src/integrators/LDForceManager.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 <fstream> 
#include "integrators/LDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/OOPSEConstant.hpp"
namespace oopse {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
    Globals* simParams = info->getSimParams();
    std::map<std::string, HydroProp> hydroPropMap;
    if (simParams->haveHydroPropFile()) {
        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
    } else {
        //error
    }

    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
              integrableObject = mol->nextIntegrableObject(j)) {
            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
            if (iter != hydroPropMap.end()) {
                hydroProps_.push_back(iter->second);
            } else {
                //error
            }
            
           }
    }
    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
  }
  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
    std::map<std::string, HydroProp> props;
    std::ifstream ifs(filename.c_str());
    if (ifs.is_open()) {

    }

    const unsigned int BufferSize = 65535;
    char buffer[BufferSize];   
    while (ifs.getline(buffer, BufferSize)) {
        StringTokenizer tokenizer(buffer);
        HydroProp currProp;
        if (tokenizer.countTokens() >= 67) {
            std::string atomName = tokenizer.nextToken();
            currProp.cod[0] = tokenizer.nextTokenAsDouble();
            currProp.cod[1] = tokenizer.nextTokenAsDouble();
            currProp.cod[2] = tokenizer.nextTokenAsDouble();

            currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();                

            currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
            
            currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble(); 
            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
        }
    }

    return props;
  }
  
  void LDForceManager::postCalculation() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Mat3x3d A;
    Mat3x3d Atrans;
    Vector3d Tb;
    Vector3d ji;
    double mass;
    unsigned int index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

          vel =integrableObject->getVel(); 
          if (integrableObject->isDirectional()){
             //calculate angular velocity in lab frame
             Mat3x3d I = integrableObject->getI();
             Vector3d angMom = integrableObject->getJ();
             Vector3d omega;

             if (integrableObject->isLinear()) {
                int linearAxis = integrableObject->linearAxis();
                int l = (linearAxis +1 )%3;
                int m = (linearAxis +2 )%3;
                omega[l] = angMom[l] /I(l, l);
                omega[m] = angMom[m] /I(m, m);
                
             } else {
                 omega[0] = angMom[0] /I(0, 0);
                 omega[1] = angMom[1] /I(1, 1);
                 omega[2] = angMom[2] /I(2, 2);
             }

             //apply friction force and torque at center of diffusion
             A = integrableObject->getA();
             Atrans = A.transpose();
             Vector3d rcd = Atrans * hydroProps_[index].cod;  
             Vector3d vcd = vel + cross(omega, rcd);
             vcd = A* vcd;
             Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
             frictionForce = Atrans*frictionForce;
             integrableObject->addFrc(frictionForce);
             Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
             frictionTorque = Atrans*frictionTorque;
             integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
             
             //apply random force and torque at center of diffustion
             Vector3d randomForce;
             Vector3d randomTorque;
             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
             randomForce = Atrans*randomForce;
             randomTorque = Atrans* randomTorque;
             integrableObject->addFrc(randomForce);            
             integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
             
          } else {
             //spheric atom
             Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);     
             Vector3d randomForce;
             Vector3d randomTorque;
             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);

             //randomForce /= OOPSEConstant::energyConvert;
             //randomTorque /= OOPSEConstant::energyConvert;
             integrableObject->addFrc(frictionForce+randomForce);             
          }

        ++index;
    
      }
    }    

    ForceManager::postCalculation();


  }

void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
    /*
    SquareMatrix<double, 6> Dd;
    SquareMatrix<double, 6> S;
    Vector<double, 6> Z;
    Vector<double, 6> generalForce;
    Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
    Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
    Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
    Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
    CholeskyDecomposition(Dd, S);
    */

    SquareMatrix<double, 6> Xid;
    SquareMatrix<double, 6> S;
    Vector<double, 6> Z;
    Vector<double, 6> generalForce;
    Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt);
    Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt);
    Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr);
    Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr);
    CholeskyDecomposition(Xid, S);

    /*
    Xid *= variance;
    Z[0] = randNumGen_.randNorm(0, 1.0);
    Z[1] = randNumGen_.randNorm(0, 1.0);
    Z[2] = randNumGen_.randNorm(0, 1.0);
    Z[3] = randNumGen_.randNorm(0, 1.0);
    Z[4] = randNumGen_.randNorm(0, 1.0);
    Z[5] = randNumGen_.randNorm(0, 1.0);
    */
        
