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 <iostream>
#include "integrators/LDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/OOPSEConstant.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "utils/ElementsTable.hpp"

namespace oopse {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
    simParams = info->getSimParams();
    veloMunge = new Velocitizer(info);

    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();  
      }
    }

    // Build the hydroProp map:
    std::map<std::string, HydroProp*> hydroPropMap;

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;              
    bool needHydroPropFile = false;
    
    for (mol = info->beginMolecule(i); mol != NULL; 
         mol = info->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); 
           integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
        
        if (integrableObject->isRigidBody()) {
          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
        }
        
      }
    }
        

    if (needHydroPropFile) {               
      if (simParams->haveHydroPropFile()) {
        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
      } else {               
        sprintf( painCave.errMsg,
                 "HydroPropFile must be set to a file name if Langevin Dynamics\n"
                 "\tis specified for rigidBodies which contain more than one atom\n"
                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
      }      

      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();  
          }        
        }
      }
    } else {
      
      std::map<std::string, HydroProp*> hydroPropMap;
      for (mol = info->beginMolecule(i); mol != NULL; 
           mol = info->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); 
             integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {
          Shape* currShape = NULL;

          if (integrableObject->isAtom()){
            Atom* atom = static_cast<Atom*>(integrableObject);
            AtomType* atomType = atom->getAtomType();
            if (atomType->isGayBerne()) {
              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
              GenericData* data = dAtomType->getPropertyByName("GayBerne");
              if (data != NULL) {
                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
                
                if (gayBerneData != NULL) {  
                  GayBerneParam gayBerneParam = gayBerneData->getData();
                  currShape = new Ellipsoid(V3Zero, 
                                            gayBerneParam.GB_l / 2.0, 
                                            gayBerneParam.GB_d / 2.0, 
                                            Mat3x3d::identity());
                } else {
                  sprintf( painCave.errMsg,
                           "Can not cast GenericData to GayBerneParam\n");
                  painCave.severity = OOPSE_ERROR;
                  painCave.isFatal = 1;
                  simError();   
                }
              } else {
                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();    
              }
            } else {
              if (atomType->isLennardJones()){
                GenericData* data = atomType->getPropertyByName("LennardJones");
                if (data != NULL) {
                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
                  if (ljData != NULL) {
                    LJParam ljParam = ljData->getData();
                    currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
                  } else {
                    sprintf( painCave.errMsg,
                             "Can not cast GenericData to LJParam\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
                  }       
                }
              } else {
                int aNum = etab.GetAtomicNum((atom->getType()).c_str());
                if (aNum != 0) {
                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
                } else {
                  sprintf( painCave.errMsg,
                           "Could not find atom type in default element.txt\n");
                  painCave.severity = OOPSE_ERROR;
                  painCave.isFatal = 1;
                  simError();          
                }
              }
            }
          }
          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
          if (iter != hydroPropMap.end()) 
            hydroProps_.push_back(iter->second);
          else {
            currHydroProp->complete();
            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
            hydroProps_.push_back(currHydroProp);
          }
        }
      }
    }
    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)) {
      HydroProp* currProp = new HydroProp(buffer);
      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
    }

    return props;
  }
   
  void LDForceManager::postCalculation(bool needStress){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    RealType mass;
    Vector3d pos;
    Vector3d frc;
    Mat3x3d A;
    Mat3x3d Atrans;
    Vector3d Tb;
    Vector3d ji;
    unsigned int index = 0;
    bool doLangevinForces;
    bool freezeMolecule;
    int fdf;

    fdf = 0;

    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {

      doLangevinForces = true;           
      freezeMolecule = false;

      if (sphericalBoundaryConditions_) {
        
        Vector3d molPos = mol->getCom();
        RealType molRad = molPos.length();

        doLangevinForces = false;
        
        if (molRad > langevinBufferRadius_) { 
          doLangevinForces = true;
          freezeMolecule = false;
        }
        if (molRad > frozenBufferRadius_) {
          doLangevinForces = false;
          freezeMolecule = true;
        }
      }
      
