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 < 3*nElements; 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 < 9*nElements; 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 |
|
|
} |