OOPSE/libmdtools/AtomVisitor.cpp

#include <cstring>
#include "AtomVisitor.hpp"
#include "DirectionalAtom.hpp"
#include "MatVec3.h"
#include "RigidBody.hpp"

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->getProperty("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->getProperty("VISITED");
  return data == NULL ?  false : true;
}

void SSDAtomVisitor::visit(DirectionalAtom* datom){

  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
  double h1[3] = {0.0, -0.75695, 0.5206};
  double h2[3] = {0.0, 0.75695, 0.5206};
  double ox[3] = {0.0, 0.0, -0.0654};
  double u[3] = {0, 0, 1};
  double rotMatrix[3][3];
  AtomInfo* atomInfo;
  double pos[3];
  double vel[3];
  double newVec[3];
  double q[4];
  AtomData* atomData;
  GenericData* data;
  bool haveAtomData;
  
  //if atom is not SSD atom, just skip it
  if(strcmp(datom->getType(), "SSD"))
    return;

  data = datom->getProperty("ATOMDATA");
  if(data != NULL){

    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData == NULL){
      cerr << "can not get Atom Data from " << datom->getType() << endl;
      atomData = new AtomData; 
      haveAtomData = false;      
    }
    else
      haveAtomData = true;
  }
  else{
    atomData = new AtomData;
    haveAtomData = false;
  }
   
  
  datom->getPos(pos);
  datom->getQ(q);
  datom->getA(rotMatrix);
  
  //center of mass of the water molecule
  matVecMul3(rotMatrix, u, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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(rotMatrix, ox, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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(rotMatrix, h1, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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(rotMatrix, h2, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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 string SSDAtomVisitor::toString(){
  char buffer[65535];
  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 differnet atoms\n");
  result += buffer;

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

  return result;
}

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

void DefaultAtomVisitor::visit(Atom* atom){
  AtomData* atomData;
  AtomInfo* atomInfo;
  double pos[3];

  if(isVisited(atom))
    return;

 atomInfo =new AtomInfo;

  atomData = new AtomData; 
  atomData->setID("ATOMDATA");
 
  atom->getPos(pos);
  atomInfo->AtomType = 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;
  double pos[3];
  double u[3];

  if(isVisited(datom))
    return;
  
  datom->getPos(pos);
  datom->getU(u);

  atomData = new AtomData; 
  atomData->setID("ATOMDATA");
  atomInfo =new AtomInfo;
  
