src/primitives/RigidBody.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. 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 <algorithm>
#include <math.h>
#include "primitives/RigidBody.hpp"
#include "utils/simError.h"
#include "utils/NumericConstant.hpp"
namespace oopse {
  
  RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData),
                           inertiaTensor_(0.0){    
  }
  
  void RigidBody::setPrevA(const RotMat3x3d& a) {
    ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
    
    for (int i =0 ; i < atoms_.size(); ++i){
      if (atoms_[i]->isDirectional()) {
        atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
      }
    }
    
  }
  
  
  void RigidBody::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;

    for (int i =0 ; i < atoms_.size(); ++i){
      if (atoms_[i]->isDirectional()) {
        atoms_[i]->setA(refOrients_[i].transpose() * a);
      }
    }
  }    
  
  void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
    ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
    
    //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
    
    for (int i =0 ; i < atoms_.size(); ++i){
      if (atoms_[i]->isDirectional()) {
        atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
      }
    }
    
  }   
  
  Mat3x3d RigidBody::getI() {
    return inertiaTensor_;
  }    
  
  std::vector<RealType> RigidBody::getGrad() {
    std::vector<RealType> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    RealType phi, theta, psi;
    RealType cphi, sphi, ctheta, stheta;
    Vector3d ephi;
    Vector3d etheta;
    Vector3d epsi;
    
    force = getFrc();
    torque =getTrq();
    myEuler = getA().toEulerAngles();
    
    phi = myEuler[0];
    theta = myEuler[1];
    psi = myEuler[2];
    
    cphi = cos(phi);
    sphi = sin(phi);
    ctheta = cos(theta);
    stheta = sin(theta);
    
    // get unit vectors along the phi, theta and psi rotation axes
    
    ephi[0] = 0.0;
    ephi[1] = 0.0;
    ephi[2] = 1.0;
    
    etheta[0] = cphi;
    etheta[1] = sphi;
    etheta[2] = 0.0;
    
    epsi[0] = stheta * cphi;
    epsi[1] = stheta * sphi;
    epsi[2] = ctheta;
    
    //gradient is equal to -force
    for (int j = 0 ; j<3; j++)
      grad[j] = -force[j];
    
    for (int j = 0; j < 3; j++ ) {
      
      grad[3] += torque[j]*ephi[j];
      grad[4] += torque[j]*etheta[j];
      grad[5] += torque[j]*epsi[j];
      
    }
    
    return grad;
  }    
  
  void RigidBody::accept(BaseVisitor* v) {
    v->visit(this);
  }    

  /**@todo need modification */
  void  RigidBody::calcRefCoords() {
    RealType mtmp;
    Vector3d refCOM(0.0);
    mass_ = 0.0;
    for (std::size_t i = 0; i < atoms_.size(); ++i) {
      mtmp = atoms_[i]->getMass();
      mass_ += mtmp;
      refCOM += refCoords_[i]*mtmp;
    }
    refCOM /= mass_;
    
    // Next, move the origin of the reference coordinate system to the COM:
    for (std::size_t i = 0; i < atoms_.size(); ++i) {
      refCoords_[i] -= refCOM;
    }

    // Moment of Inertia calculation
    Mat3x3d Itmp(0.0);    
    for (std::size_t i = 0; i < atoms_.size(); i++) {
      Mat3x3d IAtom(0.0);  
      mtmp = atoms_[i]->getMass();
      IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
      RealType r2 = refCoords_[i].lengthSquare();
      IAtom(0, 0) += mtmp * r2;
      IAtom(1, 1) += mtmp * r2;
      IAtom(2, 2) += mtmp * r2;
      Itmp += IAtom;
      
      //project the inertial moment of directional atoms into this rigid body
      if (atoms_[i]->isDirectional()) {
        Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
      } 
    }

    //    std::cout << Itmp << std::endl;

    //diagonalize 
    Vector3d evals;
    Mat3x3d::diagonalize(Itmp, evals, sU_);

