38 |
|
* University of Notre Dame has been advised of the possibility of |
39 |
|
* such damages. |
40 |
|
*/ |
41 |
+ |
#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
42 |
+ |
#include "applications/hydrodynamics/Spheric.hpp" |
43 |
+ |
#include "applications/hydrodynamics/Ellipsoid.hpp" |
44 |
+ |
#include "applications/hydrodynamics/CompositeShape.hpp" |
45 |
|
|
42 |
– |
#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
43 |
– |
#include "math/LU.hpp" |
44 |
– |
#include "math/DynamicRectMatrix.hpp" |
45 |
– |
#include "math/SquareMatrix3.hpp" |
46 |
– |
#include "utils/OOPSEConstant.hpp" |
46 |
|
namespace oopse { |
48 |
– |
/** |
49 |
– |
* Reference: |
50 |
– |
* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
51 |
– |
* Comparison of Different Modeling and Computational Procedures. |
52 |
– |
* Biophysical Journal, 75(6), 3044, 1999 |
53 |
– |
*/ |
47 |
|
|
48 |
< |
HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){ |
49 |
< |
DynamicProperty::const_iterator iter; |
48 |
> |
bool HydrodynamicsModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) { |
49 |
> |
return false; |
50 |
> |
} |
51 |
|
|
52 |
< |
iter = extraParams.find("Viscosity"); |
53 |
< |
if (iter != extraParams.end()) { |
54 |
< |
boost::any param = iter->second; |
61 |
< |
viscosity_ = boost::any_cast<double>(param); |
62 |
< |
}else { |
63 |
< |
std::cout << "HydrodynamicsModel Error\n" ; |
64 |
< |
} |
52 |
> |
bool HydrodynamicsModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { |
53 |
> |
return false; |
54 |
> |
} |
55 |
|
|
56 |
< |
iter = extraParams.find("Temperature"); |
57 |
< |
if (iter != extraParams.end()) { |
68 |
< |
boost::any param = iter->second; |
69 |
< |
temperature_ = boost::any_cast<double>(param); |
70 |
< |
}else { |
71 |
< |
std::cout << "HydrodynamicsModel Error\n" ; |
72 |
< |
} |
56 |
> |
bool HydrodynamicsModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) { |
57 |
> |
return false; |
58 |
|
} |
74 |
– |
|
75 |
– |
bool HydrodynamicsModel::calcHydrodyanmicsProps() { |
76 |
– |
if (!createBeads(beads_)) { |
77 |
– |
std::cout << "can not create beads" << std::endl; |
78 |
– |
return false; |
79 |
– |
} |
80 |
– |
|
81 |
– |
int nbeads = beads_.size(); |
82 |
– |
DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
83 |
– |
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
84 |
– |
Mat3x3d I; |
85 |
– |
I(0, 0) = 1.0; |
86 |
– |
I(1, 1) = 1.0; |
87 |
– |
I(2, 2) = 1.0; |
88 |
– |
|
89 |
– |
for (std::size_t i = 0; i < nbeads; ++i) { |
90 |
– |
for (std::size_t j = 0; j < nbeads; ++j) { |
91 |
– |
Mat3x3d Tij; |
92 |
– |
if (i != j ) { |
93 |
– |
Vector3d Rij = beads_[i].pos - beads_[j].pos; |
94 |
– |
double rij = Rij.length(); |
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(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 { |
102 |
– |
