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;
    RealType mass;
    unsigned int index = 0;
    bool doLangevinForces;
    bool freezeMolecule;
    int fdf;
    int nIntegrated;
    int nFrozen;

    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:	3126
Committed:	Fri Apr 6 21:53:43 2007 UTC (17 years, 3 months ago) by gezelter
File size:	15384 byte(s)
Log Message:	Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
#	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	chuckv	3118	#include <iostream>
43	tim	2611	#include "integrators/LDForceManager.hpp"
44			#include "math/CholeskyDecomposition.hpp"
45	tim	2632	#include "utils/OOPSEConstant.hpp"
46	gezelter	2752	#include "hydrodynamics/Sphere.hpp"
47			#include "hydrodynamics/Ellipsoid.hpp"
48			#include "openbabel/mol.hpp"
49
50			using namespace OpenBabel;
51	tim	2611	namespace oopse {
52
53			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54	gezelter	2802	simParams = info->getSimParams();
55			veloMunge = new Velocitizer(info);
56
57	gezelter	2733	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	2611
82	gezelter	2733	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	2752
92			// Build the hydroProp map:
93	gezelter	2787	std::map<std::string, HydroProp*> hydroPropMap;
94	gezelter	2752
95	tim	2611	Molecule* mol;
96			StuntDouble* integrableObject;
97	gezelter	2752	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	2733	integrableObject = mol->nextIntegrableObject(j)) {
106	gezelter	2752
107			if (integrableObject->isRigidBody()) {
108			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110	gezelter	2733	}
111
112			}
113	tim	2611	}
114	gezelter	2752
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	2767
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	2787	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136	tim	2767	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	2752	}
147			} else {
148	gezelter	2787
149			std::map<std::string, HydroProp*> hydroPropMap;
150	gezelter	2752	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	2787	gayBerneParam.GB_d / 2.0,
170			gayBerneParam.GB_l / 2.0,
171	gezelter	2752	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	2787	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
219			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
220	gezelter	2752	if (iter != hydroPropMap.end())
221			hydroProps_.push_back(iter->second);
222			else {
223	gezelter	2787	currHydroProp->complete();
224			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
225			hydroProps_.push_back(currHydroProp);
226	gezelter	2752	}
227			}
228			}
229			}
230	tim	2632	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
231	gezelter	2787	}
232	gezelter	2752
233	gezelter	2787	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
234			std::map<std::string, HydroProp*> props;
235	tim	2611	std::ifstream ifs(filename.c_str());
236			if (ifs.is_open()) {
237	gezelter	2733
238	tim	2611	}
239	gezelter	2733
240	tim	2611	const unsigned int BufferSize = 65535;
241			char buffer[BufferSize];
242			while (ifs.getline(buffer, BufferSize)) {
243	gezelter	2787	HydroProp* currProp = new HydroProp(buffer);
244			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
245	tim	2611	}
246	gezelter	2787
247	tim	2611	return props;
248			}
249	gezelter	2787
250	gezelter	3126	void LDForceManager::postCalculation(bool needStress){
251	tim	2611	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	2632	Mat3x3d Atrans;
260	tim	2611	Vector3d Tb;
261			Vector3d ji;
262	tim	2759	RealType mass;
263	tim	2611	unsigned int index = 0;
264	gezelter	2733	bool doLangevinForces;
265			bool freezeMolecule;
266			int fdf;
267	chuckv	3118	int nIntegrated;
268			int nFrozen;
269	gezelter	2802
270	chuckv	3118	fdf = 0;
271	gezelter	2802
272	tim	2611	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
273	gezelter	2766
274			doLangevinForces = true;
275			freezeMolecule = false;
276
277	gezelter	2733	if (sphericalBoundaryConditions_) {
278
279			Vector3d molPos = mol->getCom();
