src/integrators/SMIPDForceManager.cpp

/*
 * Copyright (c) 2008 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#include <fstream> 
#include <iostream>
#include "integrators/SMIPDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/OOPSEConstant.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "utils/ElementsTable.hpp"
#include "math/ConvexHull.hpp"
#include "math/Triangle.hpp"


namespace oopse {

  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
    simParams = info->getSimParams();
    veloMunge = new Velocitizer(info);
    
    // Create Hull, Convex Hull for now, other options later.
    surfaceMesh_ = new ConvexHull();
    
    
    /* Check that the simulation has target pressure and target
       temperature set*/

    if (!simParams->haveTargetTemp()) {
      sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n");
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    } else {
      targetTemp_ = simParams->getTargetTemp();
    }

    if (!simParams->haveTargetPressure()) {
      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   without a targetPressure!\n");
      
      painCave.isFatal = 1;
      simError();
    } else {
      targetPressure_ = simParams->getTargetPressure();
    }

   
    if (simParams->getUsePeriodicBoundaryConditions()) {
      sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   with periodic boundary conditions !\n");
      
      painCave.isFatal = 1;
      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 = OOPSE_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 = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();  
          }        
        }
      }
    } else {
      
      std::map<std::string, HydroProp*> hydroPropMap;
      for (mol = info->beginMolecule(i); mol != NULL; 
           mol = info->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); 
             integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {
          Shape* currShape = NULL;

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

    /* Compute hull first time through to get the area of t=0*/

    /* Build a vector of integrable objects to determine if the are surface atoms */
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {          
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {   
        localSites_.push_back(integrableObject);
      }
    }

    surfaceMesh_->computeHull(localSites_);
    Area0_ = surfaceMesh_->getArea();
    //variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
    
  }  

  std::map<std::string, HydroProp*> SMIPDForceManager::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 SMIPDForceManager::postCalculation(bool needStress){
    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;
    int fdf;
   
    fdf = 0;
  
    /*Compute surface Mesh*/
    surfaceMesh_->computeHull(localSites_);

    /* Get area and number of surface stunt doubles and compute new variance */
     //RealType area = surfaceMesh_->getArea();
     //RealType nSurfaceSDs = surfaceMesh_->getNs();

//    std::cerr << "Surface Area is: " << area << " nSurfaceSDs is: " << nSurfaceSDs << std::endl;

    /* Compute variance for random forces */
    
//    variance_ = sqrt(2.0*NumericConstant::PI)*(targetPressure_*area/nSurfaceSDs);
    
//    std::vector<Triangle*> sMesh = surfaceMesh_->getMesh();
//    std::vector<RealType>  randNums = genTriangleForces(sMesh.size(),variance_);
  
    /* Loop over the mesh faces and apply random force to each of the faces*/
    
    
//    std::vector<Triangle*>::iterator face;
//    std::vector<StuntDouble*>::iterator vertex;
/*    
    for (face = sMesh.begin(); face != sMesh.end(); ++face){
     
      Triangle* thisTriangle = *face;
      std::vector<StuntDouble*> vertexSDs = thisTriangle->getVertices();

      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
            std::cout << (*vertex)->getPos() << std::endl;
         // mass = integrableObject->getMass();

         //      integrableObject->addFrc(randomForce);           
      }


    }
  */ 
    /*
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {

      
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
          
          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 * OOPSEConstant::energyConvert) * frc;

            Tb = integrableObject->lab2Body(integrableObject->getTrq());
            Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::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 * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
              angMomStep = angMom + (dt2_ * OOPSEConstant::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 * OOPSEConstant::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 * OOPSEConstant::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(needStress);   
  }

void SMIPDForceManager::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];
    
} 
  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) {

    // zero fill the random vector before starting:
    std::vector<RealType> gaussRand;
    gaussRand.resize(nTriangles);
    std::fill(gaussRand.begin(), gaussRand.end(), 0.0);


#ifdef IS_MPI
    if (worldRank == 0) {
#endif
      for (int i = 0; i < nTriangles; i++) {
        gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0));     
      }
#ifdef IS_MPI
    }
#endif