    // zero out I and then fill the diagonals with the moments of inertia:
    inertiaTensor_(0, 0) = evals[0];
    inertiaTensor_(1, 1) = evals[1];
    inertiaTensor_(2, 2) = evals[2];
        
    int nLinearAxis = 0;
    for (int i = 0; i < 3; i++) {    
      if (fabs(evals[i]) < oopse::epsilon) {
        linear_ = true;
        linearAxis_ = i;
        ++ nLinearAxis;
      }
    }

    if (nLinearAxis > 1) {
      sprintf( painCave.errMsg,
               "RigidBody error.\n"
               "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
               "\tmoment of inertia.  This can happen in one of three ways:\n"
               "\t 1) Only one atom was specified, or \n"
               "\t 2) All atoms were specified at the same location, or\n"
               "\t 3) The programmers did something stupid.\n"
               "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
               );
      painCave.isFatal = 1;
      simError();
    }
  
  }

  void  RigidBody::calcForcesAndTorques() {
    Vector3d afrc;
    Vector3d atrq;
    Vector3d apos;
    Vector3d rpos;
    Vector3d frc(0.0);
    Vector3d trq(0.0);    
    Vector3d pos = this->getPos();
    for (int i = 0; i < atoms_.size(); i++) {

      afrc = atoms_[i]->getFrc();
      apos = atoms_[i]->getPos();
      rpos = apos - pos;
        
      frc += afrc;

      trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
      trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
      trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];

      // If the atom has a torque associated with it, then we also need to 
      // migrate the torques onto the center of mass:

      if (atoms_[i]->isDirectional()) {
        atrq = atoms_[i]->getTrq();
        trq += atrq;
      }      
    }         
    addFrc(frc);
    addTrq(trq);    
  }

  Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
    Vector3d afrc;
    Vector3d atrq;
    Vector3d apos;
    Vector3d rpos;
    Vector3d dfrc;
    Vector3d frc(0.0);
    Vector3d trq(0.0);    
    Vector3d pos = this->getPos();
    Mat3x3d tau_(0.0);

    for (int i = 0; i < atoms_.size(); i++) {
      
      afrc = atoms_[i]->getFrc();
      apos = atoms_[i]->getPos();
      rpos = apos - pos;
        
      frc += afrc;

      trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
      trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
      trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];

      // If the atom has a torque associated with it, then we also need to 
      // migrate the torques onto the center of mass:

      if (atoms_[i]->isDirectional()) {
        atrq = atoms_[i]->getTrq();
        trq += atrq;
      }
      
      tau_(0,0) -= rpos[0]*afrc[0];
      tau_(0,1) -= rpos[0]*afrc[1];
      tau_(0,2) -= rpos[0]*afrc[2];
      tau_(1,0) -= rpos[1]*afrc[0];
      tau_(1,1) -= rpos[1]*afrc[1];
      tau_(1,2) -= rpos[1]*afrc[2];
      tau_(2,0) -= rpos[2]*afrc[0];
      tau_(2,1) -= rpos[2]*afrc[1];
      tau_(2,2) -= rpos[2]*afrc[2];

    }
    addFrc(frc);
    addTrq(trq);
    return tau_;
  }

  void  RigidBody::updateAtoms() {
    unsigned int i;
    Vector3d ref;
    Vector3d apos;
    DirectionalAtom* dAtom;
    Vector3d pos = getPos();
    RotMat3x3d a = getA();
    
    for (i = 0; i < atoms_.size(); i++) {
     
      ref = body2Lab(refCoords_[i]);

      apos = pos + ref;

      atoms_[i]->setPos(apos);

      if (atoms_[i]->isDirectional()) {
          
        dAtom = (DirectionalAtom *) atoms_[i];
        dAtom->setA(refOrients_[i].transpose() * a);
      }

    }
  
  }


  void  RigidBody::updateAtoms(int frame) {
    unsigned int i;
    Vector3d ref;
    Vector3d apos;
    DirectionalAtom* dAtom;
    Vector3d pos = getPos(frame);
    RotMat3x3d a = getA(frame);
    
    for (i = 0; i < atoms_.size(); i++) {
     
      ref = body2Lab(refCoords_[i], frame);

      apos = pos + ref;

      atoms_[i]->setPos(apos, frame);

      if (atoms_[i]->isDirectional()) {
          
        dAtom = (DirectionalAtom *) atoms_[i];
        dAtom->setA(refOrients_[i].transpose() * a, frame);
      }

    }
  
  }

  void RigidBody::updateAtomVel() {
    Mat3x3d skewMat;;

