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;

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

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

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

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

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

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

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

    outStream << buffer << std::endl;

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

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

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

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

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

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

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

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

    return result;
  }

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

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

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

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

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

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

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

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

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

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

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

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

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

    myAtoms = rb->getAtoms();

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

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

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

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

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

    rbName = rb->getType();

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

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

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

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

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

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

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

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

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

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

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

    return result;
  }

} //namespace oopse
Revision:	1290
Committed:	Wed Sep 10 19:51:45 2008 UTC (16 years, 7 months ago) by cli2
Original Path:	*trunk/src/visitors/OtherVisitor.cpp*
File size:	15804 byte(s)
Log Message:	Inversion fixes and amber mostly working
#	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			* 1. Acknowledgement of the program authors must be made in any
9			* publication of scientific results based in part on use of the
10			* program. An acceptable form of acknowledgement is citation of
11			* the article in which the program was described (Matthew
12			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14			* Parallel Simulation Engine for Molecular Dynamics,"
15			* J. Comput. Chem. 26, pp. 252-271 (2005))
16			*
17			* 2. Redistributions of source code must retain the above copyright
18			* notice, this list of conditions and the following disclaimer.
19			*
20			* 3. Redistributions in binary form must reproduce the above copyright
21			* notice, this list of conditions and the following disclaimer in the
22			* documentation and/or other materials provided with the
23			* distribution.
24			*
25			* This software is provided "AS IS," without a warranty of any
26			* kind. All express or implied conditions, representations and
27			* warranties, including any implied warranty of merchantability,
28			* fitness for a particular purpose or non-infringement, are hereby
29			* excluded. The University of Notre Dame and its licensors shall not
30			* be liable for any damages suffered by licensee as a result of
31			* using, modifying or distributing the software or its
32			* derivatives. In no event will the University of Notre Dame or its
33			* licensors be liable for any lost revenue, profit or data, or for
