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 "openbabel/mol.hpp"

using namespace OpenBabel;
namespace oopse {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
    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\n"
                 "\tDynamics is specified for rigidBodies which contain more\n"
                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\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 obanum = etab.GetAtomicNum((atom->getType()).c_str());
                if (obanum != 0) {
                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
                } 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 vel;
    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) {  
          vel =integrableObject->getVel(); 
          mass = integrableObject->getMass();
          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);
            }

            //std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";

            //apply friction force and torque at center of resistance
            A = integrableObject->getA();
            Atrans = A.transpose();
            //std::cerr << "A = " << integrableObject->getA() << "\n";
            //std::cerr << "Atrans = " << A.transpose() << "\n\n";
            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
            //std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
            //std::cerr << "rcr = " << rcr << "\n\n";
            Vector3d vcdLab = vel + cross(omega, rcr);
        
            //std::cerr << "velL = " << vel << "\n\n";
            //std::cerr << "vcdL = " << vcdLab << "\n\n";
            Vector3d vcdBody = A* vcdLab;
            //std::cerr << "vcdB = " << vcdBody << "\n\n";
            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);

            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
            //std::cerr << "ffB = " << frictionForceBody << "\n\n";
            Vector3d frictionForceLab = Atrans*frictionForceBody;
            //std::cerr << "ffL = " << frictionForceLab << "\n\n";
            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n"; 
            integrableObject->addFrc(frictionForceLab);
            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n"; 
            //std::cerr << "ome = " << omega << "\n\n";
            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
            //std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
            //std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
            //std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n"; 
            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n"; 

            //apply random force and torque at center of resistance
            Vector3d randomForceBody;
            Vector3d randomTorqueBody;
            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
            //std::cerr << "rfB = " << randomForceBody << "\n\n";
            //std::cerr << "rtB = " << randomTorqueBody << "\n\n";
            Vector3d randomForceLab = Atrans*randomForceBody;
            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
            integrableObject->addFrc(randomForceLab);            
            //std::cerr << "rfL = " << randomForceLab << "\n\n";
            //std::cerr << "rtL = " << randomTorqueLab << "\n\n";
            //std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));             
            
          } else {
            //spherical atom
            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            
            integrableObject->addFrc(frictionForce+randomForce);             
          }
        }
          
