applications/hydrodynamics/HydrodynamicsModel.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include "applications/hydrodynamics/HydrodynamicsModel.hpp" 
#include "math/LU.hpp"
#include "math/DynamicRectMatrix.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/OOPSEConstant.hpp"
namespace oopse {
/**
 * Reference:
 * Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles:
 * Comparison of Different Modeling and Computational Procedures. 
 * Biophysical Journal, 75(6), 3044, 1999
 */

HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){
    DynamicProperty::const_iterator iter;

    iter = extraParams.find("Viscosity");
    if (iter != extraParams.end()) {
        boost::any param = iter->second;
        viscosity_ = boost::any_cast<double>(param);
    }else {
        std::cout << "HydrodynamicsModel Error\n" ;
    }

    iter = extraParams.find("Temperature");
    if (iter != extraParams.end()) {
        boost::any param = iter->second;
        temperature_ = boost::any_cast<double>(param);
    }else {
        std::cout << "HydrodynamicsModel Error\n" ;
    }    
}
 
bool HydrodynamicsModel::calcHydrodyanmicsProps() {
    if (!createBeads(beads_)) {
        std::cout << "can not create beads" << std::endl;
        return false;
    }

    //calcResistanceTensor();
    calcDiffusionTensor();    
    return true;    
}

void HydrodynamicsModel::calcResistanceTensor() {
}

void HydrodynamicsModel::calcDiffusionTensor() {
    int nbeads = beads_.size();
    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
    Mat3x3d I;
    I(0, 0) = 1.0;
    I(1, 1) = 1.0;
    I(2, 2) = 1.0;
    
    for (std::size_t i = 0; i < nbeads; ++i) {
        for (std::size_t j = 0; j < nbeads; ++j) {
            Mat3x3d Tij;
            if (i != j ) {
                Vector3d Rij = beads_[i].pos - beads_[j].pos;
                double rij = Rij.length();
                double rij2 = rij * rij;
                double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2;                
                Mat3x3d tmpMat;
                tmpMat = outProduct(Rij, Rij) / rij2;
                double constant = 8.0 * NumericConstant::PI * viscosity_ * rij;
                Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
            }else {
                double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius);
                Tij(0, 0) = constant;
                Tij(1, 1) = constant;
                Tij(2, 2) = constant;
            }
            B.setSubMatrix(i*3, j*3, Tij);
        }
    }

    //invert B Matrix
    invertMatrix(B, C);

    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
    std::vector<Mat3x3d> U;
    for (int i = 0; i < nbeads; ++i) {
        Mat3x3d currU;
        currU.setupSkewMat(beads_[i].pos);
        U.push_back(currU);
    }
    
    //calculate Xi matrix at arbitrary origin O
    Mat3x3d Xitt;
    Mat3x3d Xirr;
    Mat3x3d Xitr;

    //calculate the total volume

    double volume = 0.0;
    for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) {
        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
    }
        
    for (std::size_t i = 0; i < nbeads; ++i) {
        for (std::size_t j = 0; j < nbeads; ++j) {
            Mat3x3d Cij;
            C.getSubMatrix(i*3, j*3, Cij);
            
            Xitt += Cij;
            Xitr += U[i] * Cij;
            Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I;            
        }
    }

    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
    Xitt *= convertConstant;
    Xitr *= convertConstant;
    Xirr *= convertConstant;

    double kt = OOPSEConstant::kB * temperature_;

    Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
    Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
    Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O

    const static Mat3x3d zeroMat(0.0);
    
    Mat3x3d XittInv(0.0);
    XittInv = Xitt.inverse();
    
    Mat3x3d XirrInv;
    XirrInv = Xirr.inverse();

    Mat3x3d tmp;
    Mat3x3d tmpInv;
    tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
    tmpInv = tmp.inverse();

    Dott = tmpInv;
    Dotr = -XirrInv * Xitr * tmpInv;
    
    tmp = Xirr - Xitr * XittInv * Xitr.transpose();    
    tmpInv = tmp.inverse();
    
    Dorr = tmpInv;

    //calculate center of diffusion
    tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2);
    tmp(0, 1) = - Dorr(0, 1);
    tmp(0, 2) = -Dorr(0, 2);
    tmp(1, 0) = -Dorr(0, 1);
    tmp(1, 1) = Dorr(0, 0)  + Dorr(2, 2);
    tmp(1, 2) = -Dorr(1, 2);
    tmp(2, 0) = -Dorr(0, 2);
    tmp(2, 1) = -Dorr(1, 2);
    tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0);

