hpp"
47	tim	1625	namespace oopse {
48
49	gezelter	2204	void WrappingVisitor::visit(Atom *atom) {
50			internalVisit(atom);
51			}
52	gezelter	1930
53	gezelter	2204	void WrappingVisitor::visit(DirectionalAtom *datom) {
54			internalVisit(datom);
55			}
56	gezelter	1490
57	gezelter	2204	void WrappingVisitor::visit(RigidBody *rb) {
58			internalVisit(rb);
59			}
60	gezelter	1490
61	gezelter	2204	void WrappingVisitor::internalVisit(StuntDouble *sd) {
62	gezelter	1930	GenericData * data;
63			AtomData * atomData;
64			AtomInfo * atomInfo;
65			std::vector<AtomInfo *>::iterator i;
66	gezelter	1490
67	gezelter	1930	data = sd->getPropertyByName("ATOMDATA");
68	gezelter	1490
69	gezelter	1930	if (data != NULL) {
70	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
71	gezelter	1490
72	gezelter	2204	if (atomData == NULL)
73			return;
74	gezelter	1930	} else
75	gezelter	2204	return;
76	gezelter	1930
77			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78
79			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80	tim	2240	Vector3d newPos = atomInfo->pos - origin_;
81			currSnapshot->wrapVector(newPos);
82			atomInfo->pos = newPos;
83	gezelter	1930	}
84	gezelter	2204	}
85	gezelter	1490
86	tim	2240	void WrappingVisitor::update() {
87			if (useCom_){
88			origin_ = info->getCom();
89			}
90			}
91
92	gezelter	2204	const std::string WrappingVisitor::toString() {
93	gezelter	1930	char buffer[65535];
94			std::string result;
95	gezelter	1490
96	gezelter	1930	sprintf(buffer,
97			"------------------------------------------------------------------\n");
98			result += buffer;
99	gezelter	1490
100	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
101			result += buffer;
102	gezelter	1490
103	gezelter	1930	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	2204	}
113	gezelter	1490
114	gezelter	2204	//----------------------------------------------------------------------------//
115	gezelter	1490
116	gezelter	2204	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
117	gezelter	1930	BaseVisitor() {
118	gezelter	2204	this->info = info;
119			visitorName = "ReplicateVisitor";
120			this->replicateOpt = opt;
121	gezelter	1930
122	gezelter	2204	//generate the replicate directions
123			for( int i = 0; i <= replicateOpt[0]; i++ ) {
124	gezelter	1930	for( int j = 0; j <= replicateOpt[1]; j++ ) {
125	gezelter	2204	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	1930	}
134	gezelter	2204	}
135
136	gezelter	1930	}
137
138	gezelter	2204	void ReplicateVisitor::visit(Atom *atom) {
139			internalVisit(atom);
140			}
141	gezelter	1930
142	gezelter	2204	void ReplicateVisitor::visit(DirectionalAtom *datom) {
143			internalVisit(datom);
144			}
145	gezelter	1490
146	gezelter	2204	void ReplicateVisitor::visit(RigidBody *rb) {
147			internalVisit(rb);
148			}
149	gezelter	1490
150	gezelter	2204	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
151	gezelter	1930	GenericData * data;
152			AtomData * atomData;
153	gezelter	1490
154	gezelter	1930	//if there is not atom data, just skip it
155			data = sd->getPropertyByName("ATOMDATA");
156	gezelter	1490
157	gezelter	1930	if (data != NULL) {
158	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
159	gezelter	1490
160	gezelter	2204	if (atomData == NULL) {
161			return;
162			}
163	gezelter	1930	} else {
164	gezelter	2204	return;
165	gezelter	1930	}
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	2204	}
174	gezelter	1490
175	gezelter	2204	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
176	gezelter	1930	AtomInfo* newAtomInfo;
177			std::vector<Vector3i>::iterator dirIter;
178			std::vector<AtomInfo *>::iterator i;
179	gezelter	1490
180	gezelter	1930	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
181	gezelter	2204	for( i = infoList.begin(); i != infoList.end(); i++ ) {
182			newAtomInfo = new AtomInfo();
183			newAtomInfo = (*i);
184	gezelter	1490
185	gezelter	2204	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	1930
188	gezelter	2204	data->addAtomInfo(newAtomInfo);
189			}
190	gezelter	1930	} // end for(dirIter)