        ++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)*(2.0*M_PI);
    //Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
    //Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
    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:	1185
Committed:	Fri Oct 5 19:02:09 2007 UTC (17 years, 6 months ago) by xsun
Original Path:	*trunk/src/integrators/LDForceManager.cpp*
File size:	17242 byte(s)
Log Message:	Fixed some bugs in LDForceManager.cpp
#	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			#include "openbabel/mol.hpp"
49
50			using namespace OpenBabel;
51	tim	895	namespace oopse {
52
53			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54	gezelter	983	simParams = info->getSimParams();
55			veloMunge = new Velocitizer(info);
56
57	gezelter	945	sphericalBoundaryConditions_ = false;
58			if (simParams->getUseSphericalBoundaryConditions()) {
59			sphericalBoundaryConditions_ = true;
60			if (simParams->haveLangevinBufferRadius()) {
61			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
62			} else {
63			sprintf( painCave.errMsg,
64			"langevinBufferRadius must be specified "
65			"when useSphericalBoundaryConditions is turned on.\n");
66			painCave.severity = OOPSE_ERROR;
67			painCave.isFatal = 1;
68			simError();
69			}
70
71			if (simParams->haveFrozenBufferRadius()) {
72			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
73			} else {
74			sprintf( painCave.errMsg,
75			"frozenBufferRadius must be specified "
76			"when useSphericalBoundaryConditions is turned on.\n");
77			painCave.severity = OOPSE_ERROR;
78			painCave.isFatal = 1;
79			simError();
80			}
81	tim	895
82	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
83			sprintf( painCave.errMsg,
84			"frozenBufferRadius has been set smaller than the "
85			"langevinBufferRadius. This is probably an error.\n");
86			painCave.severity = OOPSE_WARNING;
87			painCave.isFatal = 0;
88			simError();
89			}
90			}
91	gezelter	956
92			// Build the hydroProp map:
93	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
94	gezelter	956
95	tim	895	Molecule* mol;
96			StuntDouble* integrableObject;
97	gezelter	956	SimInfo::MoleculeIterator i;
98			Molecule::IntegrableObjectIterator j;
99			bool needHydroPropFile = false;
100
101			for (mol = info->beginMolecule(i); mol != NULL;
102			mol = info->nextMolecule(i)) {
103			for (integrableObject = mol->beginIntegrableObject(j);
104			integrableObject != NULL;
105	gezelter	945	integrableObject = mol->nextIntegrableObject(j)) {
106	gezelter	956
107			if (integrableObject->isRigidBody()) {
108			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110	gezelter	945	}
111
112			}
113	tim	895	}
114	gezelter	956
115
116			if (needHydroPropFile) {
117			if (simParams->haveHydroPropFile()) {
118			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119			} else {
120			sprintf( painCave.errMsg,
121			"HydroPropFile must be set to a file name if Langevin\n"
122			"\tDynamics is specified for rigidBodies which contain more\n"
123			"\tthan one atom. To create a HydroPropFile, run \"Hydro\".\n");
124			painCave.severity = OOPSE_ERROR;
125			painCave.isFatal = 1;
126			simError();
127			}
128	tim	971
129			for (mol = info->beginMolecule(i); mol != NULL;
130			mol = info->nextMolecule(i)) {
131			for (integrableObject = mol->beginIntegrableObject(j);
132			integrableObject != NULL;
133			integrableObject = mol->nextIntegrableObject(j)) {
134
135	gezelter	981	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136	tim	971	if (iter != hydroPropMap.end()) {
137			hydroProps_.push_back(iter->second);
138			} else {
139			sprintf( painCave.errMsg,
140			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141			painCave.severity = OOPSE_ERROR;
142			painCave.isFatal = 1;
143			simError();
144			}
145			}
146	gezelter	956	}
147			} else {
148	gezelter	981
149			std::map<std::string, HydroProp*> hydroPropMap;
150	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
151			mol = info->nextMolecule(i)) {
152			for (integrableObject = mol->beginIntegrableObject(j);
153			integrableObject != NULL;
154			integrableObject = mol->nextIntegrableObject(j)) {
155			Shape* currShape = NULL;
156	xsun	1185
157			if (integrableObject->isAtom()){
158			Atom* atom = static_cast<Atom*>(integrableObject);
159			AtomType* atomType = atom->getAtomType();
160	gezelter	956	if (atomType->isGayBerne()) {
161	xsun	1185	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
162	gezelter	956	GenericData* data = dAtomType->getPropertyByName("GayBerne");
163			if (data != NULL) {
164			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165
166			if (gayBerneData != NULL) {
167			GayBerneParam gayBerneParam = gayBerneData->getData();