    Vector3d tmpVec;
    tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
    tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
    tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);

    tmpInv = tmp.inverse();
    
    Vector3d rod = tmpInv * tmpVec;

    //calculate Diffusion Tensor at center of diffusion
    Mat3x3d Uod;
    Uod.setupSkewMat(rod);
    
    Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
    Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
    Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
    
    Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
    Ddrr = Dorr;
    Ddtr = Dotr + Dorr * Uod;

    SquareMatrix<double, 6> Dd;
    Dd.setSubMatrix(0, 0, Ddtt);
    Dd.setSubMatrix(0, 3, Ddtr.transpose());
    Dd.setSubMatrix(3, 0, Ddtr);
    Dd.setSubMatrix(3, 3, Ddrr);    
    SquareMatrix<double, 6> Xid;
    Ddtt *= kt;
    Ddtr *=kt;
    Ddrr *= kt;
    invertMatrix(Dd, Xid);


    //Xidtt in units of kcal*fs*mol^-1*Ang^-2
    //Xid /= OOPSEConstant::energyConvert;
    Xid *= OOPSEConstant::kb * temperature_;
    props_.diffCenter = rod;
    props_.Ddtt = Ddtt;
    props_.Ddtr = Ddtr;
    props_.Ddrr = Ddrr;
    Xid.getSubMatrix(0, 0, props_.Xidtt);
    Xid.getSubMatrix(0, 3, props_.Xidrt);
    Xid.getSubMatrix(3, 0, props_.Xidtr);
    Xid.getSubMatrix(3, 3, props_.Xidrr);


    std::cout << "viscosity = " << viscosity_ << std::endl;
    std::cout << "temperature = " << temperature_ << std::endl;
    std::cout << "center of diffusion :" << std::endl;
    std::cout << rod << std::endl;
    std::cout << "diffusion tensor at center of diffusion " << std::endl;
    std::cout << "translation(A^2/fs) :" << std::endl;
    std::cout << Ddtt << std::endl;
    std::cout << "translation-rotation(A^3/fs):" << std::endl;
    std::cout << Ddtr << std::endl;
    std::cout << "rotation(A^4/fs):" << std::endl;
    std::cout << Ddrr << std::endl;

    std::cout << "resistance tensor at center of diffusion " << std::endl;
    std::cout << "translation(kcal*fs*mol^-1*Ang^-2) :" << std::endl;
    std::cout << props_.Xidtt << std::endl;
    std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl;
    std::cout << props_.Xidrt << std::endl;
    std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl;
    std::cout << props_.Xidtr << std::endl;
    std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl;
    std::cout << props_.Xidrr << std::endl;
    
      
}

void HydrodynamicsModel::writeBeads(std::ostream& os) {
    std::vector<BeadParam>::iterator iter;
    os << beads_.size() << std::endl;
    os << "Generated by Hydro" << std::endl;
    for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
        os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
    }

}

void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {

    os << sd_->getType() << "\t";
    os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t";

    os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t"
        << props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t"
        << props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t";
    
    os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t"
        << props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t"
        << props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t";

    os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t"
        << props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t"
        << props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t";        

    os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t"
        << props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t"
        << props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t";

    os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t"
        << props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t"
        << props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t";
    
    os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t"
        << props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t"
        << props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t";

    os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t"
        << props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t"
        << props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl;
    
