src/visitors/AtomVisitor.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 <cstring>
#include "visitors/AtomVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"

namespace oopse {
  void BaseAtomVisitor::visit(RigidBody *rb) {
    //vector<Atom*> myAtoms;
    //vector<Atom*>::iterator atomIter;

    //myAtoms = rb->getAtoms();

    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    //  (*atomIter)->accept(this);
  }

  void BaseAtomVisitor::setVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");

    //if visited property is not existed, add it as new property
    if (data == NULL) {
      data = new GenericData();
      data->setID("VISITED");
      atom->addProperty(data);
    }
  }

  bool BaseAtomVisitor::isVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");
    return data == NULL ? false : true;
  }

  bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
    std::set<std::string>::iterator strIter;
    strIter = ssdAtomType.find(atomType);
    return strIter != ssdAtomType.end() ? true : false;
  }

  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
    std::vector<AtomInfo*>atoms;

    //we need to convert SSD into 4 differnet atoms
    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
    //of the water with a dipole moment
    Vector3d h1(0.0, -0.75695, 0.5206);
    Vector3d h2(0.0, 0.75695, 0.5206);
    Vector3d ox(0.0, 0.0, -0.0654);
    Vector3d u(0, 0, 1);
    RotMat3x3d   rotMatrix;
    RotMat3x3d   rotTrans;
    AtomInfo *   atomInfo;
    Vector3d     pos;
    Vector3d     newVec;
    Quat4d       q;
    AtomData *   atomData;
    GenericData *data;
    bool         haveAtomData;

    //if atom is not SSD atom, just skip it
    if (!isSSDAtom(datom->getType()))
      return;

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

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

      if (atomData == NULL) {
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData;
        haveAtomData = false;
      } else
        haveAtomData = true;
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }

    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:
    //transposeMat3(rotMatrix, rotTrans);
    rotTrans = rotMatrix.transpose();

    //center of mass of the water molecule
    //matVecMul3(rotTrans, u, newVec);
    newVec = rotTrans * u;

    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "X";
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = newVec[0];
    atomInfo->dipole[1] = newVec[1];
    atomInfo->dipole[2] = newVec[2];

    atomData->addAtomInfo(atomInfo);

    //oxygen
    //matVecMul3(rotTrans, ox, newVec);
    newVec = rotTrans * ox;

    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "O";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //hydrogen1
    //matVecMul3(rotTrans, h1, newVec);
    newVec = rotTrans * h1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "H";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //hydrogen2
    //matVecMul3(rotTrans, h2, newVec);
    newVec = rotTrans * h2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "H";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if (!haveAtomData) {
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);
  }

  const std::string SSDAtomVisitor::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: Convert SSD into 4 different atoms\n");
    result += buffer;

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

    return result;
  }

  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
    std::set<std::string>::iterator strIter;
    strIter = linearAtomType.find(atomType);

    return strIter != linearAtomType.end() ? true : false;
  }

  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
   linearAtomType.insert(atomType); 
  }

  void LinearAtomVisitor::visit(DirectionalAtom* datom){
    std::vector<AtomInfo*> atoms;
    //we need to convert linear into 4 different atoms
    Vector3d c1(0.0, 0.0, -1.8);
    Vector3d c2(0.0, 0.0, -0.6);
    Vector3d c3(0.0, 0.0,  0.6);
    Vector3d c4(0.0, 0.0,  1.8);
    RotMat3x3d rotMatrix;
    RotMat3x3d rotTrans;
    AtomInfo* atomInfo;
    Vector3d pos;
    Vector3d newVec;
    Quat4d q;
    AtomData* atomData;
    GenericData* data;
    bool haveAtomData;

    //if atom is not SSD atom, just skip it
    if(!isLinearAtom(datom->getType()))
      return;

    data = datom->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData; 
        haveAtomData = false;      
      } else {
        haveAtomData = true;
      }
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }
   
