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"
#include "types/LennardJonesAdapter.hpp"
#include "types/GayBerneAdapter.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();
            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(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:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	18154 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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	1710	#include "types/LennardJonesAdapter.hpp"
51			#include "types/GayBerneAdapter.hpp"
52	gezelter	956
53	gezelter	1390	namespace OpenMD {
54	tim	895
55	gezelter	1237	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
56	gezelter	983	simParams = info->getSimParams();
57			veloMunge = new Velocitizer(info);
58
59	gezelter	945	sphericalBoundaryConditions_ = false;
60			if (simParams->getUseSphericalBoundaryConditions()) {
61			sphericalBoundaryConditions_ = true;
62			if (simParams->haveLangevinBufferRadius()) {
63			langevinBufferRadius_ = simParams->getLangevinBufferRadius();
64			} else {
65			sprintf( painCave.errMsg,
66			"langevinBufferRadius must be specified "
67			"when useSphericalBoundaryConditions is turned on.\n");
68	gezelter	1390	painCave.severity = OPENMD_ERROR;
69	gezelter	945	painCave.isFatal = 1;
70			simError();
71			}
72
73			if (simParams->haveFrozenBufferRadius()) {
74			frozenBufferRadius_ = simParams->getFrozenBufferRadius();
75			} else {
76			sprintf( painCave.errMsg,
77			"frozenBufferRadius must be specified "
78			"when useSphericalBoundaryConditions is turned on.\n");
79	gezelter	1390	painCave.severity = OPENMD_ERROR;
80	gezelter	945	painCave.isFatal = 1;
81			simError();
82			}
83	tim	895
84	gezelter	945	if (frozenBufferRadius_ < langevinBufferRadius_) {
85			sprintf( painCave.errMsg,
86			"frozenBufferRadius has been set smaller than the "
87			"langevinBufferRadius. This is probably an error.\n");
88	gezelter	1390	painCave.severity = OPENMD_WARNING;
89	gezelter	945	painCave.isFatal = 0;
90			simError();
91			}
92			}
93	gezelter	956
94			// Build the hydroProp map:
95	gezelter	981	std::map<std::string, HydroProp*> hydroPropMap;
96	gezelter	956
97	tim	895	Molecule* mol;
98			StuntDouble* integrableObject;
99	gezelter	956	SimInfo::MoleculeIterator i;
100			Molecule::IntegrableObjectIterator j;
101			bool needHydroPropFile = false;
102
103			for (mol = info->beginMolecule(i); mol != NULL;
104			mol = info->nextMolecule(i)) {
105			for (integrableObject = mol->beginIntegrableObject(j);
106			integrableObject != NULL;
107	gezelter	945	integrableObject = mol->nextIntegrableObject(j)) {
108	gezelter	956
109			if (integrableObject->isRigidBody()) {
110			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
111			if (rb->getNumAtoms() > 1) needHydroPropFile = true;
112	gezelter	945	}
113
114			}
115	tim	895	}
116	gezelter	956
117
118			if (needHydroPropFile) {
119			if (simParams->haveHydroPropFile()) {
120			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
121			} else {
122			sprintf( painCave.errMsg,
123	gezelter	1237	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
124			"\tis specified for rigidBodies which contain more than one atom\n"
125			"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
126	gezelter	1390	painCave.severity = OPENMD_ERROR;
127	gezelter	956	painCave.isFatal = 1;
128			simError();
129			}
130	tim	971
131			for (mol = info->beginMolecule(i); mol != NULL;
132			mol = info->nextMolecule(i)) {
133			for (integrableObject = mol->beginIntegrableObject(j);
134			integrableObject != NULL;
135			integrableObject = mol->nextIntegrableObject(j)) {
136
137	gezelter	981	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
138	tim	971	if (iter != hydroPropMap.end()) {
139			hydroProps_.push_back(iter->second);
140			} else {
141			sprintf( painCave.errMsg,
142			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
143	gezelter	1390	painCave.severity = OPENMD_ERROR;
144	tim	971	painCave.isFatal = 1;
145			simError();
146			}
147			}
148	gezelter	956	}
149			} else {
150	gezelter	981
151			std::map<std::string, HydroProp*> hydroPropMap;
152	gezelter	956	for (mol = info->beginMolecule(i); mol != NULL;
153			mol = info->nextMolecule(i)) {
154			for (integrableObject = mol->beginIntegrableObject(j);
155			integrableObject != NULL;
156			integrableObject = mol->nextIntegrableObject(j)) {
157			Shape* currShape = NULL;
158	xsun	1185
159			if (integrableObject->isAtom()){
160			Atom* atom = static_cast<Atom*>(integrableObject);
161			AtomType* atomType = atom->getAtomType();
162	gezelter	1710	GayBerneAdapter gba = GayBerneAdapter(atomType);
163			if (gba.isGayBerne()) {
164			currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
165			gba.getD() / 2.0,
166			Mat3x3d::identity());