191	gezelter	2204	}
192	gezelter	1490
193	gezelter	2204	const std::string ReplicateVisitor::toString() {
194	gezelter	1930	char buffer[65535];
195			std::string result;
196			std::set<std::string>::iterator i;
197	gezelter	1490
198	gezelter	1930	sprintf(buffer,
199			"------------------------------------------------------------------\n");
200			result += buffer;
201	gezelter	1490
202	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
203			result += buffer;
204	gezelter	1490
205	gezelter	1930	sprintf(buffer,
206			"Visitor Description: replicate the atoms in different direction\n");
207			result += buffer;
208	gezelter	1490
209	gezelter	1930	//print the replicate direction
210			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
211			result += buffer;
212	gezelter	1490
213	gezelter	1930	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
214			result += buffer;
215	gezelter	1490
216	gezelter	1930	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
217			result += buffer;
218	gezelter	1490
219	gezelter	1930	sprintf(buffer,
220			"------------------------------------------------------------------\n");
221			result += buffer;
222
223			return result;
224	gezelter	2204	}
225	gezelter	1490
226	gezelter	2204	//----------------------------------------------------------------------------//
227	gezelter	1490
228	gezelter	2204	XYZVisitor::XYZVisitor(SimInfo *info) :
229	tim	2097	BaseVisitor(), seleMan(info), evaluator(info){
230	gezelter	2204	this->info = info;
231			visitorName = "XYZVisitor";
232	tim	2097
233	gezelter	2204	evaluator.loadScriptString("select all");
234	tim	2097
235	gezelter	2204	if (!evaluator.isDynamic()) {
236	tim	2097	seleMan.setSelectionSet(evaluator.evaluate());
237	gezelter	2204	}
238	chuckv	3116	posOnly_ = false;
239	tim	2097	}
240
241	gezelter	2204	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
242	tim	2097	BaseVisitor(), seleMan(info), evaluator(info) {
243	gezelter	2204	this->info = info;
244			visitorName = "XYZVisitor";
245	tim	2097
246	gezelter	2204	evaluator.loadScriptString(script);
247	tim	2097
248	gezelter	2204	if (!evaluator.isDynamic()) {
249	tim	2097	seleMan.setSelectionSet(evaluator.evaluate());
250	gezelter	2204	}
251	chuckv	3116	posOnly_ = false;
252	tim	2097	}
253
254	gezelter	2204	void XYZVisitor::visit(Atom *atom) {
255	tim	1977	if (isSelected(atom))
256	gezelter	2204	internalVisit(atom);
257			}
258	gezelter	1490
259	gezelter	2204	void XYZVisitor::visit(DirectionalAtom *datom) {
260	tim	1977	if (isSelected(datom))
261	gezelter	2204	internalVisit(datom);
262			}
263	gezelter	1490
264	gezelter	2204	void XYZVisitor::visit(RigidBody *rb) {
265	tim	1977	if (isSelected(rb))
266	gezelter	2204	internalVisit(rb);
267			}
268	gezelter	1490
269	gezelter	2204	void XYZVisitor::update() {
270	tim	2097	//if dynamic, we need to re-evaluate the selection
271			if (evaluator.isDynamic()) {
272	gezelter	2204	seleMan.setSelectionSet(evaluator.evaluate());
273	tim	2097	}
274	gezelter	2204	}
275	tim	2097
276	gezelter	2204	void XYZVisitor::internalVisit(StuntDouble *sd) {
277	gezelter	1930	GenericData * data;
278			AtomData * atomData;
279			AtomInfo * atomInfo;
280			std::vector<AtomInfo *>::iterator i;
281			char buffer[1024];
282	gezelter	1490
283	gezelter	1930	//if there is not atom data, just skip it
284			data = sd->getPropertyByName("ATOMDATA");
285	gezelter	1490
286	gezelter	1930	if (data != NULL) {
287	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
288	gezelter	1490
289	gezelter	2204	if (atomData == NULL)
290			return;
291	gezelter	1930	} else
292	gezelter	2204	return;
293	gezelter	1490
294	chuckv	3116	if (posOnly_){
295			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
296			atomInfo = atomData->nextAtomInfo(i) ) {
297	xsun	3328	if (atomInfo->hasCharge) {
298			sprintf(buffer,
299			"%s%15.8f%15.8f%15.8f%15.8f",
300			atomInfo->atomTypeName.c_str(),
301			atomInfo->pos[0],
302			atomInfo->pos[1],
303			atomInfo->pos[2],
304			atomInfo->charge);
305			} else {
306			sprintf(buffer,
307	chuckv	3116	"%s%15.8f%15.8f%15.8f",
