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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include <fstream> 
#include <iostream>
#include "integrators/LDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/PhysicalConstants.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "utils/ElementsTable.hpp"

namespace OpenMD {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
    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 = OPENMD_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 = OPENMD_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 = OPENMD_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 Dynamics\n"
                 "\tis specified for rigidBodies which contain more than one atom\n"
                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
        painCave.severity = OPENMD_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 = OPENMD_ERROR;
            painCave.isFatal = 1;
            simError();  
          }        
        }
      }
    } else {
      
      std::map<std::string, HydroProp*> hydroPropMap;
      for (mol = info->beginMolecule(i); mol != NULL; 
           mol = info->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); 
             integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {
          Shape* currShape = NULL;

          if (integrableObject->isAtom()){
            Atom* atom = static_cast<Atom*>(integrableObject);
            AtomType* atomType = atom->getAtomType();
            if (atomType->isGayBerne()) {
              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
              GenericData* data = dAtomType->getPropertyByName("GayBerne");
              if (data != NULL) {
                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
                
                if (gayBerneData != NULL) {  
                  GayBerneParam gayBerneParam = gayBerneData->getData();
                  currShape = new Ellipsoid(V3Zero, 
                                            gayBerneParam.GB_l / 2.0, 
                                            gayBerneParam.GB_d / 2.0, 
                                            Mat3x3d::identity());
                } else {
                  sprintf( painCave.errMsg,
                           "Can not cast GenericData to GayBerneParam\n");
                  painCave.severity = OPENMD_ERROR;
                  painCave.isFatal = 1;
                  simError();   
                }
              } else {
                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
                painCave.severity = OPENMD_ERROR;
                painCave.isFatal = 1;
                simError();    
              }
            } else {
              if (atomType->isLennardJones()){
                GenericData* data = atomType->getPropertyByName("LennardJones");
                if (data != NULL) {
                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
                  if (ljData != NULL) {
                    LJParam ljParam = ljData->getData();
                    currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
                  } else {
                    sprintf( painCave.errMsg,
                             "Can not cast GenericData to LJParam\n");
                    painCave.severity = OPENMD_ERROR;
                    painCave.isFatal = 1;
                    simError();          
                  }       
                }
              } else {
                int aNum = etab.GetAtomicNum((atom->getType()).c_str());
                if (aNum != 0) {
                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
                } else {
                  sprintf( painCave.errMsg,
                           "Could not find atom type in default element.txt\n");
                  painCave.severity = OPENMD_ERROR;
                  painCave.isFatal = 1;
                  simError();          
                }
              }
            }
          }

          if (!simParams->haveTargetTemp()) {
            sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
            painCave.isFatal = 1;
            painCave.severity = OPENMD_ERROR;
            simError();
          }

          if (!simParams->haveViscosity()) {
            sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
            painCave.isFatal = 1;
            painCave.severity = OPENMD_ERROR;
            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 * PhysicalConstants::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;
    RealType mass;
    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) {  
          mass = integrableObject->getMass();
          if (integrableObject->isDirectional()){

            // preliminaries for directional objects:

            A = integrableObject->getA();
            Atrans = A.transpose();
            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  

            //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(rcrLab, randomForceLab ));             

            Mat3x3d I = integrableObject->getI();
            Vector3d omegaBody;

            // What remains contains velocity explicitly, but the velocity required
            // is at the full step: v(t + h), while we have initially the velocity
            // at the half step: v(t + h/2).  We need to iterate to converge the
            // friction force and friction torque vectors.

