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;
    //((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;

    for (int i =0 ; i < atoms_.size(); ++i){
      if (atoms_[i]->isDirectional()) {
        atoms_[i]->setPrevA(a * refOrients_[i]);
      }
    }

  }

      
  void RigidBody::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
    //((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;

    for (int i =0 ; i < atoms_.size(); ++i){
      if (atoms_[i]->isDirectional()) {
        atoms_[i]->setA(a * refOrients_[i]);
      }
    }
  }    
    
  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(a * refOrients_[i], snapshotNo);
      }
    }

  }   

  Mat3x3d RigidBody::getI() {
    return inertiaTensor_;
  }    

  std::vector<double> RigidBody::getGrad() {
    std::vector<double> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    double phi, theta, psi;
    double 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() {
    double 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++) {
      mtmp = atoms_[i]->getMass();
      Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
      double r2 = refCoords_[i].lengthSquare();
      Itmp(0, 0) += mtmp * r2;
      Itmp(1, 1) += mtmp * r2;
      Itmp(2, 2) += mtmp * r2;
    }

    //project the inertial moment of directional atoms into this rigid body
    for (std::size_t i = 0; i < atoms_.size(); i++) {
      if (atoms_[i]->isDirectional()) {
        RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI();
        Itmp(0, 0) += Iproject(0, 0);
        Itmp(1, 1) += Iproject(1, 1);
        Itmp(2, 2) += Iproject(2, 2);
      }
    }

    //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;
      }
        
    }
    
    setFrc(frc);
    setTrq(trq);
    