308			atomInfo->atomTypeName.c_str(),
309			atomInfo->pos[0],
310			atomInfo->pos[1],
311			atomInfo->pos[2]);
312	xsun	3328	}
313	chuckv	3116	frame.push_back(buffer);
314			}
315			}else{
316			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
317			atomInfo = atomData->nextAtomInfo(i) ) {
318	xsun	3328	if (atomInfo->hasCharge) {
319	chuckv	3116	sprintf(buffer,
320	xsun	3328	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
321			atomInfo->atomTypeName.c_str(),
322			atomInfo->pos[0],
323			atomInfo->pos[1],
324			atomInfo->pos[2],
325			atomInfo->charge,
326			atomInfo->dipole[0],
327			atomInfo->dipole[1],
328			atomInfo->dipole[2]);
329			} else {
330			sprintf(buffer,
331	chuckv	3116	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
332			atomInfo->atomTypeName.c_str(),
333			atomInfo->pos[0],
334			atomInfo->pos[1],
335			atomInfo->pos[2],
336			atomInfo->dipole[0],
337			atomInfo->dipole[1],
338			atomInfo->dipole[2]);
339	xsun	3328	}
340	chuckv	3116	frame.push_back(buffer);
341			}
342	gezelter	1930	}
343	gezelter	2204	}
344	gezelter	1490
345	gezelter	2204	bool XYZVisitor::isSelected(StuntDouble *sd) {
346	tim	2097	return seleMan.isSelected(sd);
347	gezelter	2204	}
348	gezelter	1490
349	gezelter	2204	void XYZVisitor::writeFrame(std::ostream &outStream) {
350	gezelter	1930	std::vector<std::string>::iterator i;
351			char buffer[1024];
352	gezelter	1490
353	gezelter	1930	if (frame.size() == 0)
354	gezelter	2204	std::cerr << "Current Frame does not contain any atoms" << std::endl;
355	gezelter	1490
356	gezelter	1930	//total number of atoms
357			outStream << frame.size() << std::endl;
358	gezelter	1490
359	gezelter	1930	//write comment line
360			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
361			Mat3x3d box = currSnapshot->getHmat();
362
363			sprintf(buffer,
364			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
365			currSnapshot->getTime(),
366			box(0, 0), box(0, 1), box(0, 2),
367			box(1, 0), box(1, 1), box(1, 2),
368			box(2, 0), box(2, 1), box(2, 2));
369	gezelter	1490
370	gezelter	1930	outStream << buffer << std::endl;
371	gezelter	1490
372	gezelter	1930	for( i = frame.begin(); i != frame.end(); ++i )
373	gezelter	2204	outStream << *i << std::endl;
374			}
375	gezelter	1490
376	gezelter	2204	const std::string XYZVisitor::toString() {
377	gezelter	1930	char buffer[65535];
378			std::string result;
379	gezelter	1490
380	gezelter	1930	sprintf(buffer,
381			"------------------------------------------------------------------\n");
382			result += buffer;
383	gezelter	1490
384	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
385			result += buffer;
386	gezelter	1490
387	gezelter	1930	sprintf(buffer,
388			"Visitor Description: assemble the atom data and output xyz file\n");
389			result += buffer;
390
391			sprintf(buffer,
392			"------------------------------------------------------------------\n");
393			result += buffer;
394
395			return result;
396	gezelter	2204	}
397	gezelter	1490
398	gezelter	2204	//----------------------------------------------------------------------------//
399	gezelter	1490
400	gezelter	2204	void PrepareVisitor::internalVisit(Atom *atom) {
401	gezelter	1930	GenericData *data;
402			AtomData * atomData;
403	gezelter	1490
404	gezelter	1930	//if visited property is existed, remove it
405			data = atom->getPropertyByName("VISITED");
406	gezelter	1490
407	gezelter	1930	if (data != NULL) {
408	gezelter	2204	atom->removeProperty("VISITED");
409	gezelter	1930	}
410
411			//remove atomdata
412			data = atom->getPropertyByName("ATOMDATA");
413
414			if (data != NULL) {
415	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
416	gezelter	1930
417	gezelter	2204	if (atomData != NULL)
418			atom->removeProperty("ATOMDATA");
419	gezelter	1930	}
420	gezelter	2204	}
421	gezelter	1490
422	gezelter	2204	void PrepareVisitor::internalVisit(RigidBody *rb) {
423	gezelter	1930	GenericData* data;
424			AtomData* atomData;
425			std::vector<Atom *> myAtoms;
426			std::vector<Atom *>::iterator atomIter;
427	gezelter	1490