            // this is the velocity at the half-step:
            
            Vector3d vel =integrableObject->getVel();
            Vector3d angMom = integrableObject->getJ();

            //estimate velocity at full-step using everything but friction forces:           

            frc = integrableObject->getFrc();
            Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;

            Tb = integrableObject->lab2Body(integrableObject->getTrq());
            Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;                             

            Vector3d omegaLab;
            Vector3d vcdLab;
            Vector3d vcdBody;
            Vector3d frictionForceBody;
            Vector3d frictionForceLab(0.0);
            Vector3d oldFFL;  // used to test for convergence
            Vector3d frictionTorqueBody(0.0);
            Vector3d oldFTB;  // used to test for convergence
            Vector3d frictionTorqueLab;
            RealType fdot;
            RealType tdot;

            //iteration starts here:

            for (int k = 0; k < maxIterNum_; k++) {
                            
              if (integrableObject->isLinear()) {
                int linearAxis = integrableObject->linearAxis();
                int l = (linearAxis +1 )%3;
                int m = (linearAxis +2 )%3;
                omegaBody[l] = angMomStep[l] /I(l, l);
                omegaBody[m] = angMomStep[m] /I(m, m);
                
              } else {
                omegaBody[0] = angMomStep[0] /I(0, 0);
                omegaBody[1] = angMomStep[1] /I(1, 1);
                omegaBody[2] = angMomStep[2] /I(2, 2);
              }
              
              omegaLab = Atrans * omegaBody;
              
              // apply friction force and torque at center of resistance
              
              vcdLab = velStep + cross(omegaLab, rcrLab);       
              vcdBody = A * vcdLab;
              frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
              oldFFL = frictionForceLab;
              frictionForceLab = Atrans * frictionForceBody;
              oldFTB = frictionTorqueBody;
              frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
              frictionTorqueLab = Atrans * frictionTorqueBody;
              
              // re-estimate velocities at full-step using friction forces:
              
              velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
              angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);

              // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
              
              fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
              tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
              
              if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
                break; // iteration ends here
            }

            integrableObject->addFrc(frictionForceLab);
            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));

            
          } else {
            //spherical atom

            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            integrableObject->addFrc(randomForce);            

            // What remains contains velocity explicitly, but the velocity required
            // is at the full step: v(t + h), while we have initially the velocity
            // at the half step: v(t + h/2).  We need to iterate to converge the
            // friction force vector.

            // this is the velocity at the half-step:
            
            Vector3d vel =integrableObject->getVel();

            //estimate velocity at full-step using everything but friction forces:           

            frc = integrableObject->getFrc();
            Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;

            Vector3d frictionForce(0.0);
            Vector3d oldFF;  // used to test for convergence
            RealType fdot;

            //iteration starts here:

            for (int k = 0; k < maxIterNum_; k++) {

              oldFF = frictionForce;                            
              frictionForce = -hydroProps_[index]->getXitt() * velStep;

              // re-estimate velocities at full-step using friction forces:
              
              velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);

              // check for convergence (if the vector has converged, fdot will be 1.0):
              
              fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
              
              if (fabs(1.0 - fdot) <= forceTolerance_)
                break; // iteration ends here
            }

            integrableObject->addFrc(frictionForce);

