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, 234107 (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"
#include "types/LennardJonesAdapter.hpp"
#include "types/GayBerneAdapter.hpp"

namespace OpenMD {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), 
                                                  maxIterNum_(4), 
                                                  forceTolerance_(1e-6) {
    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* sd;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;              
    bool needHydroPropFile = false;
    
    for (mol = info->beginMolecule(i); mol != NULL; 
         mol = info->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        
        if (sd->isRigidBody()) {
          RigidBody* rb = static_cast<RigidBody*>(sd);
          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 (sd = mol->beginIntegrableObject(j);  sd != NULL;
             sd = mol->nextIntegrableObject(j)) {

          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
          if (iter != hydroPropMap.end()) {
            hydroProps_.push_back(iter->second);
          } else {
            sprintf( painCave.errMsg,
                     "Can not find resistance tensor for atom [%s]\n", sd->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 (sd = mol->beginIntegrableObject(j); sd != NULL;
             sd = mol->nextIntegrableObject(j)) {

          Shape* currShape = NULL;

          if (sd->isAtom()){
            Atom* atom = static_cast<Atom*>(sd);
            AtomType* atomType = atom->getAtomType();
            GayBerneAdapter gba = GayBerneAdapter(atomType);
            if (gba.isGayBerne()) {
              currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
                                        gba.getD() / 2.0,
                                        Mat3x3d::identity());
            } else {
              LennardJonesAdapter lja = LennardJonesAdapter(atomType);
              if (lja.isLennardJones()){
                currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
              } 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(sd->getType());
          if (iter != hydroPropMap.end()) 
            hydroProps_.push_back(iter->second);
          else {
            currHydroProp->complete();
            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp));
            hydroProps_.push_back(currHydroProp);
          }
          delete currShape;
        }
      }
    }
    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* sd;
    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 (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
          
        if (freezeMolecule) 
          fdf += sd->freeze();
        
        if (doLangevinForces) {  
          mass = sd->getMass();
          if (sd->isDirectional()){

            // preliminaries for directional objects:

            A = sd->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;
            sd->addFrc(randomForceLab);            
            sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));             

            Mat3x3d I = sd->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 =sd->getVel();
            Vector3d angMom = sd->getJ();

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

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

            Tb = sd->lab2Body(sd->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 (sd->isLinear()) {
                int linearAxis = sd->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
            }

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

            
          } else {
            //spherical atom

            Vector3d randomForce;
            Vector3d randomTorque;
            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
            sd->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 =sd->getVel();