  
    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:  
    rotTrans = rotMatrix.transpose();

    newVec = rotTrans * c1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c3;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c4;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if(!haveAtomData){
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);

  }

  const std::string LinearAtomVisitor::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: Convert linear into 4 different atoms\n");
    result += buffer;

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

    return result;
  }

  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
    std::set<std::string>::iterator strIter;
    strIter = GBLipidAtomType.find(atomType);

    return strIter != GBLipidAtomType.end() ? true : false;
  }

  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
    std::vector<AtomInfo*> atoms;
    //we need to convert linear into 4 different atoms
    Vector3d c1(0.0, 0.0, -6.25);
    Vector3d c2(0.0, 0.0, -2.1);
    Vector3d c3(0.0, 0.0,  2.1);
    Vector3d c4(0.0, 0.0,  6.25);
    RotMat3x3d rotMatrix;
    RotMat3x3d rotTrans;
    AtomInfo* atomInfo;
    Vector3d pos;
    Vector3d newVec;
    Quat4d q;
    AtomData* atomData;
    GenericData* data;
    bool haveAtomData;

    //if atom is not GBlipid atom, just skip it
    if(!isGBLipidAtom(datom->getType()))
      return;

    data = datom->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData; 
        haveAtomData = false;      
      } else {
        haveAtomData = true;
      }
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }
   
  
    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:  
    rotTrans = rotMatrix.transpose();

    newVec = rotTrans * c1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c3;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c4;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if(!haveAtomData){
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);

  }

  const std::string GBLipidAtomVisitor::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: Convert GBlipid into 4 different K atoms\n");
    result += buffer;

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

    return result;
  }

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

  void DefaultAtomVisitor::visit(Atom *atom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;

    if (isVisited(atom))
      return;

    atomInfo = new AtomInfo;

    atomData = new AtomData;
    atomData->setID("ATOMDATA");

    pos = atom->getPos();
    atomInfo->atomTypeName = atom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;

    atomData->addAtomInfo(atomInfo);

    atom->addProperty(atomData);

    setVisited(atom);
  }

  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  u;

    if (isVisited(datom))
      return;

    pos = datom->getPos();
    u = datom->getElectroFrame().getColumn(2);

    atomData = new AtomData;
    atomData->setID("ATOMDATA");
    atomInfo = new AtomInfo;

    atomInfo->atomTypeName = datom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = u[0];
    atomInfo->dipole[1] = u[1];
    atomInfo->dipole[2] = u[2];

    atomData->addAtomInfo(atomInfo);

    datom->addProperty(atomData);

    setVisited(datom);
  }

  const std::string DefaultAtomVisitor::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: copy atom infomation into atom data\n");
    result += buffer;

