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++) {
      Mat3x3d IAtom(0.0);  
      mtmp = atoms_[i]->getMass();
      IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
      double r2 = refCoords_[i].lengthSquare();
      IAtom(0, 0) += mtmp * r2;
      IAtom(1, 1) += mtmp * r2;
      IAtom(2, 2) += mtmp * r2;

      //project the inertial moment of directional atoms into this rigid body
      if (atoms_[i]->isDirectional()) {
        //IAtom += atoms_[i]->getI();
        Itmp += IAtom;
        Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
      } else {
        Itmp += IAtom;
      }
    }

    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;
      }
        
    }
    
    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(refOrients_[i] * 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] * 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() );
      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:	2345
Committed:	Wed Oct 5 19:12:02 2005 UTC (18 years, 9 months ago) by tim
File size:	14343 byte(s)
Log Message:	fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	1937	#include <math.h>
43	tim	1492	#include "primitives/RigidBody.hpp"
44			#include "utils/simError.h"
45	tim	2058	#include "utils/NumericConstant.hpp"
46	gezelter	1930	namespace oopse {
47	gezelter	1490
48	gezelter	2204	RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){
49	gezelter	1490
50	gezelter	2204	}
51	gezelter	1490
52	gezelter	2204	void RigidBody::setPrevA(const RotMat3x3d& a) {
53	gezelter	1930	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
54			//((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() sU_;
55	gezelter	1490
56	gezelter	1930	for (int i =0 ; i < atoms_.size(); ++i){
57	gezelter	2204	if (atoms_[i]->isDirectional()) {
58			atoms_[i]->setPrevA(a * refOrients_[i]);
59			}
60	gezelter	1930	}
61	gezelter	1490
62	gezelter	2204	}
63	gezelter	1490
64	gezelter	1930
65	gezelter	2204	void RigidBody::setA(const RotMat3x3d& a) {
66	gezelter	1930	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67			//((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() sU_;
68	gezelter	1490
69	gezelter	1930	for (int i =0 ; i < atoms_.size(); ++i){
70	gezelter	2204	if (atoms_[i]->isDirectional()) {
71			atoms_[i]->setA(a * refOrients_[i]);
72			}
73	gezelter	1930	}
74	gezelter	2204	}
75	gezelter	1490
76	gezelter	2204	void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
77	gezelter	1930	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
78			//((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() sU_;
79	gezelter	1490
80	gezelter	1930	for (int i =0 ; i < atoms_.size(); ++i){
81	gezelter	2204	if (atoms_[i]->isDirectional()) {
82			atoms_[i]->setA(a * refOrients_[i], snapshotNo);
83			}
84	gezelter	1490	}
85
86	gezelter	2204	}
87	gezelter	1490
88	gezelter	2204	Mat3x3d RigidBody::getI() {
89	gezelter	1930	return inertiaTensor_;
90	gezelter	2204	}
91	gezelter	1490
92	gezelter	2204	std::vector<double> RigidBody::getGrad() {
93			std::vector<double> grad(6, 0.0);
94	gezelter	1930	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	1490
103	gezelter	1930	force = getFrc();
104			torque =getTrq();
105			myEuler = getA().toEulerAngles();
106	gezelter	1490
107	gezelter	1930	phi = myEuler[0];
108			theta = myEuler[1];
109			psi = myEuler[2];
110	gezelter	1490
111	gezelter	1930	cphi = cos(phi);
112			sphi = sin(phi);
113			ctheta = cos(theta);
114			stheta = sin(theta);
115	gezelter	1490
116	gezelter	1930	// get unit vectors along the phi, theta and psi rotation axes
117	gezelter	1490
118	gezelter	1930	ephi[0] = 0.0;
119			ephi[1] = 0.0;
120			ephi[2] = 1.0;
121	gezelter	1490
122	gezelter	1930	etheta[0] = cphi;
123			etheta[1] = sphi;
124			etheta[2] = 0.0;
125	gezelter	1490
126	gezelter	1930	epsi[0] = stheta * cphi;
127			epsi[1] = stheta * sphi;
128			epsi[2] = ctheta;
129	gezelter	1490
130	gezelter	1930	//gradient is equal to -force
131			for (int j = 0 ; j<3; j++)
132	gezelter	2204	grad[j] = -force[j];
133	gezelter	1490
134	gezelter	1930	for (int j = 0; j < 3; j++ ) {
