OOPSE/libmdtools/Atom.cpp

#include "Atom.hpp"

Atom::Atom(int theIndex) {
  c_n_hyd = 0; 
  has_dipole = 0;
  is_VDW = 0;
  is_LJ = 0;
  
  index = theIndex;
  offset = 3 * index;
  offsetX = offset;
  offsetY = offset+1;
  offsetZ = offset+2;
  
  Axx = index*9;
  Axy = Axx+1;
  Axz = Axx+2;
  
  Ayx = Axx+3;
  Ayy = Axx+4;
  Ayz = Axx+5;
  
  Azx = Axx+6;
  Azy = Axx+7;
  Azz = Axx+8;
}

void Atom::createArrays (int nElements) {
  int i;
  
  pos = new double[nElements*3];
  vel = new double[nElements*3];
  frc = new double[nElements*3];
  trq = new double[nElements*3];
  Amat = new double[nElements*9];
  mu = new double[nElements];
  ul = new double[nElements*3];
  
  // init directional values to zero
  
  for( i=0; i<nElements; i++){
    trq[i] = 0.0;
    trq[i+1] = 0.0;
    trq[i+2] = 0.0;
    
    Amat[i] = 1.0;
    Amat[i+1] = 0.0;
    Amat[i+2] = 0.0;
    
    Amat[i+3] = 0.0;
    Amat[i+4] = 1.0;
    Amat[i+5] = 0.0;
    
    Amat[i+6] = 0.0;
    Amat[i+7] = 0.0;
    Amat[i+8] = 1.0;
    
    mu[i] = 0.0;    
    
    ul[i] = 1.0;
    ul[i+1] = 0.0;
    ul[i+2] = 0.0;
  }
}

void Atom::destroyArrays(void) {
  delete[] pos;
  delete[] vel;
  delete[] frc;
  delete[] trq;
  delete[] Amat;
  delete[] mu;
}

void Atom::setIndex(int theIndex) {
  index = theIndex; 
  offset = index*3;
  offsetX = offset;
  offsetY = offset+1;
  offsetZ = offset+2;
  
  Axx = index*9;
  Axy = Axx+1;
  Axz = Axx+2;
  
  Ayx = Axx+3;
  Ayy = Axx+4;
  Ayz = Axx+5;
  
  Azx = Axx+6;
  Azy = Axx+7;
  Azz = Axx+8;
}

void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
                   double* Atrq, double* AAmat, double* Amu, 
                   double* Aul) {

  int nNew = nElements+nAdded;

  double* new_pos = new double[nNew*3];
  double* new_vel = new double[nNew*3];
  double* new_frc = new double[nNew*3];
  double* new_trq = new double[nNew*3];
  double* new_Amat = new double[nNew*9];
  double* new_mu = new double[nNew];
  double* new_ul = new double[nNew*3];
  int i, j;
  
  for (i = 0; i < 3*nElements; i++) {
    new_pos[i] = pos[i];
    new_vel[i] = vel[i];
    new_frc[i] = frc[i];
    new_trq[i] = trq[i];
    new_ul[i] = ul[i];
  }

  for(i = 0; i < 3*nAdded; i++) {
    j = i + 3*nElements;
    new_pos[j] = Apos[i];
    new_vel[j] = Avel[i];
    new_frc[j] = Afrc[i];
    new_trq[j] = Atrq[i];
    new_ul[j] = Aul[i]; 
  }

  for (i = 0; i < 9*nElements; i++) {
    new_Amat[i] = Amat[i];
  }

  for(i = 0; i < 9*nAdded; i++) {
    j = i + 9*nElements;
    new_Amat[j] = AAmat[i];
  }

  for (i = 0; i < nElements; i++) {
    new_mu[i] = mu[i];
  }

  for(i = 0; i < nAdded; i++) {
    j = i + nElements;
    new_mu[j] = Amu[i];
  }

  delete[] pos;
  delete[] vel;
  delete[] frc;
  delete[] trq;
  delete[] Amat;
  delete[] mu;

  pos = new_pos;
  vel = new_vel;
  frc = new_frc;
  trq = new_trq;
  ul = new_ul;
  Amat = new_Amat;
  mu = new_mu;

  nElements = nNew;
}

void Atom::deleteAtom(int theIndex) {
  deleteRange(theIndex, theIndex);
}

void Atom::deleteRange(int startIndex, int stopIndex) {
 
  int nNew = nElements-(stopIndex-startIndex+1);

