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 {
      sprintf( painCave.errMsg,
               "HydroPropFile must be set if Langevin Dynamics is specified.\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
    
    sphericalBoundaryConditions_ = false;
    if (simParams->getUseSphericalBoundaryConditions()) {
      sphericalBoundaryConditions_ = true;
      if (simParams->haveLangevinBufferRadius()) {
        langevinBufferRadius_ = simParams->getLangevinBufferRadius();
      } else {
        sprintf( painCave.errMsg,
                 "langevinBufferRadius must be specified " 
                 "when useSphericalBoundaryConditions is turned on.\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
      }
    
      if (simParams->haveFrozenBufferRadius()) {
        frozenBufferRadius_ = simParams->getFrozenBufferRadius();
      } else {
        sprintf( painCave.errMsg,
                 "frozenBufferRadius must be specified " 
                 "when useSphericalBoundaryConditions is turned on.\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
      }

      if (frozenBufferRadius_ < langevinBufferRadius_) {
        sprintf( painCave.errMsg,
                 "frozenBufferRadius has been set smaller than the " 
                 "langevinBufferRadius.  This is probably an error.\n");
        painCave.severity = OOPSE_WARNING;
        painCave.isFatal = 0;
        simError();  
      }
    }
      
    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 {
          sprintf( painCave.errMsg,
                   "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();  
        }
        
      }
    }
    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() >= 40) {
        std::string atomName = tokenizer.nextToken();
        currProp.cor[0] = tokenizer.nextTokenAsDouble();
        currProp.cor[1] = tokenizer.nextTokenAsDouble();
        currProp.cor[2] = tokenizer.nextTokenAsDouble();
        
        currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
        
        currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
        
        currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
        
        currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
        currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); 
        
        SquareMatrix<double, 6> Xir;
        Xir.setSubMatrix(0, 0, currProp.Xirtt);
        Xir.setSubMatrix(0, 3, currProp.Xirrt);
        Xir.setSubMatrix(3, 0, currProp.Xirtr);
        Xir.setSubMatrix(3, 3, currProp.Xirrr);
        CholeskyDecomposition(Xir, currProp.S);            
        
        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;
    bool doLangevinForces;
    bool freezeMolecule;
    int fdf;
    
    fdf = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      
      if (sphericalBoundaryConditions_) {
        
        Vector3d molPos = mol->getCom();
        double molRad = molPos.length();
        
        doLangevinForces = false;
        freezeMolecule = false;
        
        if (molRad > langevinBufferRadius_) { 
          doLangevinForces = true;
          freezeMolecule = false;
        }
        if (molRad > frozenBufferRadius_) {
          doLangevinForces = false;
          freezeMolecule = true;
        }
      }
      
      if (doLangevinForces) {
        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 resistance
            A = integrableObject->getA();
            Atrans = A.transpose();
            Vector3d rcr = Atrans * hydroProps_[index].cor;  
            Vector3d vcdLab = vel + cross(omega, rcr);
            Vector3d vcdBody = A* vcdLab;
            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
            Vector3d frictionForceLab = Atrans*frictionForceBody;
            integrableObject->addFrc(frictionForceLab);
            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
            
            //apply random force and torque at center of resistance
            Vector3d randomForceBody;
            Vector3d randomTorqueBody;
            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
            Vector3d randomForceLab = Atrans*randomForceBody;
            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
            integrableObject->addFrc(randomForceLab);            
            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));             
            
          } else {
            //spherical atom
            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);     
            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            
            integrableObject->addFrc(frictionForce+randomForce);             
          }
          
          ++index;
    
        }
      }
      if (freezeMolecule) 
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {          
          fdf += integrableObject->freeze();
        }
    }
    
    info_->setFdf(fdf);
    
    ForceManager::postCalculation();   
  }

void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {


    Vector<double, 6> Z;
    Vector<double, 6> generalForce;

