| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "applications/hydrodynamics/ApproximationModel.hpp" |
| 43 |
|
#include "math/LU.hpp" |
| 44 |
|
#include "math/DynamicRectMatrix.hpp" |
| 45 |
|
#include "math/SquareMatrix3.hpp" |
| 46 |
< |
#include "utils/OOPSEConstant.hpp" |
| 47 |
< |
#include "applications/hydrodynamics/Spheric.hpp" |
| 48 |
< |
#include "applications/hydrodynamics/Ellipsoid.hpp" |
| 46 |
> |
#include "utils/PhysicalConstants.hpp" |
| 47 |
> |
#include "hydrodynamics/Sphere.hpp" |
| 48 |
> |
#include "hydrodynamics/Ellipsoid.hpp" |
| 49 |
|
#include "applications/hydrodynamics/CompositeShape.hpp" |
| 50 |
|
#include "math/LU.hpp" |
| 51 |
|
#include "utils/simError.h" |
| 52 |
< |
namespace oopse { |
| 52 |
> |
namespace OpenMD { |
| 53 |
|
/** |
| 54 |
|
* Reference: |
| 55 |
|
* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
| 57 |
|
* Biophysical Journal, 75(6), 3044, 1999 |
| 58 |
|
*/ |
| 59 |
|
|
| 60 |
< |
ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){ |
| 61 |
< |
|
| 62 |
< |
} |
| 63 |
< |
|
| 64 |
< |
bool ApproximationModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) { |
| 65 |
< |
return internalCalcHydroProps(static_cast<Shape*>(spheric), viscosity, temperature); |
| 66 |
< |
} |
| 67 |
< |
|
| 68 |
< |
bool ApproximationModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { |
| 69 |
< |
return internalCalcHydroProps(static_cast<Shape*>(ellipsoid), viscosity, temperature); |
| 70 |
< |
} |
| 71 |
< |
bool ApproximationModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) { |
| 72 |
< |
return internalCalcHydroProps(static_cast<Shape*>(compositeShape), viscosity, temperature); |
| 73 |
< |
} |
| 74 |
< |
|
| 75 |
< |
void ApproximationModel::init() { |
| 60 |
> |
ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){ |
| 61 |
> |
} |
| 62 |
> |
|
| 63 |
> |
void ApproximationModel::init() { |
| 64 |
|
if (!createBeads(beads_)) { |
| 65 |
|
sprintf(painCave.errMsg, "ApproximationModel::init() : Can not create beads\n"); |
| 66 |
|
painCave.isFatal = 1; |
| 67 |
|
simError(); |
| 68 |
|
} |
| 69 |
< |
|
| 70 |
< |
} |
| 71 |
< |
|
| 72 |
< |
bool ApproximationModel::internalCalcHydroProps(Shape* shape, double viscosity, double temperature) { |
| 73 |
< |
|
| 69 |
> |
|
| 70 |
> |
} |
| 71 |
> |
|
| 72 |
> |
bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
| 73 |
> |
|
| 74 |
|
bool ret = true; |
| 75 |
< |
HydroProps cr; |
| 76 |
< |
HydroProps cd; |
| 75 |
> |
HydroProp* cr = new HydroProp(); |
| 76 |
> |
HydroProp* cd = new HydroProp(); |
| 77 |
|
calcHydroPropsAtCR(beads_, viscosity, temperature, cr); |
| 78 |
< |
//calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
| 78 |
> |
calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
| 79 |
|
setCR(cr); |
| 80 |
|
setCD(cd); |
| 93 |
– |
|
| 81 |
|
return true; |
| 82 |
< |
} |
| 83 |
< |
|
| 84 |
< |
bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) { |
| 85 |
< |
|
| 82 |
> |
} |
| 83 |
> |
|
| 84 |
> |
bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cr) { |
| 85 |
> |
|
| 86 |
|
int nbeads = beads.size(); |