    Vector3d ji = getJ();
    Mat3x3d I =  getI();

    skewMat(0, 0) =0;
    skewMat(0, 1) = ji[2] /I(2, 2);
    skewMat(0, 2) = -ji[1] /I(1, 1);

    skewMat(1, 0) = -ji[2] /I(2, 2);
    skewMat(1, 1) = 0;
    skewMat(1, 2) = ji[0]/I(0, 0);

    skewMat(2, 0) =ji[1] /I(1, 1);
    skewMat(2, 1) = -ji[0]/I(0, 0);
    skewMat(2, 2) = 0;

    Mat3x3d mat = (getA() * skewMat).transpose();
    Vector3d rbVel = getVel();


    Vector3d velRot;        
    for (int i =0 ; i < refCoords_.size(); ++i) {
      atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
    }

  }

  void RigidBody::updateAtomVel(int frame) {
    Mat3x3d skewMat;;

    Vector3d ji = getJ(frame);
    Mat3x3d I =  getI();

    skewMat(0, 0) =0;
    skewMat(0, 1) = ji[2] /I(2, 2);
    skewMat(0, 2) = -ji[1] /I(1, 1);

    skewMat(1, 0) = -ji[2] /I(2, 2);
    skewMat(1, 1) = 0;
    skewMat(1, 2) = ji[0]/I(0, 0);

    skewMat(2, 0) =ji[1] /I(1, 1);
    skewMat(2, 1) = -ji[0]/I(0, 0);
    skewMat(2, 2) = 0;

    Mat3x3d mat = (getA(frame) * skewMat).transpose();
    Vector3d rbVel = getVel(frame);


    Vector3d velRot;        
    for (int i =0 ; i < refCoords_.size(); ++i) {
      atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
    }

  }

        
  bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
    if (index < atoms_.size()) {

      Vector3d ref = body2Lab(refCoords_[index]);
      pos = getPos() + ref;
      return true;
    } else {
      std::cerr << index << " is an invalid index, current rigid body contains " 
                << atoms_.size() << "atoms" << std::endl;
      return false;
    }    
  }

  bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
    std::vector<Atom*>::iterator i;
    i = std::find(atoms_.begin(), atoms_.end(), atom);
    if (i != atoms_.end()) {
      //RigidBody class makes sure refCoords_ and atoms_ match each other 
      Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
      pos = getPos() + ref;
      return true;
    } else {
      std::cerr << "Atom " << atom->getGlobalIndex() 
                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; 
      return false;
    }
  }
  bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {

    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$

    if (index < atoms_.size()) {

      Vector3d velRot;
      Mat3x3d skewMat;;
      Vector3d ref = refCoords_[index];
      Vector3d ji = getJ();
      Mat3x3d I =  getI();

      skewMat(0, 0) =0;
      skewMat(0, 1) = ji[2] /I(2, 2);
      skewMat(0, 2) = -ji[1] /I(1, 1);

      skewMat(1, 0) = -ji[2] /I(2, 2);
      skewMat(1, 1) = 0;
      skewMat(1, 2) = ji[0]/I(0, 0);

      skewMat(2, 0) =ji[1] /I(1, 1);
      skewMat(2, 1) = -ji[0]/I(0, 0);
      skewMat(2, 2) = 0;

      velRot = (getA() * skewMat).transpose() * ref;

      vel =getVel() + velRot;
      return true;
        
    } else {
      std::cerr << index << " is an invalid index, current rigid body contains " 
                << atoms_.size() << "atoms" << std::endl;
      return false;
    }
  }

  bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {

    std::vector<Atom*>::iterator i;
    i = std::find(atoms_.begin(), atoms_.end(), atom);
    if (i != atoms_.end()) {
      return getAtomVel(vel, i - atoms_.begin());
    } else {
      std::cerr << "Atom " << atom->getGlobalIndex() 
                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
      return false;
    }    
  }

  bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
    if (index < atoms_.size()) {

      coor = refCoords_[index];
      return true;
    } else {
      std::cerr << index << " is an invalid index, current rigid body contains " 
                << atoms_.size() << "atoms" << std::endl;
      return false;
    }

  }

  bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
    std::vector<Atom*>::iterator i;
    i = std::find(atoms_.begin(), atoms_.end(), atom);
    if (i != atoms_.end()) {
      //RigidBody class makes sure refCoords_ and atoms_ match each other 
      coor = refCoords_[i - atoms_.begin()];
      return true;
    } else {
      std::cerr << "Atom " << atom->getGlobalIndex() 
                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
      return false;
    }