        
    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 = hydroProps_[index].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:	2733
Committed:	Tue Apr 25 02:09:01 2006 UTC (18 years, 4 months ago) by gezelter
File size:	13164 byte(s)
Log Message:	Adding spherical boundary conditions to LD integrator
#	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	tim	2632	#include "utils/OOPSEConstant.hpp"
45	tim	2611	namespace oopse {
46
47			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
48			Globals* simParams = info->getSimParams();
49	gezelter	2733
50	tim	2611	std::map<std::string, HydroProp> hydroPropMap;
51			if (simParams->haveHydroPropFile()) {
52	gezelter	2733	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
53	tim	2611	} else {
54	gezelter	2733	sprintf( painCave.errMsg,
55			"HydroPropFile must be set if Langevin Dynamics is specified.\n");
56			painCave.severity = OOPSE_ERROR;
57			painCave.isFatal = 1;
58			simError();
59	tim	2611	}
60	gezelter	2733
61			sphericalBoundaryConditions_ = false;
62			if (simParams->getUseSphericalBoundaryConditions()) {
63			sphericalBoundaryConditions_ = true;
64			if (simParams->haveLangevinBufferRadius()) {
65			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
66			} else {
67			sprintf( painCave.errMsg,
68			"langevinBufferRadius must be specified "
69			"when useSphericalBoundaryConditions is turned on.\n");
70			painCave.severity = OOPSE_ERROR;
71			painCave.isFatal = 1;
72			simError();
73			}
74
75			if (simParams->haveFrozenBufferRadius()) {
76			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
77			} else {
78			sprintf( painCave.errMsg,
79			"frozenBufferRadius must be specified "
80			"when useSphericalBoundaryConditions is turned on.\n");
81			painCave.severity = OOPSE_ERROR;
82			painCave.isFatal = 1;
83			simError();
84			}
85	tim	2611
86	gezelter	2733	if (frozenBufferRadius_ < langevinBufferRadius_) {
87			sprintf( painCave.errMsg,
88			"frozenBufferRadius has been set smaller than the "
89			"langevinBufferRadius. This is probably an error.\n");
90			painCave.severity = OOPSE_WARNING;
91			painCave.isFatal = 0;
92			simError();
93			}
94			}
95
96	tim	2611	SimInfo::MoleculeIterator i;
97			Molecule::IntegrableObjectIterator j;
98			Molecule* mol;
99			StuntDouble* integrableObject;
100			for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
101			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
102	gezelter	2733	integrableObject = mol->nextIntegrableObject(j)) {
103			std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
104			if (iter != hydroPropMap.end()) {
105			hydroProps_.push_back(iter->second);
106			} else {
107			sprintf( painCave.errMsg,
108			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
109			painCave.severity = OOPSE_ERROR;
110			painCave.isFatal = 1;
111			simError();
112			}
113
114			}
115	tim	2611	}
116	tim	2632	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
117	tim	2611	}
118			std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
119			std::map<std::string, HydroProp> props;
120			std::ifstream ifs(filename.c_str());
121			if (ifs.is_open()) {
122	gezelter	2733
123	tim	2611	}
124	gezelter	2733
125	tim	2611	const unsigned int BufferSize = 65535;
126			char buffer[BufferSize];
127			while (ifs.getline(buffer, BufferSize)) {
128	gezelter	2733	StringTokenizer tokenizer(buffer);
129			HydroProp currProp;
130			if (tokenizer.countTokens() >= 40) {
131			std::string atomName = tokenizer.nextToken();
132			currProp.cor[0] = tokenizer.nextTokenAsDouble();
133			currProp.cor[1] = tokenizer.nextTokenAsDouble();
134			currProp.cor[2] = tokenizer.nextTokenAsDouble();
135
136			currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
137			currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
138			currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
139			currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
140			currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
141			currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
142			currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
143			currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
144			currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
145
146			currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
147			currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
148			currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
149			currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
150			currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
151			currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
152			currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
153			currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
154			currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
155
156			currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
157			currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
158			currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
159			currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
160			currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
161			currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
162			currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
163			currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