| 87 |
< |
DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
| 88 |
< |
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
| 87 |
> |
DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
| 88 |
> |
DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
| 89 |
|
Mat3x3d I; |
| 90 |
|
I(0, 0) = 1.0; |
| 91 |
|
I(1, 1) = 1.0; |
| 92 |
|
I(2, 2) = 1.0; |
| 93 |
|
|
| 94 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
| 95 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 96 |
< |
Mat3x3d Tij; |
| 95 |
> |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 96 |
> |
Mat3x3d Tij; |
| 97 |
|
if (i != j ) { |
| 98 |
< |
Vector3d Rij = beads[i].pos - beads[j].pos; |
| 99 |
< |
double rij = Rij.length(); |
| 100 |
< |
double rij2 = rij * rij; |
| 101 |
< |
double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; |
| 102 |
< |
Mat3x3d tmpMat; |
| 103 |
< |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 104 |
< |
double constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 105 |
< |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 98 |
> |
Vector3d Rij = beads[i].pos - beads[j].pos; |
| 99 |
> |
RealType rij = Rij.length(); |
| 100 |
> |
RealType rij2 = rij * rij; |
| 101 |
> |
RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; |
| 102 |
> |
Mat3x3d tmpMat; |
| 103 |
> |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 104 |
> |
RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 105 |
> |
RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; |
| 106 |
> |
RealType tmp2 = 1.0 - sumSigma2OverRij2; |
| 107 |
> |
Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; |
| 108 |
|
}else { |
| 109 |
< |
double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 110 |
< |
Tij(0, 0) = constant; |
| 111 |
< |
Tij(1, 1) = constant; |
| 112 |
< |
Tij(2, 2) = constant; |
| 109 |
> |
RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 110 |
> |
Tij(0, 0) = constant; |
| 111 |
> |
Tij(1, 1) = constant; |
| 112 |
> |
Tij(2, 2) = constant; |
| 113 |
|
} |
| 114 |
|
B.setSubMatrix(i*3, j*3, Tij); |
| 115 |
< |
} |
| 115 |
> |
} |
| 116 |
|
} |
| 117 |
< |
|
| 117 |
> |
|
| 118 |
|
//invert B Matrix |
| 119 |
|
invertMatrix(B, C); |
| 120 |
|
|
| 121 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 122 |
|
std::vector<Mat3x3d> U; |
| 123 |
|
for (int i = 0; i < nbeads; ++i) { |
| 124 |
< |
Mat3x3d currU; |
| 125 |
< |
currU.setupSkewMat(beads[i].pos); |
| 126 |
< |
U.push_back(currU); |
| 124 |
> |
Mat3x3d currU; |
| 125 |
> |
currU.setupSkewMat(beads[i].pos); |
| 126 |
> |
U.push_back(currU); |
| 127 |
|
} |
| 128 |
|
|
| 129 |
|
//calculate Xi matrix at arbitrary origin O |
| 130 |
|
Mat3x3d Xiott; |
| 131 |
|
Mat3x3d Xiorr; |
| 132 |
|
Mat3x3d Xiotr; |
| 133 |
< |
|
| 133 |
> |
|
| 134 |
|
//calculate the total volume |
| 135 |
< |
|
| 136 |
< |
double volume = 0.0; |
| 135 |
> |
|
| 136 |
> |
RealType volume = 0.0; |
| 137 |
|
for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) { |
| 138 |
< |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
| 138 |
> |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