  }


  void RigidBody::addAtom(Atom* at, AtomStamp* ats) {

    Vector3d coords;
    Vector3d euler;
  

    atoms_.push_back(at);
 
    if( !ats->havePosition() ){
      sprintf( painCave.errMsg,
               "RigidBody error.\n"
               "\tAtom %s does not have a position specified.\n"
               "\tThis means RigidBody cannot set up reference coordinates.\n",
               ats->getType().c_str() );
      painCave.isFatal = 1;
      simError();
    }
  
    coords[0] = ats->getPosX();
    coords[1] = ats->getPosY();
    coords[2] = ats->getPosZ();

    refCoords_.push_back(coords);

    RotMat3x3d identMat = RotMat3x3d::identity();
  
    if (at->isDirectional()) {   

      if( !ats->haveOrientation() ){
        sprintf( painCave.errMsg,
                 "RigidBody error.\n"
                 "\tAtom %s does not have an orientation specified.\n"
                 "\tThis means RigidBody cannot set up reference orientations.\n",
                 ats->getType().c_str() );
        painCave.isFatal = 1;
        simError();
      }    
    
      euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
      euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
      euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;

      RotMat3x3d Atmp(euler);
      refOrients_.push_back(Atmp);
    
    }else {
      refOrients_.push_back(identMat);
    }
  
  
  }

}

Revision:	1211
Committed:	Wed Jan 23 16:38:22 2008 UTC (17 years, 3 months ago) by gezelter
File size:	15478 byte(s)
Log Message:	A few formatting changes to prettify the code
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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. 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 <algorithm>
42	tim	253	#include <math.h>
43	tim	3	#include "primitives/RigidBody.hpp"
44			#include "utils/simError.h"
45	tim	374	#include "utils/NumericConstant.hpp"
46	gezelter	246	namespace oopse {
47	gezelter	1211
48			RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData),
49			inertiaTensor_(0.0){
50	gezelter	507	}
51	gezelter	1211
52	gezelter	507	void RigidBody::setPrevA(const RotMat3x3d& a) {
53	gezelter	246	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
54	gezelter	1211
55	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
56	gezelter	507	if (atoms_[i]->isDirectional()) {
57	gezelter	882	atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
58	gezelter	507	}
59	gezelter	246	}
60	gezelter	1211
61	gezelter	507	}
62	gezelter	1211
63
64	gezelter	507	void RigidBody::setA(const RotMat3x3d& a) {
65	gezelter	246	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
66	gezelter	2
67	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
68	gezelter	507	if (atoms_[i]->isDirectional()) {
69	gezelter	882	atoms_[i]->setA(refOrients_[i].transpose() * a);
70	gezelter	507	}
71	gezelter	246	}
72	gezelter	507	}
73	gezelter	1211
74	gezelter	507	void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
75	gezelter	246	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
76	gezelter	1211
77	gezelter	246	//((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() sU_;
78	gezelter	1211
79	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
80	gezelter	507	if (atoms_[i]->isDirectional()) {
81	gezelter	882	atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
82	gezelter	507	}
83	gezelter	2	}
84	gezelter	1211
85	gezelter	507	}
86	gezelter	1211
87	gezelter	507	Mat3x3d RigidBody::getI() {
88	gezelter	246	return inertiaTensor_;
89	gezelter	507	}
90	gezelter	1211
91	tim	963	std::vector<RealType> RigidBody::getGrad() {
92			std::vector<RealType> grad(6, 0.0);
93	gezelter	246	Vector3d force;
94			Vector3d torque;