    // push these out to the other processors

#ifdef IS_MPI
    if (worldRank == 0) {
      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
    } else {
      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
    }
#endif

    for (int i = 0; i < nTriangles; i++) {
      gaussRand[i] = gaussRand[i] * variance;
    }

    return gaussRand;
  }

}
Revision:	3458
Committed:	Fri Oct 3 17:47:08 2008 UTC (15 years, 8 months ago) by chuckv
File size:	20944 byte(s)
Log Message:	Fixed makefile.
#	Content
1	/*
2	* Copyright (c) 2008 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. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41	#include <fstream>
42	#include <iostream>
43	#include "integrators/SMIPDForceManager.hpp"
44	#include "math/CholeskyDecomposition.hpp"
45	#include "utils/OOPSEConstant.hpp"
46	#include "hydrodynamics/Sphere.hpp"
47	#include "hydrodynamics/Ellipsoid.hpp"
48	#include "utils/ElementsTable.hpp"
49	#include "math/ConvexHull.hpp"
50	#include "math/Triangle.hpp"
51
52
53	namespace oopse {
54
55	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
56	simParams = info->getSimParams();
57	veloMunge = new Velocitizer(info);
58
59	// Create Hull, Convex Hull for now, other options later.
60	surfaceMesh_ = new ConvexHull();
61
62
63	/* Check that the simulation has target pressure and target
64	temperature set*/
65
66	if (!simParams->haveTargetTemp()) {
67	sprintf(painCave.errMsg, "You can't use the SMIPDynamics integrator without a targetTemp!\n");
68	painCave.isFatal = 1;
69	painCave.severity = OOPSE_ERROR;
70	simError();
71	} else {
72	targetTemp_ = simParams->getTargetTemp();
73	}
74
75	if (!simParams->haveTargetPressure()) {
76	sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
77	" without a targetPressure!\n");
78
79	painCave.isFatal = 1;
80	simError();
81	} else {
82	targetPressure_ = simParams->getTargetPressure();
83	}
84
85
86	if (simParams->getUsePeriodicBoundaryConditions()) {
87	sprintf(painCave.errMsg, "SMIPDynamics error: You can't use the SMIPD integrator\n"
88	" with periodic boundary conditions !\n");
89
90	painCave.isFatal = 1;
91	simError();
92	}
93
94
95	// Build the hydroProp map:
96	std::map<std::string, HydroProp*> hydroPropMap;
97
98	Molecule* mol;
99	StuntDouble* integrableObject;
100	SimInfo::MoleculeIterator i;
101	Molecule::IntegrableObjectIterator j;
102	bool needHydroPropFile = false;
103
104	for (mol = info->beginMolecule(i); mol != NULL;
105	mol = info->nextMolecule(i)) {
106	for (integrableObject = mol->beginIntegrableObject(j);
107	integrableObject != NULL;
108	integrableObject = mol->nextIntegrableObject(j)) {
109
110	if (integrableObject->isRigidBody()) {
111	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
112	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
113	}
114
115	}
116	}
117
118
119	if (needHydroPropFile) {
120	if (simParams->haveHydroPropFile()) {
121	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
122	} else {
123	sprintf( painCave.errMsg,
124	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
125	"\tis specified for rigidBodies which contain more than one atom\n"
126	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
127	painCave.severity = OOPSE_ERROR;
128	painCave.isFatal = 1;
129	simError();
130	}
131
132	for (mol = info->beginMolecule(i); mol != NULL;
133	mol = info->nextMolecule(i)) {
134	for (integrableObject = mol->beginIntegrableObject(j);
135	integrableObject != NULL;
136	integrableObject = mol->nextIntegrableObject(j)) {
137
138	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
139	if (iter != hydroPropMap.end()) {
140	hydroProps_.push_back(iter->second);
141	} else {
142	sprintf( painCave.errMsg,
143	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
144	painCave.severity = OOPSE_ERROR;
145	painCave.isFatal = 1;
146	simError();
147	}
148	}
149	}
150	} else {
151
152	std::map<std::string, HydroProp*> hydroPropMap;
153	for (mol = info->beginMolecule(i); mol != NULL;
