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"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "openbabel/mol.hpp"

using namespace OpenBabel;
namespace oopse {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
    Globals* simParams = info->getSimParams();
        
    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->isDirectionalAtom()) {
            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
            AtomType* atomType = dAtom->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_d / 2.0, 
                                            gayBerneParam.GB_l / 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 {
            Atom* atom = static_cast<Atom*>(integrableObject);
            AtomType* atomType = atom->getAtomType();
            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() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Mat3x3d A;
    Mat3x3d Atrans;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    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(); 
          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]->getCOR();  
            Vector3d vcdLab = vel + cross(omega, rcr);
            Vector3d vcdBody = A* vcdLab;
            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
            Vector3d frictionForceLab = Atrans*frictionForceBody;
            integrableObject->addFrc(frictionForceLab);
            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * 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]->getXitt() * vel);
            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            
            integrableObject->addFrc(frictionForce+randomForce);             
          }
        }
          
        ++index;
    
      }
    }    
    info_->setFdf(fdf);
    
    ForceManager::postCalculation();   
  }

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:	981
Committed:	Mon Jun 5 18:24:45 2006 UTC (18 years, 10 months ago) by gezelter
File size:	15097 byte(s)
Log Message:	Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
#	User	Rev	Content
1	tim	895	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include <fstream>
42			#include "integrators/LDForceManager.hpp"
43			#include "math/CholeskyDecomposition.hpp"
44	tim	904	#include "utils/OOPSEConstant.hpp"
45	gezelter	956	#include "hydrodynamics/Sphere.hpp"
46			#include "hydrodynamics/Ellipsoid.hpp"
47			#include "openbabel/mol.hpp"
48
49			using namespace OpenBabel;
50	tim	895	namespace oopse {
51
52			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
53			Globals* simParams = info->getSimParams();
54	gezelter	956
55	gezelter	945	sphericalBoundaryConditions_ = false;
56			if (simParams->getUseSphericalBoundaryConditions()) {
57			sphericalBoundaryConditions_ = true;
58			if (simParams->haveLangevinBufferRadius()) {
59			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
60			} else {
61			sprintf( painCave.errMsg,
62			"langevinBufferRadius must be specified "
63			"when useSphericalBoundaryConditions is turned on.\n");
64			painCave.severity = OOPSE_ERROR;
65			painCave.isFatal = 1;
66			simError();
67			}
68
69			if (simParams->haveFrozenBufferRadius()) {
70			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
71			} else {
72			sprintf( painCave.errMsg,
73			"frozenBufferRadius must be specified "
74			"when useSphericalBoundaryConditions is turned on.\n");
75			painCave.severity = OOPSE_ERROR;
76			painCave.isFatal = 1;
77			simError();
78			}
79	tim	895
80	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
81			sprintf( painCave.errMsg,
82			"frozenBufferRadius has been set smaller than the "
83			"langevinBufferRadius. This is probably an error.\n");
84			painCave.severity = OOPSE_WARNING;
85			painCave.isFatal = 0;
86			simError();
87			}
88			}
89	gezelter	956
90			// Build the hydroProp map:
91	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
92	gezelter	956
93	tim	895	Molecule* mol;
94			StuntDouble* integrableObject;
95	gezelter	956	SimInfo::MoleculeIterator i;
96			Molecule::IntegrableObjectIterator j;
97			bool needHydroPropFile = false;
98
99			for (mol = info->beginMolecule(i); mol != NULL;
100			mol = info->nextMolecule(i)) {
101			for (integrableObject = mol->beginIntegrableObject(j);
102			integrableObject != NULL;
103	gezelter	945	integrableObject = mol->nextIntegrableObject(j)) {
104	gezelter	956
105			if (integrableObject->isRigidBody()) {
106			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