34			* direct, indirect, special, consequential, incidental or punitive
35			* damages, however caused and regardless of the theory of liability,
36			* arising out of the use of or inability to use software, even if the
37			* University of Notre Dame has been advised of the possibility of
38			* such damages.
39			*/
40	tim	324	#include "selection/SelectionManager.hpp"
41	tim	3	#include "visitors/OtherVisitor.hpp"
42			#include "primitives/DirectionalAtom.hpp"
43			#include "primitives/RigidBody.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "brains/SimInfo.hpp"
46	tim	132	namespace oopse {
47
48	gezelter	507	void WrappingVisitor::visit(Atom *atom) {
49			internalVisit(atom);
50			}
51	gezelter	246
52	gezelter	507	void WrappingVisitor::visit(DirectionalAtom *datom) {
53			internalVisit(datom);
54			}
55	gezelter	2
56	gezelter	507	void WrappingVisitor::visit(RigidBody *rb) {
57			internalVisit(rb);
58			}
59	gezelter	2
60	gezelter	507	void WrappingVisitor::internalVisit(StuntDouble *sd) {
61	gezelter	246	GenericData * data;
62			AtomData * atomData;
63			AtomInfo * atomInfo;
64			std::vector<AtomInfo *>::iterator i;
65	gezelter	2
66	gezelter	246	data = sd->getPropertyByName("ATOMDATA");
67	gezelter	2
68	gezelter	246	if (data != NULL) {
69	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
70	gezelter	2
71	gezelter	507	if (atomData == NULL)
72			return;
73	gezelter	246	} else
74	gezelter	507	return;
75	gezelter	246
76			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
77
78			for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
79	tim	543	Vector3d newPos = atomInfo->pos - origin_;
80			currSnapshot->wrapVector(newPos);
81			atomInfo->pos = newPos;
82	gezelter	246	}
83	gezelter	507	}
84	gezelter	2
85	tim	543	void WrappingVisitor::update() {
86			if (useCom_){
87			origin_ = info->getCom();
88			}
89			}
90
91	gezelter	507	const std::string WrappingVisitor::toString() {
92	gezelter	246	char buffer[65535];
93			std::string result;
94	gezelter	2
95	gezelter	246	sprintf(buffer,
96			"------------------------------------------------------------------\n");
97			result += buffer;
98	gezelter	2
99	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
100			result += buffer;
101	gezelter	2
102	gezelter	246	sprintf(buffer,
103			"Visitor Description: wrapping atoms back to periodic box\n");
104			result += buffer;
105
106			sprintf(buffer,
107			"------------------------------------------------------------------\n");
108			result += buffer;
109
110			return result;
111	gezelter	507	}
112	gezelter	2
113	gezelter	507	//----------------------------------------------------------------------------//
114	gezelter	2
115	gezelter	507	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
116	gezelter	246	BaseVisitor() {
117	gezelter	507	this->info = info;
118			visitorName = "ReplicateVisitor";
119			this->replicateOpt = opt;
120	gezelter	246
121	gezelter	507	//generate the replicate directions
122			for( int i = 0; i <= replicateOpt[0]; i++ ) {
123	gezelter	246	for( int j = 0; j <= replicateOpt[1]; j++ ) {
124	gezelter	507	for( int k = 0; k <= replicateOpt[2]; k++ ) {
125			//skip original frame
126			if (i == 0 && j == 0 && k == 0) {
127			continue;
128			} else {
129			dir.push_back(Vector3i(i, j, k));
130			}
131			}
132	gezelter	246	}
133	gezelter	507	}
134
135	gezelter	246	}
136
137	gezelter	507	void ReplicateVisitor::visit(Atom *atom) {
138			internalVisit(atom);
139			}
140	gezelter	246
141	gezelter	507	void ReplicateVisitor::visit(DirectionalAtom *datom) {
142			internalVisit(datom);
143			}
144	gezelter	2
145	gezelter	507	void ReplicateVisitor::visit(RigidBody *rb) {
146			internalVisit(rb);
147			}
148	gezelter	2
149	gezelter	507	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
150	gezelter	246	GenericData * data;
151			AtomData * atomData;
152	gezelter	2
153	gezelter	246	//if there is not atom data, just skip it
154			data = sd->getPropertyByName("ATOMDATA");
155	gezelter	2
156	gezelter	246	if (data != NULL) {
157	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
158	gezelter	2
159	gezelter	507	if (atomData == NULL) {
160			return;
161			}
162	gezelter	246	} else {
163	gezelter	507	return;
164	gezelter	246	}
165
166			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
167			Mat3x3d box = currSnapshot->getHmat();
168
169			std::vector<AtomInfo *> atomInfoList = atomData->getData();