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
          
        if (freezeMolecule) 
          fdf += integrableObject->freeze();
        
        if (doLangevinForces) {  
          mass = integrableObject->getMass();
          if (integrableObject->isDirectional()){

            // preliminaries for directional objects:

            A = integrableObject->getA();
            Atrans = A.transpose();
            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  

            //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(rcrLab, randomForceLab ));             

            Mat3x3d I = integrableObject->getI();
            Vector3d omegaBody;

            // What remains contains velocity explicitly, but the velocity required
            // is at the full step: v(t + h), while we have initially the velocity
            // at the half step: v(t + h/2).  We need to iterate to converge the
            // friction force and friction torque vectors.

            // this is the velocity at the half-step:
            
            Vector3d vel =integrableObject->getVel();
            Vector3d angMom = integrableObject->getJ();

            //estimate velocity at full-step using everything but friction forces:           

            frc = integrableObject->getFrc();
            Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;

            Tb = integrableObject->lab2Body(integrableObject->getTrq());
            Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                             

            Vector3d omegaLab;
            Vector3d vcdLab;
            Vector3d vcdBody;
            Vector3d frictionForceBody;
            Vector3d frictionForceLab(0.0);
            Vector3d oldFFL;  // used to test for convergence
            Vector3d frictionTorqueBody(0.0);
            Vector3d oldFTB;  // used to test for convergence
            Vector3d frictionTorqueLab;
            RealType fdot;
            RealType tdot;

            //iteration starts here:

            for (int k = 0; k < maxIterNum_; k++) {
                            
              if (integrableObject->isLinear()) {
                int linearAxis = integrableObject->linearAxis();
                int l = (linearAxis +1 )%3;
                int m = (linearAxis +2 )%3;
                omegaBody[l] = angMomStep[l] /I(l, l);
                omegaBody[m] = angMomStep[m] /I(m, m);
                
              } else {
                omegaBody[0] = angMomStep[0] /I(0, 0);
                omegaBody[1] = angMomStep[1] /I(1, 1);
                omegaBody[2] = angMomStep[2] /I(2, 2);
              }
              
              omegaLab = Atrans * omegaBody;
              
              // apply friction force and torque at center of resistance
              
              vcdLab = velStep + cross(omegaLab, rcrLab);       
              vcdBody = A * vcdLab;
              frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
              oldFFL = frictionForceLab;
              frictionForceLab = Atrans * frictionForceBody;
              oldFTB = frictionTorqueBody;
              frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
              frictionTorqueLab = Atrans * frictionTorqueBody;
              
              // re-estimate velocities at full-step using friction forces:
              
              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
              angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);

              // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
              
              fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
              tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
              
              if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
                break; // iteration ends here
            }

            integrableObject->addFrc(frictionForceLab);
            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));

            
          } else {
            //spherical atom

            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            integrableObject->addFrc(randomForce);            

            // What remains contains velocity explicitly, but the velocity required
            // is at the full step: v(t + h), while we have initially the velocity
            // at the half step: v(t + h/2).  We need to iterate to converge the
            // friction force vector.

            // this is the velocity at the half-step:
            
            Vector3d vel =integrableObject->getVel();

            //estimate velocity at full-step using everything but friction forces:           

            frc = integrableObject->getFrc();
            Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;

            Vector3d frictionForce(0.0);
            Vector3d oldFF;  // used to test for convergence
            RealType fdot;

            //iteration starts here:

            for (int k = 0; k < maxIterNum_; k++) {

              oldFF = frictionForce;                            
              frictionForce = -hydroProps_[index]->getXitt() * velStep;

              // re-estimate velocities at full-step using friction forces:
              
              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);

              // check for convergence (if the vector has converged, fdot will be 1.0):
              
              fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
              
              if (fabs(1.0 - fdot) <= forceTolerance_)
                break; // iteration ends here
            }

            integrableObject->addFrc(frictionForce);