167	xsun	1185	} else {
168	gezelter	1710	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
169			if (lja.isLennardJones()){
170			currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
171	xsun	1185	} else {
172	gezelter	1237	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
173			if (aNum != 0) {
174			currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
175	gezelter	956	} else {
176			sprintf( painCave.errMsg,
177	xsun	1185	"Could not find atom type in default element.txt\n");
178	gezelter	1390	painCave.severity = OPENMD_ERROR;
179	gezelter	956	painCave.isFatal = 1;
180			simError();
181	xsun	1185	}
182	gezelter	956	}
183			}
184			}
185	chuckv	1293
186			if (!simParams->haveTargetTemp()) {
187			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
188			painCave.isFatal = 1;
189	gezelter	1390	painCave.severity = OPENMD_ERROR;
190	chuckv	1293	simError();
191			}
192
193			if (!simParams->haveViscosity()) {
194			sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
195			painCave.isFatal = 1;
196	gezelter	1390	painCave.severity = OPENMD_ERROR;
197	chuckv	1293	simError();
198			}
199
200
201	gezelter	981	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
202			std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
203	gezelter	956	if (iter != hydroPropMap.end())
204			hydroProps_.push_back(iter->second);
205			else {
206	gezelter	981	currHydroProp->complete();
207			hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
208			hydroProps_.push_back(currHydroProp);
209	gezelter	956	}
210			}
211			}
212			}
213	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
214	gezelter	981	}
215	gezelter	956
216	gezelter	981	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
217			std::map<std::string, HydroProp*> props;
218	tim	895	std::ifstream ifs(filename.c_str());
219			if (ifs.is_open()) {
220	gezelter	945
221	tim	895	}
222	gezelter	945
223	tim	895	const unsigned int BufferSize = 65535;
224			char buffer[BufferSize];
225			while (ifs.getline(buffer, BufferSize)) {
226	gezelter	981	HydroProp* currProp = new HydroProp(buffer);
227			props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
228	tim	895	}
229	gezelter	981
230	tim	895	return props;
231			}
232	gezelter	981
233	gezelter	1464	void LDForceManager::postCalculation(){
234	tim	895	SimInfo::MoleculeIterator i;
235			Molecule::IntegrableObjectIterator j;
236			Molecule* mol;
237			StuntDouble* integrableObject;
238	xsun	1185	RealType mass;
239	tim	895	Vector3d pos;
240			Vector3d frc;
241			Mat3x3d A;
242	tim	904	Mat3x3d Atrans;
243	tim	895	Vector3d Tb;
244			Vector3d ji;
245			unsigned int index = 0;
246	gezelter	945	bool doLangevinForces;
247			bool freezeMolecule;
248			int fdf;
249	gezelter	983
250	chuckv	1120	fdf = 0;
251	gezelter	983
252	tim	895	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
253	gezelter	970
254			doLangevinForces = true;
255			freezeMolecule = false;
256
257	gezelter	945	if (sphericalBoundaryConditions_) {
258
259			Vector3d molPos = mol->getCom();
260	tim	963	RealType molRad = molPos.length();
261	chuckv	1120
262	gezelter	945	doLangevinForces = false;
263
264			if (molRad > langevinBufferRadius_) {
265			doLangevinForces = true;
266			freezeMolecule = false;
267			}
268			if (molRad > frozenBufferRadius_) {
269			doLangevinForces = false;
270			freezeMolecule = true;
271			}
272			}
273
274	gezelter	956	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
275			integrableObject = mol->nextIntegrableObject(j)) {
276	gezelter	945
277	gezelter	956	if (freezeMolecule)
278			fdf += integrableObject->freeze();
279
280	chuckv	1120	if (doLangevinForces) {
281	xsun	1185	mass = integrableObject->getMass();
282	tim	895	if (integrableObject->isDirectional()){
283	gezelter	1237
284			// preliminaries for directional objects:
285
286	xsun	1216	A = integrableObject->getA();
287			Atrans = A.transpose();
288			Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
289	xsun	1185
290	gezelter	1237	//apply random force and torque at center of resistance
291	xsun	1185
292	gezelter	945	Vector3d randomForceBody;
293			Vector3d randomTorqueBody;
294			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
295	xsun	1216	Vector3d randomForceLab = Atrans * randomForceBody;
296			Vector3d randomTorqueLab = Atrans * randomTorqueBody;
297	gezelter	945	integrableObject->addFrc(randomForceLab);
298	xsun	1216	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
299	gezelter	1237
300			Mat3x3d I = integrableObject->getI();
301			Vector3d omegaBody;
302
303			// What remains contains velocity explicitly, but the velocity required
304			// is at the full step: v(t + h), while we have initially the velocity
305			// at the half step: v(t + h/2). We need to iterate to converge the
306			// friction force and friction torque vectors.
