OOPSE/libmdtools/Atom.cpp

#include "Atom.hpp"

double* Atom::pos; // the position array
double* Atom::vel; // the velocity array
double* Atom::frc; // the forc array
double* Atom::trq; // the torque vector  ( space fixed )
double* Atom::Amat; // the rotation matrix
double* Atom::mu;   // the array of dipole moments
double* Atom::ul;   // the lab frame unit directional vector
int Atom::nElements;

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 the_nElements) {
  int i;
  
  nElements = the_nElements;

  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:	413
Committed:	Wed Mar 26 21:54:49 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	4734 byte(s)
Log Message:	fixed a couple of the "static" bugs in Atom and Exclude
#	Content
1	#include "Atom.hpp"
2
3	double* Atom::pos; // the position array
4	double* Atom::vel; // the velocity array
5	double* Atom::frc; // the forc array
6	double* Atom::trq; // the torque vector ( space fixed )
7	double* Atom::Amat; // the rotation matrix
8	double* Atom::mu; // the array of dipole moments
9	double* Atom::ul; // the lab frame unit directional vector
10	int Atom::nElements;
11
12	Atom::Atom(int theIndex) {
13	c_n_hyd = 0;
14	has_dipole = 0;
15	is_VDW = 0;
16	is_LJ = 0;
17
18	index = theIndex;
19	offset = 3 * index;
20	offsetX = offset;
21	offsetY = offset+1;
22	offsetZ = offset+2;
23
24	Axx = index*9;
25	Axy = Axx+1;
26	Axz = Axx+2;
27
28	Ayx = Axx+3;
29	Ayy = Axx+4;
30	Ayz = Axx+5;
31
32	Azx = Axx+6;
33	Azy = Axx+7;
34	Azz = Axx+8;
35	}
36
37	void Atom::createArrays (int the_nElements) {
38	int i;
39
40	nElements = the_nElements;
41
42	pos = new double[nElements*3];
43	vel = new double[nElements*3];
44	frc = new double[nElements*3];
45	trq = new double[nElements*3];
46	Amat = new double[nElements*9];
47	mu = new double[nElements];
48	ul = new double[nElements*3];
49
50	// init directional values to zero
51
52	for( i=0; i<nElements; i++){
53	trq[i] = 0.0;
54	trq[i+1] = 0.0;
55	trq[i+2] = 0.0;
56
57	Amat[i] = 1.0;
58	Amat[i+1] = 0.0;
59	Amat[i+2] = 0.0;
60
61	Amat[i+3] = 0.0;
62	Amat[i+4] = 1.0;
63	Amat[i+5] = 0.0;
64
65	Amat[i+6] = 0.0;
66	Amat[i+7] = 0.0;
67	Amat[i+8] = 1.0;
68
69	mu[i] = 0.0;
70
71	ul[i] = 1.0;
72	ul[i+1] = 0.0;
73	ul[i+2] = 0.0;
74	}
75	}
76
77	void Atom::destroyArrays(void) {
78	delete[] pos;
79	delete[] vel;
80	delete[] frc;
81	delete[] trq;
82	delete[] Amat;
83	delete[] mu;
84	}
85
86	void Atom::setIndex(int theIndex) {
87	index = theIndex;
88	offset = index*3;
89	offsetX = offset;
90	offsetY = offset+1;
91	offsetZ = offset+2;
92
93	Axx = index*9;
94	Axy = Axx+1;
95	Axz = Axx+2;
96
97	Ayx = Axx+3;
98	Ayy = Axx+4;
99	Ayz = Axx+5;
100
101	Azx = Axx+6;
102	Azy = Axx+7;
103	Azz = Axx+8;
104	}
105
106	void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
107	double* Atrq, double* AAmat, double* Amu,
108	double* Aul) {
109
110	int nNew = nElements+nAdded;