          }
        }
          
        ++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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	19651 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	895	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	895	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	895	*/
42			#include <fstream>
43	chuckv	1120	#include <iostream>
44	tim	895	#include "integrators/LDForceManager.hpp"
45			#include "math/CholeskyDecomposition.hpp"
46	gezelter	1390	#include "utils/PhysicalConstants.hpp"
47	gezelter	956	#include "hydrodynamics/Sphere.hpp"
48			#include "hydrodynamics/Ellipsoid.hpp"
49	gezelter	1210	#include "utils/ElementsTable.hpp"
50	gezelter	956
51	gezelter	1390	namespace OpenMD {
52	tim	895
53	gezelter	1237	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
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	gezelter	1390	painCave.severity = OPENMD_ERROR;
67	gezelter	945	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
78	gezelter	945	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	gezelter	1390	painCave.severity = OPENMD_WARNING;
87	gezelter	945	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	gezelter	1237	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
122			"\tis specified for rigidBodies which contain more than one atom\n"
123			"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
124	gezelter	1390	painCave.severity = OPENMD_ERROR;
125	gezelter	956	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
142	tim	971	painCave.isFatal = 1;
143			simError();
144			}
145			}
146	gezelter	956	}
147			} else {
148	gezelter	981
149			std::map<std::string, HydroProp*> hydroPropMap;
150	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
151			mol = info->nextMolecule(i)) {
152			for (integrableObject = mol->beginIntegrableObject(j);
153			integrableObject != NULL;
154			integrableObject = mol->nextIntegrableObject(j)) {
155			Shape* currShape = NULL;
156	xsun	1185
157			if (integrableObject->isAtom()){
158			Atom* atom = static_cast<Atom*>(integrableObject);
159			AtomType* atomType = atom->getAtomType();
160	gezelter	956	if (atomType->isGayBerne()) {
161	xsun	1185	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
162	gezelter	956	GenericData* data = dAtomType->getPropertyByName("GayBerne");
163			if (data != NULL) {
164			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165
166			if (gayBerneData != NULL) {
167			GayBerneParam gayBerneParam = gayBerneData->getData();
168			currShape = new Ellipsoid(V3Zero,
169	xsun	1185	gayBerneParam.GB_l / 2.0,
170	gezelter	981	gayBerneParam.GB_d / 2.0,
171	gezelter	956	Mat3x3d::identity());
172			} else {
173			sprintf( painCave.errMsg,
174			"Can not cast GenericData to GayBerneParam\n");
175	gezelter	1390	painCave.severity = OPENMD_ERROR;
176	gezelter	956	painCave.isFatal = 1;
177			simError();
178			}
179			} else {
180			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
181	gezelter	1390	painCave.severity = OPENMD_ERROR;
182	gezelter	956	painCave.isFatal = 1;
183			simError();
184			}
185	xsun	1185	} else {
186			if (atomType->isLennardJones()){
187			GenericData* data = atomType->getPropertyByName("LennardJones");
188			if (data != NULL) {
189			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
190			if (ljData != NULL) {
191			LJParam ljParam = ljData->getData();
192			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
193			} else {
194			sprintf( painCave.errMsg,
195			"Can not cast GenericData to LJParam\n");
196	gezelter	1390	painCave.severity = OPENMD_ERROR;
197	xsun	1185	painCave.isFatal = 1;
198			simError();
199			}
200			}
201			} else {
202	gezelter	1237	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
203			if (aNum != 0) {
204			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
205	gezelter	956	} else {
206			sprintf( painCave.errMsg,
207	xsun	1185	"Could not find atom type in default element.txt\n");
208	gezelter	1390	painCave.severity = OPENMD_ERROR;
209	gezelter	956	painCave.isFatal = 1;
210			simError();
211	xsun	1185	}
212	gezelter	956	}
213			}
214			}
215	chuckv	1293
216			if (!simParams->haveTargetTemp()) {
217			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
218			painCave.isFatal = 1;
219	gezelter	1390	painCave.severity = OPENMD_ERROR;
220	chuckv	1293	simError();
221			}
222
223			if (!simParams->haveViscosity()) {
224			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
225			painCave.isFatal = 1;
226	gezelter	1390	painCave.severity = OPENMD_ERROR;
227	chuckv	1293	simError();
