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]  Vardeman & Gezelter, in progress (2009).                        
 */
#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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	19585 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	895	*/
41			#include <fstream>
42	chuckv	1120	#include <iostream>
43	tim	895	#include "integrators/LDForceManager.hpp"
44			#include "math/CholeskyDecomposition.hpp"
45	gezelter	1390	#include "utils/PhysicalConstants.hpp"
46	gezelter	956	#include "hydrodynamics/Sphere.hpp"
47			#include "hydrodynamics/Ellipsoid.hpp"
48	gezelter	1210	#include "utils/ElementsTable.hpp"
49	gezelter	956
50	gezelter	1390	namespace OpenMD {
51	tim	895
52	gezelter	1237	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53	gezelter	983	simParams = info->getSimParams();
54			veloMunge = new Velocitizer(info);
55
56	gezelter	945	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
66	gezelter	945	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
77	gezelter	945	painCave.isFatal = 1;
78			simError();
79			}
80	tim	895
81	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
82			sprintf( painCave.errMsg,
83			"frozenBufferRadius has been set smaller than the "
84			"langevinBufferRadius. This is probably an error.\n");
85	gezelter	1390	painCave.severity = OPENMD_WARNING;
86	gezelter	945	painCave.isFatal = 0;
87			simError();
88			}
89			}
90	gezelter	956
91			// Build the hydroProp map:
92	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
93	gezelter	956
94	tim	895	Molecule* mol;
95			StuntDouble* integrableObject;
96	gezelter	956	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	945	integrableObject = mol->nextIntegrableObject(j)) {
105	gezelter	956
106			if (integrableObject->isRigidBody()) {
107			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
108			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
109	gezelter	945	}
110
111			}
112	tim	895	}
113	gezelter	956
114
115			if (needHydroPropFile) {
116			if (simParams->haveHydroPropFile()) {
117			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118			} else {
119			sprintf( painCave.errMsg,
120	gezelter	1237	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
121			"\tis specified for rigidBodies which contain more than one atom\n"
122			"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
123	gezelter	1390	painCave.severity = OPENMD_ERROR;
124	gezelter	956	painCave.isFatal = 1;
125			simError();
126			}
127	tim	971
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	981	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
135	tim	971	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
141	tim	971	painCave.isFatal = 1;
142			simError();
143			}
144			}
145	gezelter	956	}
146			} else {
147	gezelter	981
148			std::map<std::string, HydroProp*> hydroPropMap;
149	gezelter	956	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	xsun	1185
156			if (integrableObject->isAtom()){
157			Atom* atom = static_cast<Atom*>(integrableObject);
158			AtomType* atomType = atom->getAtomType();
159	gezelter	956	if (atomType->isGayBerne()) {
160	xsun	1185	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161	gezelter	956	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	xsun	1185	gayBerneParam.GB_l / 2.0,
169	gezelter	981	gayBerneParam.GB_d / 2.0,
170	gezelter	956	Mat3x3d::identity());
171			} else {
172			sprintf( painCave.errMsg,
173			"Can not cast GenericData to GayBerneParam\n");
174	gezelter	1390	painCave.severity = OPENMD_ERROR;
175	gezelter	956	painCave.isFatal = 1;
176			simError();
177			}
178			} else {
179			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180	gezelter	1390	painCave.severity = OPENMD_ERROR;
181	gezelter	956	painCave.isFatal = 1;
182			simError();
183			}
184	xsun	1185	} else {
185			if (atomType->isLennardJones()){
186			GenericData* data = atomType->getPropertyByName("LennardJones");
187			if (data != NULL) {
188			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
189			if (ljData != NULL) {
190			LJParam ljParam = ljData->getData();
191			currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
192			} else {
193			sprintf( painCave.errMsg,
194			"Can not cast GenericData to LJParam\n");
195	gezelter	1390	painCave.severity = OPENMD_ERROR;
196	xsun	1185	painCave.isFatal = 1;
197			simError();
198			}
199			}
200			} else {
201	gezelter	1237	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
