6 |
|
double* Atom::vel; // the velocity array |
7 |
|
double* Atom::frc; // the forc array |
8 |
|
double* Atom::trq; // the torque vector ( space fixed ) |
9 |
+ |
double* Atom::Amat; // the rotation matrix |
10 |
+ |
double* Atom::mu; // the array of dipole moments |
11 |
+ |
double* Atom::ul; // the lab frame unit directional vector |
12 |
|
|
13 |
|
void DirectionalAtom::setA( double the_A[3][3] ){ |
14 |
|
|
15 |
< |
Axx = the_A[0][0]; Axy = the_A[0][1]; Axz = the_A[0][2]; |
16 |
< |
Ayx = the_A[1][0]; Ayy = the_A[1][1]; Ayz = the_A[1][2]; |
17 |
< |
Azx = the_A[2][0]; Azy = the_A[2][1]; Azz = the_A[2][2]; |
15 |
> |
Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
16 |
> |
Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
17 |
> |
Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
18 |
> |
|
19 |
> |
this->updateU(); |
20 |
|
} |
21 |
|
|
22 |
|
void DirectionalAtom::setI( double the_I[3][3] ){ |
36 |
|
q3Sqr = the_q[3] * the_q[3]; |
37 |
|
|
38 |
|
|
39 |
< |
Axx = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
40 |
< |
Axy = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
41 |
< |
Axz = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
39 |
> |
Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
40 |
> |
Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
41 |
> |
Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
42 |
|
|
43 |
< |
Ayx = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
44 |
< |
Ayy = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
45 |
< |
Ayz = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
43 |
> |
Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
44 |
> |
Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
45 |
> |
Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
46 |
|
|
47 |
< |
Azx = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
48 |
< |
Azy = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
49 |
< |
Azz = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
47 |
> |
Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
48 |
> |
Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
49 |
> |
Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
50 |
> |
|
51 |
> |
this->updateU(); |
52 |
|
} |
53 |
|
|
54 |
|
void DirectionalAtom::getA( double the_A[3][3] ){ |
55 |
|
|
56 |
< |
the_A[0][0] = Axx; |
57 |
< |
the_A[0][1] = Axy; |
58 |
< |
the_A[0][2] = Axz; |
56 |
> |
the_A[0][0] = Amat[Axx]; |
57 |
> |
the_A[0][1] = Amat[Axy]; |
58 |
> |
the_A[0][2] = Amat[Axz]; |
59 |
|
|
60 |
< |
the_A[1][0] = Ayx; |
61 |
< |
the_A[1][1] = Ayy; |
62 |
< |
the_A[1][2] = Ayz; |
60 |
> |
the_A[1][0] = Amat[Ayx]; |
61 |
> |
the_A[1][1] = Amat[Ayy]; |
62 |
> |
the_A[1][2] = Amat[Ayz]; |
63 |
|
|
64 |
< |
the_A[2][0] = Azx; |
65 |
< |
the_A[2][1] = Azy; |
66 |
< |
the_A[2][2] = Azz; |
64 |
> |
the_A[2][0] = Amat[Azx]; |
65 |
> |
the_A[2][1] = Amat[Azy]; |
66 |
> |
the_A[2][2] = Amat[Azz]; |
67 |
|
} |
68 |
|
|
69 |
|
|
81 |
|
double t, s; |
82 |
|
double ad1, ad2, ad3; |
83 |
|
|
84 |
< |
t = Axx + Ayy + Azz + 1.0; |
84 |
> |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
85 |
|
if( t > 0.0 ){ |
86 |
|
|
87 |
|
s = 0.5 / sqrt( t ); |
88 |
|
q[0] = 0.25 / s; |
89 |
< |
q[1] = (Ayz - Azy) * s; |
90 |
< |
q[2] = (Azx - Axz) * s; |
91 |
< |
q[3] = (Axy - Ayx) * s; |
89 |
> |
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
90 |
> |
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
91 |
> |
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
92 |
|
} |
93 |
|
else{ |
94 |
|
|
95 |
< |
ad1 = fabs( Axx ); |
96 |
< |
ad2 = fabs( Ayy ); |
97 |
< |
ad3 = fabs( Azz ); |
95 |
> |
ad1 = fabs( Amat[Axx] ); |
96 |
> |
ad2 = fabs( Amat[Ayy] ); |
97 |
> |
ad3 = fabs( Amat[Azz] ); |
98 |
|
|
99 |
|
if( ad1 >= ad2 && ad1 >= ad3 ){ |
100 |
|
|
101 |
< |
