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) ) {
      currSnapshot->wrapVector(atomInfo->pos);
    }
  }

  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());
      }

    }

  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());
      }
          
    }
    
  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) ) {
      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:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years ago) by gezelter
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	14439 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	407	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41	tim	324	#include "selection/SelectionManager.hpp"
42	tim	3	#include "visitors/OtherVisitor.hpp"
43			#include "primitives/DirectionalAtom.hpp"
44			#include "primitives/RigidBody.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "brains/SimInfo.hpp"
47	tim	132	namespace oopse {
48
49	gezelter	507	void WrappingVisitor::visit(Atom *atom) {
50			internalVisit(atom);
51			}
52	gezelter	246
53	gezelter	507	void WrappingVisitor::visit(DirectionalAtom *datom) {
54			internalVisit(datom);
55			}
56	gezelter	2
57	gezelter	507	void WrappingVisitor::visit(RigidBody *rb) {
58			internalVisit(rb);
59			}
60	gezelter	2
61	gezelter	507	void WrappingVisitor::internalVisit(StuntDouble *sd) {
62	gezelter	246	GenericData * data;
63			AtomData * atomData;
64			AtomInfo * atomInfo;
65			std::vector<AtomInfo *>::iterator i;
66	gezelter	2
67	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
68	gezelter	2
69	gezelter	246	if (data != NULL) {
70	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
71	gezelter	2
72	gezelter	507	if (atomData == NULL)
73			return;
74	gezelter	246	} else
75	gezelter	507	return;
76	gezelter	246
77			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78
79			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80	gezelter	507	currSnapshot->wrapVector(atomInfo->pos);
81	gezelter	246	}
82	gezelter	507	}
83	gezelter	2
84	gezelter	507	const std::string WrappingVisitor::toString() {
85	gezelter	246	char buffer[65535];
86			std::string result;
87	gezelter	2
88	gezelter	246	sprintf(buffer,
89			"------------------------------------------------------------------\n");
90			result += buffer;
91	gezelter	2
92	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
93			result += buffer;
94	gezelter	2
95	gezelter	246	sprintf(buffer,
96			"Visitor Description: wrapping atoms back to periodic box\n");
97			result += buffer;
98
99			sprintf(buffer,
100			"------------------------------------------------------------------\n");
101			result += buffer;
102
103			return result;
104	gezelter	507	}
105	gezelter	2
106	gezelter	507	//----------------------------------------------------------------------------//
107	gezelter	2
108	gezelter	507	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
109	gezelter	246	BaseVisitor() {
110	gezelter	507	this->info = info;
111			visitorName = "ReplicateVisitor";
112			this->replicateOpt = opt;
113	gezelter	246
114	gezelter	507	//generate the replicate directions
115			for( int i = 0; i <= replicateOpt[0]; i++ ) {
116	gezelter	246	for( int j = 0; j <= replicateOpt[1]; j++ ) {
117	gezelter	507	for( int k = 0; k <= replicateOpt[2]; k++ ) {
118			//skip original frame
119			if (i == 0 && j == 0 && k == 0) {
120			continue;
121			} else {
122			dir.push_back(Vector3i(i, j, k));
123			}
124			}
125	gezelter	246	}
126	gezelter	507	}
127
128	gezelter	246	}
129
130	gezelter	507	void ReplicateVisitor::visit(Atom *atom) {
131			internalVisit(atom);
132			}
133	gezelter	246
134	gezelter	507	void ReplicateVisitor::visit(DirectionalAtom *datom) {
135			internalVisit(datom);
136			}
137	gezelter	2
138	gezelter	507	void ReplicateVisitor::visit(RigidBody *rb) {
139			internalVisit(rb);
140			}
141	gezelter	2
142	gezelter	507	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
143	gezelter	246	GenericData * data;
144			AtomData * atomData;