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

    return result;
  }
} //namespace oopse
Revision:	2749
Committed:	Wed May 10 01:44:48 2006 UTC (18 years, 4 months ago) by tim
File size:	16115 byte(s)
Log Message:	adding a gay-berne switch to Dump2XYZ
#	User	Rev	Content
1	gezelter	2204	/*
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
42	gezelter	1490	#include <cstring>
43	tim	1492	#include "visitors/AtomVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "primitives/RigidBody.hpp"
46	gezelter	1490
47	tim	1625	namespace oopse {
48	gezelter	2204	void BaseAtomVisitor::visit(RigidBody *rb) {
49			//vector<Atom*> myAtoms;
50			//vector<Atom*>::iterator atomIter;
51	tim	1625
52	gezelter	2204	//myAtoms = rb->getAtoms();
53	gezelter	1490
54	gezelter	2204	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55			// (*atomIter)->accept(this);
56			}
57	gezelter	1490
58	gezelter	2204	void BaseAtomVisitor::setVisited(Atom *atom) {
59	gezelter	1930	GenericData *data;
60			data = atom->getPropertyByName("VISITED");
61	gezelter	1490
62	gezelter	1930	//if visited property is not existed, add it as new property
63			if (data == NULL) {
64	gezelter	2204	data = new GenericData();
65			data->setID("VISITED");
66			atom->addProperty(data);
67	gezelter	1930	}
68	gezelter	2204	}
69	gezelter	1490
70	gezelter	2204	bool BaseAtomVisitor::isVisited(Atom *atom) {
71	gezelter	1930	GenericData *data;
72			data = atom->getPropertyByName("VISITED");
73			return data == NULL ? false : true;
74	gezelter	2204	}
75	gezelter	1490
76	gezelter	2204	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77	tim	1931	std::set<std::string>::iterator strIter;
78			strIter = ssdAtomType.find(atomType);
79			return strIter != ssdAtomType.end() ? true : false;
80	gezelter	2204	}
81	gezelter	1490
82	gezelter	2204	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83	tim	1931	std::vector<AtomInfo*>atoms;
84	gezelter	1490
85	gezelter	1930	//we need to convert SSD into 4 differnet atoms
86			//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87			//of the water with a dipole moment
88			Vector3d h1(0.0, -0.75695, 0.5206);
89			Vector3d h2(0.0, 0.75695, 0.5206);
90			Vector3d ox(0.0, 0.0, -0.0654);
91			Vector3d u(0, 0, 1);
92			RotMat3x3d rotMatrix;
93			RotMat3x3d rotTrans;
94			AtomInfo * atomInfo;
95			Vector3d pos;
96			Vector3d newVec;
97			Quat4d q;
98			AtomData * atomData;
99			GenericData *data;
100			bool haveAtomData;
101	gezelter	1490
102	gezelter	1930	//if atom is not SSD atom, just skip it
103			if (!isSSDAtom(datom->getType()))
104	gezelter	2204	return;
105	gezelter	1490
106	gezelter	1930	data = datom->getPropertyByName("ATOMDATA");
107	gezelter	1490
108	gezelter	1930	if (data != NULL) {
109	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
110	gezelter	1930
111	gezelter	2204	if (atomData == NULL) {
112			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113			atomData = new AtomData;
114			haveAtomData = false;
115			} else
116			haveAtomData = true;
117	gezelter	1930	} else {
118	gezelter	2204	atomData = new AtomData;
119			haveAtomData = false;
120	gezelter	1490	}
121
122	gezelter	1930	pos = datom->getPos();
123			q = datom->getQ();
124			rotMatrix = datom->getA();
125	gezelter	1490
126	gezelter	1930	// We need A^T to convert from body-fixed to space-fixed:
127			//transposeMat3(rotMatrix, rotTrans);
128			rotTrans = rotMatrix.transpose();
129	gezelter	1490
130	gezelter	1930	//center of mass of the water molecule