| 139 |
|
} |
| 140 |
< |
|
| 140 |
> |
|
| 141 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
| 142 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 143 |
< |
Mat3x3d Cij; |
| 144 |
< |
C.getSubMatrix(i*3, j*3, Cij); |
| 145 |
< |
|
| 146 |
< |
Xiott += Cij; |
| 147 |
< |
Xiotr += U[i] * Cij; |
| 148 |
< |
//Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
| 149 |
< |
Xiorr += -U[i] * Cij * U[j]; |
| 150 |
< |
} |
| 142 |
> |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 143 |
> |
Mat3x3d Cij; |
| 144 |
> |
C.getSubMatrix(i*3, j*3, Cij); |
| 145 |
> |
|
| 146 |
> |
Xiott += Cij; |
| 147 |
> |
Xiotr += U[i] * Cij; |
| 148 |
> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
| 149 |
> |
Xiorr += -U[i] * Cij * U[j]; |
| 150 |
> |
} |
| 151 |
|
} |
| 152 |
|
|
| 153 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 154 |
< |
Xiott *= convertConstant; |
| 166 |
< |
Xiotr *= convertConstant; |
| 167 |
< |
Xiorr *= convertConstant; |
| 153 |
> |
// add the volume correction |
| 154 |
> |
Xiorr += (6.0 * viscosity * volume) * I; |
| 155 |
|
|
| 156 |
< |
|
| 156 |
> |
Xiott *= PhysicalConstants::viscoConvert; |
| 157 |
> |
Xiotr *= PhysicalConstants::viscoConvert; |
| 158 |
> |
Xiorr *= PhysicalConstants::viscoConvert; |
| 159 |
|
|
| 160 |
|
Mat3x3d tmp; |
| 161 |
|
Mat3x3d tmpInv; |
| 186 |
|
Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose(); |
| 187 |
|
|
| 188 |
|
|
| 189 |
< |
SquareMatrix<double,6> Xir6x6; |
| 190 |
< |
SquareMatrix<double,6> Dr6x6; |
| 189 |
> |
SquareMatrix<RealType,6> Xir6x6; |
| 190 |
> |
SquareMatrix<RealType,6> Dr6x6; |
| 191 |
|
|
| 192 |
|
Xir6x6.setSubMatrix(0, 0, Xirtt); |
| 193 |
|
Xir6x6.setSubMatrix(0, 3, Xirtr.transpose()); |
| 203 |
|
Dr6x6.getSubMatrix(0, 3, Drrt); |
| 204 |
|
Dr6x6.getSubMatrix(3, 0, Drtr); |
| 205 |
|
Dr6x6.getSubMatrix(3, 3, Drrr); |
| 206 |
< |
double kt = OOPSEConstant::kB * temperature ; |
| 206 |
> |
RealType kt = PhysicalConstants::kb * temperature ; // in kcal mol^-1 |
| 207 |
|
Drtt *= kt; |
| 208 |
|
Drrt *= kt; |
| 209 |
|
Drtr *= kt; |
| 210 |
|
Drrr *= kt; |
| 211 |
< |
Xirtt *= OOPSEConstant::kb * temperature; |
| 212 |
< |
Xirtr *= OOPSEConstant::kb * temperature; |
| 213 |
< |
Xirrr *= OOPSEConstant::kb * temperature; |
| 211 |
> |
//Xirtt *= PhysicalConstants::kb * temperature; |
| 212 |
> |
//Xirtr *= PhysicalConstants::kb * temperature; |
| 213 |
> |
//Xirrr *= PhysicalConstants::kb * temperature; |
| 214 |
|
|
| 215 |
+ |
Mat6x6d Xi, D; |
| 216 |
|
|
| 217 |
< |
cr.center = ror; |
| 218 |
< |
cr.Xi.setSubMatrix(0, 0, Xirtt); |
| 219 |
< |
cr.Xi.setSubMatrix(0, 3, Xirtr); |
| 220 |
< |
cr.Xi.setSubMatrix(3, 0, Xirtr); |
| 221 |
< |
cr.Xi.setSubMatrix(3, 3, Xirrr); |
| 222 |
< |
cr.D.setSubMatrix(0, 0, Drtt); |
| 223 |
< |
cr.D.setSubMatrix(0, 3, Drrt); |
| 224 |
< |
cr.D.setSubMatrix(3, 0, Drtr); |
| 225 |
< |
cr.D.setSubMatrix(3, 3, Drrr); |
| 217 |
> |
cr->setCOR(ror); |
| 218 |
> |
|
| 219 |
> |
Xi.setSubMatrix(0, 0, Xirtt); |
| 220 |
> |
Xi.setSubMatrix(0, 3, Xirtr); |
| 221 |
> |
Xi.setSubMatrix(3, 0, Xirtr); |
| 222 |
> |