228			}
229
230
231	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
232			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
233	gezelter	956	if (iter != hydroPropMap.end())
234			hydroProps_.push_back(iter->second);
235			else {
236	gezelter	981	currHydroProp->complete();
237			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
238			hydroProps_.push_back(currHydroProp);
239	gezelter	956	}
240			}
241			}
242			}
243	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
244	gezelter	981	}
245	gezelter	956
246	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
247			std::map<std::string, HydroProp*> props;
248	tim	895	std::ifstream ifs(filename.c_str());
249			if (ifs.is_open()) {
250	gezelter	945
251	tim	895	}
252	gezelter	945
253	tim	895	const unsigned int BufferSize = 65535;
254			char buffer[BufferSize];
255			while (ifs.getline(buffer, BufferSize)) {
256	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
257			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
258	tim	895	}
259	gezelter	981
260	tim	895	return props;
261			}
262	gezelter	981
263	gezelter	1464	void LDForceManager::postCalculation(){
264	tim	895	SimInfo::MoleculeIterator i;
265			Molecule::IntegrableObjectIterator j;
266			Molecule* mol;
267			StuntDouble* integrableObject;
268	xsun	1185	RealType mass;
269	tim	895	Vector3d pos;
270			Vector3d frc;
271			Mat3x3d A;
272	tim	904	Mat3x3d Atrans;
273	tim	895	Vector3d Tb;
274			Vector3d ji;
275			unsigned int index = 0;
276	gezelter	945	bool doLangevinForces;
277			bool freezeMolecule;
278			int fdf;
279	gezelter	983
280	chuckv	1120	fdf = 0;
281	gezelter	983
282	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
283	gezelter	970
284			doLangevinForces = true;
285			freezeMolecule = false;
286
287	gezelter	945	if (sphericalBoundaryConditions_) {
288
289			Vector3d molPos = mol->getCom();
290	tim	963	RealType molRad = molPos.length();
291	chuckv	1120
292	gezelter	945	doLangevinForces = false;
293
294			if (molRad > langevinBufferRadius_) {
295			doLangevinForces = true;
296			freezeMolecule = false;
297			}
298			if (molRad > frozenBufferRadius_) {
299			doLangevinForces = false;
300			freezeMolecule = true;
301			}
302			}
303
304	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305			integrableObject = mol->nextIntegrableObject(j)) {
306	gezelter	945
307	gezelter	956	if (freezeMolecule)
308			fdf += integrableObject->freeze();
309
310	chuckv	1120	if (doLangevinForces) {
311	xsun	1185	mass = integrableObject->getMass();
312	tim	895	if (integrableObject->isDirectional()){
313	gezelter	1237
314			// preliminaries for directional objects:
315
316	xsun	1216	A = integrableObject->getA();
317			Atrans = A.transpose();
318			Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
319	xsun	1185
320	gezelter	1237	//apply random force and torque at center of resistance
321	xsun	1185
322	gezelter	945	Vector3d randomForceBody;
323			Vector3d randomTorqueBody;
324			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
325	xsun	1216	Vector3d randomForceLab = Atrans * randomForceBody;
326			Vector3d randomTorqueLab = Atrans * randomTorqueBody;
327	gezelter	945	integrableObject->addFrc(randomForceLab);
328	xsun	1216	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
329	gezelter	1237
330			Mat3x3d I = integrableObject->getI();
331			Vector3d omegaBody;
332
333			// What remains contains velocity explicitly, but the velocity required
334			// is at the full step: v(t + h), while we have initially the velocity
335			// at the half step: v(t + h/2). We need to iterate to converge the
336			// friction force and friction torque vectors.
337
338			// this is the velocity at the half-step:
339	gezelter	945
340	gezelter	1237	Vector3d vel =integrableObject->getVel();
341			Vector3d angMom = integrableObject->getJ();
342
343			//estimate velocity at full-step using everything but friction forces:
344
345			frc = integrableObject->getFrc();
346	gezelter	1390	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
347	gezelter	1237
348			Tb = integrableObject->lab2Body(integrableObject->getTrq());
349	gezelter	1390	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
350	gezelter	1237
351			Vector3d omegaLab;
352			Vector3d vcdLab;
353			Vector3d vcdBody;
354			Vector3d frictionForceBody;
355			Vector3d frictionForceLab(0.0);
356			Vector3d oldFFL; // used to test for convergence
357			Vector3d frictionTorqueBody(0.0);
358			Vector3d oldFTB; // used to test for convergence
359			Vector3d frictionTorqueLab;
360			RealType fdot;
