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->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(bool needStress){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    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(); 
          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);
    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:	1129
Committed:	Fri Apr 20 18:15:48 2007 UTC (18 years, 6 months ago) by chrisfen
Original Path:	*trunk/src/integrators/LDForceManager.cpp*
File size:	15327 byte(s)
Log Message:	SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
#	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			if (integrableObject->isDirectionalAtom()) {
157			DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
158			AtomType* atomType = dAtom->getAtomType();
159			if (atomType->isGayBerne()) {
160			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161
162			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	gezelter	981	gayBerneParam.GB_d / 2.0,
170			gayBerneParam.GB_l / 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			}
186			} else {
187			Atom* atom = static_cast<Atom*>(integrableObject);
188			AtomType* atomType = atom->getAtomType();
189			if (atomType->isLennardJones()){
190			GenericData* data = atomType->getPropertyByName("LennardJones");
191			if (data != NULL) {
192			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
193
194			if (ljData != NULL) {
195			LJParam ljParam = ljData->getData();
196			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
197			} else {
198			sprintf( painCave.errMsg,
199			"Can not cast GenericData to LJParam\n");
200			painCave.severity = OOPSE_ERROR;
201			painCave.isFatal = 1;
202			simError();
203			}
204			}
205			} else {
206			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
207			if (obanum != 0) {
208			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
209			} else {
210			sprintf( painCave.errMsg,
211			"Could not find atom type in default element.txt\n");
212			painCave.severity = OOPSE_ERROR;
213			painCave.isFatal = 1;
214			simError();
215			}
216			}
217			}
218	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
219			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
220	gezelter	956	if (iter != hydroPropMap.end())
221			hydroProps_.push_back(iter->second);
222			else {
223	gezelter	981	currHydroProp->complete();
224			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
225			hydroProps_.push_back(currHydroProp);
226	gezelter	956	}
227			}
228			}
229			}
230	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
231	gezelter	981	}
232	gezelter	956
233	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
234			std::map<std::string, HydroProp*> props;
235	tim	895	std::ifstream ifs(filename.c_str());
236			if (ifs.is_open()) {
237	gezelter	945
238	tim	895	}
239	gezelter	945
240	tim	895	const unsigned int BufferSize = 65535;
241			char buffer[BufferSize];
242			while (ifs.getline(buffer, BufferSize)) {
243	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
244			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
245	tim	895	}
246	gezelter	981
247	tim	895	return props;
248			}
249	gezelter	981
250	gezelter	1126	void LDForceManager::postCalculation(bool needStress){
251	tim	895	SimInfo::MoleculeIterator i;
252			Molecule::IntegrableObjectIterator j;
253			Molecule* mol;
254			StuntDouble* integrableObject;
255			Vector3d vel;
256			Vector3d pos;
257			Vector3d frc;
258			Mat3x3d A;
259	tim	904	Mat3x3d Atrans;
260	tim	895	Vector3d Tb;
261			Vector3d ji;
262			unsigned int index = 0;
263	gezelter	945	bool doLangevinForces;
264			bool freezeMolecule;
265			int fdf;
266	gezelter	983
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			if (integrableObject->isDirectional()){
300	gezelter	945	//calculate angular velocity in lab frame
301			Mat3x3d I = integrableObject->getI();
302			Vector3d angMom = integrableObject->getJ();
303			Vector3d omega;
304
305			if (integrableObject->isLinear()) {
306			int linearAxis = integrableObject->linearAxis();
307			int l = (linearAxis +1 )%3;
308			int m = (linearAxis +2 )%3;
309			omega[l] = angMom[l] /I(l, l);
310			omega[m] = angMom[m] /I(m, m);
311
312			} else {
313			omega[0] = angMom[0] /I(0, 0);
314			omega[1] = angMom[1] /I(1, 1);
315			omega[2] = angMom[2] /I(2, 2);
316			}
317
318			//apply friction force and torque at center of resistance
319			A = integrableObject->getA();
320			Atrans = A.transpose();
321	gezelter	981	Vector3d rcr = Atrans * hydroProps_[index]->getCOR();
322	gezelter	945	Vector3d vcdLab = vel + cross(omega, rcr);
323			Vector3d vcdBody = A* vcdLab;
324	gezelter	981	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
325	gezelter	945	Vector3d frictionForceLab = Atrans*frictionForceBody;
326			integrableObject->addFrc(frictionForceLab);
327	gezelter	981	Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
328	gezelter	945	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
329			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
330
331			//apply random force and torque at center of resistance
332			Vector3d randomForceBody;
333			Vector3d randomTorqueBody;
334			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
335			Vector3d randomForceLab = Atrans*randomForceBody;
336			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
337			integrableObject->addFrc(randomForceLab);
338			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
339
340	tim	895	} else {
341	gezelter	945	//spherical atom
342	gezelter	981	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
343	gezelter	945	Vector3d randomForce;
344			Vector3d randomTorque;
345			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
346
347			integrableObject->addFrc(frictionForce+randomForce);
348	tim	895	}
349	gezelter	956	}
350	gezelter	945
351	gezelter	956	++index;
352	tim	895
353			}
354	gezelter	956	}
355	chuckv	1120
356	gezelter	945	info_->setFdf(fdf);
357	gezelter	983	veloMunge->removeComDrift();
358			// Remove angular drift if we are not using periodic boundary conditions.
359			if(!simParams->getUsePeriodicBoundaryConditions())
360			veloMunge->removeAngularDrift();
361
362	gezelter	1126	ForceManager::postCalculation(needStress);
363	tim	895	}
364
365	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
366	tim	904
367	tim	906
368	tim	963	Vector<RealType, 6> Z;
369			Vector<RealType, 6> generalForce;
370	tim	904
371	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
372			Z[1] = randNumGen_.randNorm(0, variance);
373			Z[2] = randNumGen_.randNorm(0, variance);
374			Z[3] = randNumGen_.randNorm(0, variance);
375			Z[4] = randNumGen_.randNorm(0, variance);
376			Z[5] = randNumGen_.randNorm(0, variance);
377	tim	904
378
379	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
380	tim	904
381	tim	895	force[0] = generalForce[0];
382			force[1] = generalForce[1];
383			force[2] = generalForce[2];
384			torque[0] = generalForce[3];
385			torque[1] = generalForce[4];
386			torque[2] = generalForce[5];
387
388			}
389
390			}