145	gezelter	2
146	gezelter	246	//if there is not atom data, just skip it
147			data = sd->getPropertyByName("ATOMDATA");
148	gezelter	2
149	gezelter	246	if (data != NULL) {
150	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
151	gezelter	2
152	gezelter	507	if (atomData == NULL) {
153			return;
154			}
155	gezelter	246	} else {
156	gezelter	507	return;
157	gezelter	246	}
158
159			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
160			Mat3x3d box = currSnapshot->getHmat();
161
162			std::vector<AtomInfo *> atomInfoList = atomData->getData();
163
164			replicate(atomInfoList, atomData, box);
165	gezelter	507	}
166	gezelter	2
167	gezelter	507	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
168	gezelter	246	AtomInfo* newAtomInfo;
169			std::vector<Vector3i>::iterator dirIter;
170			std::vector<AtomInfo *>::iterator i;
171	gezelter	2
172	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
173	gezelter	507	for( i = infoList.begin(); i != infoList.end(); i++ ) {
174			newAtomInfo = new AtomInfo();
175			newAtomInfo = (*i);
176	gezelter	2
177	gezelter	507	for( int j = 0; j < 3; j++ )
178			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
179	gezelter	246
180	gezelter	507	data->addAtomInfo(newAtomInfo);
181			}
182	gezelter	246	} // end for(dirIter)
183	gezelter	507	}
184	gezelter	2
185	gezelter	507	const std::string ReplicateVisitor::toString() {
186	gezelter	246	char buffer[65535];
187			std::string result;
188			std::set<std::string>::iterator i;
189	gezelter	2
190	gezelter	246	sprintf(buffer,
191			"------------------------------------------------------------------\n");
192			result += buffer;
193	gezelter	2
194	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
195			result += buffer;
196	gezelter	2
197	gezelter	246	sprintf(buffer,
198			"Visitor Description: replicate the atoms in different direction\n");
199			result += buffer;
200	gezelter	2
201	gezelter	246	//print the replicate direction
202			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
203			result += buffer;
204	gezelter	2
205	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
206			result += buffer;
207	gezelter	2
208	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
209			result += buffer;
210	gezelter	2
211	gezelter	246	sprintf(buffer,
212			"------------------------------------------------------------------\n");
213			result += buffer;
214
215			return result;
216	gezelter	507	}
217	gezelter	2
218	gezelter	507	//----------------------------------------------------------------------------//
219	gezelter	2
220	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info) :
221	tim	413	BaseVisitor(), seleMan(info), evaluator(info){
222	gezelter	507	this->info = info;
223			visitorName = "XYZVisitor";
224	tim	413
225	gezelter	507	evaluator.loadScriptString("select all");
226	tim	413
227	gezelter	507	if (!evaluator.isDynamic()) {
228	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
229	gezelter	507	}
230
231	tim	413	}
232
233	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
234	tim	413	BaseVisitor(), seleMan(info), evaluator(info) {
235	gezelter	507	this->info = info;
236			visitorName = "XYZVisitor";
237	tim	413
238	gezelter	507	evaluator.loadScriptString(script);
239	tim	413
240	gezelter	507	if (!evaluator.isDynamic()) {
241	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
242	gezelter	507	}
243
244	tim	413	}
245
246	gezelter	507	void XYZVisitor::visit(Atom *atom) {
247	tim	293	if (isSelected(atom))
248	gezelter	507	internalVisit(atom);
249			}
250	gezelter	2
251	gezelter	507	void XYZVisitor::visit(DirectionalAtom *datom) {
252	tim	293	if (isSelected(datom))
253	gezelter	507	internalVisit(datom);
254			}
255	gezelter	2
256	gezelter	507	void XYZVisitor::visit(RigidBody *rb) {
257	tim	293	if (isSelected(rb))
258	gezelter	507	internalVisit(rb);
259			}
260	gezelter	2
261	gezelter	507	void XYZVisitor::update() {
262	tim	413	//if dynamic, we need to re-evaluate the selection