107			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
108	gezelter	945	}
109
110			}
111	tim	895	}
112	gezelter	956
113
114			if (needHydroPropFile) {
115			if (simParams->haveHydroPropFile()) {
116			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
117			} else {
118			sprintf( painCave.errMsg,
119			"HydroPropFile must be set to a file name if Langevin\n"
120			"\tDynamics is specified for rigidBodies which contain more\n"
121			"\tthan one atom. To create a HydroPropFile, run \"Hydro\".\n");
122			painCave.severity = OOPSE_ERROR;
123			painCave.isFatal = 1;
124			simError();
125			}
126	tim	971
127			for (mol = info->beginMolecule(i); mol != NULL;
128			mol = info->nextMolecule(i)) {
129			for (integrableObject = mol->beginIntegrableObject(j);
130			integrableObject != NULL;
131			integrableObject = mol->nextIntegrableObject(j)) {
132
133	gezelter	981	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
134	tim	971	if (iter != hydroPropMap.end()) {
135			hydroProps_.push_back(iter->second);
136			} else {
137			sprintf( painCave.errMsg,
138			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
139			painCave.severity = OOPSE_ERROR;
140			painCave.isFatal = 1;
141			simError();
142			}
143			}
144	gezelter	956	}
145			} else {
146	gezelter	981
147			std::map<std::string, HydroProp*> hydroPropMap;
148	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
149			mol = info->nextMolecule(i)) {
150			for (integrableObject = mol->beginIntegrableObject(j);
151			integrableObject != NULL;
152			integrableObject = mol->nextIntegrableObject(j)) {
153			Shape* currShape = NULL;
154			if (integrableObject->isDirectionalAtom()) {
155			DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
156			AtomType* atomType = dAtom->getAtomType();
157			if (atomType->isGayBerne()) {
158			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
159
160			GenericData* data = dAtomType->getPropertyByName("GayBerne");
161			if (data != NULL) {
162			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
163
164			if (gayBerneData != NULL) {
165			GayBerneParam gayBerneParam = gayBerneData->getData();
166			currShape = new Ellipsoid(V3Zero,
167	gezelter	981	gayBerneParam.GB_d / 2.0,
168			gayBerneParam.GB_l / 2.0,
169	gezelter	956	Mat3x3d::identity());
170			} else {
171			sprintf( painCave.errMsg,
172			"Can not cast GenericData to GayBerneParam\n");
173			painCave.severity = OOPSE_ERROR;
174			painCave.isFatal = 1;
175			simError();
176			}
177			} else {
178			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
179			painCave.severity = OOPSE_ERROR;
180			painCave.isFatal = 1;
181			simError();
182			}
183			}
184			} else {
185			Atom* atom = static_cast<Atom*>(integrableObject);
186			AtomType* atomType = atom->getAtomType();
187			if (atomType->isLennardJones()){
188			GenericData* data = atomType->getPropertyByName("LennardJones");
189			if (data != NULL) {
190			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
191
192			if (ljData != NULL) {
193			LJParam ljParam = ljData->getData();
194			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
195			} else {
196			sprintf( painCave.errMsg,
197			"Can not cast GenericData to LJParam\n");
198			painCave.severity = OOPSE_ERROR;
199			painCave.isFatal = 1;
200			simError();
201			}
202			}
203			} else {
204			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
205			if (obanum != 0) {
206			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
207			} else {
208			sprintf( painCave.errMsg,
209			"Could not find atom type in default element.txt\n");
210			painCave.severity = OOPSE_ERROR;
211			painCave.isFatal = 1;
212			simError();
213			}
214			}
215			}
216	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
217			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
218	gezelter	956	if (iter != hydroPropMap.end())
219			hydroProps_.push_back(iter->second);
220			else {
221	gezelter	981	currHydroProp->complete();
222			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
223			hydroProps_.push_back(currHydroProp);
224	gezelter	956	}
225			}
226			}
227			}
228	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
229	gezelter	981	}
230	gezelter	956
231	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
232			std::map<std::string, HydroProp*> props;
233	tim	895	std::ifstream ifs(filename.c_str());
234			if (ifs.is_open()) {
235	gezelter	945
236	tim	895	}
237	gezelter	945
238	tim	895	const unsigned int BufferSize = 65535;
239			char buffer[BufferSize];
240			while (ifs.getline(buffer, BufferSize)) {