168			currShape = new Ellipsoid(V3Zero,
169	xsun	1185	gayBerneParam.GB_l / 2.0,
170	gezelter	981	gayBerneParam.GB_d / 2.0,
171	gezelter	956	Mat3x3d::identity());
172			} else {
173			sprintf( painCave.errMsg,
174			"Can not cast GenericData to GayBerneParam\n");
175			painCave.severity = OOPSE_ERROR;
176			painCave.isFatal = 1;
177			simError();
178			}
179			} else {
180			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
181			painCave.severity = OOPSE_ERROR;
182			painCave.isFatal = 1;
183			simError();
184			}
185	xsun	1185	} else {
186			if (atomType->isLennardJones()){
187			GenericData* data = atomType->getPropertyByName("LennardJones");
188			if (data != NULL) {
189			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
190			if (ljData != NULL) {
191			LJParam ljParam = ljData->getData();
192			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
193			} else {
194			sprintf( painCave.errMsg,
195			"Can not cast GenericData to LJParam\n");
196			painCave.severity = OOPSE_ERROR;
197			painCave.isFatal = 1;
198			simError();
199			}
200			}
201			} else {
202			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
203			if (obanum != 0) {
204			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
205	gezelter	956	} else {
206			sprintf( painCave.errMsg,
207	xsun	1185	"Could not find atom type in default element.txt\n");
208	gezelter	956	painCave.severity = OOPSE_ERROR;
209			painCave.isFatal = 1;
210			simError();
211	xsun	1185	}
212	gezelter	956	}
213			}
214			}
215	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
216			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
217	gezelter	956	if (iter != hydroPropMap.end())
218			hydroProps_.push_back(iter->second);
219			else {
220	gezelter	981	currHydroProp->complete();
221			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
222			hydroProps_.push_back(currHydroProp);
223	gezelter	956	}
224			}
225			}
226			}
227	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
228	gezelter	981	}
229	gezelter	956
230	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
231			std::map<std::string, HydroProp*> props;
232	tim	895	std::ifstream ifs(filename.c_str());
233			if (ifs.is_open()) {
234	gezelter	945
235	tim	895	}
236	gezelter	945
237	tim	895	const unsigned int BufferSize = 65535;
238			char buffer[BufferSize];
239			while (ifs.getline(buffer, BufferSize)) {
240	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
241			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
242	tim	895	}
243	gezelter	981
244	tim	895	return props;
245			}
246	gezelter	981
247	gezelter	1126	void LDForceManager::postCalculation(bool needStress){
248	tim	895	SimInfo::MoleculeIterator i;
249			Molecule::IntegrableObjectIterator j;
250			Molecule* mol;
251			StuntDouble* integrableObject;
252	xsun	1185	RealType mass;
253	tim	895	Vector3d vel;
254			Vector3d pos;
255			Vector3d frc;
256			Mat3x3d A;
257	tim	904	Mat3x3d Atrans;
258	tim	895	Vector3d Tb;
259			Vector3d ji;
260			unsigned int index = 0;
261	gezelter	945	bool doLangevinForces;
262			bool freezeMolecule;
263			int fdf;
264	gezelter	983
265	xsun	1185
266
267	chuckv	1120	fdf = 0;
268	gezelter	983
269	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
270	gezelter	970
271			doLangevinForces = true;
272			freezeMolecule = false;
273
274	gezelter	945	if (sphericalBoundaryConditions_) {
275
276			Vector3d molPos = mol->getCom();
277	tim	963	RealType molRad = molPos.length();
278	chuckv	1120
279	gezelter	945	doLangevinForces = false;
280
281			if (molRad > langevinBufferRadius_) {
282			doLangevinForces = true;
283			freezeMolecule = false;
284			}
285			if (molRad > frozenBufferRadius_) {
286			doLangevinForces = false;
287			freezeMolecule = true;
288			}
289			}
290
291	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292			integrableObject = mol->nextIntegrableObject(j)) {
293	gezelter	945
294	gezelter	956	if (freezeMolecule)
295			fdf += integrableObject->freeze();
296
297	chuckv	1120	if (doLangevinForces) {
298	tim	895	vel =integrableObject->getVel();
299	xsun	1185	mass = integrableObject->getMass();
300	tim	895	if (integrableObject->isDirectional()){
301	gezelter	945	//calculate angular velocity in lab frame
302			Mat3x3d I = integrableObject->getI();
303			Vector3d angMom = integrableObject->getJ();
304			Vector3d omega;
305
306			if (integrableObject->isLinear()) {
307			int linearAxis = integrableObject->linearAxis();
308			int l = (linearAxis +1 )%3;
309			int m = (linearAxis +2 )%3;
310			omega[l] = angMom[l] /I(l, l);
311			omega[m] = angMom[m] /I(m, m);
312
313			} else {
314			omega[0] = angMom[0] /I(0, 0);
315			omega[1] = angMom[1] /I(1, 1);