131			//matVecMul3(rotTrans, u, newVec);
132			newVec = rotTrans * u;
133	gezelter	1490
134	gezelter	1930	atomInfo = new AtomInfo;
135	gezelter	2091	atomInfo->atomTypeName = "X";
136	gezelter	1930	atomInfo->pos[0] = pos[0];
137			atomInfo->pos[1] = pos[1];
138			atomInfo->pos[2] = pos[2];
139			atomInfo->dipole[0] = newVec[0];
140			atomInfo->dipole[1] = newVec[1];
141			atomInfo->dipole[2] = newVec[2];
142	gezelter	1490
143	gezelter	1930	atomData->addAtomInfo(atomInfo);
144	gezelter	1490
145	gezelter	1930	//oxygen
146			//matVecMul3(rotTrans, ox, newVec);
147			newVec = rotTrans * ox;
148	gezelter	1490
149	gezelter	1930	atomInfo = new AtomInfo;
150	gezelter	2091	atomInfo->atomTypeName = "O";
151	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
152			atomInfo->pos[1] = pos[1] + newVec[1];
153			atomInfo->pos[2] = pos[2] + newVec[2];
154			atomInfo->dipole[0] = 0.0;
155			atomInfo->dipole[1] = 0.0;
156			atomInfo->dipole[2] = 0.0;
157			atomData->addAtomInfo(atomInfo);
158	gezelter	1490
159	gezelter	1930	//hydrogen1
160			//matVecMul3(rotTrans, h1, newVec);
161			newVec = rotTrans * h1;
162			atomInfo = new AtomInfo;
163	gezelter	2091	atomInfo->atomTypeName = "H";
164	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
165			atomInfo->pos[1] = pos[1] + newVec[1];
166			atomInfo->pos[2] = pos[2] + newVec[2];
167			atomInfo->dipole[0] = 0.0;
168			atomInfo->dipole[1] = 0.0;
169			atomInfo->dipole[2] = 0.0;
170			atomData->addAtomInfo(atomInfo);
171	gezelter	1490
172	gezelter	1930	//hydrogen2
173			//matVecMul3(rotTrans, h2, newVec);
174			newVec = rotTrans * h2;
175			atomInfo = new AtomInfo;
176	gezelter	2091	atomInfo->atomTypeName = "H";
177	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
178			atomInfo->pos[1] = pos[1] + newVec[1];
179			atomInfo->pos[2] = pos[2] + newVec[2];
180			atomInfo->dipole[0] = 0.0;
181			atomInfo->dipole[1] = 0.0;
182			atomInfo->dipole[2] = 0.0;
183			atomData->addAtomInfo(atomInfo);
184	gezelter	1490
185	gezelter	1930	//add atom data into atom's property
186
187			if (!haveAtomData) {
188	gezelter	2204	atomData->setID("ATOMDATA");
189			datom->addProperty(atomData);
190	gezelter	1930	}
191
192			setVisited(datom);
193	gezelter	2204	}
194	gezelter	1490
195	gezelter	2204	const std::string SSDAtomVisitor::toString() {
196	gezelter	1930	char buffer[65535];
197			std::string result;
198	gezelter	1490
199	gezelter	1930	sprintf(buffer,
200			"------------------------------------------------------------------\n");
201			result += buffer;
202	gezelter	1490
203	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204			result += buffer;
205	gezelter	1490
206	gezelter	1930	sprintf(buffer,
207			"Visitor Description: Convert SSD into 4 different atoms\n");
208			result += buffer;
209	gezelter	1490
210	gezelter	1930	sprintf(buffer,
211			"------------------------------------------------------------------\n");
212			result += buffer;
213
214			return result;
215	gezelter	2204	}
216	gezelter	1490
217	gezelter	2204	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218	tim	1931	std::set<std::string>::iterator strIter;
219			strIter = linearAtomType.find(atomType);
220
221			return strIter != linearAtomType.end() ? true : false;
222	gezelter	2204	}
223	chrisfen	1718
224	tim	2749	void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225			linearAtomType.insert(atomType);
226			}
227
228	gezelter	2204	void LinearAtomVisitor::visit(DirectionalAtom* datom){
229	tim	1931	std::vector<AtomInfo*> atoms;