  }

  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(a * refOrients_[i]);
        //dAtom->rotateBy( 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(a * refOrients_[i], 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() );
      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() );
        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:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years ago) by gezelter
Original Path:	*trunk/src/primitives/RigidBody.cpp*
File size:	14362 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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	2
48	gezelter	507	RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){
49	gezelter	2
50	gezelter	507	}
51	gezelter	2
52	gezelter	507	void RigidBody::setPrevA(const RotMat3x3d& a) {
53	gezelter	246	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
54			//((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() sU_;
55	gezelter	2
56	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
57	gezelter	507	if (atoms_[i]->isDirectional()) {
58			atoms_[i]->setPrevA(a * refOrients_[i]);
59			}
60	gezelter	246	}
61	gezelter	2
62	gezelter	507	}
63	gezelter	2
64	gezelter	246
65	gezelter	507	void RigidBody::setA(const RotMat3x3d& a) {
66	gezelter	246	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67			//((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() sU_;
68	gezelter	2
69	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
70	gezelter	507	if (atoms_[i]->isDirectional()) {
71			atoms_[i]->setA(a * refOrients_[i]);
72			}
73	gezelter	246	}
74	gezelter	507	}
75	gezelter	2
76	gezelter	507	void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
77	gezelter	246	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
78			//((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() sU_;
79	gezelter	2
80	gezelter	246	for (int i =0 ; i < atoms_.size(); ++i){
81	gezelter	507	if (atoms_[i]->isDirectional()) {
82			atoms_[i]->setA(a * refOrients_[i], snapshotNo);
83			}
84	gezelter	2	}
85
86	gezelter	507	}
87	gezelter	2
88	gezelter	507	Mat3x3d RigidBody::getI() {
89	gezelter	246	return inertiaTensor_;
90	gezelter	507	}
91	gezelter	2
92	gezelter	507	std::vector<double> RigidBody::getGrad() {
93			std::vector<double> grad(6, 0.0);
94	gezelter	246	Vector3d force;
95			Vector3d torque;
96			Vector3d myEuler;
97			double phi, theta, psi;
98			double cphi, sphi, ctheta, stheta;
99			Vector3d ephi;
100			Vector3d etheta;
101			Vector3d epsi;
102	gezelter	2
103	gezelter	246	force = getFrc();
104			torque =getTrq();
105			myEuler = getA().toEulerAngles();
106	gezelter	2
107	gezelter	246	phi = myEuler[0];
108			theta = myEuler[1];
109			psi = myEuler[2];
110	gezelter	2
111	gezelter	246	cphi = cos(phi);
112			sphi = sin(phi);
113			ctheta = cos(theta);
114			stheta = sin(theta);
115	gezelter	2
116	gezelter	246	// get unit vectors along the phi, theta and psi rotation axes
117	gezelter	2
118	gezelter	246	ephi[0] = 0.0;
119			ephi[1] = 0.0;
120			ephi[2] = 1.0;
121	gezelter	2
122	gezelter	246	etheta[0] = cphi;
123			etheta[1] = sphi;
124			etheta[2] = 0.0;
125	gezelter	2
126	gezelter	246	epsi[0] = stheta * cphi;
127			epsi[1] = stheta * sphi;
128			epsi[2] = ctheta;
129	gezelter	2
130	gezelter	246	//gradient is equal to -force
131			for (int j = 0 ; j<3; j++)
132	gezelter	507	grad[j] = -force[j];
133	gezelter	2
134	gezelter	246	for (int j = 0; j < 3; j++ ) {
135	gezelter	2
136	gezelter	507	grad[3] += torque[j]*ephi[j];
137			grad[4] += torque[j]*etheta[j];
138			grad[5] += torque[j]*epsi[j];
139	gezelter	2
140	gezelter	246	}
141
142			return grad;
143	gezelter	507	}
144	gezelter	2
145	gezelter	507	void RigidBody::accept(BaseVisitor* v) {
146	gezelter	246	v->visit(this);
147	gezelter	507	}
148	gezelter	2
149	gezelter	507	/*@todo need modification /
150			void RigidBody::calcRefCoords() {
151	gezelter	246	double mtmp;
152			Vector3d refCOM(0.0);