154	mol = info->nextMolecule(i)) {
155	for (integrableObject = mol->beginIntegrableObject(j);
156	integrableObject != NULL;
157	integrableObject = mol->nextIntegrableObject(j)) {
158	Shape* currShape = NULL;
159
160	if (integrableObject->isAtom()){
161	Atom* atom = static_cast<Atom*>(integrableObject);
162	AtomType* atomType = atom->getAtomType();
163	if (atomType->isGayBerne()) {
164	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
165	GenericData* data = dAtomType->getPropertyByName("GayBerne");
166	if (data != NULL) {
167	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
168
169	if (gayBerneData != NULL) {
170	GayBerneParam gayBerneParam = gayBerneData->getData();
171	currShape = new Ellipsoid(V3Zero,
172	gayBerneParam.GB_l / 2.0,
173	gayBerneParam.GB_d / 2.0,
174	Mat3x3d::identity());
175	} else {
176	sprintf( painCave.errMsg,
177	"Can not cast GenericData to GayBerneParam\n");
178	painCave.severity = OOPSE_ERROR;
179	painCave.isFatal = 1;
180	simError();
181	}
182	} else {
183	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
184	painCave.severity = OOPSE_ERROR;
185	painCave.isFatal = 1;
186	simError();
187	}
188	} else {
189	if (atomType->isLennardJones()){
190	GenericData* data = atomType->getPropertyByName("LennardJones");
191	if (data != NULL) {
192	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
193	if (ljData != NULL) {
194	LJParam ljParam = ljData->getData();
195	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
196	} else {
197	sprintf( painCave.errMsg,
198	"Can not cast GenericData to LJParam\n");
199	painCave.severity = OOPSE_ERROR;
200	painCave.isFatal = 1;
201	simError();
202	}
203	}
204	} else {
205	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
206	if (aNum != 0) {
207	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
208	} else {
209	sprintf( painCave.errMsg,
210	"Could not find atom type in default element.txt\n");
211	painCave.severity = OOPSE_ERROR;
212	painCave.isFatal = 1;
213	simError();
214	}
215	}
216	}
217	}
218	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
219	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
220	if (iter != hydroPropMap.end())
221	hydroProps_.push_back(iter->second);
222	else {
223	currHydroProp->complete();
224	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
225	hydroProps_.push_back(currHydroProp);
226	}
227	}
228	}
229	}
230
231	/* Compute hull first time through to get the area of t=0*/
232
233	/* Build a vector of integrable objects to determine if the are surface atoms */
234	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
235	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
236	integrableObject = mol->nextIntegrableObject(j)) {
237	localSites_.push_back(integrableObject);
238	}
239	}
240
241	surfaceMesh_->computeHull(localSites_);
242	Area0_ = surfaceMesh_->getArea();
243	//variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
244
245	}
246
247	std::map<std::string, HydroProp*> SMIPDForceManager::parseFrictionFile(const std::string& filename) {
248	std::map<std::string, HydroProp*> props;
249	std::ifstream ifs(filename.c_str());
250	if (ifs.is_open()) {
251
252	}
253
254	const unsigned int BufferSize = 65535;
255	char buffer[BufferSize];
256	while (ifs.getline(buffer, BufferSize)) {
257	HydroProp* currProp = new HydroProp(buffer);
258	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
259	}
260
261	return props;
262	}
263
264	void SMIPDForceManager::postCalculation(bool needStress){
265	SimInfo::MoleculeIterator i;
266	Molecule::IntegrableObjectIterator j;
267	Molecule* mol;
268	StuntDouble* integrableObject;
269	RealType mass;
270	Vector3d pos;
271	Vector3d frc;
272	Mat3x3d A;
273	Mat3x3d Atrans;
274	Vector3d Tb;
275	Vector3d ji;
276	unsigned int index = 0;
277	int fdf;
278
279	fdf = 0;
280
281	/Compute surface Mesh/
282	surfaceMesh_->computeHull(localSites_);
283
284	/* Get area and number of surface stunt doubles and compute new variance */
285	//RealType area = surfaceMesh_->getArea();
