95 |
|
double rij2 = rij * rij; |
96 |
|
double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
97 |
|
Mat3x3d tmpMat; |
98 |
< |
tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; |
98 |
> |
tmpMat = outProduct(Rij, Rij) / rij2; |
99 |
|
double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
100 |
|
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
101 |
|
}else { |
105 |
|
Tij(2, 2) = constant; |
106 |
|
} |
107 |
|
B.setSubMatrix(i*3, j*3, Tij); |
108 |
+ |
std::cout << Tij << std::endl; |
109 |
|
} |
110 |
|
} |
111 |
|
|
112 |
+ |
std::cout << "B=\n" |
113 |
+ |
<< B << std::endl; |
114 |
|
//invert B Matrix |
115 |
|
invertMatrix(B, C); |
116 |
+ |
|
117 |
+ |
std::cout << "C=\n" |
118 |
+ |
<< C << std::endl; |
119 |
+ |
|
120 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
121 |
|
std::vector<Mat3x3d> U; |
122 |
|
for (int i = 0; i < nbeads; ++i) { |
129 |
|
Mat3x3d Xitt; |
130 |
|
Mat3x3d Xirr; |
131 |
|
Mat3x3d Xitr; |
132 |
+ |
|
133 |
+ |
//calculate the total volume |
134 |
+ |
|
135 |
+ |
double volume = 0.0; |
136 |
+ |
for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
137 |
+ |
volume = 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
138 |
+ |
} |
139 |
|
|
140 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
141 |
|
for (std::size_t j = 0; j < nbeads; ++j) { |
143 |
|
C.getSubMatrix(i*3, j*3, Cij); |
144 |
|
|
145 |
|
Xitt += Cij; |
146 |
< |
Xirr += U[i] * Cij; |
147 |
< |
Xitr += U[i] * Cij * U[j]; |
146 |
> |
Xitr += U[i] * Cij; |
147 |
> |
Xirr += -U[i] * Cij * U[j]; |
148 |
> |
//Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I; |
149 |
|
} |
150 |
|
} |
151 |
|
|
165 |
|
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
166 |
|
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
167 |
|
|
168 |
< |
Mat3x3d XirrInv(0.0); |
154 |
< |
Mat3x3d XirrCopy; |
155 |
< |
XirrCopy = Xirr; |
168 |
> |
const static Mat3x3d zeroMat(0.0); |
169 |
|
|
170 |
|
Mat3x3d XittInv(0.0); |
171 |
< |
Mat3x3d XittCopy; |
172 |
< |
XittCopy = Xitt; |
173 |
< |
invertMatrix(XittCopy, XittInv); |
171 |
> |
XittInv = Xitt.inverse(); |
172 |
> |
|
173 |
> |
//Xirr may not be inverted,if it one of the diagonal element is zero, for example |
174 |
> |
//( a11 a12 0) |
175 |
> |
//( a21 a22 0) |
176 |
> |
//( 0 0 0) |
177 |
> |
Mat3x3d XirrInv; |
178 |
> |
XirrInv = Xirr.inverse(); |
179 |
|
|
180 |
|
Mat3x3d tmp; |
181 |
|
Mat3x3d tmpInv; |
182 |
|
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
183 |
+ |
tmpInv = tmp.inverse(); |
184 |
|
|
166 |
– |
const static Mat3x3d zeroMat(0.0); |
167 |
– |
if (!invertMatrix(tmp, tmpInv)) { |
168 |
– |
tmpInv = zeroMat; |
169 |
– |
} |
170 |
– |
|
185 |
|
Dott = kt * tmpInv; |
186 |
< |
Dotr = -kt*XirrInv * Xitr * tmpInv; |
186 |
> |
Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8; |
187 |
|
|
188 |
< |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
188 |
> |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
189 |
> |
tmpInv = tmp.inverse(); |
190 |
|
|
191 |
< |
if(!invertMatrix(tmp, tmpInv)) { |
177 |
< |
tmpInv = zeroMat; |
178 |
< |
} |
179 |
< |
Dorr = kt * tmpInv; |
191 |
> |
Dorr = kt * tmpInv*1.0E16; |
192 |
|
|
193 |
|
//Do.getSubMatrix(0, 0 , Dott); |
194 |
|
//Do.getSubMatrix(3, 0, Dotr); |
210 |
|
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
211 |
|
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
212 |
|
|
213 |
< |
if(!invertMatrix(tmp, tmpInv)) { |
202 |
< |
tmpInv = zeroMat; |
203 |
< |
} |
213 |
> |
tmpInv = tmp.inverse(); |
214 |
|
|
215 |
|
Vector3d rod = tmpInv * tmpVec; |
216 |
|
|
256 |
|
os << "//translational diffusion tensor" << std::endl; |
257 |
|
os << props_.transDiff << std::endl; |
258 |
|
|
259 |
< |
os << "//translational diffusion tensor" << std::endl; |
259 |
> |
os << "//translation-rotation coupling diffusion tensor" << std::endl; |
260 |
|
os << props_.transRotDiff << std::endl; |
261 |
|
|
262 |
|
os << "//rotational diffusion tensor" << std::endl; |