153			mass_ = 0.0;
154			for (std::size_t i = 0; i < atoms_.size(); ++i) {
155	gezelter	507	mtmp = atoms_[i]->getMass();
156			mass_ += mtmp;
157			refCOM += refCoords_[i]*mtmp;
158	gezelter	246	}
159			refCOM /= mass_;
160	gezelter	2
161	gezelter	246	// Next, move the origin of the reference coordinate system to the COM:
162			for (std::size_t i = 0; i < atoms_.size(); ++i) {
163	gezelter	507	refCoords_[i] -= refCOM;
164	gezelter	246	}
165	gezelter	2
166	gezelter	507	// Moment of Inertia calculation
167	gezelter	246	Mat3x3d Itmp(0.0);
168	gezelter	2
169	gezelter	246	for (std::size_t i = 0; i < atoms_.size(); i++) {
170	gezelter	507	mtmp = atoms_[i]->getMass();
171			Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
172			double r2 = refCoords_[i].lengthSquare();
173			Itmp(0, 0) += mtmp * r2;
174			Itmp(1, 1) += mtmp * r2;
175			Itmp(2, 2) += mtmp * r2;
176	gezelter	246	}
177	gezelter	2
178	tim	273	//project the inertial moment of directional atoms into this rigid body
179			for (std::size_t i = 0; i < atoms_.size(); i++) {
180	gezelter	507	if (atoms_[i]->isDirectional()) {
181			RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI();
182			Itmp(0, 0) += Iproject(0, 0);
183			Itmp(1, 1) += Iproject(1, 1);
184			Itmp(2, 2) += Iproject(2, 2);
185			}
186	tim	273	}
187
188	gezelter	246	//diagonalize
189			Vector3d evals;
190			Mat3x3d::diagonalize(Itmp, evals, sU_);
191	gezelter	2
192	gezelter	246	// zero out I and then fill the diagonals with the moments of inertia:
193			inertiaTensor_(0, 0) = evals[0];
194			inertiaTensor_(1, 1) = evals[1];
195			inertiaTensor_(2, 2) = evals[2];
196
197			int nLinearAxis = 0;
198			for (int i = 0; i < 3; i++) {
199	gezelter	507	if (fabs(evals[i]) < oopse::epsilon) {
200			linear_ = true;
201			linearAxis_ = i;
202			++ nLinearAxis;
203			}
204	gezelter	246	}
205	gezelter	2
206	gezelter	246	if (nLinearAxis > 1) {
207	gezelter	507	sprintf( painCave.errMsg,
208			"RigidBody error.\n"
209			"\tOOPSE found more than one axis in this rigid body with a vanishing \n"
210			"\tmoment of inertia. This can happen in one of three ways:\n"
211			"\t 1) Only one atom was specified, or \n"
212			"\t 2) All atoms were specified at the same location, or\n"
213			"\t 3) The programmers did something stupid.\n"
214			"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n"
215			);
216			painCave.isFatal = 1;
217			simError();
218	gezelter	246	}
219	gezelter	2
220	gezelter	507	}
221	gezelter	2
222	gezelter	507	void RigidBody::calcForcesAndTorques() {
223	gezelter	246	Vector3d afrc;
224			Vector3d atrq;
225			Vector3d apos;
226			Vector3d rpos;
227			Vector3d frc(0.0);
228			Vector3d trq(0.0);
229			Vector3d pos = this->getPos();
230			for (int i = 0; i < atoms_.size(); i++) {
231	gezelter	2
232	gezelter	507	afrc = atoms_[i]->getFrc();
233			apos = atoms_[i]->getPos();
234			rpos = apos - pos;
235	gezelter	246
236	gezelter	507	frc += afrc;
237	gezelter	2
238	gezelter	507	trq[0] += rpos[1]afrc[2] - rpos[2]afrc[1];
239			trq[1] += rpos[2]afrc[0] - rpos[0]afrc[2];
240			trq[2] += rpos[0]afrc[1] - rpos[1]afrc[0];
241	gezelter	2
242	gezelter	507	// If the atom has a torque associated with it, then we also need to
243			// migrate the torques onto the center of mass:
244	gezelter	2
245	gezelter	507	if (atoms_[i]->isDirectional()) {
246			atrq = atoms_[i]->getTrq();
247			trq += atrq;
248			}
249	gezelter	246
250			}
251
252			setFrc(frc);
253			setTrq(trq);
254
255	gezelter	507	}
256	gezelter	2
257	gezelter	507	void RigidBody::updateAtoms() {
258	gezelter	246	unsigned int i;
259			Vector3d ref;
260			Vector3d apos;
261			DirectionalAtom* dAtom;
262			Vector3d pos = getPos();
263			RotMat3x3d a = getA();
264	gezelter	2
265	gezelter	246	for (i = 0; i < atoms_.size(); i++) {
266
267	gezelter	507	ref = body2Lab(refCoords_[i]);
268	gezelter	2
269	gezelter	507	apos = pos + ref;
270	gezelter	2
271	gezelter	507	atoms_[i]->setPos(apos);