          }
        }
          
        ++index;
    
      }
    }    

    info_->setFdf(fdf);
    veloMunge->removeComDrift();
    // Remove angular drift if we are not using periodic boundary conditions.
    if(!simParams->getUsePeriodicBoundaryConditions()) 
      veloMunge->removeAngularDrift();

    ForceManager::postCalculation(needStress);   
  }

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


    Vector<RealType, 6> Z;
    Vector<RealType, 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]->getS()*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:	1237
Committed:	Fri Apr 18 16:55:15 2008 UTC (17 years ago) by gezelter
Original Path:	*trunk/src/integrators/LDForceManager.cpp*
File size:	19093 byte(s)
Log Message:	Adding iterative looping to get better estimates of friction forces from full-step velocities
#	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	chuckv	1120	#include <iostream>
43	tim	895	#include "integrators/LDForceManager.hpp"
44			#include "math/CholeskyDecomposition.hpp"
45	tim	904	#include "utils/OOPSEConstant.hpp"
46	gezelter	956	#include "hydrodynamics/Sphere.hpp"
47			#include "hydrodynamics/Ellipsoid.hpp"
48	gezelter	1210	#include "utils/ElementsTable.hpp"
49	gezelter	956
50	tim	895	namespace oopse {
51
52	gezelter	1237	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53	gezelter	983	simParams = info->getSimParams();
54			veloMunge = new Velocitizer(info);
55
56	gezelter	945	sphericalBoundaryConditions_ = false;
57			if (simParams->getUseSphericalBoundaryConditions()) {
58			sphericalBoundaryConditions_ = true;
59			if (simParams->haveLangevinBufferRadius()) {
60			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
61			} else {
62			sprintf( painCave.errMsg,
63			"langevinBufferRadius must be specified "
64			"when useSphericalBoundaryConditions is turned on.\n");
65			painCave.severity = OOPSE_ERROR;
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			if (simParams->haveFrozenBufferRadius()) {
71			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
72			} else {
73			sprintf( painCave.errMsg,
74			"frozenBufferRadius must be specified "
75			"when useSphericalBoundaryConditions is turned on.\n");
76			painCave.severity = OOPSE_ERROR;
77			painCave.isFatal = 1;
78			simError();
79			}
80	tim	895
81	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
82			sprintf( painCave.errMsg,
83			"frozenBufferRadius has been set smaller than the "
84			"langevinBufferRadius. This is probably an error.\n");
85			painCave.severity = OOPSE_WARNING;
86			painCave.isFatal = 0;
87			simError();
88			}
89			}
90	gezelter	956
91			// Build the hydroProp map:
92	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
93	gezelter	956
94	tim	895	Molecule* mol;
95			StuntDouble* integrableObject;
96	gezelter	956	SimInfo::MoleculeIterator i;
97			Molecule::IntegrableObjectIterator j;
98			bool needHydroPropFile = false;
99
100			for (mol = info->beginMolecule(i); mol != NULL;
101			mol = info->nextMolecule(i)) {
102			for (integrableObject = mol->beginIntegrableObject(j);
103			integrableObject != NULL;
104	gezelter	945	integrableObject = mol->nextIntegrableObject(j)) {
105	gezelter	956
106			if (integrableObject->isRigidBody()) {
107			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
108			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
109	gezelter	945	}
110
111			}
112	tim	895	}
113	gezelter	956
114
115			if (needHydroPropFile) {
116			if (simParams->haveHydroPropFile()) {
117			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118			} else {
119			sprintf( painCave.errMsg,
120	gezelter	1237	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
121			"\tis specified for rigidBodies which contain more than one atom\n"
122			"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
123	gezelter	956	painCave.severity = OOPSE_ERROR;
124			painCave.isFatal = 1;
125			simError();
126			}
127	tim	971
128			for (mol = info->beginMolecule(i); mol != NULL;