202			if (aNum != 0) {
203			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
204	gezelter	956	} else {
205			sprintf( painCave.errMsg,
206	xsun	1185	"Could not find atom type in default element.txt\n");
207	gezelter	1390	painCave.severity = OPENMD_ERROR;
208	gezelter	956	painCave.isFatal = 1;
209			simError();
210	xsun	1185	}
211	gezelter	956	}
212			}
213			}
214	chuckv	1293
215			if (!simParams->haveTargetTemp()) {
216			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
217			painCave.isFatal = 1;
218	gezelter	1390	painCave.severity = OPENMD_ERROR;
219	chuckv	1293	simError();
220			}
221
222			if (!simParams->haveViscosity()) {
223			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
224			painCave.isFatal = 1;
225	gezelter	1390	painCave.severity = OPENMD_ERROR;
226	chuckv	1293	simError();
227			}
228
229
230	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
231			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
232	gezelter	956	if (iter != hydroPropMap.end())
233			hydroProps_.push_back(iter->second);
234			else {
235	gezelter	981	currHydroProp->complete();
236			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
237			hydroProps_.push_back(currHydroProp);
238	gezelter	956	}
239			}
240			}
241			}
242	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
243	gezelter	981	}
244	gezelter	956
245	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
246			std::map<std::string, HydroProp*> props;
247	tim	895	std::ifstream ifs(filename.c_str());
248			if (ifs.is_open()) {
249	gezelter	945
250	tim	895	}
251	gezelter	945
252	tim	895	const unsigned int BufferSize = 65535;
253			char buffer[BufferSize];
254			while (ifs.getline(buffer, BufferSize)) {
255	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
256			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
257	tim	895	}
258	gezelter	981
259	tim	895	return props;
260			}
261	gezelter	981
262	gezelter	1464	void LDForceManager::postCalculation(){
263	tim	895	SimInfo::MoleculeIterator i;
264			Molecule::IntegrableObjectIterator j;
265			Molecule* mol;
266			StuntDouble* integrableObject;
267	xsun	1185	RealType mass;
268	tim	895	Vector3d pos;
269			Vector3d frc;
270			Mat3x3d A;
271	tim	904	Mat3x3d Atrans;
272	tim	895	Vector3d Tb;
273			Vector3d ji;
274			unsigned int index = 0;
275	gezelter	945	bool doLangevinForces;
276			bool freezeMolecule;
277			int fdf;
278	gezelter	983
279	chuckv	1120	fdf = 0;
280	gezelter	983
281	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
282	gezelter	970
283			doLangevinForces = true;
284			freezeMolecule = false;
285
286	gezelter	945	if (sphericalBoundaryConditions_) {
287
288			Vector3d molPos = mol->getCom();
289	tim	963	RealType molRad = molPos.length();
290	chuckv	1120
291	gezelter	945	doLangevinForces = false;
292
293			if (molRad > langevinBufferRadius_) {
294			doLangevinForces = true;
295			freezeMolecule = false;
296			}
297			if (molRad > frozenBufferRadius_) {
298			doLangevinForces = false;
299			freezeMolecule = true;
300			}
301			}
302
303	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304			integrableObject = mol->nextIntegrableObject(j)) {
305	gezelter	945
306	gezelter	956	if (freezeMolecule)
307			fdf += integrableObject->freeze();
308
309	chuckv	1120	if (doLangevinForces) {
310	xsun	1185	mass = integrableObject->getMass();
311	tim	895	if (integrableObject->isDirectional()){
312	gezelter	1237
313			// preliminaries for directional objects:
314
315	xsun	1216	A = integrableObject->getA();
316			Atrans = A.transpose();
317			Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
318	xsun	1185
319	gezelter	1237	//apply random force and torque at center of resistance
320	xsun	1185
321	gezelter	945	Vector3d randomForceBody;
322			Vector3d randomTorqueBody;
323			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
324	xsun	1216	Vector3d randomForceLab = Atrans * randomForceBody;
325			Vector3d randomTorqueLab = Atrans * randomTorqueBody;
326	gezelter	945	integrableObject->addFrc(randomForceLab);
327	xsun	1216	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
328	gezelter	1237
329			Mat3x3d I = integrableObject->getI();
330			Vector3d omegaBody;
331
332			// What remains contains velocity explicitly, but the velocity required
333			// is at the full step: v(t + h), while we have initially the velocity
334			// at the half step: v(t + h/2). We need to iterate to converge the
335			// friction force and friction torque vectors.