164			currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
165
166			currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
167			currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
168			currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
169			currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
170			currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
171			currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
172			currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
173			currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
174			currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
175
176			SquareMatrix<double, 6> Xir;
177			Xir.setSubMatrix(0, 0, currProp.Xirtt);
178			Xir.setSubMatrix(0, 3, currProp.Xirrt);
179			Xir.setSubMatrix(3, 0, currProp.Xirtr);
180			Xir.setSubMatrix(3, 3, currProp.Xirrr);
181			CholeskyDecomposition(Xir, currProp.S);
182
183			props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
184			}
185	tim	2611	}
186	gezelter	2733
187	tim	2611	return props;
188			}
189
190			void LDForceManager::postCalculation() {
191			SimInfo::MoleculeIterator i;
192			Molecule::IntegrableObjectIterator j;
193			Molecule* mol;
194			StuntDouble* integrableObject;
195			Vector3d vel;
196			Vector3d pos;
197			Vector3d frc;
198			Mat3x3d A;
199	tim	2632	Mat3x3d Atrans;
200	tim	2611	Vector3d Tb;
201			Vector3d ji;
202			double mass;
203			unsigned int index = 0;
204	gezelter	2733	bool doLangevinForces;
205			bool freezeMolecule;
206			int fdf;
207
208			fdf = 0;
209	tim	2611	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
210	gezelter	2733
211			if (sphericalBoundaryConditions_) {
212
213			Vector3d molPos = mol->getCom();
214			double molRad = molPos.length();
215
216			doLangevinForces = false;
217			freezeMolecule = false;
218
219			if (molRad > langevinBufferRadius_) {
220			doLangevinForces = true;
221			freezeMolecule = false;
222			}
223			if (molRad > frozenBufferRadius_) {
224			doLangevinForces = false;
225			freezeMolecule = true;
226			}
227			}
228
229			if (doLangevinForces) {
230			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231			integrableObject = mol->nextIntegrableObject(j)) {
232
233	tim	2611	vel =integrableObject->getVel();
234			if (integrableObject->isDirectional()){
235	gezelter	2733	//calculate angular velocity in lab frame
236			Mat3x3d I = integrableObject->getI();
237			Vector3d angMom = integrableObject->getJ();
238			Vector3d omega;
239
240			if (integrableObject->isLinear()) {
241			int linearAxis = integrableObject->linearAxis();
242			int l = (linearAxis +1 )%3;
243			int m = (linearAxis +2 )%3;
244			omega[l] = angMom[l] /I(l, l);
245			omega[m] = angMom[m] /I(m, m);
246
247			} else {
248			omega[0] = angMom[0] /I(0, 0);
249			omega[1] = angMom[1] /I(1, 1);
250			omega[2] = angMom[2] /I(2, 2);
251			}
252
253			//apply friction force and torque at center of resistance
254			A = integrableObject->getA();
255			Atrans = A.transpose();
256			Vector3d rcr = Atrans * hydroProps_[index].cor;
257			Vector3d vcdLab = vel + cross(omega, rcr);
258			Vector3d vcdBody = A* vcdLab;
259			Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
260			Vector3d frictionForceLab = Atrans*frictionForceBody;
261			integrableObject->addFrc(frictionForceLab);
262			Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
263			Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
264			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
265
266			//apply random force and torque at center of resistance
267			Vector3d randomForceBody;
268			Vector3d randomTorqueBody;
269			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
270			Vector3d randomForceLab = Atrans*randomForceBody;
271			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
272			integrableObject->addFrc(randomForceLab);
273			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
274
275	tim	2611	} else {
276	gezelter	2733	//spherical atom
277			Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
278			Vector3d randomForce;
279			Vector3d randomTorque;
280			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
281
282			integrableObject->addFrc(frictionForce+randomForce);
283	tim	2611	}
284	gezelter	2733
285			++index;
286	tim	2611
287	gezelter	2733	}
288	tim	2611	}
289	gezelter	2733	if (freezeMolecule)
290			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291			integrableObject = mol->nextIntegrableObject(j)) {
292			fdf += integrableObject->freeze();
293			}
294			}
295
296			info_->setFdf(fdf);
297
298			ForceManager::postCalculation();
299	tim	2611	}
300
301			void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
302	tim	2632
303	tim	2634
304	tim	2632	Vector<double, 6> Z;
305			Vector<double, 6> generalForce;
306
307
308	tim	2611	Z[0] = randNumGen_.randNorm(0, variance);
309			Z[1] = randNumGen_.randNorm(0, variance);
310			Z[2] = randNumGen_.randNorm(0, variance);
311			Z[3] = randNumGen_.randNorm(0, variance);
312			Z[4] = randNumGen_.randNorm(0, variance);
313			Z[5] = randNumGen_.randNorm(0, variance);
314	tim	2632
315
316	tim	2634	generalForce = hydroProps_[index].S*Z;
317	tim	2632
318	tim	2611	force[0] = generalForce[0];
319			force[1] = generalForce[1];
320			force[2] = generalForce[2];
321			torque[0] = generalForce[3];
322			torque[1] = generalForce[4];
323			torque[2] = generalForce[5];
324
325			}
326
327			}