263			if (evaluator.isDynamic()) {
264	gezelter	507	seleMan.setSelectionSet(evaluator.evaluate());
265	tim	413	}
266	gezelter	507	}
267	tim	413
268	gezelter	507	void XYZVisitor::internalVisit(StuntDouble *sd) {
269	gezelter	246	GenericData * data;
270			AtomData * atomData;
271			AtomInfo * atomInfo;
272			std::vector<AtomInfo *>::iterator i;
273			char buffer[1024];
274	gezelter	2
275	gezelter	246	//if there is not atom data, just skip it
276			data = sd->getPropertyByName("ATOMDATA");
277	gezelter	2
278	gezelter	246	if (data != NULL) {
279	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
280	gezelter	2
281	gezelter	507	if (atomData == NULL)
282			return;
283	gezelter	246	} else
284	gezelter	507	return;
285	gezelter	2
286	gezelter	246	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
287	gezelter	507	atomInfo = atomData->nextAtomInfo(i) ) {
288			sprintf(buffer,
289			"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
290			atomInfo->atomTypeName.c_str(),
291			atomInfo->pos[0],
292			atomInfo->pos[1],
293			atomInfo->pos[2],
294			atomInfo->dipole[0],
295			atomInfo->dipole[1],
296			atomInfo->dipole[2]);
297			frame.push_back(buffer);
298	gezelter	246	}
299	gezelter	507	}
300	gezelter	2
301	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
302	tim	413	return seleMan.isSelected(sd);
303	gezelter	507	}
304	gezelter	2
305	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
306	gezelter	246	std::vector<std::string>::iterator i;
307			char buffer[1024];
308	gezelter	2
309	gezelter	246	if (frame.size() == 0)
310	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
311	gezelter	2
312	gezelter	246	//total number of atoms
313			outStream << frame.size() << std::endl;
314	gezelter	2
315	gezelter	246	//write comment line
316			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
317			Mat3x3d box = currSnapshot->getHmat();
318
319			sprintf(buffer,
320			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
321			currSnapshot->getTime(),
322			box(0, 0), box(0, 1), box(0, 2),
323			box(1, 0), box(1, 1), box(1, 2),
324			box(2, 0), box(2, 1), box(2, 2));
325	gezelter	2
326	gezelter	246	outStream << buffer << std::endl;
327	gezelter	2
328	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
329	gezelter	507	outStream << *i << std::endl;
330			}
331	gezelter	2
332	gezelter	507	const std::string XYZVisitor::toString() {
333	gezelter	246	char buffer[65535];
334			std::string result;
335	gezelter	2
336	gezelter	246	sprintf(buffer,
337			"------------------------------------------------------------------\n");
338			result += buffer;
339	gezelter	2
340	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
341			result += buffer;
342	gezelter	2
343	gezelter	246	sprintf(buffer,
344			"Visitor Description: assemble the atom data and output xyz file\n");
345			result += buffer;
346
347			sprintf(buffer,
348			"------------------------------------------------------------------\n");
349			result += buffer;
350
351			return result;
352	gezelter	507	}
353	gezelter	2
354	gezelter	507	//----------------------------------------------------------------------------//
355	gezelter	2
356	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
357	gezelter	246	GenericData *data;
358			AtomData * atomData;
359	gezelter	2
360	gezelter	246	//if visited property is existed, remove it
361			data = atom->getPropertyByName("VISITED");
362	gezelter	2
363	gezelter	246	if (data != NULL) {
364	gezelter	507	atom->removeProperty("VISITED");
365	gezelter	246	}
366
367			//remove atomdata
368			data = atom->getPropertyByName("ATOMDATA");
369
370			if (data != NULL) {
371	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
372	gezelter	246
373	gezelter	507	if (atomData != NULL)
374			atom->removeProperty("ATOMDATA");
375	gezelter	246	}
376	gezelter	507	}
377	gezelter	2
378	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
379	gezelter	246	GenericData* data;
380			AtomData* atomData;