95			Vector3d myEuler;
96	tim	963	RealType phi, theta, psi;
97			RealType cphi, sphi, ctheta, stheta;
98	gezelter	246	Vector3d ephi;
99			Vector3d etheta;
100			Vector3d epsi;
101	gezelter	1211
102	gezelter	246	force = getFrc();
103			torque =getTrq();
104			myEuler = getA().toEulerAngles();
105	gezelter	1211
106	gezelter	246	phi = myEuler[0];
107			theta = myEuler[1];
108			psi = myEuler[2];
109	gezelter	1211
110	gezelter	246	cphi = cos(phi);
111			sphi = sin(phi);
112			ctheta = cos(theta);
113			stheta = sin(theta);
114	gezelter	1211
115	gezelter	246	// get unit vectors along the phi, theta and psi rotation axes
116	gezelter	1211
117	gezelter	246	ephi[0] = 0.0;
118			ephi[1] = 0.0;
119			ephi[2] = 1.0;
120	gezelter	1211
121	gezelter	246	etheta[0] = cphi;
122			etheta[1] = sphi;
123			etheta[2] = 0.0;
124	gezelter	1211
125	gezelter	246	epsi[0] = stheta * cphi;
126			epsi[1] = stheta * sphi;
127			epsi[2] = ctheta;
128	gezelter	1211
129	gezelter	246	//gradient is equal to -force
130			for (int j = 0 ; j<3; j++)
131	gezelter	507	grad[j] = -force[j];
132	gezelter	1211
133	gezelter	246	for (int j = 0; j < 3; j++ ) {
134	gezelter	1211
135	gezelter	507	grad[3] += torque[j]*ephi[j];
136			grad[4] += torque[j]*etheta[j];
137			grad[5] += torque[j]*epsi[j];
138	gezelter	1211
139	gezelter	246	}
140
141			return grad;
142	gezelter	507	}
143	gezelter	1211
144	gezelter	507	void RigidBody::accept(BaseVisitor* v) {
145	gezelter	246	v->visit(this);
146	gezelter	507	}
147	gezelter	2
148	gezelter	507	/*@todo need modification /
149			void RigidBody::calcRefCoords() {
150	tim	963	RealType mtmp;
151	gezelter	246	Vector3d refCOM(0.0);
152			mass_ = 0.0;
153			for (std::size_t i = 0; i < atoms_.size(); ++i) {
154	gezelter	507	mtmp = atoms_[i]->getMass();
155			mass_ += mtmp;
156			refCOM += refCoords_[i]*mtmp;
157	gezelter	246	}
158			refCOM /= mass_;
159	gezelter	1211
160	gezelter	246	// Next, move the origin of the reference coordinate system to the COM:
161			for (std::size_t i = 0; i < atoms_.size(); ++i) {
162	gezelter	507	refCoords_[i] -= refCOM;
163	gezelter	246	}
164	gezelter	2
165	gezelter	507	// Moment of Inertia calculation
166	tim	642	Mat3x3d Itmp(0.0);
167	gezelter	246	for (std::size_t i = 0; i < atoms_.size(); i++) {
168	tim	642	Mat3x3d IAtom(0.0);
169	gezelter	507	mtmp = atoms_[i]->getMass();
170	tim	642	IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
171	tim	963	RealType r2 = refCoords_[i].lengthSquare();
172	tim	642	IAtom(0, 0) += mtmp * r2;
173			IAtom(1, 1) += mtmp * r2;
174			IAtom(2, 2) += mtmp * r2;
175	tim	648	Itmp += IAtom;
176	gezelter	1211
177	tim	642	//project the inertial moment of directional atoms into this rigid body
178	gezelter	507	if (atoms_[i]->isDirectional()) {
179	tim	646	Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
180	tim	648	}
181	tim	273	}
182
183	chrisfen	695	// std::cout << Itmp << std::endl;
184	gezelter	663
185	gezelter	246	//diagonalize
186			Vector3d evals;
187			Mat3x3d::diagonalize(Itmp, evals, sU_);
188	gezelter	2
189	gezelter	246	// zero out I and then fill the diagonals with the moments of inertia:
190			inertiaTensor_(0, 0) = evals[0];
191			inertiaTensor_(1, 1) = evals[1];
192			inertiaTensor_(2, 2) = evals[2];
193
194			int nLinearAxis = 0;
195			for (int i = 0; i < 3; i++) {
196	gezelter	507	if (fabs(evals[i]) < oopse::epsilon) {
197			linear_ = true;
198			linearAxis_ = i;
199			++ nLinearAxis;
200			}
201	gezelter	246	}
202	gezelter	2
203	gezelter	246	if (nLinearAxis > 1) {
204	gezelter	507	sprintf( painCave.errMsg,
205			"RigidBody error.\n"
206			"\tOOPSE found more than one axis in this rigid body with a vanishing \n"
207			"\tmoment of inertia. This can happen in one of three ways:\n"