}

}
Revision:	904
Committed:	Thu Mar 16 22:50:48 2006 UTC (19 years, 7 months ago) by tim
Original Path:	*trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp*
File size:	12099 byte(s)
Log Message:	LagevinDynamics is working?
#	User	Rev	Content
1	tim	891	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
43			#include "math/LU.hpp"
44			#include "math/DynamicRectMatrix.hpp"
45			#include "math/SquareMatrix3.hpp"
46	tim	892	#include "utils/OOPSEConstant.hpp"
47	tim	891	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			*/
54	tim	892
55			HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){
56			DynamicProperty::const_iterator iter;
57
58			iter = extraParams.find("Viscosity");
59			if (iter != extraParams.end()) {
60			boost::any param = iter->second;
61			viscosity_ = boost::any_cast<double>(param);
62			}else {
63			std::cout << "HydrodynamicsModel Error\n" ;
64			}
65
66			iter = extraParams.find("Temperature");
67			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			}
73			}
74
75			bool HydrodynamicsModel::calcHydrodyanmicsProps() {
76	tim	891	if (!createBeads(beads_)) {
77			std::cout << "can not create beads" << std::endl;
78			return false;
79			}
80	tim	895
81			//calcResistanceTensor();
82	tim	900	calcDiffusionTensor();
83	tim	891	return true;
84			}
85
86	tim	895	void HydrodynamicsModel::calcResistanceTensor() {
87			}
88
89			void HydrodynamicsModel::calcDiffusionTensor() {
90			int nbeads = beads_.size();
91			DynamicRectMatrix<double> B(3nbeads, 3nbeads);
92			DynamicRectMatrix<double> C(3nbeads, 3nbeads);
93			Mat3x3d I;
94			I(0, 0) = 1.0;
95			I(1, 1) = 1.0;
96			I(2, 2) = 1.0;
97
98			for (std::size_t i = 0; i < nbeads; ++i) {
99			for (std::size_t j = 0; j < nbeads; ++j) {
100			Mat3x3d Tij;
101			if (i != j ) {
102			Vector3d Rij = beads_[i].pos - beads_[j].pos;
103			double rij = Rij.length();
104			double rij2 = rij * rij;
105			double sumSigma2OverRij2 = ((beads_[i].radiusbeads_[i].radius) + (beads_[i].radiusbeads_[i].radius)) / rij2;
106			Mat3x3d tmpMat;
107			tmpMat = outProduct(Rij, Rij) / rij2;
108			double constant = 8.0 * NumericConstant::PI * viscosity_ * rij;
109			Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
110			}else {
111			double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius);
112			Tij(0, 0) = constant;
113			Tij(1, 1) = constant;
114			Tij(2, 2) = constant;
115			}
116			B.setSubMatrix(i3, j3, Tij);
117			}
118			}
119
120			//invert B Matrix
121			invertMatrix(B, C);
122
123			//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
124			std::vector<Mat3x3d> U;
125			for (int i = 0; i < nbeads; ++i) {
126			Mat3x3d currU;
127			currU.setupSkewMat(beads_[i].pos);
128			U.push_back(currU);
129			}
130
131			//calculate Xi matrix at arbitrary origin O
132			Mat3x3d Xitt;
133			Mat3x3d Xirr;
134			Mat3x3d Xitr;
135
136			//calculate the total volume
137
138			double volume = 0.0;
139			for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) {
140			volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
141			}
142
143			for (std::size_t i = 0; i < nbeads; ++i) {
144			for (std::size_t j = 0; j < nbeads; ++j) {
145			Mat3x3d Cij;
146			C.getSubMatrix(i3, j3, Cij);
147
148			Xitt += Cij;
149			Xitr += U[i] * Cij;
150			Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I;
151			}
152			}
153
154	tim	900	const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
155			Xitt *= convertConstant;
156			Xitr *= convertConstant;
157			Xirr *= convertConstant;
158	tim	895
159	tim	900	double kt = OOPSEConstant::kB * temperature_;
160	tim	895
161			Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
162			Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
163			Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
164
165			const static Mat3x3d zeroMat(0.0);
166
167			Mat3x3d XittInv(0.0);
168			XittInv = Xitt.inverse();
169
170			Mat3x3d XirrInv;
171			XirrInv = Xirr.inverse();
172
173			Mat3x3d tmp;
174			Mat3x3d tmpInv;
175			tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
176			tmpInv = tmp.inverse();
177
178	tim	901	Dott = tmpInv;
179			Dotr = -XirrInv * Xitr * tmpInv;
180	tim	895
181			tmp = Xirr - Xitr * XittInv * Xitr.transpose();
182			tmpInv = tmp.inverse();
183
184	tim	901	Dorr = tmpInv;
185	tim	900
186	tim	895	//calculate center of diffusion
187			tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2);
188			tmp(0, 1) = - Dorr(0, 1);
189			tmp(0, 2) = -Dorr(0, 2);
190			tmp(1, 0) = -Dorr(0, 1);
191			tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2);
192			tmp(1, 2) = -Dorr(1, 2);
193			tmp(2, 0) = -Dorr(0, 2);
194			tmp(2, 1) = -Dorr(1, 2);
195			tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0);
196
197			Vector3d tmpVec;
198			tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