129			mol = info->nextMolecule(i)) {
130			for (integrableObject = mol->beginIntegrableObject(j);
131			integrableObject != NULL;
132			integrableObject = mol->nextIntegrableObject(j)) {
133
134	gezelter	981	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
135	tim	971	if (iter != hydroPropMap.end()) {
136			hydroProps_.push_back(iter->second);
137			} else {
138			sprintf( painCave.errMsg,
139			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
140			painCave.severity = OOPSE_ERROR;
141			painCave.isFatal = 1;
142			simError();
143			}
144			}
145	gezelter	956	}
146			} else {
147	gezelter	981
148			std::map<std::string, HydroProp*> hydroPropMap;
149	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
150			mol = info->nextMolecule(i)) {
151			for (integrableObject = mol->beginIntegrableObject(j);
152			integrableObject != NULL;
153			integrableObject = mol->nextIntegrableObject(j)) {
154			Shape* currShape = NULL;
155	xsun	1185
156			if (integrableObject->isAtom()){
157			Atom* atom = static_cast<Atom*>(integrableObject);
158			AtomType* atomType = atom->getAtomType();
159	gezelter	956	if (atomType->isGayBerne()) {
160	xsun	1185	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161	gezelter	956	GenericData* data = dAtomType->getPropertyByName("GayBerne");
162			if (data != NULL) {
163			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
164
165			if (gayBerneData != NULL) {
166			GayBerneParam gayBerneParam = gayBerneData->getData();
167			currShape = new Ellipsoid(V3Zero,
168	xsun	1185	gayBerneParam.GB_l / 2.0,
169	gezelter	981	gayBerneParam.GB_d / 2.0,
170	gezelter	956	Mat3x3d::identity());
171			} else {
172			sprintf( painCave.errMsg,
173			"Can not cast GenericData to GayBerneParam\n");
174			painCave.severity = OOPSE_ERROR;
175			painCave.isFatal = 1;
176			simError();
177			}
178			} else {
179			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180			painCave.severity = OOPSE_ERROR;
181			painCave.isFatal = 1;
182			simError();
183			}
184	xsun	1185	} else {
185			if (atomType->isLennardJones()){
186			GenericData* data = atomType->getPropertyByName("LennardJones");
187			if (data != NULL) {
188			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
189			if (ljData != NULL) {
190			LJParam ljParam = ljData->getData();
191			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
192			} else {
193			sprintf( painCave.errMsg,
194			"Can not cast GenericData to LJParam\n");
195			painCave.severity = OOPSE_ERROR;
196			painCave.isFatal = 1;
197			simError();
198			}
199			}
200			} else {
201	gezelter	1237	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
202			if (aNum != 0) {
203			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
204	gezelter	956	} else {
205			sprintf( painCave.errMsg,
206	xsun	1185	"Could not find atom type in default element.txt\n");
207	gezelter	956	painCave.severity = OOPSE_ERROR;
208			painCave.isFatal = 1;
209			simError();
210	xsun	1185	}
211	gezelter	956	}
212			}
213			}
214	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
215			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
216	gezelter	956	if (iter != hydroPropMap.end())
217			hydroProps_.push_back(iter->second);
218			else {
219	gezelter	981	currHydroProp->complete();
220			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
221			hydroProps_.push_back(currHydroProp);
222	gezelter	956	}
223			}
224			}
225			}
226	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
227	gezelter	981	}
228	gezelter	956
229	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
230			std::map<std::string, HydroProp*> props;
231	tim	895	std::ifstream ifs(filename.c_str());
232			if (ifs.is_open()) {
233	gezelter	945
234	tim	895	}
235	gezelter	945
236	tim	895	const unsigned int BufferSize = 65535;
237			char buffer[BufferSize];
238			while (ifs.getline(buffer, BufferSize)) {
239	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
240			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
241	tim	895	}