Xi.setSubMatrix(3, 3, Xirrr); |
| 223 |
> |
|
| 224 |
> |
cr->setXi(Xi); |
| 225 |
> |
|
| 226 |
> |
D.setSubMatrix(0, 0, Drtt); |
| 227 |
> |
D.setSubMatrix(0, 3, Drrt); |
| 228 |
> |
D.setSubMatrix(3, 0, Drtr); |
| 229 |
> |
D.setSubMatrix(3, 3, Drrr); |
| 230 |
> |
|
| 231 |
> |
cr->setD(D); |
| 232 |
|
|
| 233 |
|
std::cout << "-----------------------------------------\n"; |
| 234 |
|
std::cout << "center of resistance :" << std::endl; |
| 253 |
|
|
| 254 |
|
return true; |
| 255 |
|
} |
| 256 |
< |
|
| 257 |
< |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) { |
| 258 |
< |
|
| 256 |
> |
|
| 257 |
> |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) { |
| 258 |
> |
|
| 259 |
|
int nbeads = beads.size(); |
| 260 |
< |
DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
| 261 |
< |
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
| 260 |
> |
DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
| 261 |
> |
DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
| 262 |
|
Mat3x3d I; |
| 263 |
|
I(0, 0) = 1.0; |
| 264 |
|
I(1, 1) = 1.0; |
| 265 |
|
I(2, 2) = 1.0; |
| 266 |
|
|
| 267 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
| 268 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 269 |
< |
Mat3x3d Tij; |
| 270 |
< |
if (i != j ) { |
| 271 |
< |
Vector3d Rij = beads[i].pos - beads[j].pos; |
| 272 |
< |
double rij = Rij.length(); |
| 273 |
< |
double rij2 = rij * rij; |
| 274 |
< |
double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; |
| 275 |
< |
Mat3x3d tmpMat; |
| 276 |
< |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 277 |
< |
double constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 278 |
< |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 279 |
< |
}else { |
| 280 |
< |
double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 281 |
< |
Tij(0, 0) = constant; |
| 282 |
< |
Tij(1, 1) = constant; |
| 283 |
< |
Tij(2, 2) = constant; |
| 284 |
< |
} |
| 285 |
< |
B.setSubMatrix(i*3, j*3, Tij); |
| 268 |
> |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 269 |
> |
Mat3x3d Tij; |
| 270 |
> |
if (i != j ) { |
| 271 |
> |
Vector3d Rij = beads[i].pos - beads[j].pos; |
| 272 |
> |
RealType rij = Rij.length(); |
| 273 |
> |
RealType rij2 = rij * rij; |
| 274 |
> |
RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; |
| 275 |
> |
Mat3x3d tmpMat; |
| 276 |
> |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 277 |
> |
RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 278 |
> |
RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; |
| 279 |
> |
RealType tmp2 = 1.0 - sumSigma2OverRij2; |
| 280 |
> |
Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; |
| 281 |
> |
}else { |
| 282 |
> |
RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 283 |
> |
Tij(0, 0) = constant; |
| 284 |
> |
Tij(1, 1) = constant; |
| 285 |
> |
Tij(2, 2) = constant; |
| 286 |
|
} |
| 287 |
+ |
B.setSubMatrix(i*3, j*3, Tij); |
| 288 |
+ |
} |
| 289 |
|
} |
| 290 |
< |
|
| 290 |
> |
|
| 291 |
|
//invert B Matrix |
| 292 |
|
invertMatrix(B, C); |
| 293 |
< |
|
| 293 |
> |
|