208			"\t 1) Only one atom was specified, or \n"
209			"\t 2) All atoms were specified at the same location, or\n"
210			"\t 3) The programmers did something stupid.\n"
211			"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n"
212			);
213			painCave.isFatal = 1;
214			simError();
215	gezelter	246	}
216	gezelter	2
217	gezelter	507	}
218	gezelter	2
219	gezelter	507	void RigidBody::calcForcesAndTorques() {
220	gezelter	246	Vector3d afrc;
221			Vector3d atrq;
222			Vector3d apos;
223			Vector3d rpos;
224			Vector3d frc(0.0);
225	gezelter	1126	Vector3d trq(0.0);
226	gezelter	246	Vector3d pos = this->getPos();
227			for (int i = 0; i < atoms_.size(); i++) {
228	gezelter	2
229	gezelter	507	afrc = atoms_[i]->getFrc();
230			apos = atoms_[i]->getPos();
231			rpos = apos - pos;
232	gezelter	246
233	gezelter	507	frc += afrc;
234	gezelter	2
235	gezelter	507	trq[0] += rpos[1]afrc[2] - rpos[2]afrc[1];
236			trq[1] += rpos[2]afrc[0] - rpos[0]afrc[2];
237			trq[2] += rpos[0]afrc[1] - rpos[1]afrc[0];
238	gezelter	2
239	gezelter	507	// If the atom has a torque associated with it, then we also need to
240			// migrate the torques onto the center of mass:
241	gezelter	2
242	gezelter	507	if (atoms_[i]->isDirectional()) {
243			atrq = atoms_[i]->getTrq();
244			trq += atrq;
245	gezelter	1126	}
246			}
247			addFrc(frc);
248			addTrq(trq);
249			}
250
251			Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
252			Vector3d afrc;
253			Vector3d atrq;
254			Vector3d apos;
255			Vector3d rpos;
256	gezelter	1211	Vector3d dfrc;
257	gezelter	1126	Vector3d frc(0.0);
258			Vector3d trq(0.0);
259			Vector3d pos = this->getPos();
260			Mat3x3d tau_(0.0);
261
262			for (int i = 0; i < atoms_.size(); i++) {
263	gezelter	1211
264	gezelter	1126	afrc = atoms_[i]->getFrc();
265			apos = atoms_[i]->getPos();
266			rpos = apos - pos;
267
268			frc += afrc;
269
270			trq[0] += rpos[1]afrc[2] - rpos[2]afrc[1];
271			trq[1] += rpos[2]afrc[0] - rpos[0]afrc[2];
272			trq[2] += rpos[0]afrc[1] - rpos[1]afrc[0];
273
274			// If the atom has a torque associated with it, then we also need to
275			// migrate the torques onto the center of mass:
276
277			if (atoms_[i]->isDirectional()) {
278			atrq = atoms_[i]->getTrq();
279			trq += atrq;
280	gezelter	507	}
281	gezelter	1126
282			tau_(0,0) -= rpos[0]*afrc[0];
283			tau_(0,1) -= rpos[0]*afrc[1];
284			tau_(0,2) -= rpos[0]*afrc[2];
285			tau_(1,0) -= rpos[1]*afrc[0];
286			tau_(1,1) -= rpos[1]*afrc[1];
287			tau_(1,2) -= rpos[1]*afrc[2];
288			tau_(2,0) -= rpos[2]*afrc[0];
289			tau_(2,1) -= rpos[2]*afrc[1];
290			tau_(2,2) -= rpos[2]*afrc[2];
291	gezelter	1211
292			}
293	tim	899	addFrc(frc);
294			addTrq(trq);
295	gezelter	1126	return tau_;
296	gezelter	507	}
297	gezelter	2
298	gezelter	507	void RigidBody::updateAtoms() {
299	gezelter	246	unsigned int i;
300			Vector3d ref;
301			Vector3d apos;
302			DirectionalAtom* dAtom;
303			Vector3d pos = getPos();
304			RotMat3x3d a = getA();
305	gezelter	2
306	gezelter	246	for (i = 0; i < atoms_.size(); i++) {
307
308	gezelter	507	ref = body2Lab(refCoords_[i]);
309	gezelter	2
310	gezelter	507	apos = pos + ref;
311	gezelter	2
312	gezelter	507	atoms_[i]->setPos(apos);
313	gezelter	2
314	gezelter	507	if (atoms_[i]->isDirectional()) {
315	gezelter	246
316	gezelter	507	dAtom = (DirectionalAtom *) atoms_[i];
317	gezelter	882	dAtom->setA(refOrients_[i].transpose() * a);
318	gezelter	507	}
319	gezelter	2
320			}
321
322	gezelter	507	}
323	gezelter	2
324
325	gezelter	507	void RigidBody::updateAtoms(int frame) {
326	tim	318	unsigned int i;
327			Vector3d ref;
328			Vector3d apos;
329			DirectionalAtom* dAtom;
330			Vector3d pos = getPos(frame);
331			RotMat3x3d a = getA(frame);