double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
103 |
– |
Tij(0, 0) = constant; |
104 |
– |
Tij(1, 1) = constant; |
105 |
– |
Tij(2, 2) = constant; |
106 |
– |
} |
107 |
– |
B.setSubMatrix(i*3, j*3, Tij); |
108 |
– |
std::cout << Tij << std::endl; |
109 |
– |
} |
110 |
– |
} |
59 |
|
|
60 |
< |
std::cout << "B=\n" |
113 |
< |
<< B << std::endl; |
114 |
< |
//invert B Matrix |
115 |
< |
invertMatrix(B, C); |
60 |
> |
void HydrodynamicsModel::writeHydroProps(std::ostream& os) { |
61 |
|
|
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) { |
123 |
– |
Mat3x3d currU; |
124 |
– |
currU.setupSkewMat(beads_[i].pos); |
125 |
– |
U.push_back(currU); |
126 |
– |
} |
62 |
|
|
63 |
< |
//calculate Xi matrix at arbitrary origin O |
64 |
< |
Mat3x3d Xitt; |
65 |
< |
Mat3x3d Xirr; |
66 |
< |
Mat3x3d Xitr; |
63 |
> |
os << sd_->getType() << "\t"; |
64 |
> |
|
65 |
> |
//center of resistance |
66 |
> |
os << cr_.center[0] << "\t" << cr_.center[1] << "\t" << cr_.center[2] << "\t"; |
67 |
|
|
68 |
< |
//calculate the total volume |
68 |
> |
//resistance tensor at center of resistance |
69 |
> |
//translation |
70 |
> |
os << cr_.Xi(0, 0) << "\t" << cr_.Xi(0, 1) << "\t" << cr_.Xi(0, 2) << "\t" |
71 |
> |
<< cr_.Xi(1, 0) << "\t" << cr_.Xi(1, 1) << "\t" << cr_.Xi(1, 2) << "\t" |
72 |
> |
<< cr_.Xi(2, 0) << "\t" << cr_.Xi(2, 1) << "\t" << cr_.Xi(2, 2) << "\t"; |
73 |
|
|
74 |
< |
double volume = 0.0; |
75 |
< |
for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
76 |
< |
volume = 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
77 |
< |
} |
139 |
< |
|
140 |
< |
for (std::size_t i = 0; i < nbeads; ++i) { |
141 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
142 |
< |
Mat3x3d Cij; |
143 |
< |
C.getSubMatrix(i*3, j*3, Cij); |
144 |
< |
|
145 |
< |
Xitt += Cij; |
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 |
< |
} |
74 |
> |
//rotation-translation |
75 |
> |
os << cr_.Xi(0, 3) << "\t" << cr_.Xi(0, 4) << "\t" << cr_.Xi(0, 5) << "\t" |
76 |
> |
<< cr_.Xi(1, 3) << "\t" << cr_.Xi(1, 4) << "\t" << cr_.Xi(1, 5) << "\t" |
77 |
> |
<< cr_.Xi(2, 3) << "\t" << cr_.Xi(2, 4) << "\t" << cr_.Xi(2, 5) << "\t"; |
78 |
|
|
79 |
< |
//invert Xi to get Diffusion Tensor at arbitrary origin O |
80 |
< |
RectMatrix<double, 6, 6> Xi; |
81 |
< |
RectMatrix<double, 6, 6> Do; |
82 |
< |
Xi.setSubMatrix(0, 0, Xitt); |
156 |
< |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
157 |
< |
Xi.setSubMatrix(3, 0, Xitr); |
158 |
< |
Xi.setSubMatrix(3, 3, Xirr); |
159 |
< |
//invertMatrix(Xi, Do); |
160 |
< |
double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
161 |
< |
//Do *= kt; |
79 |
> |
//translation-rotation |
80 |
> |
os << cr_.Xi(3, 0) << "\t" << cr_.Xi(3, 1) << "\t" << cr_.Xi(3, 2) << "\t" |
81 |
> |
<< cr_.Xi(4, 0) << "\t" << cr_.Xi(4, 1) << "\t" << cr_.Xi(4, 2) << "\t" |
82 |
> |
<< cr_.Xi(5, 0) << "\t" << cr_.Xi(5, 1) << "\t" << cr_.Xi(5, 2) << "\t"; |
