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){
    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() {
    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);

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

    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:	2802
Committed:	Tue Jun 6 17:43:28 2006 UTC (18 years, 1 month ago) by gezelter
File size:	15319 byte(s)
Log Message:	testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
#	User	Rev	Content
1	tim	2611	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include <fstream>
42			#include "integrators/LDForceManager.hpp"
43			#include "math/CholeskyDecomposition.hpp"
44	tim	2632	#include "utils/OOPSEConstant.hpp"
45	gezelter	2752	#include "hydrodynamics/Sphere.hpp"
46			#include "hydrodynamics/Ellipsoid.hpp"
47			#include "openbabel/mol.hpp"
48
49			using namespace OpenBabel;
50	tim	2611	namespace oopse {
51
52			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
53	gezelter	2802	simParams = info->getSimParams();
54			veloMunge = new Velocitizer(info);
55
56	gezelter	2733	sphericalBoundaryConditions_ = false;
57			if (simParams->getUseSphericalBoundaryConditions()) {
58			sphericalBoundaryConditions_ = true;
59			if (simParams->haveLangevinBufferRadius()) {
60			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
61			} else {
62			sprintf( painCave.errMsg,
63			"langevinBufferRadius must be specified "
64			"when useSphericalBoundaryConditions is turned on.\n");
65			painCave.severity = OOPSE_ERROR;
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			if (simParams->haveFrozenBufferRadius()) {
71			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
72			} else {
73			sprintf( painCave.errMsg,
74			"frozenBufferRadius must be specified "
75			"when useSphericalBoundaryConditions is turned on.\n");
76			painCave.severity = OOPSE_ERROR;
77			painCave.isFatal = 1;
78			simError();
79			}
80	tim	2611
81	gezelter	2733	if (frozenBufferRadius_ < langevinBufferRadius_) {
82			sprintf( painCave.errMsg,
83			"frozenBufferRadius has been set smaller than the "
84			"langevinBufferRadius. This is probably an error.\n");
85			painCave.severity = OOPSE_WARNING;
86			painCave.isFatal = 0;
87			simError();
88			}
89			}
90	gezelter	2752
91			// Build the hydroProp map:
92	gezelter	2787	std::map<std::string, HydroProp*> hydroPropMap;
93	gezelter	2752
94	tim	2611	Molecule* mol;
95			StuntDouble* integrableObject;
96	gezelter	2752	SimInfo::MoleculeIterator i;
97			Molecule::IntegrableObjectIterator j;
98			bool needHydroPropFile = false;
99
100			for (mol = info->beginMolecule(i); mol != NULL;
101			mol = info->nextMolecule(i)) {
102			for (integrableObject = mol->beginIntegrableObject(j);
103			integrableObject != NULL;
104	gezelter	2733	integrableObject = mol->nextIntegrableObject(j)) {
105	gezelter	2752
106			if (integrableObject->isRigidBody()) {
107			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
108			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
109	gezelter	2733	}
110
111			}
112	tim	2611	}
113	gezelter	2752
114
115			if (needHydroPropFile) {
116			if (simParams->haveHydroPropFile()) {
117			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118			} else {
119			sprintf( painCave.errMsg,
120			"HydroPropFile must be set to a file name if Langevin\n"
121			"\tDynamics is specified for rigidBodies which contain more\n"
122			"\tthan one atom. To create a HydroPropFile, run \"Hydro\".\n");
123			painCave.severity = OOPSE_ERROR;
124			painCave.isFatal = 1;
125			simError();
126			}
127	tim	2767
128			for (mol = info->beginMolecule(i); mol != NULL;
129			mol = info->nextMolecule(i)) {
130			for (integrableObject = mol->beginIntegrableObject(j);
131			integrableObject != NULL;
132			integrableObject = mol->nextIntegrableObject(j)) {
133
134	gezelter	2787	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
135	tim	2767	if (iter != hydroPropMap.end()) {
136			hydroProps_.push_back(iter->second);
137			} else {
138			sprintf( painCave.errMsg,
139			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
140			painCave.severity = OOPSE_ERROR;
141			painCave.isFatal = 1;
142			simError();
143			}
144			}
145	gezelter	2752	}
146			} else {
147	gezelter	2787
148			std::map<std::string, HydroProp*> hydroPropMap;
149	gezelter	2752	for (mol = info->beginMolecule(i); mol != NULL;
150			mol = info->nextMolecule(i)) {
151			for (integrableObject = mol->beginIntegrableObject(j);
152			integrableObject != NULL;
153			integrableObject = mol->nextIntegrableObject(j)) {
154			Shape* currShape = NULL;
155			if (integrableObject->isDirectionalAtom()) {
156			DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
157			AtomType* atomType = dAtom->getAtomType();
158			if (atomType->isGayBerne()) {
159			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
160
161			GenericData* data = dAtomType->getPropertyByName("GayBerne");
162			if (data != NULL) {
163			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
164
165			if (gayBerneData != NULL) {
166			GayBerneParam gayBerneParam = gayBerneData->getData();
167			currShape = new Ellipsoid(V3Zero,
168	gezelter	2787	gayBerneParam.GB_d / 2.0,
169			gayBerneParam.GB_l / 2.0,
170	gezelter	2752	Mat3x3d::identity());
171			} else {
172			sprintf( painCave.errMsg,
173			"Can not cast GenericData to GayBerneParam\n");
174			painCave.severity = OOPSE_ERROR;
175			painCave.isFatal = 1;
176			simError();
177			}
178			} else {
179			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180			painCave.severity = OOPSE_ERROR;
181			painCave.isFatal = 1;