272	gezelter	2
273	gezelter	507	if (atoms_[i]->isDirectional()) {
274	gezelter	246
275	gezelter	507	dAtom = (DirectionalAtom *) atoms_[i];
276			dAtom->setA(a * refOrients_[i]);
277			//dAtom->rotateBy( A );
278			}
279	gezelter	2
280			}
281
282	gezelter	507	}
283	gezelter	2
284
285	gezelter	507	void RigidBody::updateAtoms(int frame) {
286	tim	318	unsigned int i;
287			Vector3d ref;
288			Vector3d apos;
289			DirectionalAtom* dAtom;
290			Vector3d pos = getPos(frame);
291			RotMat3x3d a = getA(frame);
292
293			for (i = 0; i < atoms_.size(); i++) {
294
295	gezelter	507	ref = body2Lab(refCoords_[i], frame);
296	tim	318
297	gezelter	507	apos = pos + ref;
298	tim	318
299	gezelter	507	atoms_[i]->setPos(apos, frame);
300	tim	318
301	gezelter	507	if (atoms_[i]->isDirectional()) {
302	tim	318
303	gezelter	507	dAtom = (DirectionalAtom *) atoms_[i];
304			dAtom->setA(a * refOrients_[i], frame);
305			}
306	tim	318
307			}
308
309	gezelter	507	}
310	tim	318
311	gezelter	507	void RigidBody::updateAtomVel() {
312	tim	318	Mat3x3d skewMat;;
313
314			Vector3d ji = getJ();
315			Mat3x3d I = getI();
316
317			skewMat(0, 0) =0;
318			skewMat(0, 1) = ji[2] /I(2, 2);
319			skewMat(0, 2) = -ji[1] /I(1, 1);
320
321			skewMat(1, 0) = -ji[2] /I(2, 2);
322			skewMat(1, 1) = 0;
323			skewMat(1, 2) = ji[0]/I(0, 0);
324
325			skewMat(2, 0) =ji[1] /I(1, 1);
326			skewMat(2, 1) = -ji[0]/I(0, 0);
327			skewMat(2, 2) = 0;
328
329			Mat3x3d mat = (getA() * skewMat).transpose();
330			Vector3d rbVel = getVel();
331
332
333			Vector3d velRot;
334			for (int i =0 ; i < refCoords_.size(); ++i) {
335	gezelter	507	atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
336	tim	318	}
337
338	gezelter	507	}
339	tim	318
340	gezelter	507	void RigidBody::updateAtomVel(int frame) {
341	tim	318	Mat3x3d skewMat;;
342
343			Vector3d ji = getJ(frame);
344			Mat3x3d I = getI();
345
346			skewMat(0, 0) =0;
347			skewMat(0, 1) = ji[2] /I(2, 2);
348			skewMat(0, 2) = -ji[1] /I(1, 1);
349
350			skewMat(1, 0) = -ji[2] /I(2, 2);
351			skewMat(1, 1) = 0;
352			skewMat(1, 2) = ji[0]/I(0, 0);
353
354			skewMat(2, 0) =ji[1] /I(1, 1);
355			skewMat(2, 1) = -ji[0]/I(0, 0);
356			skewMat(2, 2) = 0;
357
358			Mat3x3d mat = (getA(frame) * skewMat).transpose();
359			Vector3d rbVel = getVel(frame);
360
361
362			Vector3d velRot;
363			for (int i =0 ; i < refCoords_.size(); ++i) {
364	gezelter	507	atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
365	tim	318	}
366
367	gezelter	507	}
368	tim	318
369
370
371	gezelter	507	bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
372	gezelter	246	if (index < atoms_.size()) {
373	gezelter	2
374	gezelter	507	Vector3d ref = body2Lab(refCoords_[index]);
375			pos = getPos() + ref;
376			return true;
377	gezelter	246	} else {
378	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
379			<< atoms_.size() << "atoms" << std::endl;
380			return false;
381	gezelter	246	}
382	gezelter	507	}
383	gezelter	2
384	gezelter	507	bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
385	gezelter	246	std::vector<Atom*>::iterator i;
386			i = std::find(atoms_.begin(), atoms_.end(), atom);
387			if (i != atoms_.end()) {
388	gezelter	507	//RigidBody class makes sure refCoords_ and atoms_ match each other
389			Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
390			pos = getPos() + ref;
391			return true;
392	gezelter	246	} else {
393	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
394			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
395			return false;
396	gezelter	2	}
397	gezelter	507	}
398			bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
399	gezelter	2
400	gezelter	246	//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
401	gezelter	2
402	gezelter	246	if (index < atoms_.size()) {
403	gezelter	2
404	gezelter	507	Vector3d velRot;
405			Mat3x3d skewMat;;
406			Vector3d ref = refCoords_[index];
407			Vector3d ji = getJ();
408			Mat3x3d I = getI();