230			//we need to convert linear into 4 different atoms
231			Vector3d c1(0.0, 0.0, -1.8);
232			Vector3d c2(0.0, 0.0, -0.6);
233			Vector3d c3(0.0, 0.0, 0.6);
234			Vector3d c4(0.0, 0.0, 1.8);
235			RotMat3x3d rotMatrix;
236			RotMat3x3d rotTrans;
237			AtomInfo* atomInfo;
238			Vector3d pos;
239			Vector3d newVec;
240			Quat4d q;
241			AtomData* atomData;
242			GenericData* data;
243			bool haveAtomData;
244	chrisfen	1718
245	tim	1931	//if atom is not SSD atom, just skip it
246			if(!isLinearAtom(datom->getType()))
247	gezelter	2204	return;
248	chrisfen	1718
249	tim	1931	data = datom->getPropertyByName("ATOMDATA");
250			if(data != NULL){
251	gezelter	2204	atomData = dynamic_cast<AtomData*>(data);
252			if(atomData == NULL){
253			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
254			atomData = new AtomData;
255			haveAtomData = false;
256			} else {
257			haveAtomData = true;
258			}
259	tim	1931	} else {
260	gezelter	2204	atomData = new AtomData;
261			haveAtomData = false;
262	chrisfen	1718	}
263
264
265	tim	1931	pos = datom->getPos();
266			q = datom->getQ();
267			rotMatrix = datom->getA();
268	chrisfen	1718
269	tim	1931	// We need A^T to convert from body-fixed to space-fixed:
270			rotTrans = rotMatrix.transpose();
271	chrisfen	1718
272	tim	1931	newVec = rotTrans * c1;
273			atomInfo = new AtomInfo;
274	gezelter	2091	atomInfo->atomTypeName = "C";
275	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
276			atomInfo->pos[1] = pos[1] + newVec[1];
277			atomInfo->pos[2] = pos[2] + newVec[2];
278			atomInfo->dipole[0] = 0.0;
279			atomInfo->dipole[1] = 0.0;
280			atomInfo->dipole[2] = 0.0;
281			atomData->addAtomInfo(atomInfo);
282	chrisfen	1718
283	tim	1931	newVec = rotTrans * c2;
284			atomInfo = new AtomInfo;
285	gezelter	2091	atomInfo->atomTypeName = "C";
286	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
287			atomInfo->pos[1] = pos[1] + newVec[1];
288			atomInfo->pos[2] = pos[2] + newVec[2];
289			atomInfo->dipole[0] = 0.0;
290			atomInfo->dipole[1] = 0.0;
291			atomInfo->dipole[2] = 0.0;
292			atomData->addAtomInfo(atomInfo);
293	chrisfen	1718
294	tim	1931	newVec = rotTrans * c3;
295			atomInfo = new AtomInfo;
296	gezelter	2091	atomInfo->atomTypeName = "C";
297	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
298			atomInfo->pos[1] = pos[1] + newVec[1];
299			atomInfo->pos[2] = pos[2] + newVec[2];
300			atomInfo->dipole[0] = 0.0;
301			atomInfo->dipole[1] = 0.0;
302			atomInfo->dipole[2] = 0.0;
303			atomData->addAtomInfo(atomInfo);
304	chrisfen	1718
305	tim	1931	newVec = rotTrans * c4;
306			atomInfo = new AtomInfo;
307	gezelter	2091	atomInfo->atomTypeName = "C";
308	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
309			atomInfo->pos[1] = pos[1] + newVec[1];
310			atomInfo->pos[2] = pos[2] + newVec[2];
311			atomInfo->dipole[0] = 0.0;
312			atomInfo->dipole[1] = 0.0;
313			atomInfo->dipole[2] = 0.0;
314			atomData->addAtomInfo(atomInfo);
315	chrisfen	1718
316	tim	1931	//add atom data into atom's property
317	chrisfen	1718
318	tim	1931	if(!haveAtomData){
319	gezelter	2204	atomData->setID("ATOMDATA");
320			datom->addProperty(atomData);
321	tim	1931	}
322	chrisfen	1718
323	tim	1931	setVisited(datom);
324
325	gezelter	2204	}
326	chrisfen	1718
327	gezelter	2204	const std::string LinearAtomVisitor::toString(){
328			char buffer[65535];
329			std::string result;
330	chrisfen	1718
331	gezelter	2204	sprintf(buffer ,"------------------------------------------------------------------\n");
332			result += buffer;