332
333			for (i = 0; i < atoms_.size(); i++) {
334
335	gezelter	507	ref = body2Lab(refCoords_[i], frame);
336	tim	318
337	gezelter	507	apos = pos + ref;
338	tim	318
339	gezelter	507	atoms_[i]->setPos(apos, frame);
340	tim	318
341	gezelter	507	if (atoms_[i]->isDirectional()) {
342	tim	318
343	gezelter	507	dAtom = (DirectionalAtom *) atoms_[i];
344	gezelter	882	dAtom->setA(refOrients_[i].transpose() * a, frame);
345	gezelter	507	}
346	tim	318
347			}
348
349	gezelter	507	}
350	tim	318
351	gezelter	507	void RigidBody::updateAtomVel() {
352	tim	318	Mat3x3d skewMat;;
353
354			Vector3d ji = getJ();
355			Mat3x3d I = getI();
356
357			skewMat(0, 0) =0;
358			skewMat(0, 1) = ji[2] /I(2, 2);
359			skewMat(0, 2) = -ji[1] /I(1, 1);
360
361			skewMat(1, 0) = -ji[2] /I(2, 2);
362			skewMat(1, 1) = 0;
363			skewMat(1, 2) = ji[0]/I(0, 0);
364
365			skewMat(2, 0) =ji[1] /I(1, 1);
366			skewMat(2, 1) = -ji[0]/I(0, 0);
367			skewMat(2, 2) = 0;
368
369			Mat3x3d mat = (getA() * skewMat).transpose();
370			Vector3d rbVel = getVel();
371
372
373			Vector3d velRot;
374			for (int i =0 ; i < refCoords_.size(); ++i) {
375	gezelter	507	atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
376	tim	318	}
377
378	gezelter	507	}
379	tim	318
380	gezelter	507	void RigidBody::updateAtomVel(int frame) {
381	tim	318	Mat3x3d skewMat;;
382
383			Vector3d ji = getJ(frame);
384			Mat3x3d I = getI();
385
386			skewMat(0, 0) =0;
387			skewMat(0, 1) = ji[2] /I(2, 2);
388			skewMat(0, 2) = -ji[1] /I(1, 1);
389
390			skewMat(1, 0) = -ji[2] /I(2, 2);
391			skewMat(1, 1) = 0;
392			skewMat(1, 2) = ji[0]/I(0, 0);
393
394			skewMat(2, 0) =ji[1] /I(1, 1);
395			skewMat(2, 1) = -ji[0]/I(0, 0);
396			skewMat(2, 2) = 0;
397
398			Mat3x3d mat = (getA(frame) * skewMat).transpose();
399			Vector3d rbVel = getVel(frame);
400
401
402			Vector3d velRot;
403			for (int i =0 ; i < refCoords_.size(); ++i) {
404	gezelter	507	atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
405	tim	318	}
406
407	gezelter	507	}
408	tim	318
409
410
411	gezelter	507	bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
412	gezelter	246	if (index < atoms_.size()) {
413	gezelter	2
414	gezelter	507	Vector3d ref = body2Lab(refCoords_[index]);
415			pos = getPos() + ref;
416			return true;
417	gezelter	246	} else {
418	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
419			<< atoms_.size() << "atoms" << std::endl;
420			return false;
421	gezelter	246	}
422	gezelter	507	}
423	gezelter	2
424	gezelter	507	bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
425	gezelter	246	std::vector<Atom*>::iterator i;
426			i = std::find(atoms_.begin(), atoms_.end(), atom);
427			if (i != atoms_.end()) {
428	gezelter	507	//RigidBody class makes sure refCoords_ and atoms_ match each other
429			Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
430			pos = getPos() + ref;
431			return true;
432	gezelter	246	} else {
433	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
434			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
435			return false;
436	gezelter	2	}
437	gezelter	507	}
438			bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
439	gezelter	2
440	gezelter	246	//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
441	gezelter	2
442	gezelter	246	if (index < atoms_.size()) {
443	gezelter	2
444	gezelter	507	Vector3d velRot;
445			Mat3x3d skewMat;;
446			Vector3d ref = refCoords_[index];
447			Vector3d ji = getJ();
448			Mat3x3d I = getI();
449	gezelter	2
450	gezelter	507	skewMat(0, 0) =0;
451			skewMat(0, 1) = ji[2] /I(2, 2);
452			skewMat(0, 2) = -ji[1] /I(1, 1);
453	gezelter	2
454	gezelter	507	skewMat(1, 0) = -ji[2] /I(2, 2);
455			skewMat(1, 1) = 0;
456			skewMat(1, 2) = ji[0]/I(0, 0);
