| 6 |
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* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "applications/hydrodynamics/ApproximationModel.hpp" |
| 44 |
|
#include "math/LU.hpp" |
| 45 |
|
#include "math/DynamicRectMatrix.hpp" |
| 46 |
|
#include "math/SquareMatrix3.hpp" |
| 47 |
< |
#include "utils/OOPSEConstant.hpp" |
| 47 |
> |
#include "utils/PhysicalConstants.hpp" |
| 48 |
|
#include "hydrodynamics/Sphere.hpp" |
| 49 |
|
#include "hydrodynamics/Ellipsoid.hpp" |
| 50 |
|
#include "applications/hydrodynamics/CompositeShape.hpp" |
| 51 |
|
#include "math/LU.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 53 |
< |
namespace oopse { |
| 53 |
> |
namespace OpenMD { |
| 54 |
|
/** |
| 55 |
|
* Reference: |
| 56 |
|
* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
| 73 |
|
bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
| 74 |
|
|
| 75 |
|
bool ret = true; |
| 76 |
< |
HydroProps cr; |
| 77 |
< |
HydroProps cd; |
| 76 |
> |
HydroProp* cr = new HydroProp(); |
| 77 |
> |
HydroProp* cd = new HydroProp(); |
| 78 |
|
calcHydroPropsAtCR(beads_, viscosity, temperature, cr); |
| 79 |
< |
//calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
| 79 |
> |
calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
| 80 |
|
setCR(cr); |
| 81 |
|
setCD(cd); |
| 81 |
– |
|
| 82 |
|
return true; |
| 83 |
|
} |
| 84 |
|
|
| 85 |
< |
bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProps& cr) { |
| 85 |
> |
bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cr) { |
| 86 |
|
|
| 87 |
< |
int nbeads = beads.size(); |
| 87 |
> |
unsigned int nbeads = beads.size(); |
| 88 |
|
DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
| 89 |
|
DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
| 90 |
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Mat3x3d I; |
| 103 |
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Mat3x3d tmpMat; |
| 104 |
|
tmpMat = outProduct(Rij, Rij) / rij2; |
| 105 |
|
RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 106 |
< |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 106 |
> |
RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; |
| 107 |
> |
RealType tmp2 = 1.0 - sumSigma2OverRij2; |
| 108 |
> |
Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; |
| 109 |
|
}else { |
| 110 |
|
RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 111 |
|
Tij(0, 0) = constant; |
| 121 |
|
|
| 122 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 123 |
|
std::vector<Mat3x3d> U; |
| 124 |
< |
for (int i = 0; i < nbeads; ++i) { |
| 124 |
> |
for (unsigned int i = 0; i < nbeads; ++i) { |
| 125 |
|
Mat3x3d currU; |
| 126 |
|
currU.setupSkewMat(beads[i].pos); |
| 127 |
|
U.push_back(currU); |
| 146 |
|
|
| 147 |
|
Xiott += Cij; |
| 148 |
|
Xiotr += U[i] * Cij; |
| 149 |
< |
//Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
| 149 |
> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
| 150 |
|
Xiorr += -U[i] * Cij * U[j]; |
| 151 |
|
} |
| 152 |
|
} |
| 153 |
+ |
|
| 154 |
+ |
// add the volume correction |
| 155 |
+ |
Xiorr += (RealType(6.0) * viscosity * volume) * I; |
| 156 |
|
|
| 157 |
< |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 158 |
< |
Xiott *= convertConstant; |
| 159 |
< |
Xiotr *= convertConstant; |
| 155 |
< |
Xiorr *= convertConstant; |
| 157 |
> |
Xiott *= PhysicalConstants::viscoConvert; |
| 158 |
> |
Xiotr *= PhysicalConstants::viscoConvert; |
| 159 |
> |