    Z[0] = randNumGen_.randNorm(0, variance);
    Z[1] = randNumGen_.randNorm(0, variance);
    Z[2] = randNumGen_.randNorm(0, variance);
    Z[3] = randNumGen_.randNorm(0, variance);
    Z[4] = randNumGen_.randNorm(0, variance);
    Z[5] = randNumGen_.randNorm(0, variance);
     

    generalForce = S*Z;
    
    force[0] = generalForce[0];
    force[1] = generalForce[1];
    force[2] = generalForce[2];
    torque[0] = generalForce[3];
    torque[1] = generalForce[4];
    torque[2] = generalForce[5];
    
}

}
Revision:	904
Committed:	Thu Mar 16 22:50:48 2006 UTC (19 years, 1 month ago) by tim
Original Path:	*trunk/src/integrators/LDForceManager.cpp*
File size:	13095 byte(s)
Log Message:	LagevinDynamics is working?
#	User	Rev	Content
1	tim	895	/*
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			#include <fstream>
42			#include "integrators/LDForceManager.hpp"
43			#include "math/CholeskyDecomposition.hpp"
44	tim	904	#include "utils/OOPSEConstant.hpp"
45	tim	895	namespace oopse {
46
47			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
48			Globals* simParams = info->getSimParams();
49			std::map<std::string, HydroProp> hydroPropMap;
50			if (simParams->haveHydroPropFile()) {
51			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
52			} else {
53			//error
54			}
55
56			SimInfo::MoleculeIterator i;
57			Molecule::IntegrableObjectIterator j;
58			Molecule* mol;
59			StuntDouble* integrableObject;
60			for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
61			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
62			integrableObject = mol->nextIntegrableObject(j)) {
63			std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
64			if (iter != hydroPropMap.end()) {
65			hydroProps_.push_back(iter->second);
66			} else {
67			//error
68			}
69
70			}
71			}
72	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
73	tim	895	}
74			std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
75			std::map<std::string, HydroProp> props;
76			std::ifstream ifs(filename.c_str());
77			if (ifs.is_open()) {
78
79			}
80
81			const unsigned int BufferSize = 65535;
82			char buffer[BufferSize];
83			while (ifs.getline(buffer, BufferSize)) {
84			StringTokenizer tokenizer(buffer);
85			HydroProp currProp;
86			if (tokenizer.countTokens() >= 67) {
87			std::string atomName = tokenizer.nextToken();
88			currProp.cod[0] = tokenizer.nextTokenAsDouble();
89			currProp.cod[1] = tokenizer.nextTokenAsDouble();
90			currProp.cod[2] = tokenizer.nextTokenAsDouble();
91
92			currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
93			currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
94			currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
95			currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
96			currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
97			currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
98			currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
99			currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
100			currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
101
102			currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
103			currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
104			currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
105			currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
106			currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
107			currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
108			currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
109			currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
110			currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
111
112			currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
113			currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
114			currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
115			currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
116			currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
117			currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
118			currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
119			currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
120			currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
121
122			currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
123			currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
124			currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
125			currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
126			currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
127			currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
128			currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
129			currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
130			currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
131
132			currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
133			currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
134			currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
135			currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
136			currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
137			currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
138			currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
139			currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
140			currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
141
142			currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
143			currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
144			currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