  double* new_pos = new double[nNew*3];
  double* new_vel = new double[nNew*3];
  double* new_frc = new double[nNew*3];
  double* new_trq = new double[nNew*3];
  double* new_Amat = new double[nNew*9];
  double* new_mu = new double[nNew];
  double* new_ul = new double[nNew*3];
  int i, j;
  
  for (i = 0; i < 3*startIndex; i++) {
    new_pos[i] = pos[i];
    new_vel[i] = vel[i];
    new_frc[i] = frc[i];
    new_trq[i] = trq[i];
    new_ul[i] = ul[i];
  }

  for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
    j = i - 3*startIndex + 1;
    new_pos[j] = pos[i];
    new_vel[j] = vel[i];
    new_frc[j] = frc[i];
    new_trq[j] = trq[i];
    new_ul[j] = ul[i]; 
  }

  for (i = 0; i < 9*startIndex; i++) {
    new_Amat[i] = Amat[i];
  }

  for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
    j = i - 9*startIndex + 1;
    new_Amat[j] = Amat[i];
  }

  for (i = 0; i < startIndex; i++) {
    new_mu[i] = mu[i];
  }

  for(i = (stopIndex+1); i < nElements; i++) {
    j = i - startIndex + 1;
    new_mu[j] = mu[i];
  }

  delete[] pos;
  delete[] vel;
  delete[] frc;
  delete[] trq;
  delete[] Amat;
  delete[] mu;

  pos = new_pos;
  vel = new_vel;
  frc = new_frc;
  trq = new_trq;
  ul = new_ul;
  Amat = new_Amat;
  mu = new_mu;