381			std::vector<Atom *> myAtoms;
382			std::vector<Atom *>::iterator atomIter;
383	gezelter	2
384	gezelter	246	//if visited property is existed, remove it
385			data = rb->getPropertyByName("VISITED");
386	gezelter	2
387	gezelter	246	if (data != NULL) {
388	gezelter	507	rb->removeProperty("VISITED");
389	gezelter	246	}
390
391			//remove atomdata
392			data = rb->getPropertyByName("ATOMDATA");
393
394			if (data != NULL) {
395	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
396	gezelter	246
397	gezelter	507	if (atomData != NULL)
398			rb->removeProperty("ATOMDATA");
399	gezelter	246	}
400
401			myAtoms = rb->getAtoms();
402
403			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
404	gezelter	507	internalVisit(*atomIter);
405			}
406	gezelter	2
407	gezelter	507	const std::string PrepareVisitor::toString() {
408			char buffer[65535];
409			std::string result;
410	tim	293
411	gezelter	507	sprintf(buffer,
412			"------------------------------------------------------------------\n");
413			result += buffer;
414	tim	293
415	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
416			result += buffer;
417	tim	293
418	gezelter	507	sprintf(buffer,
419			"Visitor Description: prepare for operation of other vistors\n");
420			result += buffer;
421	tim	293
422	gezelter	507	sprintf(buffer,
423			"------------------------------------------------------------------\n");
424			result += buffer;
425	tim	293
426	gezelter	507	return result;
427			}
428	gezelter	2
429	gezelter	507	//----------------------------------------------------------------------------//
430	gezelter	2
431	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
432	gezelter	246	visitorName = "WaterTypeVisitor";
433			waterTypeList.insert("TIP3P_RB_0");
434			waterTypeList.insert("TIP4P_RB_0");
435			waterTypeList.insert("TIP5P_RB_0");
436			waterTypeList.insert("SPCE_RB_0");
437	gezelter	507	}
438	gezelter	2
439	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
440	gezelter	246	std::string rbName;
441			std::vector<Atom *> myAtoms;
442			std::vector<Atom *>::iterator atomIter;
443			GenericData* data;
444			AtomData* atomData;
445			AtomInfo* atomInfo;
446			std::vector<AtomInfo *>::iterator i;
447	gezelter	2
448	gezelter	246	rbName = rb->getType();
449	gezelter	2
450	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
451	gezelter	507	myAtoms = rb->getAtoms();
452	gezelter	2
453	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
454			++atomIter ) {
455			data = (*atomIter)->getPropertyByName("ATOMDATA");
456	gezelter	2
457	gezelter	507	if (data != NULL) {
458			atomData = dynamic_cast<AtomData *>(data);
459	gezelter	2
460	gezelter	507	if (atomData == NULL)
461			continue;
462			} else
463			continue;
464	gezelter	246
465	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
466			atomInfo = atomData->nextAtomInfo(i) ) {
467			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
468			} //end for(atomInfo)
469			} //end for(atomIter)
470	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
471	gezelter	507	}
472	gezelter	2
473	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
474			return atomTypeName.substr(0, atomTypeName.find('_'));
475			}
476	gezelter	2
477	gezelter	507	const std::string WaterTypeVisitor::toString() {
478	gezelter	246	char buffer[65535];
479			std::string result;
480	gezelter	2
481	gezelter	246	sprintf(buffer,
482			"------------------------------------------------------------------\n");
483			result += buffer;
484	gezelter	2
485	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
486			result += buffer;
487	gezelter	2
488	gezelter	246	sprintf(buffer,
489			"Visitor Description: Replace the atom type in water model\n");
490			result += buffer;
491	gezelter	2
492	gezelter	246	sprintf(buffer,
493			"------------------------------------------------------------------\n");
494			result += buffer;
495
496			return result;
497	gezelter	507	}
498	gezelter	2
499	gezelter	246	} //namespace oopse