s = 2.0 * sqrt( 1.0 + Axx - Ayy - Azz ); |
102 |
< |
q[0] = (Ayz + Azy) / s; |
101 |
> |
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
102 |
> |
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
103 |
|
q[1] = 0.5 / s; |
104 |
< |
q[2] = (Axy + Ayx) / s; |
105 |
< |
q[3] = (Axz + Azx) / s; |
104 |
> |
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
105 |
> |
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
106 |
|
} |
107 |
|
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
108 |
|
|
109 |
< |
s = sqrt( 1.0 + Ayy - Axx - Azz ) * 2.0; |
110 |
< |
q[0] = (Axz + Azx) / s; |
111 |
< |
q[1] = (Axy + Ayx) / s; |
109 |
> |
s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
110 |
> |
q[0] = (Amat[Axz] + Amat[Azx]) / s; |
111 |
> |
q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
112 |
|
q[2] = 0.5 / s; |
113 |
< |
q[3] = (Ayz + Azy) / s; |
113 |
> |
q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
114 |
|
} |
115 |
|
else{ |
116 |
|
|
117 |
< |
s = sqrt( 1.0 + Azz - Axx - Ayy ) * 2.0; |
118 |
< |
q[0] = (Axy + Ayx) / s; |
119 |
< |
q[1] = (Axz + Azx) / s; |
120 |
< |
q[2] = (Ayz + Azy) / s; |
117 |
> |
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
118 |
> |
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
119 |
> |
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
120 |
> |
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
121 |
|
q[3] = 0.5 / s; |
122 |
|
} |
123 |
|
} |
126 |
|
|
127 |
|
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
128 |
|
|
129 |
< |
Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
130 |
< |
Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
131 |
< |
Axz = sin(theta) * sin(psi); |
129 |
> |
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
130 |
> |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
131 |
> |
Amat[Axz] = sin(theta) * sin(psi); |
132 |
|
|
133 |
< |
Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
134 |
< |
Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
135 |
< |
Ayz = sin(theta) * cos(psi); |
133 |
> |
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
134 |
> |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
135 |
> |
Amat[Ayz] = sin(theta) * cos(psi); |
136 |
|
|
137 |
< |
Azx = sin(phi) * sin(theta); |
138 |
< |
Azy = -cos(phi) * sin(theta); |
139 |
< |
Azz = cos(theta); |
137 |
> |
Amat[Azx] = sin(phi) * sin(theta); |
138 |
> |
Amat[Azy] = -cos(phi) * sin(theta); |
139 |
> |
Amat[Azz] = cos(theta); |
140 |
> |
|
141 |
> |
this->updateU(); |
142 |
|
} |
143 |
|
|
144 |
|
|
150 |
|
rl[1] = r[1]; |
151 |
|
rl[2] = r[2]; |
152 |
|
|
153 |
< |
r[0] = (Axx * rl[0]) + (Axy * rl[1]) + (Axz * rl[2]); |
154 |
< |
r[1] = (Ayx * rl[0]) + (Ayy * rl[1]) + (Ayz * rl[2]); |
155 |
< |
r[2] = (Azx * rl[0]) + (Azy * rl[1]) + (Azz * rl[2]); |
153 |
> |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
154 |
> |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
155 |
> |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
156 |
|
} |
157 |
|
|
158 |
|
void DirectionalAtom::body2Lab( double r[3] ){ |
163 |
|
rb[1] = r[1]; |
164 |
|
rb[2] = r[2]; |
165 |
|
|
166 |
< |
r[0] = (Axx * rb[0]) + (Ayx * rb[1]) + (Azx * rb[2]); |
167 |
< |
r[1] = (Axy * rb[0]) + (Ayy * rb[1]) + (Azy * rb[2]); |
168 |
< |
r[2] = (Axz * rb[0]) + (Ayz * rb[1]) + (Azz * rb[2]); |
166 |
> |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
167 |
> |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
168 |
> |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
169 |
|
} |
170 |
|
|
171 |
+ |
void DirectionalAtom::updateU( void ){ |
172 |
+ |
|
173 |
+ |
r[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
174 |
+ |
r[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
175 |
+ |
r[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
176 |
+ |
} |
177 |
+ |
|