  atomInfo->AtomType = 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 string DefaultAtomVisitor::toString(){
  char buffer[65535];
  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;
}    
Revision:	1126
Committed:	Tue Apr 20 05:39:38 2004 UTC (20 years, 2 months ago) by tim
File size:	5822 byte(s)
Log Message:	DUMP2XYZ 0.99 version
#	User	Rev	Content
1	tim	1118	#include <cstring>
2			#include "AtomVisitor.hpp"
3			#include "DirectionalAtom.hpp"
4			#include "MatVec3.h"
5	tim	1119	#include "RigidBody.hpp"
6	tim	1118
7	tim	1119	void BaseAtomVisitor::visit(RigidBody* rb){
8			//vector<Atom*> myAtoms;
9			//vector<Atom*>::iterator atomIter;
10
11			//myAtoms = rb->getAtoms();
12
13			//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14			// (*atomIter)->accept(this);
15			}
16
17	tim	1118	void BaseAtomVisitor::setVisited(Atom* atom){
18			GenericData* data;
19			data = atom->getProperty("VISITED");
20
21			//if visited property is not existed, add it as new property
22			if(data == NULL){
23			data = new GenericData();
24			data->setID("VISITED");
25			atom->addProperty(data);
26			}
27			}
28
29			bool BaseAtomVisitor::isVisited(Atom* atom){
30			GenericData* data;
31			data = atom->getProperty("VISITED");
32			return data == NULL ? false : true;
33			}
34
35			void SSDAtomVisitor::visit(DirectionalAtom* datom){
36
37			vector<AtomInfo*> atoms;
38
39			//we need to convert SSD into 4 differnet atoms
40			//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
41			//of the water with a dipole moment
42			double h1[3] = {0.0, -0.75695, 0.5206};
43			double h2[3] = {0.0, 0.75695, 0.5206};
44			double ox[3] = {0.0, 0.0, -0.0654};
45			double u[3] = {0, 0, 1};
46			double rotMatrix[3][3];
47			AtomInfo* atomInfo;
48			double pos[3];
49			double vel[3];
50			double newVec[3];
51			double q[4];
52			AtomData* atomData;
53			GenericData* data;
54			bool haveAtomData;
55
56			//if atom is not SSD atom, just skip it
57	tim	1126	if(strcmp(datom->getType(), "SSD"))
58	tim	1118	return;
59
60			data = datom->getProperty("ATOMDATA");
61			if(data != NULL){
62
63			atomData = dynamic_cast<AtomData*>(data);
64			if(atomData == NULL){
65			cerr << "can not get Atom Data from " << datom->getType() << endl;
66			atomData = new AtomData;
67			haveAtomData = false;
68			}
69			else
70			haveAtomData = true;
71			}
72			else{
73			atomData = new AtomData;
74			haveAtomData = false;
75			}
76
77
78			datom->getPos(pos);
79			datom->getQ(q);
80			datom->getA(rotMatrix);
81
82			//center of mass of the water molecule
83			matVecMul3(rotMatrix, u, newVec);
84			atomInfo = new AtomInfo;
85			atomInfo->AtomType = "X";
86			atomInfo->pos[0] = pos[0];
87			atomInfo->pos[1] = pos[1];
88			atomInfo->pos[2] = pos[2];
89			atomInfo->dipole[0] = newVec[0];
90			atomInfo->dipole[1] = newVec[1];
91			atomInfo->dipole[2] = newVec[2];
92
93			atomData->addAtomInfo(atomInfo);
94
95			//oxygen
96			matVecMul3(rotMatrix, ox, newVec);
97			atomInfo = new AtomInfo;
98			atomInfo->AtomType = "O";
99			atomInfo->pos[0] = pos[0] + newVec[0];
100			atomInfo->pos[1] = pos[1] + newVec[1];
101			atomInfo->pos[2] = pos[2] + newVec[2];
102			atomInfo->dipole[0] = 0.0;
103			atomInfo->dipole[1] = 0.0;
104			atomInfo->dipole[2] = 0.0;
105			atomData->addAtomInfo(atomInfo);
106
107
108			//hydrogen1
109			matVecMul3(rotMatrix, h1, newVec);
110			atomInfo = new AtomInfo;
111			atomInfo->AtomType = "H";
112			atomInfo->pos[0] = pos[0] + newVec[0];
113			atomInfo->pos[1] = pos[1] + newVec[1];
114			atomInfo->pos[2] = pos[2] + newVec[2];
115			atomInfo->dipole[0] = 0.0;
116			atomInfo->dipole[1] = 0.0;
117			atomInfo->dipole[2] = 0.0;
118			atomData->addAtomInfo(atomInfo);
119
120			//hydrogen2
121			matVecMul3(rotMatrix, h2, newVec);
122			atomInfo = new AtomInfo;
123			atomInfo->AtomType = "H";
124			atomInfo->pos[0] = pos[0] + newVec[0];
125			atomInfo->pos[1] = pos[1] + newVec[1];
126			atomInfo->pos[2] = pos[2] + newVec[2];
127			atomInfo->dipole[0] = 0.0;
128			atomInfo->dipole[1] = 0.0;
129			atomInfo->dipole[2] = 0.0;
130			atomData->addAtomInfo(atomInfo);
131
132			//add atom data into atom's property
133
134			if(!haveAtomData){
135			atomData->setID("ATOMDATA");
136			datom->addProperty(atomData);
137			}
138
139			setVisited(datom);
140
141			}
142
143	tim	1126	const string SSDAtomVisitor::toString(){
144			char buffer[65535];
145			string result;
146
147			sprintf(buffer ,"------------------------------------------------------------------\n");
148			result += buffer;
149
150			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
151			result += buffer;
152
153			sprintf(buffer , "Visitor Description: Convert SSD into 4 differnet atoms\n");
154			result += buffer;
155
156			sprintf(buffer ,"------------------------------------------------------------------\n");
157			result += buffer;
158
159			return result;
160			}
161
162			//----------------------------------------------------------------------------//
163
164	tim	1118	void DefaultAtomVisitor::visit(Atom* atom){
165			AtomData* atomData;
166			AtomInfo* atomInfo;
167			double pos[3];
168
169			if(isVisited(atom))
170			return;
171
172			atomInfo =new AtomInfo;
173	tim	1119
174			atomData = new AtomData;
175			atomData->setID("ATOMDATA");
176	tim	1118
177			atom->getPos(pos);
178			atomInfo->AtomType = atom->getType();
179			atomInfo->pos[0] = pos[0];
180			atomInfo->pos[1] = pos[1];
181			atomInfo->pos[2] = pos[2];
182			atomInfo->dipole[0] = 0.0;
183			atomInfo->dipole[1] = 0.0;
184			atomInfo->dipole[2] = 0.0;
185
186	tim	1119
187			atomData->addAtomInfo(atomInfo);
188
189	tim	1118	atom->addProperty(atomData);
190
191			setVisited(atom);
192			}
193			void DefaultAtomVisitor::visit(DirectionalAtom* datom){
194			AtomData* atomData;
195			AtomInfo* atomInfo;
196			double pos[3];
197			double u[3];
198
199			if(isVisited(datom))
200			return;
201
202			datom->getPos(pos);
203			datom->getU(u);
204
205	tim	1119	atomData = new AtomData;
206			atomData->setID("ATOMDATA");
207	tim	1118	atomInfo =new AtomInfo;
208
209			atomInfo->AtomType = datom->getType();
210			atomInfo->pos[0] = pos[0];
211			atomInfo->pos[1] = pos[1];
212			atomInfo->pos[2] = pos[2];
213			atomInfo->dipole[0] = u[0];
214			atomInfo->dipole[1] = u[1];
215			atomInfo->dipole[2] = u[2];
216
217	tim	1119	atomData->addAtomInfo(atomInfo);
218
219	tim	1118	datom->addProperty(atomData);
220
221			setVisited(datom);
222			}
223	tim	1126
224
225			const string DefaultAtomVisitor::toString(){
226			char buffer[65535];
227			string result;
228
229			sprintf(buffer ,"------------------------------------------------------------------\n");
230			result += buffer;
231
232			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
233			result += buffer;
234
235			sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
236			result += buffer;
237
238			sprintf(buffer ,"------------------------------------------------------------------\n");
239			result += buffer;
240
241			return result;
242			}