  nElements = nNew;
}
Revision:	410
Committed:	Wed Mar 26 21:23:00 2003 UTC (21 years, 3 months ago) by gezelter
File size:	4347 byte(s)
Log Message:	Fixes in Atom and Exclude list
#	User	Rev	Content
1	gezelter	409	#include "Atom.hpp"
2
3			Atom::Atom(int theIndex) {
4			c_n_hyd = 0;
5			has_dipole = 0;
6			is_VDW = 0;
7			is_LJ = 0;
8
9			index = theIndex;
10			offset = 3 * index;
11			offsetX = offset;
12			offsetY = offset+1;
13			offsetZ = offset+2;
14
15			Axx = index*9;
16			Axy = Axx+1;
17			Axz = Axx+2;
18
19			Ayx = Axx+3;
20			Ayy = Axx+4;
21			Ayz = Axx+5;
22
23			Azx = Axx+6;
24			Azy = Axx+7;
25			Azz = Axx+8;
26			}
27
28			void Atom::createArrays (int nElements) {
29			int i;
30
31			pos = new double[nElements*3];
32			vel = new double[nElements*3];
33			frc = new double[nElements*3];
34			trq = new double[nElements*3];
35			Amat = new double[nElements*9];
36			mu = new double[nElements];
37			ul = new double[nElements*3];
38
39			// init directional values to zero
40
41			for( i=0; i<nElements; i++){
42			trq[i] = 0.0;
43			trq[i+1] = 0.0;
44			trq[i+2] = 0.0;
45
46			Amat[i] = 1.0;
47			Amat[i+1] = 0.0;
48			Amat[i+2] = 0.0;
49
50			Amat[i+3] = 0.0;
51			Amat[i+4] = 1.0;
52			Amat[i+5] = 0.0;
53
54			Amat[i+6] = 0.0;
55			Amat[i+7] = 0.0;
56			Amat[i+8] = 1.0;
57
58			mu[i] = 0.0;
59
60			ul[i] = 1.0;
61			ul[i+1] = 0.0;
62			ul[i+2] = 0.0;
63			}
64			}
65
66			void Atom::destroyArrays(void) {
67			delete[] pos;
68			delete[] vel;
69			delete[] frc;
70			delete[] trq;
71			delete[] Amat;
72			delete[] mu;
73			}
74
75			void Atom::setIndex(int theIndex) {
76			index = theIndex;
77			offset = index*3;
78			offsetX = offset;
79			offsetY = offset+1;
80			offsetZ = offset+2;
81
82			Axx = index*9;
83			Axy = Axx+1;
84			Axz = Axx+2;
85
86			Ayx = Axx+3;
87			Ayy = Axx+4;
88			Ayz = Axx+5;
89
90			Azx = Axx+6;
91			Azy = Axx+7;
92			Azz = Axx+8;
93			}
94
95			void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
96			double* Atrq, double* AAmat, double* Amu,
97			double* Aul) {
98
99			int nNew = nElements+nAdded;
100
101			double* new_pos = new double[nNew*3];
102			double* new_vel = new double[nNew*3];
103			double* new_frc = new double[nNew*3];
104			double* new_trq = new double[nNew*3];
105			double* new_Amat = new double[nNew*9];
106			double* new_mu = new double[nNew];
107			double* new_ul = new double[nNew*3];
108			int i, j;
109
110			for (i = 0; i < 3*nElements; i++) {
111			new_pos[i] = pos[i];
112			new_vel[i] = vel[i];
113			new_frc[i] = frc[i];
114			new_trq[i] = trq[i];
115			new_ul[i] = ul[i];
116			}
117
118			for(i = 0; i < 3*nAdded; i++) {
119			j = i + 3*nElements;
120	gezelter	410	new_pos[j] = Apos[i];
121			new_vel[j] = Avel[i];
122			new_frc[j] = Afrc[i];
123			new_trq[j] = Atrq[i];
124			new_ul[j] = Aul[i];
125	gezelter	409	}
126
127			for (i = 0; i < 9*nElements; i++) {
128			new_Amat[i] = Amat[i];
129			}
130
131			for(i = 0; i < 9*nAdded; i++) {
132			j = i + 9*nElements;
133	gezelter	410	new_Amat[j] = AAmat[i];
134	gezelter	409	}
135
136			for (i = 0; i < nElements; i++) {
137			new_mu[i] = mu[i];
138			}
139
140			for(i = 0; i < nAdded; i++) {
141			j = i + nElements;
142	gezelter	410	new_mu[j] = Amu[i];
143	gezelter	409	}
144
145			delete[] pos;
146			delete[] vel;
147			delete[] frc;
148			delete[] trq;
149			delete[] Amat;
150			delete[] mu;
151
152			pos = new_pos;
153			vel = new_vel;
154			frc = new_frc;
155			trq = new_trq;
156			ul = new_ul;
157			Amat = new_Amat;
158			mu = new_mu;
159
160			nElements = nNew;
161			}
162
163			void Atom::deleteAtom(int theIndex) {
164			deleteRange(theIndex, theIndex);
165			}
166
167			void Atom::deleteRange(int startIndex, int stopIndex) {
168
169			int nNew = nElements-(stopIndex-startIndex+1);
170
171			double* new_pos = new double[nNew*3];
172			double* new_vel = new double[nNew*3];
173			double* new_frc = new double[nNew*3];
174			double* new_trq = new double[nNew*3];
175			double* new_Amat = new double[nNew*9];
176			double* new_mu = new double[nNew];
177			double* new_ul = new double[nNew*3];
178			int i, j;
179
180			for (i = 0; i < 3*startIndex; i++) {
181			new_pos[i] = pos[i];
182			new_vel[i] = vel[i];
183			new_frc[i] = frc[i];
184			new_trq[i] = trq[i];
185			new_ul[i] = ul[i];
186			}
187
188			for(i = 3(stopIndex + 1); i < 3nElements; i++) {
189			j = i - 3*startIndex + 1;
190			new_pos[j] = pos[i];
191			new_vel[j] = vel[i];
192			new_frc[j] = frc[i];
193			new_trq[j] = trq[i];
194			new_ul[j] = ul[i];
195			}
196
197			for (i = 0; i < 9*startIndex; i++) {
198			new_Amat[i] = Amat[i];
199			}
200
201			for(i = 9(stopIndex + 1); i < 9nElements; i++) {
202			j = i - 9*startIndex + 1;
203			new_Amat[j] = Amat[i];
204			}
205
206			for (i = 0; i < startIndex; i++) {
207			new_mu[i] = mu[i];
208			}
209
210			for(i = (stopIndex+1); i < nElements; i++) {
211			j = i - startIndex + 1;
212			new_mu[j] = mu[i];
213			}
214
215			delete[] pos;
216			delete[] vel;
217			delete[] frc;
218			delete[] trq;
219			delete[] Amat;
220			delete[] mu;
221
222			pos = new_pos;
223			vel = new_vel;
224			frc = new_frc;
225			trq = new_trq;
226			ul = new_ul;
227			Amat = new_Amat;
228			mu = new_mu;
229
230			nElements = nNew;
231			}