409	gezelter	2
410	gezelter	507	skewMat(0, 0) =0;
411			skewMat(0, 1) = ji[2] /I(2, 2);
412			skewMat(0, 2) = -ji[1] /I(1, 1);
413	gezelter	2
414	gezelter	507	skewMat(1, 0) = -ji[2] /I(2, 2);
415			skewMat(1, 1) = 0;
416			skewMat(1, 2) = ji[0]/I(0, 0);
417	gezelter	2
418	gezelter	507	skewMat(2, 0) =ji[1] /I(1, 1);
419			skewMat(2, 1) = -ji[0]/I(0, 0);
420			skewMat(2, 2) = 0;
421	gezelter	2
422	gezelter	507	velRot = (getA() * skewMat).transpose() * ref;
423	gezelter	2
424	gezelter	507	vel =getVel() + velRot;
425			return true;
426	gezelter	246
427			} else {
428	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
429			<< atoms_.size() << "atoms" << std::endl;
430			return false;
431	gezelter	2	}
432	gezelter	507	}
433	gezelter	2
434	gezelter	507	bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
435	gezelter	2
436	gezelter	246	std::vector<Atom*>::iterator i;
437			i = std::find(atoms_.begin(), atoms_.end(), atom);
438			if (i != atoms_.end()) {
439	gezelter	507	return getAtomVel(vel, i - atoms_.begin());
440	gezelter	246	} else {
441	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
442			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
443			return false;
444	gezelter	246	}
445	gezelter	507	}
446	gezelter	2
447	gezelter	507	bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
448	gezelter	246	if (index < atoms_.size()) {
449
450	gezelter	507	coor = refCoords_[index];
451			return true;
452	gezelter	246	} else {
453	gezelter	507	std::cerr << index << " is an invalid index, current rigid body contains "
454			<< atoms_.size() << "atoms" << std::endl;
455			return false;
456	gezelter	2	}
457
458	gezelter	507	}
459	gezelter	2
460	gezelter	507	bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
461	gezelter	246	std::vector<Atom*>::iterator i;
462			i = std::find(atoms_.begin(), atoms_.end(), atom);
463			if (i != atoms_.end()) {
464	gezelter	507	//RigidBody class makes sure refCoords_ and atoms_ match each other
465			coor = refCoords_[i - atoms_.begin()];
466			return true;
467	gezelter	246	} else {
468	gezelter	507	std::cerr << "Atom " << atom->getGlobalIndex()
469			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
470			return false;
471	gezelter	246	}
472	gezelter	2
473	gezelter	507	}
474	gezelter	2
475
476	gezelter	507	void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
477	gezelter	2
478	gezelter	507	Vector3d coords;
479			Vector3d euler;
480	gezelter	2
481
482	gezelter	507	atoms_.push_back(at);
483	gezelter	246
484	gezelter	507	if( !ats->havePosition() ){
485			sprintf( painCave.errMsg,
486			"RigidBody error.\n"
487			"\tAtom %s does not have a position specified.\n"
488			"\tThis means RigidBody cannot set up reference coordinates.\n",
489			ats->getType() );
490			painCave.isFatal = 1;
491			simError();
492			}
493	gezelter	2
494	gezelter	507	coords[0] = ats->getPosX();
495			coords[1] = ats->getPosY();
496			coords[2] = ats->getPosZ();
497	gezelter	2
498	gezelter	507	refCoords_.push_back(coords);
499	gezelter	2
500	gezelter	507	RotMat3x3d identMat = RotMat3x3d::identity();
501	gezelter	2
502	gezelter	507	if (at->isDirectional()) {
503	gezelter	2
504	gezelter	507	if( !ats->haveOrientation() ){
505			sprintf( painCave.errMsg,
506			"RigidBody error.\n"
507			"\tAtom %s does not have an orientation specified.\n"
508			"\tThis means RigidBody cannot set up reference orientations.\n",
509			ats->getType() );
510			painCave.isFatal = 1;
511			simError();
512			}
513	gezelter	246
514	gezelter	507	euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
515			euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
516			euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
517	gezelter	2
518	gezelter	507	RotMat3x3d Atmp(euler);
519			refOrients_.push_back(Atmp);
520	gezelter	2
521	gezelter	507	}else {
522			refOrients_.push_back(identMat);
523			}
524	gezelter	2
525
526	gezelter	507	}
527	gezelter	2
528			}
529