199			tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
200			tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);
201
202			tmpInv = tmp.inverse();
203
204			Vector3d rod = tmpInv * tmpVec;
205
206			//calculate Diffusion Tensor at center of diffusion
207			Mat3x3d Uod;
208			Uod.setupSkewMat(rod);
209
210			Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
211			Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
212			Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
213
214			Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
215			Ddrr = Dorr;
216			Ddtr = Dotr + Dorr * Uod;
217
218			SquareMatrix<double, 6> Dd;
219			Dd.setSubMatrix(0, 0, Ddtt);
220			Dd.setSubMatrix(0, 3, Ddtr.transpose());
221			Dd.setSubMatrix(3, 0, Ddtr);
222			Dd.setSubMatrix(3, 3, Ddrr);
223			SquareMatrix<double, 6> Xid;
224	tim	901	Ddtt *= kt;
225			Ddtr *=kt;
226			Ddrr *= kt;
227	tim	904	invertMatrix(Dd, Xid);
228	tim	901
229	tim	904
230
231	tim	900	//Xidtt in units of kcalfsmol^-1*Ang^-2
232	tim	904	//Xid /= OOPSEConstant::energyConvert;
233			Xid = OOPSEConstant::kb temperature_;
234	tim	902	props_.diffCenter = rod;
235			props_.Ddtt = Ddtt;
236			props_.Ddtr = Ddtr;
237			props_.Ddrr = Ddrr;
238	tim	895	Xid.getSubMatrix(0, 0, props_.Xidtt);
239			Xid.getSubMatrix(0, 3, props_.Xidrt);
240			Xid.getSubMatrix(3, 0, props_.Xidtr);
241			Xid.getSubMatrix(3, 3, props_.Xidrr);
242
243	tim	900
244	tim	901	std::cout << "viscosity = " << viscosity_ << std::endl;
245			std::cout << "temperature = " << temperature_ << std::endl;
246	tim	895	std::cout << "center of diffusion :" << std::endl;
247			std::cout << rod << std::endl;
248	tim	900	std::cout << "diffusion tensor at center of diffusion " << std::endl;
249			std::cout << "translation(A^2/fs) :" << std::endl;
250	tim	895	std::cout << Ddtt << std::endl;
251	tim	900	std::cout << "translation-rotation(A^3/fs):" << std::endl;
252	tim	895	std::cout << Ddtr << std::endl;
253	tim	900	std::cout << "rotation(A^4/fs):" << std::endl;
254	tim	895	std::cout << Ddrr << std::endl;
255	tim	900
256			std::cout << "resistance tensor at center of diffusion " << std::endl;
257			std::cout << "translation(kcalfsmol^-1*Ang^-2) :" << std::endl;
258			std::cout << props_.Xidtt << std::endl;
259			std::cout << "rotation-translation (kcalfsmol^-1*Ang^-3):" << std::endl;
260			std::cout << props_.Xidrt << std::endl;
261			std::cout << "translation-rotation(kcalfsmol^-1*Ang^-3):" << std::endl;
262			std::cout << props_.Xidtr << std::endl;
263			std::cout << "rotation(kcalfsmol^-1*Ang^-4):" << std::endl;
264			std::cout << props_.Xidrr << std::endl;
265
266	tim	895
267			}
268
269	tim	891	void HydrodynamicsModel::writeBeads(std::ostream& os) {
270	tim	892	std::vector<BeadParam>::iterator iter;
271			os << beads_.size() << std::endl;
272			os << "Generated by Hydro" << std::endl;
273			for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
274			os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
275			}
276	tim	891
277			}
278
279			void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {
280
281	tim	895	os << sd_->getType() << "\t";
282			os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t";
283	tim	892
284	tim	895	os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t"
285			<< props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t"
286			<< props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t";
287
288			os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t"
289			<< props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t"
290			<< props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t";
291	tim	892
292	tim	895	os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t"
293			<< props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t"
294			<< props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t";
295	tim	892
296	tim	895	os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t"
297			<< props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t"
298			<< props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t";
299
300			os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t"
301			<< props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t"
302			<< props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t";
303	tim	892
304	tim	895	os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t"
305			<< props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t"
306			<< props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t";
307	tim	892
308	tim	895	os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t"
309			<< props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t"
310			<< props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl;
311	tim	892
312	tim	891	}
313
314			}