457	gezelter	2
458	gezelter	507	skewMat(2, 0) =ji[1] /I(1, 1);
459			skewMat(2, 1) = -ji[0]/I(0, 0);
460			skewMat(2, 2) = 0;
461	gezelter	2
462	gezelter	507	velRot = (getA() * skewMat).transpose() * ref;
463	gezelter	2
464	gezelter	507	vel =getVel() + velRot;
465			return true;
466	gezelter	246
467			} else {
468	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
469			<< atoms_.size() << "atoms" << std::endl;
470			return false;
471	gezelter	2	}
472	gezelter	507	}
473	gezelter	2
474	gezelter	507	bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
475	gezelter	2
476	gezelter	246	std::vector<Atom*>::iterator i;
477			i = std::find(atoms_.begin(), atoms_.end(), atom);
478			if (i != atoms_.end()) {
479	gezelter	507	return getAtomVel(vel, i - atoms_.begin());
480	gezelter	246	} else {
481	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
482			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
483			return false;
484	gezelter	246	}
485	gezelter	507	}
486	gezelter	2
487	gezelter	507	bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
488	gezelter	246	if (index < atoms_.size()) {
489
490	gezelter	507	coor = refCoords_[index];
491			return true;
492	gezelter	246	} else {
493	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
494			<< atoms_.size() << "atoms" << std::endl;
495			return false;
496	gezelter	2	}
497
498	gezelter	507	}
499	gezelter	2
500	gezelter	507	bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
501	gezelter	246	std::vector<Atom*>::iterator i;
502			i = std::find(atoms_.begin(), atoms_.end(), atom);
503			if (i != atoms_.end()) {
504	gezelter	507	//RigidBody class makes sure refCoords_ and atoms_ match each other
505			coor = refCoords_[i - atoms_.begin()];
506			return true;
507	gezelter	246	} else {
508	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
509			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
510			return false;
511	gezelter	246	}
512	gezelter	2
513	gezelter	507	}
514	gezelter	2
515
516	gezelter	507	void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
517	gezelter	2
518	gezelter	507	Vector3d coords;
519			Vector3d euler;
520	gezelter	2
521
522	gezelter	507	atoms_.push_back(at);
523	gezelter	246
524	gezelter	507	if( !ats->havePosition() ){
525			sprintf( painCave.errMsg,
526			"RigidBody error.\n"
527			"\tAtom %s does not have a position specified.\n"
528			"\tThis means RigidBody cannot set up reference coordinates.\n",
529	tim	770	ats->getType().c_str() );
530	gezelter	507	painCave.isFatal = 1;
531			simError();
532			}
533	gezelter	2
534	gezelter	507	coords[0] = ats->getPosX();
535			coords[1] = ats->getPosY();
536			coords[2] = ats->getPosZ();
537	gezelter	2
538	gezelter	507	refCoords_.push_back(coords);
539	gezelter	2
540	gezelter	507	RotMat3x3d identMat = RotMat3x3d::identity();
541	gezelter	2
542	gezelter	507	if (at->isDirectional()) {
543	gezelter	2
544	gezelter	507	if( !ats->haveOrientation() ){
545			sprintf( painCave.errMsg,
546			"RigidBody error.\n"
547			"\tAtom %s does not have an orientation specified.\n"
548			"\tThis means RigidBody cannot set up reference orientations.\n",
549	tim	770	ats->getType().c_str() );
550	gezelter	507	painCave.isFatal = 1;
551			simError();
552			}
553	gezelter	246
554	gezelter	507	euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
555			euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
556			euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
557	gezelter	2
558	gezelter	507	RotMat3x3d Atmp(euler);
559			refOrients_.push_back(Atmp);
560	gezelter	2
561	gezelter	507	}else {
562			refOrients_.push_back(identMat);
563			}
564	gezelter	2
565
566	gezelter	507	}
567	gezelter	2
568			}
569