242	gezelter	981
243	tim	895	return props;
244			}
245	gezelter	981
246	gezelter	1126	void LDForceManager::postCalculation(bool needStress){
247	tim	895	SimInfo::MoleculeIterator i;
248			Molecule::IntegrableObjectIterator j;
249			Molecule* mol;
250			StuntDouble* integrableObject;
251	xsun	1185	RealType mass;
252	tim	895	Vector3d pos;
253			Vector3d frc;
254			Mat3x3d A;
255	tim	904	Mat3x3d Atrans;
256	tim	895	Vector3d Tb;
257			Vector3d ji;
258			unsigned int index = 0;
259	gezelter	945	bool doLangevinForces;
260			bool freezeMolecule;
261			int fdf;
262	gezelter	983
263	chuckv	1120	fdf = 0;
264	gezelter	983
265	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
266	gezelter	970
267			doLangevinForces = true;
268			freezeMolecule = false;
269
270	gezelter	945	if (sphericalBoundaryConditions_) {
271
272			Vector3d molPos = mol->getCom();
273	tim	963	RealType molRad = molPos.length();
274	chuckv	1120
275	gezelter	945	doLangevinForces = false;
276
277			if (molRad > langevinBufferRadius_) {
278			doLangevinForces = true;
279			freezeMolecule = false;
280			}
281			if (molRad > frozenBufferRadius_) {
282			doLangevinForces = false;
283			freezeMolecule = true;
284			}
285			}
286
287	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
288			integrableObject = mol->nextIntegrableObject(j)) {
289	gezelter	945
290	gezelter	956	if (freezeMolecule)
291			fdf += integrableObject->freeze();
292
293	chuckv	1120	if (doLangevinForces) {
294	xsun	1185	mass = integrableObject->getMass();
295	tim	895	if (integrableObject->isDirectional()){
296	gezelter	1237
297			// preliminaries for directional objects:
298
299	xsun	1216	A = integrableObject->getA();
300			Atrans = A.transpose();
301			Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
302	xsun	1185
303	gezelter	1237	//apply random force and torque at center of resistance
304	xsun	1185
305	gezelter	945	Vector3d randomForceBody;
306			Vector3d randomTorqueBody;
307			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
308	xsun	1216	Vector3d randomForceLab = Atrans * randomForceBody;
309			Vector3d randomTorqueLab = Atrans * randomTorqueBody;
310	gezelter	945	integrableObject->addFrc(randomForceLab);
311	xsun	1216	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
312	gezelter	1237
313			Mat3x3d I = integrableObject->getI();
314			Vector3d omegaBody;
315
316			// What remains contains velocity explicitly, but the velocity required
317			// is at the full step: v(t + h), while we have initially the velocity
318			// at the half step: v(t + h/2). We need to iterate to converge the
319			// friction force and friction torque vectors.
320
321			// this is the velocity at the half-step:
322	gezelter	945
323	gezelter	1237	Vector3d vel =integrableObject->getVel();
324			Vector3d angMom = integrableObject->getJ();
325
326			//estimate velocity at full-step using everything but friction forces:
327
328			frc = integrableObject->getFrc();
329			Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
330
331			Tb = integrableObject->lab2Body(integrableObject->getTrq());
332			Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;
333
334			Vector3d omegaLab;
335			Vector3d vcdLab;
336			Vector3d vcdBody;
337			Vector3d frictionForceBody;
338			Vector3d frictionForceLab(0.0);
339			Vector3d oldFFL; // used to test for convergence
340			Vector3d frictionTorqueBody(0.0);
341			Vector3d oldFTB; // used to test for convergence
342			Vector3d frictionTorqueLab;
343			RealType fdot;
344			RealType tdot;
345
346			//iteration starts here:
347
348			for (int k = 0; k < maxIterNum_; k++) {
349
350			if (integrableObject->isLinear()) {
351			int linearAxis = integrableObject->linearAxis();
352			int l = (linearAxis +1 )%3;
353			int m = (linearAxis +2 )%3;
354			omegaBody[l] = angMomStep[l] /I(l, l);
355			omegaBody[m] = angMomStep[m] /I(m, m);
356
357			} else {
358			omegaBody[0] = angMomStep[0] /I(0, 0);
359			omegaBody[1] = angMomStep[1] /I(1, 1);
360			omegaBody[2] = angMomStep[2] /I(2, 2);