170
171			replicate(atomInfoList, atomData, box);
172	gezelter	507	}
173	gezelter	2
174	gezelter	507	void ReplicateVisitor::replicate(std::vector<AtomInfo >&infoList, AtomData data, const Mat3x3d& box) {
175	gezelter	246	AtomInfo* newAtomInfo;
176			std::vector<Vector3i>::iterator dirIter;
177			std::vector<AtomInfo *>::iterator i;
178	gezelter	2
179	gezelter	246	for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
180	gezelter	507	for( i = infoList.begin(); i != infoList.end(); i++ ) {
181			newAtomInfo = new AtomInfo();
182			newAtomInfo = (*i);
183	gezelter	2
184	gezelter	507	for( int j = 0; j < 3; j++ )
185			newAtomInfo->pos[j] += (dirIter)[0]box(j, 0) + (dirIter)[1]box(j, 1) + (dirIter)[2]box(j, 2);
186	gezelter	246
187	gezelter	507	data->addAtomInfo(newAtomInfo);
188			}
189	gezelter	246	} // end for(dirIter)
190	gezelter	507	}
191	gezelter	2
192	gezelter	507	const std::string ReplicateVisitor::toString() {
193	gezelter	246	char buffer[65535];
194			std::string result;
195			std::set<std::string>::iterator i;
196	gezelter	2
197	gezelter	246	sprintf(buffer,
198			"------------------------------------------------------------------\n");
199			result += buffer;
200	gezelter	2
201	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
202			result += buffer;
203	gezelter	2
204	gezelter	246	sprintf(buffer,
205			"Visitor Description: replicate the atoms in different direction\n");
206			result += buffer;
207	gezelter	2
208	gezelter	246	//print the replicate direction
209			sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
210			result += buffer;
211	gezelter	2
212	gezelter	246	sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
213			result += buffer;
214	gezelter	2
215	gezelter	246	sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
216			result += buffer;
217	gezelter	2
218	gezelter	246	sprintf(buffer,
219			"------------------------------------------------------------------\n");
220			result += buffer;
221
222			return result;
223	gezelter	507	}
224	gezelter	2
225	gezelter	507	//----------------------------------------------------------------------------//
226	gezelter	2
227	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info) :
228	tim	413	BaseVisitor(), seleMan(info), evaluator(info){
229	gezelter	507	this->info = info;
230			visitorName = "XYZVisitor";
231	tim	413
232	gezelter	507	evaluator.loadScriptString("select all");
233	tim	413
234	gezelter	507	if (!evaluator.isDynamic()) {
235	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
236	gezelter	507	}
237	chuckv	1118	posOnly_ = false;
238	tim	413	}
239
240	gezelter	507	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
241	tim	413	BaseVisitor(), seleMan(info), evaluator(info) {
242	gezelter	507	this->info = info;
243			visitorName = "XYZVisitor";
244	tim	413
245	gezelter	507	evaluator.loadScriptString(script);
246	tim	413
247	gezelter	507	if (!evaluator.isDynamic()) {
248	tim	413	seleMan.setSelectionSet(evaluator.evaluate());
249	gezelter	507	}
250	chuckv	1118	posOnly_ = false;
251	tim	413	}
252
253	gezelter	507	void XYZVisitor::visit(Atom *atom) {
254	tim	293	if (isSelected(atom))
255	gezelter	507	internalVisit(atom);
256			}
257	gezelter	2
258	gezelter	507	void XYZVisitor::visit(DirectionalAtom *datom) {
259	tim	293	if (isSelected(datom))
260	gezelter	507	internalVisit(datom);
261			}
262	gezelter	2
263	gezelter	507	void XYZVisitor::visit(RigidBody *rb) {
264	tim	293	if (isSelected(rb))
265	gezelter	507	internalVisit(rb);
266			}
267	gezelter	2
268	gezelter	507	void XYZVisitor::update() {
269	tim	413	//if dynamic, we need to re-evaluate the selection
270			if (evaluator.isDynamic()) {
271	gezelter	507	seleMan.setSelectionSet(evaluator.evaluate());
272	tim	413	}
273	gezelter	507	}
274	tim	413
275	gezelter	507	void XYZVisitor::internalVisit(StuntDouble *sd) {
276	gezelter	246	GenericData * data;
277			AtomData * atomData;
278			AtomInfo * atomInfo;
279			std::vector<AtomInfo *>::iterator i;
280			char buffer[1024];
281	gezelter	2
282	gezelter	246	//if there is not atom data, just skip it
283			data = sd->getPropertyByName("ATOMDATA");
284	gezelter	2
285	gezelter	246	if (data != NULL) {
286	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
287	gezelter	2
288	gezelter	507	if (atomData == NULL)
289			return;
290	gezelter	246	} else
291	gezelter	507	return;
292	gezelter	2