280	tim	2759	RealType molRad = molPos.length();
281	chuckv	3118
282	gezelter	2733	doLangevinForces = false;
283
284			if (molRad > langevinBufferRadius_) {
285			doLangevinForces = true;
286			freezeMolecule = false;
287			}
288			if (molRad > frozenBufferRadius_) {
289			doLangevinForces = false;
290			freezeMolecule = true;
291			}
292			}
293
294	gezelter	2752	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
295			integrableObject = mol->nextIntegrableObject(j)) {
296	gezelter	2733
297	gezelter	2752	if (freezeMolecule)
298			fdf += integrableObject->freeze();
299
300	chuckv	3118	if (doLangevinForces) {
301	tim	2611	vel =integrableObject->getVel();
302			if (integrableObject->isDirectional()){
303	gezelter	2733	//calculate angular velocity in lab frame
304			Mat3x3d I = integrableObject->getI();
305			Vector3d angMom = integrableObject->getJ();
306			Vector3d omega;
307
308			if (integrableObject->isLinear()) {
309			int linearAxis = integrableObject->linearAxis();
310			int l = (linearAxis +1 )%3;
311			int m = (linearAxis +2 )%3;
312			omega[l] = angMom[l] /I(l, l);
313			omega[m] = angMom[m] /I(m, m);
314
315			} else {
316			omega[0] = angMom[0] /I(0, 0);
317			omega[1] = angMom[1] /I(1, 1);
318			omega[2] = angMom[2] /I(2, 2);
319			}
320
321			//apply friction force and torque at center of resistance
322			A = integrableObject->getA();
323			Atrans = A.transpose();
324	gezelter	2787	Vector3d rcr = Atrans * hydroProps_[index]->getCOR();
325	gezelter	2733	Vector3d vcdLab = vel + cross(omega, rcr);
326			Vector3d vcdBody = A* vcdLab;
327	gezelter	2787	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
328	gezelter	2733	Vector3d frictionForceLab = Atrans*frictionForceBody;
329			integrableObject->addFrc(frictionForceLab);
330	gezelter	2787	Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
331	gezelter	2733	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
332			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
333
334			//apply random force and torque at center of resistance
335			Vector3d randomForceBody;
336			Vector3d randomTorqueBody;
337			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
338			Vector3d randomForceLab = Atrans*randomForceBody;
339			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
340			integrableObject->addFrc(randomForceLab);
341			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
342
343	tim	2611	} else {
344	gezelter	2733	//spherical atom
345	gezelter	2787	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
346	gezelter	2733	Vector3d randomForce;
347			Vector3d randomTorque;
348			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
349
350			integrableObject->addFrc(frictionForce+randomForce);
351	tim	2611	}
352	gezelter	2752	}
353	gezelter	2733
354	gezelter	2752	++index;
355	tim	2611
356			}
357	gezelter	2752	}
358	chuckv	3118
359	gezelter	2733	info_->setFdf(fdf);
360	gezelter	2802	veloMunge->removeComDrift();
361			// Remove angular drift if we are not using periodic boundary conditions.
362			if(!simParams->getUsePeriodicBoundaryConditions())
363			veloMunge->removeAngularDrift();
364
365	gezelter	3126	ForceManager::postCalculation(needStress);
366	tim	2611	}
367
368	tim	2759	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
369	tim	2632
370	tim	2634
371	tim	2759	Vector<RealType, 6> Z;
372			Vector<RealType, 6> generalForce;
373	tim	2632
374	tim	2611	Z[0] = randNumGen_.randNorm(0, variance);
375			Z[1] = randNumGen_.randNorm(0, variance);
376			Z[2] = randNumGen_.randNorm(0, variance);
377			Z[3] = randNumGen_.randNorm(0, variance);
378			Z[4] = randNumGen_.randNorm(0, variance);
379			Z[5] = randNumGen_.randNorm(0, variance);
380	tim	2632
381
382	gezelter	2787	generalForce = hydroProps_[index]->getS()*Z;
383	tim	2632
384	tim	2611	force[0] = generalForce[0];
385			force[1] = generalForce[1];
386			force[2] = generalForce[2];
387			torque[0] = generalForce[3];
388			torque[1] = generalForce[4];
389			torque[2] = generalForce[5];
390
391			}
392
393			}