| 294 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 295 |
|
std::vector<Mat3x3d> U; |
| 296 |
|
for (int i = 0; i < nbeads; ++i) { |
| 297 |
< |
Mat3x3d currU; |
| 298 |
< |
currU.setupSkewMat(beads[i].pos); |
| 299 |
< |
U.push_back(currU); |
| 297 |
> |
Mat3x3d currU; |
| 298 |
> |
currU.setupSkewMat(beads[i].pos); |
| 299 |
> |
U.push_back(currU); |
| 300 |
|
} |
| 301 |
|
|
| 302 |
|
//calculate Xi matrix at arbitrary origin O |
| 306 |
|
|
| 307 |
|
//calculate the total volume |
| 308 |
|
|
| 309 |
< |
double volume = 0.0; |
| 309 |
> |
RealType volume = 0.0; |
| 310 |
|
for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) { |
| 311 |
< |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
| 311 |
> |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
| 312 |
|
} |
| 313 |
< |
|
| 313 |
> |
|
| 314 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
| 315 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 316 |
< |
Mat3x3d Cij; |
| 317 |
< |
C.getSubMatrix(i*3, j*3, Cij); |
| 315 |
> |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 316 |
> |
Mat3x3d Cij; |
| 317 |
> |
C.getSubMatrix(i*3, j*3, Cij); |
| 318 |
|
|
| 319 |
< |
Xitt += Cij; |
| 320 |
< |
Xitr += U[i] * Cij; |
| 321 |
< |
//Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
| 322 |
< |
Xirr += -U[i] * Cij * U[j]; |
| 323 |
< |
} |
| 319 |
> |
Xitt += Cij; |
| 320 |
> |
Xitr += U[i] * Cij; |
| 321 |
> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
| 322 |
> |
Xirr += -U[i] * Cij * U[j]; |
| 323 |
> |
} |
| 324 |
|
} |
| 325 |
< |
|
| 326 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 327 |
< |
Xitt *= convertConstant; |
| 328 |
< |
Xitr *= convertConstant; |
| 329 |
< |
Xirr *= convertConstant; |
| 330 |
< |
|
| 331 |
< |
double kt = OOPSEConstant::kB * temperature; |
| 332 |
< |
|
| 325 |
> |
// add the volume correction here: |
| 326 |
> |
Xirr += (6.0 * viscosity * volume) * I; |
| 327 |
> |
|
| 328 |
> |
Xitt *= PhysicalConstants::viscoConvert; |
| 329 |
> |
Xitr *= PhysicalConstants::viscoConvert; |
| 330 |
> |
Xirr *= PhysicalConstants::viscoConvert; |
| 331 |
> |
|
| 332 |
> |
RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
| 333 |
> |
|
| 334 |
|
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
| 335 |
|
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
| 336 |
|
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
| 337 |
< |
|
| 337 |
> |
|
| 338 |
|
const static Mat3x3d zeroMat(0.0); |
| 339 |
|
|
| 340 |
|
Mat3x3d XittInv(0.0); |
| 388 |
|
Ddrr = Dorr; |
| 389 |
|
Ddtr = Dotr + Dorr * Uod; |
| 390 |
|
|
| 391 |
< |
SquareMatrix<double, 6> Dd; |
| 391 |
> |
SquareMatrix<RealType, 6> Dd; |
| 392 |
|
Dd.setSubMatrix(0, 0, Ddtt); |
| 393 |
|
Dd.setSubMatrix(0, 3, Ddtr.transpose()); |
| 394 |
|
Dd.setSubMatrix(3, 0, Ddtr); |
| 395 |
|
Dd.setSubMatrix(3, 3, Ddrr); |
| 396 |
< |
SquareMatrix<double, 6> Xid; |
| 396 |
> |
SquareMatrix<RealType, 6> Xid; |
| 397 |
|
Ddtt *= kt; |
| 398 |
|
Ddtr *=kt; |
| 399 |
|
Ddrr *= kt; |
| 402 |
|
|
| 403 |
|
|
| 404 |
|
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
| 405 |
< |