182			simError();
183			}
184			}
185			} else {
186			Atom* atom = static_cast<Atom*>(integrableObject);
187			AtomType* atomType = atom->getAtomType();
188			if (atomType->isLennardJones()){
189			GenericData* data = atomType->getPropertyByName("LennardJones");
190			if (data != NULL) {
191			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192
193			if (ljData != NULL) {
194			LJParam ljParam = ljData->getData();
195			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
196			} else {
197			sprintf( painCave.errMsg,
198			"Can not cast GenericData to LJParam\n");
199			painCave.severity = OOPSE_ERROR;
200			painCave.isFatal = 1;
201			simError();
202			}
203			}
204			} else {
205			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
206			if (obanum != 0) {
207			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
208			} else {
209			sprintf( painCave.errMsg,
210			"Could not find atom type in default element.txt\n");
211			painCave.severity = OOPSE_ERROR;
212			painCave.isFatal = 1;
213			simError();
214			}
215			}
216			}
217	gezelter	2787	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
218			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
219	gezelter	2752	if (iter != hydroPropMap.end())
220			hydroProps_.push_back(iter->second);
221			else {
222	gezelter	2787	currHydroProp->complete();
223			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
224			hydroProps_.push_back(currHydroProp);
225	gezelter	2752	}
226			}
227			}
228			}
229	tim	2632	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
230	gezelter	2787	}
231	gezelter	2752
232	gezelter	2787	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
233			std::map<std::string, HydroProp*> props;
234	tim	2611	std::ifstream ifs(filename.c_str());
235			if (ifs.is_open()) {
236	gezelter	2733
237	tim	2611	}
238	gezelter	2733
239	tim	2611	const unsigned int BufferSize = 65535;
240			char buffer[BufferSize];
241			while (ifs.getline(buffer, BufferSize)) {
242	gezelter	2787	HydroProp* currProp = new HydroProp(buffer);
243			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
244	tim	2611	}
245	gezelter	2787
246	tim	2611	return props;
247			}
248	gezelter	2787
249	tim	2611	void LDForceManager::postCalculation() {
250			SimInfo::MoleculeIterator i;
251			Molecule::IntegrableObjectIterator j;
252			Molecule* mol;
253			StuntDouble* integrableObject;
254			Vector3d vel;
255			Vector3d pos;
256			Vector3d frc;
257			Mat3x3d A;
258	tim	2632	Mat3x3d Atrans;
259	tim	2611	Vector3d Tb;
260			Vector3d ji;
261	tim	2759	RealType mass;
262	tim	2611	unsigned int index = 0;
263	gezelter	2733	bool doLangevinForces;
264			bool freezeMolecule;
265			int fdf;
266	gezelter	2802
267
268	gezelter	2733	fdf = 0;
269	tim	2611	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
270	gezelter	2766
271			doLangevinForces = true;
272			freezeMolecule = false;
273
274	gezelter	2733	if (sphericalBoundaryConditions_) {
275
276			Vector3d molPos = mol->getCom();
277	tim	2759	RealType molRad = molPos.length();
278	gezelter	2733
279			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	2752	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292			integrableObject = mol->nextIntegrableObject(j)) {
293	gezelter	2733
294	gezelter	2752	if (freezeMolecule)
295			fdf += integrableObject->freeze();
296
297			if (doLangevinForces) {
298	tim	2611	vel =integrableObject->getVel();
299			if (integrableObject->isDirectional()){
300	gezelter	2733	//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	2787	Vector3d rcr = Atrans * hydroProps_[index]->getCOR();
322	gezelter	2733	Vector3d vcdLab = vel + cross(omega, rcr);
323			Vector3d vcdBody = A* vcdLab;
324	gezelter	2787	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
325	gezelter	2733	Vector3d frictionForceLab = Atrans*frictionForceBody;
326			integrableObject->addFrc(frictionForceLab);
327	gezelter	2787	Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
328	gezelter	2733	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	2611	} else {
341	gezelter	2733	//spherical atom
342	gezelter	2787	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
343	gezelter	2733	Vector3d randomForce;
344			Vector3d randomTorque;
345			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
346
347			integrableObject->addFrc(frictionForce+randomForce);
348	tim	2611	}
349	gezelter	2752	}
350	gezelter	2733
351	gezelter	2752	++index;
352	tim	2611
353			}
354	gezelter	2752	}
355	gezelter	2733	info_->setFdf(fdf);
356	gezelter	2802
357			veloMunge->removeComDrift();
358			// Remove angular drift if we are not using periodic boundary conditions.
359			if(!simParams->getUsePeriodicBoundaryConditions())
360			veloMunge->removeAngularDrift();
361
362	gezelter	2733	ForceManager::postCalculation();
363	tim	2611	}
364
365	tim	2759	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
366	tim	2632
367	tim	2634
368	tim	2759	Vector<RealType, 6> Z;
369			Vector<RealType, 6> generalForce;
370	tim	2632
371
372	tim	2611	Z[0] = randNumGen_.randNorm(0, variance);
373			Z[1] = randNumGen_.randNorm(0, variance);
374			Z[2] = randNumGen_.randNorm(0, variance);
375			Z[3] = randNumGen_.randNorm(0, variance);
376			Z[4] = randNumGen_.randNorm(0, variance);
377			Z[5] = randNumGen_.randNorm(0, variance);
378	tim	2632
379
380	gezelter	2787	generalForce = hydroProps_[index]->getS()*Z;
381	tim	2632
382	tim	2611	force[0] = generalForce[0];
383			force[1] = generalForce[1];
384			force[2] = generalForce[2];
385			torque[0] = generalForce[3];
386			torque[1] = generalForce[4];
387			torque[2] = generalForce[5];
388
389			}
390
391			}