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 (22 years, 7 months ago) by mmeineke
File size:	4734 byte(s)
Log Message:	fixed a couple of the "static" bugs in Atom and Exclude
#	User	Rev	Content
1	gezelter	409	#include "Atom.hpp"
2
3	mmeineke	413	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	gezelter	409	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	mmeineke	413	void Atom::createArrays (int the_nElements) {
38	gezelter	409	int i;
39
40	mmeineke	413	nElements = the_nElements;
41
42	gezelter	409	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	gezelter	410	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	gezelter	409	}
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	gezelter	410	new_Amat[j] = AAmat[i];
145	gezelter	409	}
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	gezelter	410	new_mu[j] = Amu[i];
154	gezelter	409	}
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			}