293	cli2	1290	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
294			std::string bn = baseTypeName(at);
295
296	chuckv	1118	if (posOnly_){
297			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
298			atomInfo = atomData->nextAtomInfo(i) ) {
299	xsun	1219	if (atomInfo->hasCharge) {
300			sprintf(buffer,
301	cli2	1290	"%s%15.8f%15.8f%15.8f%15.8f",
302			bn.c_str(),
303			atomInfo->pos[0],
304			atomInfo->pos[1],
305			atomInfo->pos[2],
306			atomInfo->charge);
307	xsun	1219	} else {
308			sprintf(buffer,
309	chuckv	1118	"%s%15.8f%15.8f%15.8f",
310	cli2	1290	bn.c_str(),
311			atomInfo->pos[0],
312			atomInfo->pos[1],
313			atomInfo->pos[2]);
314	xsun	1219	}
315	chuckv	1118	frame.push_back(buffer);
316			}
317			}else{
318			for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
319			atomInfo = atomData->nextAtomInfo(i) ) {
320	xsun	1219	if (atomInfo->hasCharge) {
321	chuckv	1118	sprintf(buffer,
322	xsun	1219	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
323	cli2	1290	bn.c_str(),
324	xsun	1219	atomInfo->pos[0],
325			atomInfo->pos[1],
326			atomInfo->pos[2],
327			atomInfo->charge,
328			atomInfo->dipole[0],
329			atomInfo->dipole[1],
330			atomInfo->dipole[2]);
331			} else {
332			sprintf(buffer,
333	chuckv	1118	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
334	cli2	1290	bn.c_str(),
335	chuckv	1118	atomInfo->pos[0],
336			atomInfo->pos[1],
337			atomInfo->pos[2],
338			atomInfo->dipole[0],
339			atomInfo->dipole[1],
340			atomInfo->dipole[2]);
341	xsun	1219	}
342	chuckv	1118	frame.push_back(buffer);
343			}
344	gezelter	246	}
345	gezelter	507	}
346	gezelter	2
347	gezelter	507	bool XYZVisitor::isSelected(StuntDouble *sd) {
348	tim	413	return seleMan.isSelected(sd);
349	gezelter	507	}
350	gezelter	2
351	gezelter	507	void XYZVisitor::writeFrame(std::ostream &outStream) {
352	gezelter	246	std::vector<std::string>::iterator i;
353			char buffer[1024];
354	gezelter	2
355	gezelter	246	if (frame.size() == 0)
356	gezelter	507	std::cerr << "Current Frame does not contain any atoms" << std::endl;
357	gezelter	2
358	gezelter	246	//total number of atoms
359			outStream << frame.size() << std::endl;
360	gezelter	2
361	gezelter	246	//write comment line
362			Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
363			Mat3x3d box = currSnapshot->getHmat();
364
365			sprintf(buffer,
366			"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
367			currSnapshot->getTime(),
368			box(0, 0), box(0, 1), box(0, 2),
369			box(1, 0), box(1, 1), box(1, 2),
370			box(2, 0), box(2, 1), box(2, 2));
371	gezelter	2
372	gezelter	246	outStream << buffer << std::endl;
373	gezelter	2
374	gezelter	246	for( i = frame.begin(); i != frame.end(); ++i )
375	gezelter	507	outStream << *i << std::endl;
376			}
377	gezelter	2
378	cli2	1290	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
379			return atomTypeName.substr(0, atomTypeName.find('-'));
380			}
381
382			std::string XYZVisitor::baseTypeName(AtomType* at) {
383			std::vector<AtomType*> ayb = at->allYourBase();
384			return ayb[ayb.size()-1]->getName();
385			}
386
387	gezelter	507	const std::string XYZVisitor::toString() {
388	gezelter	246	char buffer[65535];
389			std::string result;
390	gezelter	2
391	gezelter	246	sprintf(buffer,
392			"------------------------------------------------------------------\n");
393			result += buffer;
394	gezelter	2
395	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
396			result += buffer;
397	gezelter	2
398	gezelter	246	sprintf(buffer,
399			"Visitor Description: assemble the atom data and output xyz file\n");
400			result += buffer;
401
402			sprintf(buffer,
403			"------------------------------------------------------------------\n");
404			result += buffer;
405
406			return result;
407	gezelter	507	}
408	gezelter	2
409	gezelter	507	//----------------------------------------------------------------------------//
410	gezelter	2
411	gezelter	507	void PrepareVisitor::internalVisit(Atom *atom) {
412	gezelter	246	GenericData *data;
413			AtomData * atomData;
414	gezelter	2
415	gezelter	246	//if visited property is existed, remove it
416			data = atom->getPropertyByName("VISITED");
417	gezelter	2
418	gezelter	246	if (data != NULL) {
419	gezelter	507	atom->removeProperty("VISITED");
420	gezelter	246	}
421
422			//remove atomdata
423			data = atom->getPropertyByName("ATOMDATA");
424
425			if (data != NULL) {