83 |
|
|
84 |
+ |
//rotation |
85 |
+ |
os << cr_.Xi(3, 3) << "\t" << cr_.Xi(3, 4) << "\t" << cr_.Xi(3, 5) << "\t" |
86 |
+ |
<< cr_.Xi(4, 3) << "\t" << cr_.Xi(4, 4) << "\t" << cr_.Xi(4, 5) << "\t" |
87 |
+ |
<< cr_.Xi(5, 3) << "\t" << cr_.Xi(5, 4) << "\t" << cr_.Xi(5, 5) << "\t"; |
88 |
|
|
164 |
– |
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
165 |
– |
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
166 |
– |
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
89 |
|
|
90 |
< |
const static Mat3x3d zeroMat(0.0); |
91 |
< |
|
92 |
< |
Mat3x3d XittInv(0.0); |
93 |
< |
XittInv = Xitt.inverse(); |
94 |
< |
|
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(); |
90 |
> |
//diffusion tensor at center of resistance |
91 |
> |
//translation |
92 |
> |
os << cr_.D(0, 0) << "\t" << cr_.D(0, 1) << "\t" << cr_.D(0, 2) << "\t" |
93 |
> |
<< cr_.D(1, 0) << "\t" << cr_.D(1, 1) << "\t" << cr_.D(1, 2) << "\t" |
94 |
> |
<< cr_.D(2, 0) << "\t" << cr_.D(2, 1) << "\t" << cr_.D(2, 2) << "\t"; |
95 |
|
|
96 |
< |
Mat3x3d tmp; |
97 |
< |
Mat3x3d tmpInv; |
98 |
< |
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
99 |
< |
tmpInv = tmp.inverse(); |
96 |
> |
//rotation-translation |
97 |
> |
os << cr_.D(0, 3) << "\t" << cr_.D(0, 4) << "\t" << cr_.D(0, 5) << "\t" |
98 |
> |
<< cr_.D(1, 3) << "\t" << cr_.D(1, 4) << "\t" << cr_.D(1, 5) << "\t" |
99 |
> |
<< cr_.D(2, 3) << "\t" << cr_.D(2, 4) << "\t" << cr_.D(2, 5) << "\t"; |
100 |
|
|
101 |
< |
Dott = kt * tmpInv; |
102 |
< |
Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8; |
101 |
> |
//translation-rotation |
102 |
> |
os << cr_.D(3, 0) << "\t" << cr_.D(3, 1) << "\t" << cr_.D(3, 2) << "\t" |
103 |
> |
<< cr_.D(4, 0) << "\t" << cr_.D(4, 1) << "\t" << cr_.D(4, 2) << "\t" |
104 |
> |
<< cr_.D(5, 0) << "\t" << cr_.D(5, 1) << "\t" << cr_.D(5, 2) << "\t"; |
105 |
|
|
106 |
< |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
107 |
< |
tmpInv = tmp.inverse(); |
108 |
< |
|
109 |
< |
Dorr = kt * tmpInv*1.0E16; |
106 |
> |
//rotation |
107 |
> |
os << cr_.D(3, 3) << "\t" << cr_.D(3, 4) << "\t" << cr_.D(3, 5) << "\t" |
108 |
> |
<< cr_.D(4, 3) << "\t" << cr_.D(4, 4) << "\t" << cr_.D(4, 5) << "\t" |
109 |
> |
<< cr_.D(5, 3) << "\t" << cr_.D(5, 4) << "\t" << cr_.D(5, 5) << "\t"; |
110 |
> |
|
111 |
> |
//--------------------------------------------------------------------- |
112 |
|
|
113 |
< |
//Do.getSubMatrix(0, 0 , Dott); |
114 |
< |
//Do.getSubMatrix(3, 0, Dotr); |
195 |
< |
//Do.getSubMatrix(3, 3, Dorr); |
113 |
> |
//center of diffusion |
114 |
> |
os << cd_.center[0] << "\t" << cd_.center[1] << "\t" << cd_.center[2] << "\t"; |
115 |
|
|
116 |
< |
//calculate center of diffusion |
117 |
< |
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
118 |
< |
tmp(0, 1) = - Dorr(0, 1); |
119 |
< |
tmp(0, 2) = -Dorr(0, 2); |
120 |
< |