316			omega[2] = angMom[2] /I(2, 2);
317			}
318	xsun	1185
319			//std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";
320
321	gezelter	945	//apply friction force and torque at center of resistance
322			A = integrableObject->getA();
323			Atrans = A.transpose();
324	xsun	1185	//std::cerr << "A = " << integrableObject->getA() << "\n";
325			//std::cerr << "Atrans = " << A.transpose() << "\n\n";
326	gezelter	981	Vector3d rcr = Atrans * hydroProps_[index]->getCOR();
327	xsun	1185	//std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
328			//std::cerr << "rcr = " << rcr << "\n\n";
329	gezelter	945	Vector3d vcdLab = vel + cross(omega, rcr);
330	xsun	1185
331			//std::cerr << "velL = " << vel << "\n\n";
332			//std::cerr << "vcdL = " << vcdLab << "\n\n";
333	gezelter	945	Vector3d vcdBody = A* vcdLab;
334	xsun	1185	//std::cerr << "vcdB = " << vcdBody << "\n\n";
335	gezelter	981	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
336	xsun	1185
337			//std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
338			//std::cerr << "ffB = " << frictionForceBody << "\n\n";
339	gezelter	945	Vector3d frictionForceLab = Atrans*frictionForceBody;
340	xsun	1185	//std::cerr << "ffL = " << frictionForceLab << "\n\n";
341			//std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
342	gezelter	945	integrableObject->addFrc(frictionForceLab);
343	xsun	1185	//std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
344			//std::cerr << "ome = " << omega << "\n\n";
345	gezelter	981	Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
346	xsun	1185	//std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
347	gezelter	945	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
348	xsun	1185	//std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
349			//std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
350			//std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
351	gezelter	945	integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
352	xsun	1185	//std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
353
354	gezelter	945	//apply random force and torque at center of resistance
355			Vector3d randomForceBody;
356			Vector3d randomTorqueBody;
357			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
358	xsun	1185	//std::cerr << "rfB = " << randomForceBody << "\n\n";
359			//std::cerr << "rtB = " << randomTorqueBody << "\n\n";
360	gezelter	945	Vector3d randomForceLab = Atrans*randomForceBody;
361			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
362			integrableObject->addFrc(randomForceLab);
363	xsun	1185	//std::cerr << "rfL = " << randomForceLab << "\n\n";
364			//std::cerr << "rtL = " << randomTorqueLab << "\n\n";
365			//std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
366	gezelter	945	integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
367
368	tim	895	} else {
369	gezelter	945	//spherical atom
370	gezelter	981	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
371	xsun	1185	//std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
372	gezelter	945	Vector3d randomForce;
373			Vector3d randomTorque;
374			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
375
376			integrableObject->addFrc(frictionForce+randomForce);
377	tim	895	}
378	gezelter	956	}
379	gezelter	945
380	gezelter	956	++index;
381	tim	895
382			}
383	gezelter	956	}
384	chuckv	1120
385	gezelter	945	info_->setFdf(fdf);
386	gezelter	983	veloMunge->removeComDrift();
387			// Remove angular drift if we are not using periodic boundary conditions.
388			if(!simParams->getUsePeriodicBoundaryConditions())
389			veloMunge->removeAngularDrift();
390
391	gezelter	1126	ForceManager::postCalculation(needStress);
392	tim	895	}
393
394	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
395	tim	904
396	tim	906
397	tim	963	Vector<RealType, 6> Z;
398			Vector<RealType, 6> generalForce;
399	tim	904
400	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
401			Z[1] = randNumGen_.randNorm(0, variance);
402			Z[2] = randNumGen_.randNorm(0, variance);
403	xsun	1185	//Z[3] = randNumGen_.randNorm(0, variance)(2.0M_PI);
404			//Z[4] = randNumGen_.randNorm(0, variance)(2.0M_PI);
405			//Z[5] = randNumGen_.randNorm(0, variance)(2.0M_PI);
406	tim	895	Z[3] = randNumGen_.randNorm(0, variance);
407			Z[4] = randNumGen_.randNorm(0, variance);
408			Z[5] = randNumGen_.randNorm(0, variance);
409	tim	904
410
411	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
412	tim	904
413	tim	895	force[0] = generalForce[0];
414			force[1] = generalForce[1];
415			force[2] = generalForce[2];
416			torque[0] = generalForce[3];
417			torque[1] = generalForce[4];
418			torque[2] = generalForce[5];
419
420	xsun	1185	}
421	tim	895
422			}