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.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#include <fstream>
43	#include <iostream>
44	#include "integrators/LDForceManager.hpp"
45	#include "math/CholeskyDecomposition.hpp"
46	#include "utils/PhysicalConstants.hpp"
47	#include "hydrodynamics/Sphere.hpp"
48	#include "hydrodynamics/Ellipsoid.hpp"
49	#include "utils/ElementsTable.hpp"
50	#include "types/LennardJonesAdapter.hpp"
51	#include "types/GayBerneAdapter.hpp"
52
53	namespace OpenMD {
54
55	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
56	simParams = info->getSimParams();
57	veloMunge = new Velocitizer(info);
58
59	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	painCave.severity = OPENMD_ERROR;
69	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	painCave.severity = OPENMD_ERROR;
80	painCave.isFatal = 1;
81	simError();
82	}
83
84	if (frozenBufferRadius_ < langevinBufferRadius_) {
85	sprintf( painCave.errMsg,
86	"frozenBufferRadius has been set smaller than the "
87	"langevinBufferRadius. This is probably an error.\n");
88	painCave.severity = OPENMD_WARNING;
89	painCave.isFatal = 0;
90	simError();
91	}
92	}
93
94	// Build the hydroProp map:
95	std::map<std::string, HydroProp*> hydroPropMap;
96
97	Molecule* mol;
98	StuntDouble* integrableObject;
99	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	integrableObject = mol->nextIntegrableObject(j)) {
108
109	if (integrableObject->isRigidBody()) {
110	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
111	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
112	}
113
114	}
115	}
116
117
118	if (needHydroPropFile) {
119	if (simParams->haveHydroPropFile()) {
120	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
121	} else {
122	sprintf( painCave.errMsg,
123	"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	painCave.severity = OPENMD_ERROR;
127	painCave.isFatal = 1;
128	simError();
129	}
130
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	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
138	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	painCave.severity = OPENMD_ERROR;
144	painCave.isFatal = 1;
145	simError();
146	}
147	}
148	}
149	} else {
150
151	std::map<std::string, HydroProp*> hydroPropMap;
152	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
159	if (integrableObject->isAtom()){
160	Atom* atom = static_cast<Atom*>(integrableObject);
161	AtomType* atomType = atom->getAtomType();
162	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	} else {
168	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
169	if (lja.isLennardJones()){
170	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
171	} else {
172	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
173	if (aNum != 0) {
174	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
175	} else {
176	sprintf( painCave.errMsg,
177	"Could not find atom type in default element.txt\n");
178	painCave.severity = OPENMD_ERROR;
179	painCave.isFatal = 1;
180	simError();
181	}
182	}
183	}
184	}
185
186	if (!simParams->haveTargetTemp()) {
187	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
188	painCave.isFatal = 1;
189	painCave.severity = OPENMD_ERROR;
190	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	painCave.severity = OPENMD_ERROR;
197	simError();
198	}
199
200
201	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
202	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
203	if (iter != hydroPropMap.end())
204	hydroProps_.push_back(iter->second);
205	else {
206	currHydroProp->complete();
207	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
208	hydroProps_.push_back(currHydroProp);
209	}
210	}
211	}
212	}
213	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
214	}
215
216	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
217	std::map<std::string, HydroProp*> props;
218	std::ifstream ifs(filename.c_str());
219	if (ifs.is_open()) {
220
221	}
222
223	const unsigned int BufferSize = 65535;
224	char buffer[BufferSize];
225	while (ifs.getline(buffer, BufferSize)) {
226	HydroProp* currProp = new HydroProp(buffer);
227	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
228	}
229
230	return props;
231	}
232
233	void LDForceManager::postCalculation(){
234	SimInfo::MoleculeIterator i;
235	Molecule::IntegrableObjectIterator j;
236	Molecule* mol;
237	StuntDouble* integrableObject;
238	RealType mass;
239	Vector3d pos;
240	Vector3d frc;
241	Mat3x3d A;
242	Mat3x3d Atrans;
243	Vector3d Tb;
244	Vector3d ji;
245	unsigned int index = 0;
246	bool doLangevinForces;
247	bool freezeMolecule;
248	int fdf;
249
250	fdf = 0;
251
252	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
253
254	doLangevinForces = true;
255	freezeMolecule = false;
256
257	if (sphericalBoundaryConditions_) {
258
259	Vector3d molPos = mol->getCom();
260	RealType molRad = molPos.length();
261
262	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	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
275	integrableObject = mol->nextIntegrableObject(j)) {
276
277	if (freezeMolecule)
278	fdf += integrableObject->freeze();
279
280	if (doLangevinForces) {
281	mass = integrableObject->getMass();
282	if (integrableObject->isDirectional()){
283
284	// preliminaries for directional objects:
285
286	A = integrableObject->getA();
287	Atrans = A.transpose();
288	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
289
290	//apply random force and torque at center of resistance
291
292	Vector3d randomForceBody;
293	Vector3d randomTorqueBody;
294	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
295	Vector3d randomForceLab = Atrans * randomForceBody;
296	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
297	integrableObject->addFrc(randomForceLab);
298	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
299
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
310	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	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
317
318	Tb = integrableObject->lab2Body(integrableObject->getTrq());
319	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
320
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	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
366	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
367
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	} else {
382	//spherical atom
383
384	Vector3d randomForce;
385	Vector3d randomTorque;
386	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
387	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
396	Vector3d vel =integrableObject->getVel();
397
398	//estimate velocity at full-step using everything but friction forces:
399
400	frc = integrableObject->getFrc();
401	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
402
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	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
417
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	}
429	}
430
431	++index;
432
433	}
434	}
435
436	info_->setFdf(fdf);
437	veloMunge->removeComDrift();
438	// Remove angular drift if we are not using periodic boundary conditions.
439	if(!simParams->getUsePeriodicBoundaryConditions())
440	veloMunge->removeAngularDrift();
441
442	ForceManager::postCalculation();
443	}
444
445	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
446
447
448	Vector<RealType, 6> Z;
449	Vector<RealType, 6> generalForce;
450
451	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
458	generalForce = hydroProps_[index]->getS()*Z;
459
460	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	}
468
469	}