307
308			// this is the velocity at the half-step:
309	gezelter	945
310	gezelter	1237	Vector3d vel =integrableObject->getVel();
311			Vector3d angMom = integrableObject->getJ();
312
313			//estimate velocity at full-step using everything but friction forces:
314
315			frc = integrableObject->getFrc();
316	gezelter	1390	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
317	gezelter	1237
318			Tb = integrableObject->lab2Body(integrableObject->getTrq());
319	gezelter	1390	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
320	gezelter	1237
321			Vector3d omegaLab;
322			Vector3d vcdLab;
323			Vector3d vcdBody;
324			Vector3d frictionForceBody;
325			Vector3d frictionForceLab(0.0);
326			Vector3d oldFFL; // used to test for convergence
327			Vector3d frictionTorqueBody(0.0);
328			Vector3d oldFTB; // used to test for convergence
329			Vector3d frictionTorqueLab;
330			RealType fdot;
331			RealType tdot;
332
333			//iteration starts here:
334
335			for (int k = 0; k < maxIterNum_; k++) {
336
337			if (integrableObject->isLinear()) {
338			int linearAxis = integrableObject->linearAxis();
339			int l = (linearAxis +1 )%3;
340			int m = (linearAxis +2 )%3;
341			omegaBody[l] = angMomStep[l] /I(l, l);
342			omegaBody[m] = angMomStep[m] /I(m, m);
343
344			} else {
345			omegaBody[0] = angMomStep[0] /I(0, 0);
346			omegaBody[1] = angMomStep[1] /I(1, 1);
347			omegaBody[2] = angMomStep[2] /I(2, 2);
348			}
349
350			omegaLab = Atrans * omegaBody;
351
352			// apply friction force and torque at center of resistance
353
354			vcdLab = velStep + cross(omegaLab, rcrLab);
355			vcdBody = A * vcdLab;
356			frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
357			oldFFL = frictionForceLab;
358			frictionForceLab = Atrans * frictionForceBody;
359			oldFTB = frictionTorqueBody;
360			frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
361			frictionTorqueLab = Atrans * frictionTorqueBody;
362
363			// re-estimate velocities at full-step using friction forces:
364
365	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
366			angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
367	gezelter	1237
368			// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
369
370			fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
371			tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
372
373			if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
374			break; // iteration ends here
375			}
376
377			integrableObject->addFrc(frictionForceLab);
378			integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
379
380
381	tim	895	} else {
382	gezelter	945	//spherical atom
383	gezelter	1237
384	gezelter	945	Vector3d randomForce;
385			Vector3d randomTorque;
386			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
387	gezelter	1237	integrableObject->addFrc(randomForce);
388
389			// What remains contains velocity explicitly, but the velocity required
390			// is at the full step: v(t + h), while we have initially the velocity
391			// at the half step: v(t + h/2). We need to iterate to converge the
392			// friction force vector.
393
394			// this is the velocity at the half-step:
395	gezelter	945
396	gezelter	1237	Vector3d vel =integrableObject->getVel();
397
398			//estimate velocity at full-step using everything but friction forces:
399
400			frc = integrableObject->getFrc();
401	gezelter	1390	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
402	gezelter	1237
403			Vector3d frictionForce(0.0);
404			Vector3d oldFF; // used to test for convergence
405			RealType fdot;
406
407			//iteration starts here:
408
409			for (int k = 0; k < maxIterNum_; k++) {
410
411			oldFF = frictionForce;
412			frictionForce = -hydroProps_[index]->getXitt() * velStep;
413
414			// re-estimate velocities at full-step using friction forces:
415
416	gezelter	1390	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
417	gezelter	1237
418			// check for convergence (if the vector has converged, fdot will be 1.0):
419
420			fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
421
422			if (fabs(1.0 - fdot) <= forceTolerance_)
423			break; // iteration ends here
424			}
425
426			integrableObject->addFrc(frictionForce);
427
428	tim	895	}
429	gezelter	956	}
430	gezelter	945
431	gezelter	956	++index;
432	tim	895
433			}
434	gezelter	956	}
435	chuckv	1120
436	gezelter	945	info_->setFdf(fdf);
437	gezelter	983	veloMunge->removeComDrift();
438			// Remove angular drift if we are not using periodic boundary conditions.
439			if(!simParams->getUsePeriodicBoundaryConditions())
440			veloMunge->removeAngularDrift();
441
442	gezelter	1464	ForceManager::postCalculation();
443	tim	895	}
444
445	tim	963	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
446	tim	904
447	tim	906
448	tim	963	Vector<RealType, 6> Z;
449			Vector<RealType, 6> generalForce;
450	tim	904
451	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
452			Z[1] = randNumGen_.randNorm(0, variance);
453			Z[2] = randNumGen_.randNorm(0, variance);
454			Z[3] = randNumGen_.randNorm(0, variance);
455			Z[4] = randNumGen_.randNorm(0, variance);
456			Z[5] = randNumGen_.randNorm(0, variance);
457	tim	904
458	gezelter	981	generalForce = hydroProps_[index]->getS()*Z;
459	tim	904
460	tim	895	force[0] = generalForce[0];
461			force[1] = generalForce[1];
462			force[2] = generalForce[2];
463			torque[0] = generalForce[3];
464			torque[1] = generalForce[4];
465			torque[2] = generalForce[5];
466
467	xsun	1185	}
468	tim	895
469			}