145			currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
146			currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
147			currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
148			currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
149			currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
150			currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();
151
152			currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
153			currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
154			currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
155			currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
156			currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
157			currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
158			currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
159			currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
160			currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
161			props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
162			}
163			}
164
165			return props;
166			}
167
168			void LDForceManager::postCalculation() {
169			SimInfo::MoleculeIterator i;
170			Molecule::IntegrableObjectIterator j;
171			Molecule* mol;
172			StuntDouble* integrableObject;
173			Vector3d vel;
174			Vector3d pos;
175			Vector3d frc;
176			Mat3x3d A;
177	tim	904	Mat3x3d Atrans;
178	tim	895	Vector3d Tb;
179			Vector3d ji;
180			double mass;
181			unsigned int index = 0;
182			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184			integrableObject = mol->nextIntegrableObject(j)) {
185
186			vel =integrableObject->getVel();
187			if (integrableObject->isDirectional()){
188			//calculate angular velocity in lab frame
189			Mat3x3d I = integrableObject->getI();
190			Vector3d angMom = integrableObject->getJ();
191			Vector3d omega;
192
193			if (integrableObject->isLinear()) {
194			int linearAxis = integrableObject->linearAxis();
195			int l = (linearAxis +1 )%3;
196			int m = (linearAxis +2 )%3;
197			omega[l] = angMom[l] /I(l, l);
198			omega[m] = angMom[m] /I(m, m);
199
200			} else {
201			omega[0] = angMom[0] /I(0, 0);
202			omega[1] = angMom[1] /I(1, 1);
203			omega[2] = angMom[2] /I(2, 2);
204			}
205
206			//apply friction force and torque at center of diffusion
207			A = integrableObject->getA();
208	tim	904	Atrans = A.transpose();
209			Vector3d rcd = Atrans * hydroProps_[index].cod;
210	tim	895	Vector3d vcd = vel + cross(omega, rcd);
211	tim	904	vcd = A* vcd;
212	tim	895	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
213	tim	904	frictionForce = Atrans*frictionForce;
214	tim	895	integrableObject->addFrc(frictionForce);
215			Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
216	tim	904	frictionTorque = Atrans*frictionTorque;
217			integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
218	tim	895
219			//apply random force and torque at center of diffustion
220			Vector3d randomForce;
221			Vector3d randomTorque;
222			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
223	tim	904	randomForce = Atrans*randomForce;
224			randomTorque = Atrans* randomTorque;
225			integrableObject->addFrc(randomForce);
226	tim	895	integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
227
228			} else {
229			//spheric atom
230			Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
231			Vector3d randomForce;
232			Vector3d randomTorque;
233			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
234	tim	904
235			//randomForce /= OOPSEConstant::energyConvert;
236			//randomTorque /= OOPSEConstant::energyConvert;
237	tim	895	integrableObject->addFrc(frictionForce+randomForce);
238			}
239
240			++index;
241
242			}
243			}
244
245			ForceManager::postCalculation();
246
247
248
249			}
250
251			void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
252	tim	904	/*
253	tim	895	SquareMatrix<double, 6> Dd;
254			SquareMatrix<double, 6> S;
255			Vector<double, 6> Z;
256			Vector<double, 6> generalForce;
257			Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
258			Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
259			Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
260			Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
261			CholeskyDecomposition(Dd, S);
262	tim	904	*/
263
264			SquareMatrix<double, 6> Xid;
265			SquareMatrix<double, 6> S;
266			Vector<double, 6> Z;
267			Vector<double, 6> generalForce;
268			Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt);
269			Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt);
270			Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr);
271			Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr);
272			CholeskyDecomposition(Xid, S);
273
274			/*
275			Xid *= variance;
276			Z[0] = randNumGen_.randNorm(0, 1.0);
277			Z[1] = randNumGen_.randNorm(0, 1.0);
278			Z[2] = randNumGen_.randNorm(0, 1.0);
279			Z[3] = randNumGen_.randNorm(0, 1.0);
280			Z[4] = randNumGen_.randNorm(0, 1.0);
281			Z[5] = randNumGen_.randNorm(0, 1.0);
282			*/
283
284	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
285			Z[1] = randNumGen_.randNorm(0, variance);
286			Z[2] = randNumGen_.randNorm(0, variance);
287			Z[3] = randNumGen_.randNorm(0, variance);
288			Z[4] = randNumGen_.randNorm(0, variance);
289			Z[5] = randNumGen_.randNorm(0, variance);
290	tim	904
291
292	tim	895	generalForce = S*Z;
293	tim	904
294	tim	895	force[0] = generalForce[0];
295			force[1] = generalForce[1];
296			force[2] = generalForce[2];
297			torque[0] = generalForce[3];
298			torque[1] = generalForce[4];
299			torque[2] = generalForce[5];
300
301			}
302
303			}