336
337			// this is the velocity at the half-step:
338	gezelter	945
339	gezelter	1237	Vector3d vel =integrableObject->getVel();
340			Vector3d angMom = integrableObject->getJ();
341
342			//estimate velocity at full-step using everything but friction forces:
343
344			frc = integrableObject->getFrc();
345	gezelter	1390	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
346	gezelter	1237
347			Tb = integrableObject->lab2Body(integrableObject->getTrq());
348	gezelter	1390	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
349	gezelter	1237
350			Vector3d omegaLab;
351			Vector3d vcdLab;
352			Vector3d vcdBody;
353			Vector3d frictionForceBody;
354			Vector3d frictionForceLab(0.0);
355			Vector3d oldFFL; // used to test for convergence
356			Vector3d frictionTorqueBody(0.0);
357			Vector3d oldFTB; // used to test for convergence
358			Vector3d frictionTorqueLab;
359			RealType fdot;
360			RealType tdot;
361
362			//iteration starts here:
363
364			for (int k = 0; k < maxIterNum_; k++) {
365
366			if (integrableObject->isLinear()) {
367			int linearAxis = integrableObject->linearAxis();
368			int l = (linearAxis +1 )%3;
369			int m = (linearAxis +2 )%3;
370			omegaBody[l] = angMomStep[l] /I(l, l);
371			omegaBody[m] = angMomStep[m] /I(m, m);
372
373			} else {
374			omegaBody[0] = angMomStep[0] /I(0, 0);
375			omegaBody[1] = angMomStep[1] /I(1, 1);
376			omegaBody[2] = angMomStep[2] /I(2, 2);
377			}
378
379			omegaLab = Atrans * omegaBody;
380
381			// apply friction force and torque at center of resistance
382
383			vcdLab = velStep + cross(omegaLab, rcrLab);
384			vcdBody = A * vcdLab;
385			frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
386			oldFFL = frictionForceLab;
387			frictionForceLab = Atrans * frictionForceBody;
388			oldFTB = frictionTorqueBody;
389			frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
390			frictionTorqueLab = Atrans * frictionTorqueBody;
391
392			// re-estimate velocities at full-step using friction forces:
393
394	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
395			angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
396	gezelter	1237
397			// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
398
399			fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
400			tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
401
402			if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
403			break; // iteration ends here
404			}
405
406			integrableObject->addFrc(frictionForceLab);
407			integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
408
409
410	tim	895	} else {
411	gezelter	945	//spherical atom
412	gezelter	1237
413	gezelter	945	Vector3d randomForce;
414			Vector3d randomTorque;
415			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
416	gezelter	1237	integrableObject->addFrc(randomForce);
417
418			// What remains contains velocity explicitly, but the velocity required
419			// is at the full step: v(t + h), while we have initially the velocity
420			// at the half step: v(t + h/2). We need to iterate to converge the
421			// friction force vector.
422
423			// this is the velocity at the half-step:
424	gezelter	945
425	gezelter	1237	Vector3d vel =integrableObject->getVel();
426
427			//estimate velocity at full-step using everything but friction forces:
428
429			frc = integrableObject->getFrc();
430	gezelter	1390	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
431	gezelter	1237
432			Vector3d frictionForce(0.0);
433			Vector3d oldFF; // used to test for convergence
434			RealType fdot;
435
436			//iteration starts here:
437
438			for (int k = 0; k < maxIterNum_; k++) {
439
440			oldFF = frictionForce;
441			frictionForce = -hydroProps_[index]->getXitt() * velStep;
442
443			// re-estimate velocities at full-step using friction forces:
444
445	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
446	gezelter	1237
447			// check for convergence (if the vector has converged, fdot will be 1.0):
448
449			fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
450
451			if (fabs(1.0 - fdot) <= forceTolerance_)
452			break; // iteration ends here
453			}
454
455			integrableObject->addFrc(frictionForce);
456
457	tim	895	}
458	gezelter	956	}
459	gezelter	945
460	gezelter	956	++index;
461	tim	895
462			}
463	gezelter	956	}
464	chuckv	1120
465	gezelter	945	info_->setFdf(fdf);
466	gezelter	983	veloMunge->removeComDrift();
467			// Remove angular drift if we are not using periodic boundary conditions.
468			if(!simParams->getUsePeriodicBoundaryConditions())
469			veloMunge->removeAngularDrift();
470
471	gezelter	1464	ForceManager::postCalculation();
472	tim	895	}
473
474	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
475	tim	904
476	tim	906
477	tim	963	Vector<RealType, 6> Z;
478			Vector<RealType, 6> generalForce;
479	tim	904
480	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
481			Z[1] = randNumGen_.randNorm(0, variance);
482			Z[2] = randNumGen_.randNorm(0, variance);
483			Z[3] = randNumGen_.randNorm(0, variance);
484			Z[4] = randNumGen_.randNorm(0, variance);
485			Z[5] = randNumGen_.randNorm(0, variance);
486	tim	904
487	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
488	tim	904
489	tim	895	force[0] = generalForce[0];
490			force[1] = generalForce[1];
491			force[2] = generalForce[2];
492			torque[0] = generalForce[3];
493			torque[1] = generalForce[4];
494			torque[2] = generalForce[5];
495
496	xsun	1185	}
497	tim	895
498			}