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"
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*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;
    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();
             Vector3d rcd = A.transpose() * hydroProps_[index].cod;  
             Vector3d vcd = vel + cross(omega, rcd);
             Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
             integrableObject->addFrc(frictionForce);
             Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
             integrableObject->addTrq(frictionTorque);
             
             //apply random force and torque at center of diffustion
             Vector3d randomForce;
             Vector3d randomTorque;
             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
             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_);
             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);
    
    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:	2611
Committed:	Mon Mar 13 22:42:40 2006 UTC (18 years, 3 months ago) by tim
File size:	11894 byte(s)
Log Message:	LangevinDynamics in progress
#	User	Rev	Content
1	tim	2611	/*
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			namespace oopse {
45
46			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
47			Globals* simParams = info->getSimParams();
48			std::map<std::string, HydroProp> hydroPropMap;
49			if (simParams->haveHydroPropFile()) {
50			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
51			} else {
52			//error
53			}
54
55			SimInfo::MoleculeIterator i;
56			Molecule::IntegrableObjectIterator j;
57			Molecule* mol;
58			StuntDouble* integrableObject;
59			for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
60			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
61			integrableObject = mol->nextIntegrableObject(j)) {
62			std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
63			if (iter != hydroPropMap.end()) {
64			hydroProps_.push_back(iter->second);
65			} else {
66			//error
67			}
68
69			}
70			}
71			variance_ = 2.0*simParams->getDt();
72			}
73			std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
74			std::map<std::string, HydroProp> props;
75			std::ifstream ifs(filename.c_str());
76			if (ifs.is_open()) {
77
78			}
79
80			const unsigned int BufferSize = 65535;
81			char buffer[BufferSize];
82			while (ifs.getline(buffer, BufferSize)) {
83			StringTokenizer tokenizer(buffer);
84			HydroProp currProp;
85			if (tokenizer.countTokens() >= 67) {
86			std::string atomName = tokenizer.nextToken();
87			currProp.cod[0] = tokenizer.nextTokenAsDouble();
88			currProp.cod[1] = tokenizer.nextTokenAsDouble();
89			currProp.cod[2] = tokenizer.nextTokenAsDouble();
90
91			currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
92			currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
93			currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
94			currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
95			currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
96			currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
97			currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
98			currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
99			currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
100
101			currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
102			currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
103			currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
104			currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
105			currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
106			currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
107			currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
108			currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
109			currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
110
111			currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
112			currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
113			currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
114			currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
115			currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
116			currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
117			currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
118			currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
119			currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
120
121			currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
122			currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
123			currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
124			currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
125			currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
126			currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
127			currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
128			currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
129			currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
130
131			currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
132			currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
133			currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
134			currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
135			currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
136			currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
137			currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
138			currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
139			currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
140
141			currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
142			currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
143			currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
144			currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
145			currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
146			currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
147			currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
148			currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
149			currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();
150
151			currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
152			currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
153			currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
154			currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
155			currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
156			currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
157			currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
158			currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
159			currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
160			props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
161			}
162			}
163
164			return props;
165			}
166
167			void LDForceManager::postCalculation() {
168			SimInfo::MoleculeIterator i;
169			Molecule::IntegrableObjectIterator j;
170			Molecule* mol;
171			StuntDouble* integrableObject;
172			Vector3d vel;
173			Vector3d pos;
174			Vector3d frc;
175			Mat3x3d A;
176			Vector3d Tb;
177			Vector3d ji;
178			double mass;
179			unsigned int index = 0;
180			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
181			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
182			integrableObject = mol->nextIntegrableObject(j)) {
183
184			vel =integrableObject->getVel();
185			if (integrableObject->isDirectional()){
186			//calculate angular velocity in lab frame
187			Mat3x3d I = integrableObject->getI();
188			Vector3d angMom = integrableObject->getJ();
189			Vector3d omega;
190
191			if (integrableObject->isLinear()) {
192			int linearAxis = integrableObject->linearAxis();
193			int l = (linearAxis +1 )%3;
194			int m = (linearAxis +2 )%3;
195			omega[l] = angMom[l] /I(l, l);
196			omega[m] = angMom[m] /I(m, m);
197
198			} else {
199			omega[0] = angMom[0] /I(0, 0);
200			omega[1] = angMom[1] /I(1, 1);
201			omega[2] = angMom[2] /I(2, 2);
202			}
203
204			//apply friction force and torque at center of diffusion
205			A = integrableObject->getA();
206			Vector3d rcd = A.transpose() * hydroProps_[index].cod;
207			Vector3d vcd = vel + cross(omega, rcd);
208			Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
209			integrableObject->addFrc(frictionForce);
210			Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
211			integrableObject->addTrq(frictionTorque);
212
213			//apply random force and torque at center of diffustion
214			Vector3d randomForce;
215			Vector3d randomTorque;
216			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
217			integrableObject->addFrc(randomForce);
218			integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
219
220			} else {
221			//spheric atom
222			Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
223			Vector3d randomForce;
224			Vector3d randomTorque;
225			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
226			integrableObject->addFrc(frictionForce+randomForce);
227			}
228
229			++index;
230
231			}
232			}
233
234			ForceManager::postCalculation();
235
236
237
238			}
239
240			void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
241			SquareMatrix<double, 6> Dd;
242			SquareMatrix<double, 6> S;
243			Vector<double, 6> Z;
244			Vector<double, 6> generalForce;
245			Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
246			Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
247			Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
248			Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
249			CholeskyDecomposition(Dd, S);
250
251			Z[0] = randNumGen_.randNorm(0, variance);
252			Z[1] = randNumGen_.randNorm(0, variance);
253			Z[2] = randNumGen_.randNorm(0, variance);
254			Z[3] = randNumGen_.randNorm(0, variance);
255			Z[4] = randNumGen_.randNorm(0, variance);
256			Z[5] = randNumGen_.randNorm(0, variance);
257
258			generalForce = S*Z;
259			force[0] = generalForce[0];
260			force[1] = generalForce[1];
261			force[2] = generalForce[2];
262			torque[0] = generalForce[3];
263			torque[1] = generalForce[4];
264			torque[2] = generalForce[5];
265
266			}
267
268			}