tmp(1, 0) = -Dorr(0, 1); |
202 |
< |
tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
203 |
< |
tmp(1, 2) = -Dorr(1, 2); |
204 |
< |
tmp(2, 0) = -Dorr(0, 2); |
205 |
< |
tmp(2, 1) = -Dorr(1, 2); |
206 |
< |
tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
116 |
> |
//resistance tensor at center of diffusion |
117 |
> |
//translation |
118 |
> |
os << cd_.Xi(0, 0) << "\t" << cd_.Xi(0, 1) << "\t" << cd_.Xi(0, 2) << "\t" |
119 |
> |
<< cd_.Xi(1, 0) << "\t" << cd_.Xi(1, 1) << "\t" << cd_.Xi(1, 2) << "\t" |
120 |
> |
<< cd_.Xi(2, 0) << "\t" << cd_.Xi(2, 1) << "\t" << cd_.Xi(2, 2) << "\t"; |
121 |
|
|
122 |
< |
Vector3d tmpVec; |
123 |
< |
tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
124 |
< |
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
125 |
< |
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
122 |
> |
//rotation-translation |
123 |
> |
os << cd_.Xi(0, 3) << "\t" << cd_.Xi(0, 4) << "\t" << cd_.Xi(0, 5) << "\t" |
124 |
> |
<< cd_.Xi(1, 3) << "\t" << cd_.Xi(1, 4) << "\t" << cd_.Xi(1, 5) << "\t" |
125 |
> |
<< cd_.Xi(2, 3) << "\t" << cd_.Xi(2, 4) << "\t" << cd_.Xi(2, 5) << "\t"; |
126 |
|
|
127 |
< |
tmpInv = tmp.inverse(); |
128 |
< |
|
129 |
< |
Vector3d rod = tmpInv * tmpVec; |
127 |
> |
//translation-rotation |
128 |
> |
os << cd_.Xi(3, 0) << "\t" << cd_.Xi(3, 1) << "\t" << cd_.Xi(3, 2) << "\t" |
129 |
> |
<< cd_.Xi(4, 0) << "\t" << cd_.Xi(4, 1) << "\t" << cd_.Xi(4, 2) << "\t" |
130 |
> |
<< cd_.Xi(5, 0) << "\t" << cd_.Xi(5, 1) << "\t" << cd_.Xi(5, 2) << "\t"; |
131 |
|
|
132 |
< |
//calculate Diffusion Tensor at center of diffusion |
133 |
< |
Mat3x3d Uod; |
134 |
< |
Uod.setupSkewMat(rod); |
135 |
< |
|
221 |
< |
Mat3x3d Ddtt; //translational diffusion tensor at diffusion center |
222 |
< |
Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center |
223 |
< |
Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor |
224 |
< |
|
225 |
< |
Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
226 |
< |
Ddrr = Dorr; |
227 |
< |
Ddtr = Dotr + Dorr * Uod; |
228 |
< |
|
229 |
< |
props_.diffCenter = rod; |
230 |
< |
props_.transDiff = Ddtt; |
231 |
< |
props_.transRotDiff = Ddtr; |
232 |
< |
props_.rotDiff = Ddrr; |
132 |
> |
//rotation |
133 |
> |
os << cd_.Xi(3, 3) << "\t" << cd_.Xi(3, 4) << "\t" << cd_.Xi(3, 5) << "\t" |
134 |
> |
<< cd_.Xi(4, 3) << "\t" << cd_.Xi(4, 4) << "\t" << cd_.Xi(4, 5) << "\t" |
135 |
> |
<< cd_.Xi(5, 3) << "\t" << cd_.Xi(5, 4) << "\t" << cd_.Xi(5, 5) << "\t"; |
136 |
|
|
234 |
– |
return true; |
235 |
– |
} |
137 |
|
|
138 |
< |
void HydrodynamicsModel::writeBeads(std::ostream& os) { |
139 |
< |
std::vector<BeadParam>::iterator iter; |
140 |
< |
os << beads_.size() << std::endl; |
141 |
< |
os << "Generated by Hydro" << std::endl; |
142 |
< |
for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
242 |
< |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
243 |