286	//RealType nSurfaceSDs = surfaceMesh_->getNs();
287
288	// std::cerr << "Surface Area is: " << area << " nSurfaceSDs is: " << nSurfaceSDs << std::endl;
289
290	/* Compute variance for random forces */
291
292	// variance_ = sqrt(2.0NumericConstant::PI)(targetPressure_*area/nSurfaceSDs);
293
294	// std::vector<Triangle*> sMesh = surfaceMesh_->getMesh();
295	// std::vector<RealType> randNums = genTriangleForces(sMesh.size(),variance_);
296
297	/* Loop over the mesh faces and apply random force to each of the faces*/
298
299
300	// std::vector<Triangle*>::iterator face;
301	// std::vector<StuntDouble*>::iterator vertex;
302	/*
303	for (face = sMesh.begin(); face != sMesh.end(); ++face){
304
305	Triangle* thisTriangle = *face;
306	std::vector<StuntDouble*> vertexSDs = thisTriangle->getVertices();
307
308	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
309	std::cout << (*vertex)->getPos() << std::endl;
310	// mass = integrableObject->getMass();
311
312	// integrableObject->addFrc(randomForce);
313	}
314
315
316	}
317	*/
318	/*
319	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
320
321
322	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323	integrableObject = mol->nextIntegrableObject(j)) {
324
325	mass = integrableObject->getMass();
326	if (integrableObject->isDirectional()){
327
328	// preliminaries for directional objects:
329
330	A = integrableObject->getA();
331	Atrans = A.transpose();
332	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
333
334	//apply random force and torque at center of resistance
335
336	Vector3d randomForceBody;
337	Vector3d randomTorqueBody;
338	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
339	Vector3d randomForceLab = Atrans * randomForceBody;
340	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
341	integrableObject->addFrc(randomForceLab);
342	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
343
344	Mat3x3d I = integrableObject->getI();
345	Vector3d omegaBody;
346
347	// What remains contains velocity explicitly, but the velocity required
348	// is at the full step: v(t + h), while we have initially the velocity
349	// at the half step: v(t + h/2). We need to iterate to converge the
350	// friction force and friction torque vectors.
351
352	// this is the velocity at the half-step:
353
354	Vector3d vel =integrableObject->getVel();
355	Vector3d angMom = integrableObject->getJ();
356
357	//estimate velocity at full-step using everything but friction forces:
358
359	frc = integrableObject->getFrc();
360	Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
361
362	Tb = integrableObject->lab2Body(integrableObject->getTrq());
363	Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;
364
365	Vector3d omegaLab;
366	Vector3d vcdLab;
367	Vector3d vcdBody;
368	Vector3d frictionForceBody;
369	Vector3d frictionForceLab(0.0);
370	Vector3d oldFFL; // used to test for convergence
371	Vector3d frictionTorqueBody(0.0);
372	Vector3d oldFTB; // used to test for convergence
373	Vector3d frictionTorqueLab;
374	RealType fdot;
375	RealType tdot;
376
377	//iteration starts here:
378
379	for (int k = 0; k < maxIterNum_; k++) {
380
381	if (integrableObject->isLinear()) {
382	int linearAxis = integrableObject->linearAxis();
383	int l = (linearAxis +1 )%3;
384	int m = (linearAxis +2 )%3;
385	omegaBody[l] = angMomStep[l] /I(l, l);
386	omegaBody[m] = angMomStep[m] /I(m, m);
387
388	} else {
389	omegaBody[0] = angMomStep[0] /I(0, 0);
390	omegaBody[1] = angMomStep[1] /I(1, 1);
391	omegaBody[2] = angMomStep[2] /I(2, 2);
392	}
393
394	omegaLab = Atrans * omegaBody;
395
396	// apply friction force and torque at center of resistance
397
398	vcdLab = velStep + cross(omegaLab, rcrLab);
399	vcdBody = A * vcdLab;
400	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
401	oldFFL = frictionForceLab;
402	frictionForceLab = Atrans * frictionForceBody;
403	oldFTB = frictionTorqueBody;
404	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