333	chrisfen	1718
334	gezelter	2204	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
335			result += buffer;
336	chrisfen	1718
337	gezelter	2204	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
338			result += buffer;
339	chrisfen	1718
340	gezelter	2204	sprintf(buffer ,"------------------------------------------------------------------\n");
341			result += buffer;
342	chrisfen	1718
343	gezelter	2204	return result;
344			}
345	chrisfen	1718
346	xsun	2581	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
347			std::set<std::string>::iterator strIter;
348			strIter = GBLipidAtomType.find(atomType);
349
350			return strIter != GBLipidAtomType.end() ? true : false;
351			}
352
353			void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
354			std::vector<AtomInfo*> atoms;
355			//we need to convert linear into 4 different atoms
356			Vector3d c1(0.0, 0.0, -6.25);
357			Vector3d c2(0.0, 0.0, -2.1);
358			Vector3d c3(0.0, 0.0, 2.1);
359			Vector3d c4(0.0, 0.0, 6.25);
360			RotMat3x3d rotMatrix;
361			RotMat3x3d rotTrans;
362			AtomInfo* atomInfo;
363			Vector3d pos;
364			Vector3d newVec;
365			Quat4d q;
366			AtomData* atomData;
367			GenericData* data;
368			bool haveAtomData;
369
370			//if atom is not GBlipid atom, just skip it
371			if(!isGBLipidAtom(datom->getType()))
372			return;
373
374			data = datom->getPropertyByName("ATOMDATA");
375			if(data != NULL){
376			atomData = dynamic_cast<AtomData*>(data);
377			if(atomData == NULL){
378			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
379			atomData = new AtomData;
380			haveAtomData = false;
381			} else {
382			haveAtomData = true;
383			}
384			} else {
385			atomData = new AtomData;
386			haveAtomData = false;
387			}
388
389
390			pos = datom->getPos();
391			q = datom->getQ();
392			rotMatrix = datom->getA();
393
394			// We need A^T to convert from body-fixed to space-fixed:
395			rotTrans = rotMatrix.transpose();
396
397			newVec = rotTrans * c1;
398			atomInfo = new AtomInfo;
399			atomInfo->atomTypeName = "K";
400			atomInfo->pos[0] = pos[0] + newVec[0];
401			atomInfo->pos[1] = pos[1] + newVec[1];
402			atomInfo->pos[2] = pos[2] + newVec[2];
403			atomInfo->dipole[0] = 0.0;
404			atomInfo->dipole[1] = 0.0;
405			atomInfo->dipole[2] = 0.0;
406			atomData->addAtomInfo(atomInfo);
407
408			newVec = rotTrans * c2;
409			atomInfo = new AtomInfo;
410			atomInfo->atomTypeName = "K";
411			atomInfo->pos[0] = pos[0] + newVec[0];
412			atomInfo->pos[1] = pos[1] + newVec[1];
413			atomInfo->pos[2] = pos[2] + newVec[2];
414			atomInfo->dipole[0] = 0.0;
415			atomInfo->dipole[1] = 0.0;
416			atomInfo->dipole[2] = 0.0;
417			atomData->addAtomInfo(atomInfo);
418
419			newVec = rotTrans * c3;
420			atomInfo = new AtomInfo;
421			atomInfo->atomTypeName = "K";
422			atomInfo->pos[0] = pos[0] + newVec[0];
423			atomInfo->pos[1] = pos[1] + newVec[1];
424			atomInfo->pos[2] = pos[2] + newVec[2];
425			atomInfo->dipole[0] = 0.0;
426			atomInfo->dipole[1] = 0.0;
427			atomInfo->dipole[2] = 0.0;
428			atomData->addAtomInfo(atomInfo);
429
430			newVec = rotTrans * c4;
431			atomInfo = new AtomInfo;
432			atomInfo->atomTypeName = "K";
433			atomInfo->pos[0] = pos[0] + newVec[0];
434			atomInfo->pos[1] = pos[1] + newVec[1];
435			atomInfo->pos[2] = pos[2] + newVec[2];
436			atomInfo->dipole[0] = 0.0;
437			atomInfo->dipole[1] = 0.0;
438			atomInfo->dipole[2] = 0.0;
439			atomData->addAtomInfo(atomInfo);
440
441			//add atom data into atom's property
442