< |
} |
138 |
> |
//diffusion tensor at center of diffusion |
139 |
> |
//translation |
140 |
> |
os << cd_.D(0, 0) << "\t" << cd_.D(0, 1) << "\t" << cd_.D(0, 2) << "\t" |
141 |
> |
<< cd_.D(1, 0) << "\t" << cd_.D(1, 1) << "\t" << cd_.D(1, 2) << "\t" |
142 |
> |
<< cd_.D(2, 0) << "\t" << cd_.D(2, 1) << "\t" << cd_.D(2, 2) << "\t"; |
143 |
|
|
144 |
< |
} |
144 |
> |
//rotation-translation |
145 |
> |
os << cd_.D(0, 3) << "\t" << cd_.D(0, 4) << "\t" << cd_.D(0, 5) << "\t" |
146 |
> |
<< cd_.D(1, 3) << "\t" << cd_.D(1, 4) << "\t" << cd_.D(1, 5) << "\t" |
147 |
> |
<< cd_.D(2, 3) << "\t" << cd_.D(2, 4) << "\t" << cd_.D(2, 5) << "\t"; |
148 |
|
|
149 |
< |
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
150 |
< |
os << "//viscosity = " << viscosity_ << std::endl; |
151 |
< |
os << "//temperature = " << temperature_<< std::endl; |
152 |
< |
std::vector<BeadParam>::iterator iter; |
251 |
< |
os << sd_->getType() << "\n"; |
149 |
> |
//translation-rotation |
150 |
> |
os << cd_.D(3, 0) << "\t" << cd_.D(3, 1) << "\t" << cd_.D(3, 2) << "\t" |
151 |
> |
<< cd_.D(4, 0) << "\t" << cd_.D(4, 1) << "\t" << cd_.D(4, 2) << "\t" |
152 |
> |
<< cd_.D(5, 0) << "\t" << cd_.D(5, 1) << "\t" << cd_.D(5, 2) << "\t"; |
153 |
|
|
154 |
< |
os << "//diffusion center" << std::endl; |
155 |
< |
os << props_.diffCenter << std::endl; |
154 |
> |
//rotation |
155 |
> |
os << cd_.D(3, 3) << "\t" << cd_.D(3, 4) << "\t" << cd_.D(3, 5) << "\t" |
156 |
> |
<< cd_.D(4, 3) << "\t" << cd_.D(4, 4) << "\t" << cd_.D(4, 5) << "\t" |
157 |
> |
<< cd_.D(5, 3) << "\t" << cd_.D(5, 4) << "\t" << cd_.D(5, 5) << "\n"; |
158 |
|
|
256 |
– |
os << "//translational diffusion tensor" << std::endl; |
257 |
– |
os << props_.transDiff << std::endl; |
159 |
|
|
259 |
– |
os << "//translation-rotation coupling diffusion tensor" << std::endl; |
260 |
– |
os << props_.transRotDiff << std::endl; |
261 |
– |
|
262 |
– |
os << "//rotational diffusion tensor" << std::endl; |
263 |
– |
os << props_.rotDiff << std::endl; |
264 |
– |
|
265 |
– |
/* |
266 |
– |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n" |
267 |
– |
|
268 |
– |
os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t" |
269 |
– |
<< props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t" |
270 |
– |
<< props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n"; |
271 |
– |
|
272 |
– |
os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t" |
273 |
– |
<< props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t" |
274 |
– |
<< props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t" |
275 |
– |
|
276 |
– |
os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t" |
277 |
– |
<< props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t" |
278 |
– |
<< props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";" |
279 |
– |
<< std::endl; |
280 |
– |
*/ |
160 |
|
} |
161 |
|
|
162 |
|
} |