428	gezelter	1930	//if visited property is existed, remove it
429			data = rb->getPropertyByName("VISITED");
430	gezelter	1490
431	gezelter	1930	if (data != NULL) {
432	gezelter	2204	rb->removeProperty("VISITED");
433	gezelter	1930	}
434
435			//remove atomdata
436			data = rb->getPropertyByName("ATOMDATA");
437
438			if (data != NULL) {
439	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
440	gezelter	1930
441	gezelter	2204	if (atomData != NULL)
442			rb->removeProperty("ATOMDATA");
443	gezelter	1930	}
444
445			myAtoms = rb->getAtoms();
446
447			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
448	gezelter	2204	internalVisit(*atomIter);
449			}
450	gezelter	1490
451	gezelter	2204	const std::string PrepareVisitor::toString() {
452			char buffer[65535];
453			std::string result;
454	tim	1977
455	gezelter	2204	sprintf(buffer,
456			"------------------------------------------------------------------\n");
457			result += buffer;
458	tim	1977
459	gezelter	2204	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
460			result += buffer;
461	tim	1977
462	gezelter	2204	sprintf(buffer,
463			"Visitor Description: prepare for operation of other vistors\n");
464			result += buffer;
465	tim	1977
466	gezelter	2204	sprintf(buffer,
467			"------------------------------------------------------------------\n");
468			result += buffer;
469	tim	1977
470	gezelter	2204	return result;
471			}
472	gezelter	1490
473	gezelter	2204	//----------------------------------------------------------------------------//
474	gezelter	1490
475	gezelter	2204	WaterTypeVisitor::WaterTypeVisitor() {
476	gezelter	1930	visitorName = "WaterTypeVisitor";
477			waterTypeList.insert("TIP3P_RB_0");
478			waterTypeList.insert("TIP4P_RB_0");
479			waterTypeList.insert("TIP5P_RB_0");
480			waterTypeList.insert("SPCE_RB_0");
481	gezelter	2204	}
482	gezelter	1490
483	gezelter	2204	void WaterTypeVisitor::visit(RigidBody *rb) {
484	gezelter	1930	std::string rbName;
485			std::vector<Atom *> myAtoms;
486			std::vector<Atom *>::iterator atomIter;
487			GenericData* data;
488			AtomData* atomData;
489			AtomInfo* atomInfo;
490			std::vector<AtomInfo *>::iterator i;
491	gezelter	1490
492	gezelter	1930	rbName = rb->getType();
493	gezelter	1490
494	gezelter	1930	if (waterTypeList.find(rbName) != waterTypeList.end()) {
495	gezelter	2204	myAtoms = rb->getAtoms();
496	gezelter	1490
497	gezelter	2204	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
498			++atomIter ) {
499			data = (*atomIter)->getPropertyByName("ATOMDATA");
500	gezelter	1490
501	gezelter	2204	if (data != NULL) {
502			atomData = dynamic_cast<AtomData *>(data);
503	gezelter	1490
504	gezelter	2204	if (atomData == NULL)
505			continue;
506			} else
507			continue;
508	gezelter	1930
509	gezelter	2204	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
510			atomInfo = atomData->nextAtomInfo(i) ) {
511			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
512			} //end for(atomInfo)
513			} //end for(atomIter)
514	gezelter	1930	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
515	gezelter	2204	}
516	gezelter	1490
517	gezelter	2091	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
518			return atomTypeName.substr(0, atomTypeName.find('_'));
519			}
520	gezelter	1490
521	gezelter	2204	const std::string WaterTypeVisitor::toString() {
522	gezelter	1930	char buffer[65535];
523			std::string result;
524	gezelter	1490
525	gezelter	1930	sprintf(buffer,
526			"------------------------------------------------------------------\n");
527			result += buffer;
528	gezelter	1490
529	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
530			result += buffer;
531	gezelter	1490
532	gezelter	1930	sprintf(buffer,
533			"Visitor Description: Replace the atom type in water model\n");
534			result += buffer;
535	gezelter	1490
536	gezelter	1930	sprintf(buffer,
537			"------------------------------------------------------------------\n");
538			result += buffer;
539
540			return result;
541	gezelter	2204	}
542	gezelter	1490
543	gezelter	1930	} //namespace oopse