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

            frc = sd->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
            }

            sd->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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 7 months ago) by gezelter
File size:	17578 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1782	#include "types/LennardJonesAdapter.hpp"
51			#include "types/GayBerneAdapter.hpp"
52	gezelter	956
53	gezelter	1390	namespace OpenMD {
54	tim	895
55	gezelter	2071	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info),
56			maxIterNum_(4),
57			forceTolerance_(1e-6) {
58	gezelter	983	simParams = info->getSimParams();
59			veloMunge = new Velocitizer(info);
60
61	gezelter	945	sphericalBoundaryConditions_ = false;
62			if (simParams->getUseSphericalBoundaryConditions()) {
63			sphericalBoundaryConditions_ = true;
64			if (simParams->haveLangevinBufferRadius()) {
65			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
66			} else {
67			sprintf( painCave.errMsg,
68			"langevinBufferRadius must be specified "
69			"when useSphericalBoundaryConditions is turned on.\n");
70	gezelter	1390	painCave.severity = OPENMD_ERROR;
71	gezelter	945	painCave.isFatal = 1;
72			simError();
73			}
74
75			if (simParams->haveFrozenBufferRadius()) {
76			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
77			} else {
78			sprintf( painCave.errMsg,
79			"frozenBufferRadius must be specified "
80			"when useSphericalBoundaryConditions is turned on.\n");
81	gezelter	1390	painCave.severity = OPENMD_ERROR;
82	gezelter	945	painCave.isFatal = 1;
83			simError();
84			}
85	tim	895
86	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
87			sprintf( painCave.errMsg,
88			"frozenBufferRadius has been set smaller than the "
89			"langevinBufferRadius. This is probably an error.\n");
90	gezelter	1390	painCave.severity = OPENMD_WARNING;
91	gezelter	945	painCave.isFatal = 0;
92			simError();
93			}
94			}
95	gezelter	956
96			// Build the hydroProp map:
97	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
98	gezelter	956
99	tim	895	Molecule* mol;
100	gezelter	1782	StuntDouble* sd;
101	gezelter	956	SimInfo::MoleculeIterator i;
102			Molecule::IntegrableObjectIterator j;
103			bool needHydroPropFile = false;
104
105			for (mol = info->beginMolecule(i); mol != NULL;
106			mol = info->nextMolecule(i)) {
107	gezelter	1782
108			for (sd = mol->beginIntegrableObject(j); sd != NULL;
109			sd = mol->nextIntegrableObject(j)) {
110	gezelter	956
111	gezelter	1782	if (sd->isRigidBody()) {
112			RigidBody* rb = static_cast<RigidBody*>(sd);
113	gezelter	956	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
114	gezelter	945	}
115
116			}
117	tim	895	}
118	gezelter	956
119
120			if (needHydroPropFile) {
121			if (simParams->haveHydroPropFile()) {
122			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
123			} else {
124			sprintf( painCave.errMsg,
125	gezelter	1237	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
126			"\tis specified for rigidBodies which contain more than one atom\n"
127			"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
128	gezelter	1390	painCave.severity = OPENMD_ERROR;
129	gezelter	956	painCave.isFatal = 1;
130			simError();
131			}
132	tim	971
133			for (mol = info->beginMolecule(i); mol != NULL;
134			mol = info->nextMolecule(i)) {
135
136	gezelter	1782	for (sd = mol->beginIntegrableObject(j); sd != NULL;
137			sd = mol->nextIntegrableObject(j)) {
138
139			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
140	tim	971	if (iter != hydroPropMap.end()) {
141			hydroProps_.push_back(iter->second);
142			} else {
143			sprintf( painCave.errMsg,
144	gezelter	1782	"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str());
145	gezelter	1390	painCave.severity = OPENMD_ERROR;
146	tim	971	painCave.isFatal = 1;
147			simError();
148			}
149			}
150	gezelter	956	}
151			} else {
152	gezelter	981
153			std::map<std::string, HydroProp*> hydroPropMap;
154	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
155			mol = info->nextMolecule(i)) {
156	gezelter	1782
157			for (sd = mol->beginIntegrableObject(j); sd != NULL;
158			sd = mol->nextIntegrableObject(j)) {
159
160	gezelter	956	Shape* currShape = NULL;
161	xsun	1185
162	gezelter	1782	if (sd->isAtom()){
163			Atom* atom = static_cast<Atom*>(sd);
164	xsun	1185	AtomType* atomType = atom->getAtomType();
165	gezelter	1782	GayBerneAdapter gba = GayBerneAdapter(atomType);
166			if (gba.isGayBerne()) {
167			currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
168			gba.getD() / 2.0,
169			Mat3x3d::identity());
170	xsun	1185	} else {
171	gezelter	1782	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
172			if (lja.isLennardJones()){
173			currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
174	xsun	1185	} else {
175	gezelter	1237	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
176			if (aNum != 0) {
