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 (22 years, 7 months ago) by gezelter
Original Path:	*trunk/OOPSE/libmdtools/Atom.cpp*
File size:	4347 byte(s)
Log Message:	Fixes in Atom and Exclude list
#	Content
1	#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	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	}
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	new_Amat[j] = AAmat[i];
134	}
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	new_mu[j] = Amu[i];
143	}
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	}