241	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
242			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
243	tim	895	}
244	gezelter	981
245	tim	895	return props;
246			}
247	gezelter	981
248	tim	895	void LDForceManager::postCalculation() {
249			SimInfo::MoleculeIterator i;
250			Molecule::IntegrableObjectIterator j;
251			Molecule* mol;
252			StuntDouble* integrableObject;
253			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	tim	963	RealType mass;
261	tim	895	unsigned int index = 0;
262	gezelter	945	bool doLangevinForces;
263			bool freezeMolecule;
264			int fdf;
265
266			fdf = 0;
267	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
268	gezelter	970
269			doLangevinForces = true;
270			freezeMolecule = false;
271
272	gezelter	945	if (sphericalBoundaryConditions_) {
273
274			Vector3d molPos = mol->getCom();
275	tim	963	RealType molRad = molPos.length();
276	gezelter	945
277			doLangevinForces = false;
278
279			if (molRad > langevinBufferRadius_) {
280			doLangevinForces = true;
281			freezeMolecule = false;
282			}
283			if (molRad > frozenBufferRadius_) {
284			doLangevinForces = false;
285			freezeMolecule = true;
286			}
287			}
288
289	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290			integrableObject = mol->nextIntegrableObject(j)) {
291	gezelter	945
292	gezelter	956	if (freezeMolecule)
293			fdf += integrableObject->freeze();
294
295			if (doLangevinForces) {
296	tim	895	vel =integrableObject->getVel();
297			if (integrableObject->isDirectional()){
298	gezelter	945	//calculate angular velocity in lab frame
299			Mat3x3d I = integrableObject->getI();
300			Vector3d angMom = integrableObject->getJ();
301			Vector3d omega;
302
303			if (integrableObject->isLinear()) {
304			int linearAxis = integrableObject->linearAxis();
305			int l = (linearAxis +1 )%3;
306			int m = (linearAxis +2 )%3;
307			omega[l] = angMom[l] /I(l, l);
308			omega[m] = angMom[m] /I(m, m);
309
310			} else {
311			omega[0] = angMom[0] /I(0, 0);
312			omega[1] = angMom[1] /I(1, 1);
313			omega[2] = angMom[2] /I(2, 2);
314			}
315
316			//apply friction force and torque at center of resistance
317			A = integrableObject->getA();
318			Atrans = A.transpose();
319	gezelter	981	Vector3d rcr = Atrans * hydroProps_[index]->getCOR();
320	gezelter	945	Vector3d vcdLab = vel + cross(omega, rcr);
321			Vector3d vcdBody = A* vcdLab;
322	gezelter	981	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
323	gezelter	945	Vector3d frictionForceLab = Atrans*frictionForceBody;
324			integrableObject->addFrc(frictionForceLab);
325	gezelter	981	Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
326	gezelter	945	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
327			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
328
329			//apply random force and torque at center of resistance
330			Vector3d randomForceBody;
331			Vector3d randomTorqueBody;
332			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
333			Vector3d randomForceLab = Atrans*randomForceBody;
334			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
335			integrableObject->addFrc(randomForceLab);
336			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
337
338	tim	895	} else {
339	gezelter	945	//spherical atom
340	gezelter	981	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
341	gezelter	945	Vector3d randomForce;
342			Vector3d randomTorque;
343			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
344
345			integrableObject->addFrc(frictionForce+randomForce);
346	tim	895	}
347	gezelter	956	}
348	gezelter	945
349	gezelter	956	++index;
350	tim	895
351			}
352	gezelter	956	}
353	gezelter	945	info_->setFdf(fdf);
354
355			ForceManager::postCalculation();
356	tim	895	}
357
358	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
359	tim	904
360	tim	906
361	tim	963	Vector<RealType, 6> Z;
362			Vector<RealType, 6> generalForce;
363	tim	904
364
365	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
366			Z[1] = randNumGen_.randNorm(0, variance);
367			Z[2] = randNumGen_.randNorm(0, variance);
368			Z[3] = randNumGen_.randNorm(0, variance);
369			Z[4] = randNumGen_.randNorm(0, variance);
370			Z[5] = randNumGen_.randNorm(0, variance);
371	tim	904
372
373	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
374	tim	904
375	tim	895	force[0] = generalForce[0];
376			force[1] = generalForce[1];
377			force[2] = generalForce[2];
378			torque[0] = generalForce[3];
379			torque[1] = generalForce[4];
380			torque[2] = generalForce[5];
381
382			}
383
384			}