111
112	double* new_pos = new double[nNew*3];
113	double* new_vel = new double[nNew*3];
114	double* new_frc = new double[nNew*3];
115	double* new_trq = new double[nNew*3];
116	double* new_Amat = new double[nNew*9];
117	double* new_mu = new double[nNew];
118	double* new_ul = new double[nNew*3];
119	int i, j;
120
121	for (i = 0; i < 3*nElements; i++) {
122	new_pos[i] = pos[i];
123	new_vel[i] = vel[i];
124	new_frc[i] = frc[i];
125	new_trq[i] = trq[i];
126	new_ul[i] = ul[i];
127	}
128
129	for(i = 0; i < 3*nAdded; i++) {
130	j = i + 3*nElements;
131	new_pos[j] = Apos[i];
132	new_vel[j] = Avel[i];
133	new_frc[j] = Afrc[i];
134	new_trq[j] = Atrq[i];
135	new_ul[j] = Aul[i];
136	}
137
138	for (i = 0; i < 9*nElements; i++) {
139	new_Amat[i] = Amat[i];
140	}
141
142	for(i = 0; i < 9*nAdded; i++) {
143	j = i + 9*nElements;
144	new_Amat[j] = AAmat[i];
145	}
146
147	for (i = 0; i < nElements; i++) {
148	new_mu[i] = mu[i];
149	}
150
151	for(i = 0; i < nAdded; i++) {
152	j = i + nElements;
153	new_mu[j] = Amu[i];
154	}
155
156	delete[] pos;
157	delete[] vel;
158	delete[] frc;
159	delete[] trq;
160	delete[] Amat;
161	delete[] mu;
162
163	pos = new_pos;
164	vel = new_vel;
165	frc = new_frc;
166	trq = new_trq;
167	ul = new_ul;
168	Amat = new_Amat;
169	mu = new_mu;
170
171	nElements = nNew;
172	}
173
174	void Atom::deleteAtom(int theIndex) {
175	deleteRange(theIndex, theIndex);
176	}
177
178	void Atom::deleteRange(int startIndex, int stopIndex) {
179
180	int nNew = nElements-(stopIndex-startIndex+1);
181
182	double* new_pos = new double[nNew*3];
183	double* new_vel = new double[nNew*3];
184	double* new_frc = new double[nNew*3];
185	double* new_trq = new double[nNew*3];
186	double* new_Amat = new double[nNew*9];
187	double* new_mu = new double[nNew];
188	double* new_ul = new double[nNew*3];
189	int i, j;
190
191	for (i = 0; i < 3*startIndex; i++) {
192	new_pos[i] = pos[i];
193	new_vel[i] = vel[i];
194	new_frc[i] = frc[i];
195	new_trq[i] = trq[i];
196	new_ul[i] = ul[i];
197	}
198
199	for(i = 3(stopIndex + 1); i < 3nElements; i++) {
200	j = i - 3*startIndex + 1;
201	new_pos[j] = pos[i];
202	new_vel[j] = vel[i];
203	new_frc[j] = frc[i];
204	new_trq[j] = trq[i];
205	new_ul[j] = ul[i];
206	}
207
208	for (i = 0; i < 9*startIndex; i++) {
209	new_Amat[i] = Amat[i];
210	}
211
212	for(i = 9(stopIndex + 1); i < 9nElements; i++) {
213	j = i - 9*startIndex + 1;
214	new_Amat[j] = Amat[i];
215	}
216
217	for (i = 0; i < startIndex; i++) {
218	new_mu[i] = mu[i];
219	}
220
221	for(i = (stopIndex+1); i < nElements; i++) {
222	j = i - startIndex + 1;
223	new_mu[j] = mu[i];
224	}
225
226	delete[] pos;
227	delete[] vel;
228	delete[] frc;
229	delete[] trq;
230	delete[] Amat;
231	delete[] mu;
232
233	pos = new_pos;
234	vel = new_vel;
235	frc = new_frc;
236	trq = new_trq;
237	ul = new_ul;
238	Amat = new_Amat;
239	mu = new_mu;
240
241	nElements = nNew;
242	}