Xiorr *= PhysicalConstants::viscoConvert; |
| 160 |
|
|
| 157 |
– |
|
| 158 |
– |
|
| 161 |
|
Mat3x3d tmp; |
| 162 |
|
Mat3x3d tmpInv; |
| 163 |
|
Vector3d tmpVec; |
| 204 |
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Dr6x6.getSubMatrix(0, 3, Drrt); |
| 205 |
|
Dr6x6.getSubMatrix(3, 0, Drtr); |
| 206 |
|
Dr6x6.getSubMatrix(3, 3, Drrr); |
| 207 |
< |
RealType kt = OOPSEConstant::kB * temperature ; |
| 207 |
> |
RealType kt = PhysicalConstants::kb * temperature ; // in kcal mol^-1 |
| 208 |
|
Drtt *= kt; |
| 209 |
|
Drrt *= kt; |
| 210 |
|
Drtr *= kt; |
| 211 |
|
Drrr *= kt; |
| 212 |
< |
Xirtt *= OOPSEConstant::kb * temperature; |
| 213 |
< |
Xirtr *= OOPSEConstant::kb * temperature; |
| 214 |
< |
Xirrr *= OOPSEConstant::kb * temperature; |
| 212 |
> |
//Xirtt *= PhysicalConstants::kb * temperature; |
| 213 |
> |
//Xirtr *= PhysicalConstants::kb * temperature; |
| 214 |
> |
//Xirrr *= PhysicalConstants::kb * temperature; |
| 215 |
|
|
| 216 |
+ |
Mat6x6d Xi, D; |
| 217 |
|
|
| 218 |
< |
cr.center = ror; |
| 219 |
< |
cr.Xi.setSubMatrix(0, 0, Xirtt); |
| 220 |
< |
cr.Xi.setSubMatrix(0, 3, Xirtr); |
| 221 |
< |
cr.Xi.setSubMatrix(3, 0, Xirtr); |
| 222 |
< |
cr.Xi.setSubMatrix(3, 3, Xirrr); |
| 223 |
< |
cr.D.setSubMatrix(0, 0, Drtt); |
| 224 |
< |
cr.D.setSubMatrix(0, 3, Drrt); |
| 225 |
< |
cr.D.setSubMatrix(3, 0, Drtr); |
| 226 |
< |
cr.D.setSubMatrix(3, 3, Drrr); |
| 218 |
> |
cr->setCOR(ror); |
| 219 |
> |
|
| 220 |
> |
Xi.setSubMatrix(0, 0, Xirtt); |
| 221 |
> |
Xi.setSubMatrix(0, 3, Xirtr); |
| 222 |
> |
Xi.setSubMatrix(3, 0, Xirtr); |
| 223 |
> |
Xi.setSubMatrix(3, 3, Xirrr); |
| 224 |
> |
|
| 225 |
> |
cr->setXi(Xi); |
| 226 |
> |
|
| 227 |
> |
D.setSubMatrix(0, 0, Drtt); |
| 228 |
> |
D.setSubMatrix(0, 3, Drrt); |
| 229 |
> |
D.setSubMatrix(3, 0, Drtr); |
| 230 |
> |
D.setSubMatrix(3, 3, Drrr); |
| 231 |
> |
|
| 232 |
> |
cr->setD(D); |
| 233 |
|
|
| 234 |
|
std::cout << "-----------------------------------------\n"; |
| 235 |
|
std::cout << "center of resistance :" << std::endl; |
| 255 |
|
return true; |
| 256 |
|
} |
| 257 |
|
|
| 258 |
< |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProps& cr) { |
| 258 |
> |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) { |
| 259 |
|
|
| 260 |
< |
int nbeads = beads.size(); |
| 260 |
> |
unsigned int nbeads = beads.size(); |
| 261 |
|
DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
| 262 |
|
DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
| 263 |
|
Mat3x3d I; |
| 276 |
|
Mat3x3d tmpMat; |
| 277 |
|
tmpMat = outProduct(Rij, Rij) / rij2; |
| 278 |
|
RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; |
| 279 |
< |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 279 |
> |
RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; |
| 280 |
> |
RealType tmp2 = 1.0 - sumSigma2OverRij2; |
| 281 |
> |
Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; |
| 282 |
|
}else { |
| 283 |
|
RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); |
| 284 |
|
Tij(0, 0) = constant; |
| 294 |
|
|
| 295 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 296 |
|
std::vector<Mat3x3d> U; |
| 297 |
< |
for (int i = 0; i < nbeads; ++i) { |
| 297 |
> |
for (unsigned int i = 0; i < nbeads; ++i) { |
| 298 |
|
Mat3x3d currU; |
| 299 |
|
currU.setupSkewMat(beads[i].pos); |
| 300 |
|
U.push_back(currU); |
| 319 |
|
|
| 320 |
|
Xitt += Cij; |
| 321 |
|
Xitr += U[i] * Cij; |
| 322 |
< |
//Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
| 322 |
> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
| 323 |
|
Xirr += -U[i] * Cij * U[j]; |
| 324 |
|
} |
| 325 |
|
} |
| 326 |
+ |
// add the volume correction here: |
| 327 |
+ |
Xirr += (RealType(6.0) * viscosity * volume) * I; |
| 328 |
|
|
| 329 |
< |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 330 |
< |
Xitt *= convertConstant; |
| 331 |
< |
Xitr *= convertConstant; |
| 319 |
< |
Xirr *= convertConstant; |
| 329 |
> |
Xitt *= PhysicalConstants::viscoConvert; |
| 330 |
> |
Xitr *= PhysicalConstants::viscoConvert; |
| 331 |
> |
Xirr *= PhysicalConstants::viscoConvert; |
| 332 |
|
|
| 333 |
< |
RealType kt = OOPSEConstant::kB * temperature; |
| 333 |
> |
RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
| 334 |
|
|
| 335 |
|
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
| 336 |
|
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
| 403 |
|
|
| 404 |
|
|
| 405 |
|
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
| 406 |
< |
//Xid /= OOPSEConstant::energyConvert; |
| 407 |
< |
Xid *= OOPSEConstant::kb * temperature; |
| 406 |
> |
//Xid /= PhysicalConstants::energyConvert; |
| 407 |
> |
Xid *= PhysicalConstants::kb * temperature; |
| 408 |
|
|
| 409 |
< |
cr.center = rod; |
| 398 |
< |
cr.D.setSubMatrix(0, 0, Ddtt); |
| 399 |
< |
cr.D.setSubMatrix(0, 3, Ddtr); |
| 400 |
< |
cr.D.setSubMatrix(3, 0, Ddtr); |
| 401 |
< |
cr.D.setSubMatrix(3, 3, Ddrr); |
| 402 |
< |
cr.Xi = Xid; |
| 409 |
> |
Mat6x6d Xi, D; |
| 410 |
|
|
| 411 |
+ |
cd->setCOR(rod); |
| 412 |
+ |
|
| 413 |
+ |
cd->setXi(Xid); |
| 414 |
+ |
|
| 415 |
+ |
D.setSubMatrix(0, 0, Ddtt); |
| 416 |
+ |
D.setSubMatrix(0, 3, Ddtr); |
| 417 |
+ |
D.setSubMatrix(3, 0, Ddtr); |
| 418 |
+ |
D.setSubMatrix(3, 3, Ddrr); |
| 419 |
+ |
|
| 420 |
+ |
cd->setD(D); |
| 421 |
+ |
|
| 422 |
|
std::cout << "viscosity = " << viscosity << std::endl; |
| 423 |
|
std::cout << "temperature = " << temperature << std::endl; |
| 424 |
|
std::cout << "center of diffusion :" << std::endl; |
| 425 |
|
std::cout << rod << std::endl; |
| 426 |
|
std::cout << "diffusion tensor at center of diffusion " << std::endl; |
| 427 |
< |
std::cout << "translation(A^2/fs) :" << std::endl; |
| 427 |
> |
std::cout << "translation(A^2 / fs) :" << std::endl; |
| 428 |
|
std::cout << Ddtt << std::endl; |
| 429 |
< |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
| 429 |
> |
std::cout << "translation-rotation(A / fs):" << std::endl; |
| 430 |
|
std::cout << Ddtr << std::endl; |
| 431 |
< |
std::cout << "rotation(A^4/fs):" << std::endl; |
| 431 |
> |
std::cout << "rotation(fs^-1):" << std::endl; |
| 432 |
|
std::cout << Ddrr << std::endl; |
| 433 |
|
|
| 434 |
|
std::cout << "resistance tensor at center of diffusion " << std::endl; |
| 444 |
|
Xid.getSubMatrix(3, 3, Xidrr); |
| 445 |
|
|
| 446 |
|
std::cout << Xidtt << std::endl; |
| 447 |
< |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 447 |
> |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 448 |
|
std::cout << Xidrt << std::endl; |
| 449 |
< |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 449 |
> |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 450 |
|
std::cout << Xidtr << std::endl; |
| 451 |
< |
std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
| 451 |
> |
std::cout << "rotation(kcal*fs*mol^-1):" << std::endl; |
| 452 |
|
std::cout << Xidrr << std::endl; |
| 453 |
|
|
| 454 |
|
return true; |