405	frictionTorqueLab = Atrans * frictionTorqueBody;
406
407	// re-estimate velocities at full-step using friction forces:
408
409	velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
410	angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
411
412	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
413
414	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
415	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
416
417	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
418	break; // iteration ends here
419	}
420
421	integrableObject->addFrc(frictionForceLab);
422	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
423
424
425	} else {
426	//spherical atom
427
428	Vector3d randomForce;
429	Vector3d randomTorque;
430	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
431	integrableObject->addFrc(randomForce);
432
433	// What remains contains velocity explicitly, but the velocity required
434	// is at the full step: v(t + h), while we have initially the velocity
435	// at the half step: v(t + h/2). We need to iterate to converge the
436	// friction force vector.
437
438	// this is the velocity at the half-step:
439
440	Vector3d vel =integrableObject->getVel();
441
442	//estimate velocity at full-step using everything but friction forces:
443
444	frc = integrableObject->getFrc();
445	Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
446
447	Vector3d frictionForce(0.0);
448	Vector3d oldFF; // used to test for convergence
449	RealType fdot;
450
451	//iteration starts here:
452
453	for (int k = 0; k < maxIterNum_; k++) {
454
455	oldFF = frictionForce;
456	frictionForce = -hydroProps_[index]->getXitt() * velStep;
457
458	// re-estimate velocities at full-step using friction forces:
459
460	velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
461
462	// check for convergence (if the vector has converged, fdot will be 1.0):
463
464	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
465
466	if (fabs(1.0 - fdot) <= forceTolerance_)
467	break; // iteration ends here
468	}
469
470	integrableObject->addFrc(frictionForce);
471
472
473	}
474
475	++index;
476
477	}
478	}
479	*/
480	// info_->setFdf(fdf);
481	// veloMunge->removeComDrift();
482	// Remove angular drift if we are not using periodic boundary conditions.
483	//if(!simParams->getUsePeriodicBoundaryConditions())
484	// veloMunge->removeAngularDrift();
485
486	//ForceManager::postCalculation(needStress);
487	}
488
489	void SMIPDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
490
491
492	Vector<RealType, 6> Z;
493	Vector<RealType, 6> generalForce;
494
495	Z[0] = randNumGen_.randNorm(0, variance);
496	Z[1] = randNumGen_.randNorm(0, variance);
497	Z[2] = randNumGen_.randNorm(0, variance);
498	Z[3] = randNumGen_.randNorm(0, variance);
499	Z[4] = randNumGen_.randNorm(0, variance);
500	Z[5] = randNumGen_.randNorm(0, variance);
501
502	generalForce = hydroProps_[index]->getS()*Z;
503
504	force[0] = generalForce[0];
505	force[1] = generalForce[1];
506	force[2] = generalForce[2];
507	torque[0] = generalForce[3];
508	torque[1] = generalForce[4];
509	torque[2] = generalForce[5];
510
511	}
512	std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, RealType variance) {
513
514	// zero fill the random vector before starting:
515	std::vector<RealType> gaussRand;
516	gaussRand.resize(nTriangles);
517	std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
518
519
520	#ifdef IS_MPI
521	if (worldRank == 0) {
522	#endif
523	for (int i = 0; i < nTriangles; i++) {
524	gaussRand[i] = fabs(randNumGen_.randNorm(0.0, 1.0));
525	}
526	#ifdef IS_MPI
527	}
528	#endif
529
530	// push these out to the other processors
531
532	#ifdef IS_MPI
533	if (worldRank == 0) {
534	MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
535	} else {
536	MPI_Bcast(&gaussRand[0], nTriangles, MPI_REAL, 0, MPI_COMM_WORLD);
537	}
538	#endif
539
540	for (int i = 0; i < nTriangles; i++) {
541	gaussRand[i] = gaussRand[i] * variance;
542	}
543
544	return gaussRand;
545	}
546
547	}