177			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
178	gezelter	956	} else {
179			sprintf( painCave.errMsg,
180	xsun	1185	"Could not find atom type in default element.txt\n");
181	gezelter	1390	painCave.severity = OPENMD_ERROR;
182	gezelter	956	painCave.isFatal = 1;
183			simError();
184	xsun	1185	}
185	gezelter	956	}
186			}
187			}
188	chuckv	1293
189			if (!simParams->haveTargetTemp()) {
190			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
191			painCave.isFatal = 1;
192	gezelter	1390	painCave.severity = OPENMD_ERROR;
193	chuckv	1293	simError();
194			}
195
196			if (!simParams->haveViscosity()) {
197			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
198			painCave.isFatal = 1;
199	gezelter	1390	painCave.severity = OPENMD_ERROR;
200	chuckv	1293	simError();
201			}
202
203	gezelter	1782
204	gezelter	1610	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
205	gezelter	1782	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
206	gezelter	956	if (iter != hydroPropMap.end())
207			hydroProps_.push_back(iter->second);
208			else {
209	gezelter	981	currHydroProp->complete();
210	gezelter	1782	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp));
211	gezelter	981	hydroProps_.push_back(currHydroProp);
212	gezelter	956	}
213	gezelter	1879	delete currShape;
214	gezelter	956	}
215			}
216			}
217	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
218	gezelter	981	}
219	gezelter	956
220	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
221			std::map<std::string, HydroProp*> props;
222	tim	895	std::ifstream ifs(filename.c_str());
223			if (ifs.is_open()) {
224	gezelter	945
225	tim	895	}
226	gezelter	945
227	tim	895	const unsigned int BufferSize = 65535;
228			char buffer[BufferSize];
229			while (ifs.getline(buffer, BufferSize)) {
230	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
231			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
232	tim	895	}
233	gezelter	981
234	tim	895	return props;
235			}
236	gezelter	981
237	gezelter	1464	void LDForceManager::postCalculation(){
238	tim	895	SimInfo::MoleculeIterator i;
239			Molecule::IntegrableObjectIterator j;
240			Molecule* mol;
241	gezelter	1782	StuntDouble* sd;
242	xsun	1185	RealType mass;
243	tim	895	Vector3d pos;
244			Vector3d frc;
245			Mat3x3d A;
246	tim	904	Mat3x3d Atrans;
247	tim	895	Vector3d Tb;
248			Vector3d ji;
249			unsigned int index = 0;
250	gezelter	945	bool doLangevinForces;
251			bool freezeMolecule;
252			int fdf;
253	gezelter	983
254	chuckv	1120	fdf = 0;
255	gezelter	983
256	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
257	gezelter	970
258			doLangevinForces = true;
259			freezeMolecule = false;
260
261	gezelter	945	if (sphericalBoundaryConditions_) {
262
263			Vector3d molPos = mol->getCom();
264	tim	963	RealType molRad = molPos.length();
265	chuckv	1120
266	gezelter	945	doLangevinForces = false;
267
268			if (molRad > langevinBufferRadius_) {
269			doLangevinForces = true;
270			freezeMolecule = false;
271			}
272			if (molRad > frozenBufferRadius_) {
273			doLangevinForces = false;
274			freezeMolecule = true;
275			}
276			}
277
278	gezelter	1782	for (sd = mol->beginIntegrableObject(j); sd != NULL;
279			sd = mol->nextIntegrableObject(j)) {
280	gezelter	945
281	gezelter	956	if (freezeMolecule)
282	gezelter	1782	fdf += sd->freeze();
283	gezelter	956
284	chuckv	1120	if (doLangevinForces) {
285	gezelter	1782	mass = sd->getMass();
286			if (sd->isDirectional()){
287	gezelter	1237
288			// preliminaries for directional objects:
289
290	gezelter	1782	A = sd->getA();
291	xsun	1216	Atrans = A.transpose();
292			Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
293	xsun	1185
294	gezelter	1237	//apply random force and torque at center of resistance
295	xsun	1185
296	gezelter	945	Vector3d randomForceBody;
297			Vector3d randomTorqueBody;
298			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
299	xsun	1216	Vector3d randomForceLab = Atrans * randomForceBody;
300			Vector3d randomTorqueLab = Atrans * randomTorqueBody;
301	gezelter	1782	sd->addFrc(randomForceLab);
302			sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
303	gezelter	1610
304	gezelter	1782	Mat3x3d I = sd->getI();
305	gezelter	1237	Vector3d omegaBody;
306
307			// What remains contains velocity explicitly, but the velocity required
308			// is at the full step: v(t + h), while we have initially the velocity
309			// at the half step: v(t + h/2). We need to iterate to converge the
310			// friction force and friction torque vectors.
311
312			// this is the velocity at the half-step:
313	gezelter	945
314	gezelter	1782	Vector3d vel =sd->getVel();
315			Vector3d angMom = sd->getJ();
316	gezelter	1237
317			//estimate velocity at full-step using everything but friction forces:
318
319	gezelter	1782	frc = sd->getFrc();
320	gezelter	1390	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
321	gezelter	1237
322	gezelter	1782	Tb = sd->lab2Body(sd->getTrq());
323	gezelter	1390	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