361			RealType tdot;
362
363			//iteration starts here:
364
365			for (int k = 0; k < maxIterNum_; k++) {
366
367			if (integrableObject->isLinear()) {
368			int linearAxis = integrableObject->linearAxis();
369			int l = (linearAxis +1 )%3;
370			int m = (linearAxis +2 )%3;
371			omegaBody[l] = angMomStep[l] /I(l, l);
372			omegaBody[m] = angMomStep[m] /I(m, m);
373
374			} else {
375			omegaBody[0] = angMomStep[0] /I(0, 0);
376			omegaBody[1] = angMomStep[1] /I(1, 1);
377			omegaBody[2] = angMomStep[2] /I(2, 2);
378			}
379
380			omegaLab = Atrans * omegaBody;
381
382			// apply friction force and torque at center of resistance
383
384			vcdLab = velStep + cross(omegaLab, rcrLab);
385			vcdBody = A * vcdLab;
386			frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
387			oldFFL = frictionForceLab;
388			frictionForceLab = Atrans * frictionForceBody;
389			oldFTB = frictionTorqueBody;
390			frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
391			frictionTorqueLab = Atrans * frictionTorqueBody;
392
393			// re-estimate velocities at full-step using friction forces:
394
395	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
396			angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
397	gezelter	1237
398			// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
399
400			fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
401			tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
402
403			if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
404			break; // iteration ends here
405			}
406
407			integrableObject->addFrc(frictionForceLab);
408			integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
409
410
411	tim	895	} else {
412	gezelter	945	//spherical atom
413	gezelter	1237
414	gezelter	945	Vector3d randomForce;
415			Vector3d randomTorque;
416			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
417	gezelter	1237	integrableObject->addFrc(randomForce);
418
419			// What remains contains velocity explicitly, but the velocity required
420			// is at the full step: v(t + h), while we have initially the velocity
421			// at the half step: v(t + h/2). We need to iterate to converge the
422			// friction force vector.
423
424			// this is the velocity at the half-step:
425	gezelter	945
426	gezelter	1237	Vector3d vel =integrableObject->getVel();
427
428			//estimate velocity at full-step using everything but friction forces:
429
430			frc = integrableObject->getFrc();
431	gezelter	1390	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
432	gezelter	1237
433			Vector3d frictionForce(0.0);
434			Vector3d oldFF; // used to test for convergence
435			RealType fdot;
436
437			//iteration starts here:
438
439			for (int k = 0; k < maxIterNum_; k++) {
440
441			oldFF = frictionForce;
442			frictionForce = -hydroProps_[index]->getXitt() * velStep;
443
444			// re-estimate velocities at full-step using friction forces:
445
446	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
447	gezelter	1237
448			// check for convergence (if the vector has converged, fdot will be 1.0):
449
450			fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
451
452			if (fabs(1.0 - fdot) <= forceTolerance_)
453			break; // iteration ends here
454			}
455
456			integrableObject->addFrc(frictionForce);
457
458	tim	895	}
459	gezelter	956	}
460	gezelter	945
461	gezelter	956	++index;
462	tim	895
463			}
464	gezelter	956	}
465	chuckv	1120
466	gezelter	945	info_->setFdf(fdf);
467	gezelter	983	veloMunge->removeComDrift();
468			// Remove angular drift if we are not using periodic boundary conditions.
469			if(!simParams->getUsePeriodicBoundaryConditions())
470			veloMunge->removeAngularDrift();
471
472	gezelter	1464	ForceManager::postCalculation();
473	tim	895	}
474
475	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
476	tim	904
477	tim	906
478	tim	963	Vector<RealType, 6> Z;
479			Vector<RealType, 6> generalForce;
480	tim	904
481	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
482			Z[1] = randNumGen_.randNorm(0, variance);
483			Z[2] = randNumGen_.randNorm(0, variance);
484			Z[3] = randNumGen_.randNorm(0, variance);
485			Z[4] = randNumGen_.randNorm(0, variance);
486			Z[5] = randNumGen_.randNorm(0, variance);
487	tim	904
488	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
489	tim	904
490	tim	895	force[0] = generalForce[0];
491			force[1] = generalForce[1];
492			force[2] = generalForce[2];
493			torque[0] = generalForce[3];
494			torque[1] = generalForce[4];
495			torque[2] = generalForce[5];
496
497	xsun	1185	}
498	tim	895
499			}