443			if(!haveAtomData){
444			atomData->setID("ATOMDATA");
445			datom->addProperty(atomData);
446			}
447
448			setVisited(datom);
449
450			}
451
452			const std::string GBLipidAtomVisitor::toString(){
453			char buffer[65535];
454			std::string result;
455
456			sprintf(buffer ,"------------------------------------------------------------------\n");
457			result += buffer;
458
459			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
460			result += buffer;
461
462			sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
463			result += buffer;
464
465			sprintf(buffer ,"------------------------------------------------------------------\n");
466			result += buffer;
467
468			return result;
469			}
470
471	gezelter	2204	//----------------------------------------------------------------------------//
472	gezelter	1490
473	gezelter	2204	void DefaultAtomVisitor::visit(Atom *atom) {
474	gezelter	1930	AtomData *atomData;
475			AtomInfo *atomInfo;
476			Vector3d pos;
477	gezelter	1490
478	gezelter	1930	if (isVisited(atom))
479	gezelter	2204	return;
480	gezelter	1490
481	gezelter	1930	atomInfo = new AtomInfo;
482	gezelter	1490
483	gezelter	1930	atomData = new AtomData;
484			atomData->setID("ATOMDATA");
485	gezelter	1490
486	gezelter	1930	pos = atom->getPos();
487	gezelter	2091	atomInfo->atomTypeName = atom->getType();
488	gezelter	1930	atomInfo->pos[0] = pos[0];
489			atomInfo->pos[1] = pos[1];
490			atomInfo->pos[2] = pos[2];
491			atomInfo->dipole[0] = 0.0;
492			atomInfo->dipole[1] = 0.0;
493			atomInfo->dipole[2] = 0.0;
494	gezelter	1490
495	gezelter	1930	atomData->addAtomInfo(atomInfo);
496	gezelter	1490
497	gezelter	1930	atom->addProperty(atomData);
498
499			setVisited(atom);
500	gezelter	2204	}
501	gezelter	1490
502	gezelter	2204	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
503	gezelter	1930	AtomData *atomData;
504			AtomInfo *atomInfo;
505			Vector3d pos;
506			Vector3d u;
507	gezelter	1490
508	gezelter	1930	if (isVisited(datom))
509	gezelter	2204	return;
510	gezelter	1490
511	gezelter	1930	pos = datom->getPos();
512	tim	1959	u = datom->getElectroFrame().getColumn(2);
513	gezelter	1490
514	gezelter	1930	atomData = new AtomData;
515			atomData->setID("ATOMDATA");
516			atomInfo = new AtomInfo;
517	gezelter	1490
518	gezelter	2091	atomInfo->atomTypeName = datom->getType();
519	gezelter	1930	atomInfo->pos[0] = pos[0];
520			atomInfo->pos[1] = pos[1];
521			atomInfo->pos[2] = pos[2];
522			atomInfo->dipole[0] = u[0];
523			atomInfo->dipole[1] = u[1];
524			atomInfo->dipole[2] = u[2];
525
526			atomData->addAtomInfo(atomInfo);
527
528			datom->addProperty(atomData);
529
530			setVisited(datom);
531	gezelter	2204	}
532	gezelter	1490
533	gezelter	2204	const std::string DefaultAtomVisitor::toString() {
534	gezelter	1930	char buffer[65535];
535			std::string result;
536	gezelter	1490
537	gezelter	1930	sprintf(buffer,
538			"------------------------------------------------------------------\n");
539			result += buffer;
540	gezelter	1490
541	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
542			result += buffer;
543	gezelter	1490
544	gezelter	1930	sprintf(buffer,
545			"Visitor Description: copy atom infomation into atom data\n");
546			result += buffer;
547	gezelter	1490
548	gezelter	1930	sprintf(buffer,
549			"------------------------------------------------------------------\n");
550			result += buffer;
551	gezelter	1490
552	gezelter	1930	return result;
553	gezelter	2204	}
554	gezelter	1930	} //namespace oopse