426	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
427	gezelter	246
428	gezelter	507	if (atomData != NULL)
429			atom->removeProperty("ATOMDATA");
430	gezelter	246	}
431	gezelter	507	}
432	gezelter	2
433	gezelter	507	void PrepareVisitor::internalVisit(RigidBody *rb) {
434	gezelter	246	GenericData* data;
435			AtomData* atomData;
436			std::vector<Atom *> myAtoms;
437			std::vector<Atom *>::iterator atomIter;
438	gezelter	2
439	gezelter	246	//if visited property is existed, remove it
440			data = rb->getPropertyByName("VISITED");
441	gezelter	2
442	gezelter	246	if (data != NULL) {
443	gezelter	507	rb->removeProperty("VISITED");
444	gezelter	246	}
445
446			//remove atomdata
447			data = rb->getPropertyByName("ATOMDATA");
448
449			if (data != NULL) {
450	gezelter	507	atomData = dynamic_cast<AtomData *>(data);
451	gezelter	246
452	gezelter	507	if (atomData != NULL)
453			rb->removeProperty("ATOMDATA");
454	gezelter	246	}
455
456			myAtoms = rb->getAtoms();
457
458			for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
459	gezelter	507	internalVisit(*atomIter);
460			}
461	gezelter	2
462	gezelter	507	const std::string PrepareVisitor::toString() {
463			char buffer[65535];
464			std::string result;
465	tim	293
466	gezelter	507	sprintf(buffer,
467			"------------------------------------------------------------------\n");
468			result += buffer;
469	tim	293
470	gezelter	507	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
471			result += buffer;
472	tim	293
473	gezelter	507	sprintf(buffer,
474			"Visitor Description: prepare for operation of other vistors\n");
475			result += buffer;
476	tim	293
477	gezelter	507	sprintf(buffer,
478			"------------------------------------------------------------------\n");
479			result += buffer;
480	tim	293
481	gezelter	507	return result;
482			}
483	gezelter	2
484	gezelter	507	//----------------------------------------------------------------------------//
485	gezelter	2
486	gezelter	507	WaterTypeVisitor::WaterTypeVisitor() {
487	gezelter	246	visitorName = "WaterTypeVisitor";
488			waterTypeList.insert("TIP3P_RB_0");
489			waterTypeList.insert("TIP4P_RB_0");
490			waterTypeList.insert("TIP5P_RB_0");
491			waterTypeList.insert("SPCE_RB_0");
492	gezelter	507	}
493	gezelter	2
494	gezelter	507	void WaterTypeVisitor::visit(RigidBody *rb) {
495	gezelter	246	std::string rbName;
496			std::vector<Atom *> myAtoms;
497			std::vector<Atom *>::iterator atomIter;
498			GenericData* data;
499			AtomData* atomData;
500			AtomInfo* atomInfo;
501			std::vector<AtomInfo *>::iterator i;
502	gezelter	2
503	gezelter	246	rbName = rb->getType();
504	gezelter	2
505	gezelter	246	if (waterTypeList.find(rbName) != waterTypeList.end()) {
506	gezelter	507	myAtoms = rb->getAtoms();
507	gezelter	2
508	gezelter	507	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
509			++atomIter ) {
510			data = (*atomIter)->getPropertyByName("ATOMDATA");
511	gezelter	2
512	gezelter	507	if (data != NULL) {
513			atomData = dynamic_cast<AtomData *>(data);
514	gezelter	2
515	gezelter	507	if (atomData == NULL)
516			continue;
517			} else
518			continue;
519	gezelter	246
520	gezelter	507	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
521			atomInfo = atomData->nextAtomInfo(i) ) {
522			atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
523			} //end for(atomInfo)
524			} //end for(atomIter)
525	gezelter	246	} //end if (waterTypeList.find(rbName) != waterTypeList.end())
526	gezelter	507	}
527	gezelter	2
528	gezelter	407	std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
529			return atomTypeName.substr(0, atomTypeName.find('_'));
530			}
531	gezelter	2
532	gezelter	507	const std::string WaterTypeVisitor::toString() {
533	gezelter	246	char buffer[65535];
534			std::string result;
535	gezelter	2
536	gezelter	246	sprintf(buffer,
537			"------------------------------------------------------------------\n");
538			result += buffer;
539	gezelter	2
540	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
541			result += buffer;
542	gezelter	2
543	gezelter	246	sprintf(buffer,
544			"Visitor Description: Replace the atom type in water model\n");
545			result += buffer;
546	gezelter	2
547	gezelter	246	sprintf(buffer,
548			"------------------------------------------------------------------\n");
549			result += buffer;
550
551			return result;
552	gezelter	507	}
553	gezelter	2
554	gezelter	246	} //namespace oopse