324	gezelter	1237
325			Vector3d omegaLab;
326			Vector3d vcdLab;
327			Vector3d vcdBody;
328			Vector3d frictionForceBody;
329			Vector3d frictionForceLab(0.0);
330			Vector3d oldFFL; // used to test for convergence
331			Vector3d frictionTorqueBody(0.0);
332			Vector3d oldFTB; // used to test for convergence
333			Vector3d frictionTorqueLab;
334			RealType fdot;
335			RealType tdot;
336
337			//iteration starts here:
338
339			for (int k = 0; k < maxIterNum_; k++) {
340
341	gezelter	1782	if (sd->isLinear()) {
342			int linearAxis = sd->linearAxis();
343	gezelter	1237	int l = (linearAxis +1 )%3;
344			int m = (linearAxis +2 )%3;
345			omegaBody[l] = angMomStep[l] /I(l, l);
346			omegaBody[m] = angMomStep[m] /I(m, m);
347
348			} else {
349			omegaBody[0] = angMomStep[0] /I(0, 0);
350			omegaBody[1] = angMomStep[1] /I(1, 1);
351			omegaBody[2] = angMomStep[2] /I(2, 2);
352			}
353
354			omegaLab = Atrans * omegaBody;
355
356			// apply friction force and torque at center of resistance
357
358			vcdLab = velStep + cross(omegaLab, rcrLab);
359			vcdBody = A * vcdLab;
360			frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
361			oldFFL = frictionForceLab;
362			frictionForceLab = Atrans * frictionForceBody;
363			oldFTB = frictionTorqueBody;
364			frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
365			frictionTorqueLab = Atrans * frictionTorqueBody;
366
367			// re-estimate velocities at full-step using friction forces:
368
369	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
370			angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
371	gezelter	1237
372			// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
373
374			fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
375			tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
376
377			if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
378			break; // iteration ends here
379			}
380
381	gezelter	1782	sd->addFrc(frictionForceLab);
382			sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
383	gezelter	1237
384
385	tim	895	} else {
386	gezelter	945	//spherical atom
387	gezelter	1237
388	gezelter	945	Vector3d randomForce;
389			Vector3d randomTorque;
390			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
391	gezelter	1782	sd->addFrc(randomForce);
392	gezelter	1237
393			// What remains contains velocity explicitly, but the velocity required
394			// is at the full step: v(t + h), while we have initially the velocity
395			// at the half step: v(t + h/2). We need to iterate to converge the
396			// friction force vector.
397
398			// this is the velocity at the half-step:
399	gezelter	945
400	gezelter	1782	Vector3d vel =sd->getVel();
401	gezelter	1237
402			//estimate velocity at full-step using everything but friction forces:
403
404	gezelter	1782	frc = sd->getFrc();
405	gezelter	1390	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
406	gezelter	1237
407			Vector3d frictionForce(0.0);
408			Vector3d oldFF; // used to test for convergence
409			RealType fdot;
410
411			//iteration starts here:
412
413			for (int k = 0; k < maxIterNum_; k++) {
414
415			oldFF = frictionForce;
416			frictionForce = -hydroProps_[index]->getXitt() * velStep;
417
418			// re-estimate velocities at full-step using friction forces:
419
420	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
421	gezelter	1237
422			// check for convergence (if the vector has converged, fdot will be 1.0):
423
424			fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
425
426			if (fabs(1.0 - fdot) <= forceTolerance_)
427			break; // iteration ends here
428			}
429
430	gezelter	1782	sd->addFrc(frictionForce);
431	gezelter	1237
432	tim	895	}
433	gezelter	956	}
434	gezelter	945
435	gezelter	956	++index;
436	tim	895
437			}
438	gezelter	956	}
439	chuckv	1120
440	gezelter	945	info_->setFdf(fdf);
441	gezelter	983	veloMunge->removeComDrift();
442			// Remove angular drift if we are not using periodic boundary conditions.
443			if(!simParams->getUsePeriodicBoundaryConditions())
444			veloMunge->removeAngularDrift();
445
446	gezelter	1464	ForceManager::postCalculation();
447	tim	895	}
448
449	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
450	tim	904
451	tim	906
452	tim	963	Vector<RealType, 6> Z;
453			Vector<RealType, 6> generalForce;
454	tim	904
455	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
456			Z[1] = randNumGen_.randNorm(0, variance);
457			Z[2] = randNumGen_.randNorm(0, variance);
458			Z[3] = randNumGen_.randNorm(0, variance);
459			Z[4] = randNumGen_.randNorm(0, variance);
460			Z[5] = randNumGen_.randNorm(0, variance);
461	tim	904
462	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
463	tim	904
464	tim	895	force[0] = generalForce[0];
465			force[1] = generalForce[1];
466			force[2] = generalForce[2];
467			torque[0] = generalForce[3];
468			torque[1] = generalForce[4];
469			torque[2] = generalForce[5];
470
471	xsun	1185	}
472	tim	895
473			}