361			}
362
363			omegaLab = Atrans * omegaBody;
364
365			// apply friction force and torque at center of resistance
366
367			vcdLab = velStep + cross(omegaLab, rcrLab);
368			vcdBody = A * vcdLab;
369			frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
370			oldFFL = frictionForceLab;
371			frictionForceLab = Atrans * frictionForceBody;
372			oldFTB = frictionTorqueBody;
373			frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
374			frictionTorqueLab = Atrans * frictionTorqueBody;
375
376			// re-estimate velocities at full-step using friction forces:
377
378			velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
379			angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
380
381			// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
382
383			fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
384			tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
385
386			if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
387			break; // iteration ends here
388			}
389
390			integrableObject->addFrc(frictionForceLab);
391			integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
392
393
394	tim	895	} else {
395	gezelter	945	//spherical atom
396	gezelter	1237
397	gezelter	945	Vector3d randomForce;
398			Vector3d randomTorque;
399			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
400	gezelter	1237	integrableObject->addFrc(randomForce);
401
402			// What remains contains velocity explicitly, but the velocity required
403			// is at the full step: v(t + h), while we have initially the velocity
404			// at the half step: v(t + h/2). We need to iterate to converge the
405			// friction force vector.
406
407			// this is the velocity at the half-step:
408	gezelter	945
409	gezelter	1237	Vector3d vel =integrableObject->getVel();
410
411			//estimate velocity at full-step using everything but friction forces:
412
413			frc = integrableObject->getFrc();
414			Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
415
416			Vector3d frictionForce(0.0);
417			Vector3d oldFF; // used to test for convergence
418			RealType fdot;
419
420			//iteration starts here:
421
422			for (int k = 0; k < maxIterNum_; k++) {
423
424			oldFF = frictionForce;
425			frictionForce = -hydroProps_[index]->getXitt() * velStep;
426
427			// re-estimate velocities at full-step using friction forces:
428
429			velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
430
431			// check for convergence (if the vector has converged, fdot will be 1.0):
432
433			fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
434
435			if (fabs(1.0 - fdot) <= forceTolerance_)
436			break; // iteration ends here
437			}
438
439			integrableObject->addFrc(frictionForce);
440
441	tim	895	}
442	gezelter	956	}
443	gezelter	945
444	gezelter	956	++index;
445	tim	895
446			}
447	gezelter	956	}
448	chuckv	1120
449	gezelter	945	info_->setFdf(fdf);
450	gezelter	983	veloMunge->removeComDrift();
451			// Remove angular drift if we are not using periodic boundary conditions.
452			if(!simParams->getUsePeriodicBoundaryConditions())
453			veloMunge->removeAngularDrift();
454
455	gezelter	1126	ForceManager::postCalculation(needStress);
456	tim	895	}
457
458	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
459	tim	904
460	tim	906
461	tim	963	Vector<RealType, 6> Z;
462			Vector<RealType, 6> generalForce;
463	tim	904
464	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
465			Z[1] = randNumGen_.randNorm(0, variance);
466			Z[2] = randNumGen_.randNorm(0, variance);
467			Z[3] = randNumGen_.randNorm(0, variance);
468			Z[4] = randNumGen_.randNorm(0, variance);
469			Z[5] = randNumGen_.randNorm(0, variance);
470	tim	904
471	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
472	tim	904
473	tim	895	force[0] = generalForce[0];
474			force[1] = generalForce[1];
475			force[2] = generalForce[2];
476			torque[0] = generalForce[3];
477			torque[1] = generalForce[4];
478			torque[2] = generalForce[5];
479
480	xsun	1185	}
481	tim	895
482			}