//Xid /= OOPSEConstant::energyConvert; |
| 406 |
< |
Xid *= OOPSEConstant::kb * temperature; |
| 405 |
> |
//Xid /= PhysicalConstants::energyConvert; |
| 406 |
> |
Xid *= PhysicalConstants::kb * temperature; |
| 407 |
|
|
| 408 |
< |
cr.center = rod; |
| 410 |
< |
cr.D.setSubMatrix(0, 0, Ddtt); |
| 411 |
< |
cr.D.setSubMatrix(0, 3, Ddtr); |
| 412 |
< |
cr.D.setSubMatrix(3, 0, Ddtr); |
| 413 |
< |
cr.D.setSubMatrix(3, 3, Ddrr); |
| 414 |
< |
cr.Xi = Xid; |
| 408 |
> |
Mat6x6d Xi, D; |
| 409 |
|
|
| 410 |
+ |
cd->setCOR(rod); |
| 411 |
+ |
|
| 412 |
+ |
cd->setXi(Xid); |
| 413 |
+ |
|
| 414 |
+ |
D.setSubMatrix(0, 0, Ddtt); |
| 415 |
+ |
D.setSubMatrix(0, 3, Ddtr); |
| 416 |
+ |
D.setSubMatrix(3, 0, Ddtr); |
| 417 |
+ |
D.setSubMatrix(3, 3, Ddrr); |
| 418 |
+ |
|
| 419 |
+ |
cd->setD(D); |
| 420 |
+ |
|
| 421 |
|
std::cout << "viscosity = " << viscosity << std::endl; |
| 422 |
|
std::cout << "temperature = " << temperature << std::endl; |
| 423 |
|
std::cout << "center of diffusion :" << std::endl; |
| 424 |
|
std::cout << rod << std::endl; |
| 425 |
|
std::cout << "diffusion tensor at center of diffusion " << std::endl; |
| 426 |
< |
std::cout << "translation(A^2/fs) :" << std::endl; |
| 426 |
> |
std::cout << "translation(A^2 / fs) :" << std::endl; |
| 427 |
|
std::cout << Ddtt << std::endl; |
| 428 |
< |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
| 428 |
> |
std::cout << "translation-rotation(A / fs):" << std::endl; |
| 429 |
|
std::cout << Ddtr << std::endl; |
| 430 |
< |
std::cout << "rotation(A^4/fs):" << std::endl; |
| 430 |
> |
std::cout << "rotation(fs^-1):" << std::endl; |
| 431 |
|
std::cout << Ddrr << std::endl; |
| 432 |
|
|
| 433 |
|
std::cout << "resistance tensor at center of diffusion " << std::endl; |
| 443 |
|
Xid.getSubMatrix(3, 3, Xidrr); |
| 444 |
|
|
| 445 |
|
std::cout << Xidtt << std::endl; |
| 446 |
< |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 446 |
> |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 447 |
|
std::cout << Xidrt << std::endl; |
| 448 |
< |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 448 |
> |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 449 |
|
std::cout << Xidtr << std::endl; |
| 450 |
< |
std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
| 450 |
> |
std::cout << "rotation(kcal*fs*mol^-1):" << std::endl; |
| 451 |
|
std::cout << Xidrr << std::endl; |
| 452 |
|
|
| 453 |
|
return true; |
| 454 |
< |
|
| 455 |
< |
} |
| 454 |
> |
|
| 455 |
> |
} |
| 456 |
|
|
| 457 |
< |
|
| 453 |
< |
void ApproximationModel::writeBeads(std::ostream& os) { |
| 457 |
> |
void ApproximationModel::writeBeads(std::ostream& os) { |
| 458 |
|
std::vector<BeadParam>::iterator iter; |
| 459 |
|
os << beads_.size() << std::endl; |
| 460 |
|
os << "Generated by Hydro" << std::endl; |
| 461 |
|
for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
| 462 |
< |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
| 462 |
> |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
| 463 |
|
} |
| 464 |
< |
|
| 464 |
> |
|
| 465 |
> |
} |
| 466 |
|
} |
| 462 |
– |
|
| 463 |
– |
|
| 464 |
– |
|
| 465 |
– |
} |