135	gezelter	1490
136	gezelter	2204	grad[3] += torque[j]*ephi[j];
137			grad[4] += torque[j]*etheta[j];
138			grad[5] += torque[j]*epsi[j];
139	gezelter	1490
140	gezelter	1930	}
141
142			return grad;
143	gezelter	2204	}
144	gezelter	1490
145	gezelter	2204	void RigidBody::accept(BaseVisitor* v) {
146	gezelter	1930	v->visit(this);
147	gezelter	2204	}
148	gezelter	1490
149	gezelter	2204	/*@todo need modification /
150			void RigidBody::calcRefCoords() {
151	gezelter	1930	double mtmp;
152			Vector3d refCOM(0.0);
153			mass_ = 0.0;
154			for (std::size_t i = 0; i < atoms_.size(); ++i) {
155	gezelter	2204	mtmp = atoms_[i]->getMass();
156			mass_ += mtmp;
157			refCOM += refCoords_[i]*mtmp;
158	gezelter	1930	}
159			refCOM /= mass_;
160	gezelter	1490
161	gezelter	1930	// 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	2204	refCoords_[i] -= refCOM;
164	gezelter	1930	}
165	gezelter	1490
166	gezelter	2204	// Moment of Inertia calculation
167	tim	2341	Mat3x3d Itmp(0.0);
168	gezelter	1930	for (std::size_t i = 0; i < atoms_.size(); i++) {
169	tim	2341	Mat3x3d IAtom(0.0);
170	gezelter	2204	mtmp = atoms_[i]->getMass();
171	tim	2341	IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
172	gezelter	2204	double r2 = refCoords_[i].lengthSquare();
173	tim	2341	IAtom(0, 0) += mtmp * r2;
174			IAtom(1, 1) += mtmp * r2;
175			IAtom(2, 2) += mtmp * r2;
176	gezelter	1490
177	tim	2341	//project the inertial moment of directional atoms into this rigid body
178	gezelter	2204	if (atoms_[i]->isDirectional()) {
179	tim	2345	//IAtom += atoms_[i]->getI();
180			Itmp += IAtom;
181			Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
182	tim	2341	} else {
183			Itmp += IAtom;
184	gezelter	2204	}
185	tim	1957	}
186
187	tim	2345	std::cout << Itmp <<std::endl;
188	gezelter	1930	//diagonalize
189			Vector3d evals;
190			Mat3x3d::diagonalize(Itmp, evals, sU_);
191	gezelter	1490
192	gezelter	1930	// 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	2204	if (fabs(evals[i]) < oopse::epsilon) {
200			linear_ = true;
201			linearAxis_ = i;
202			++ nLinearAxis;
203			}
204	gezelter	1930	}
205	gezelter	1490
206	gezelter	1930	if (nLinearAxis > 1) {
207	gezelter	2204	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	1930	}
219	gezelter	1490
220	gezelter	2204	}
221	gezelter	1490
222	gezelter	2204	void RigidBody::calcForcesAndTorques() {
223	gezelter	1930	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	1490
232	gezelter	2204	afrc = atoms_[i]->getFrc();
233			apos = atoms_[i]->getPos();
234			rpos = apos - pos;
235	gezelter	1930
236	gezelter	2204	frc += afrc;
237	gezelter	1490
238	gezelter	2204	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	1490
242	gezelter	2204	// 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	1490
245	gezelter	2204	if (atoms_[i]->isDirectional()) {
246			atrq = atoms_[i]->getTrq();
247			trq += atrq;
248			}
249	gezelter	1930
250			}
251
252			setFrc(frc);
253			setTrq(trq);
254
255	gezelter	2204	}
256	gezelter	1490
257	gezelter	2204	void RigidBody::updateAtoms() {
258	gezelter	1930	unsigned int i;
259			Vector3d ref;
260			Vector3d apos;
261			DirectionalAtom* dAtom;
262			Vector3d pos = getPos();
263			RotMat3x3d a = getA();
264	gezelter	1490
265	gezelter	1930	for (i = 0; i < atoms_.size(); i++) {
266
267	gezelter	2204	ref = body2Lab(refCoords_[i]);
268	gezelter	1490
269	gezelter	2204	apos = pos + ref;
270	gezelter	1490
271	gezelter	2204	atoms_[i]->setPos(apos);
272	gezelter	1490
273	gezelter	2204	if (atoms_[i]->isDirectional()) {
274	gezelter	1930
275	gezelter	2204	dAtom = (DirectionalAtom *) atoms_[i];
276	gezelter	2335	dAtom->setA(refOrients_[i] * a);
277	gezelter	2204	}
278	gezelter	1490
279			}
280
281	gezelter	2204	}
282	gezelter	1490
283
284	gezelter	2204	void RigidBody::updateAtoms(int frame) {
285	tim	2002	unsigned int i;
286			Vector3d ref;
287			Vector3d apos;
288			DirectionalAtom* dAtom;
289			Vector3d pos = getPos(frame);
290			RotMat3x3d a = getA(frame);
291
292			for (i = 0; i < atoms_.size(); i++) {
293
294	gezelter	2204	ref = body2Lab(refCoords_[i], frame);
295	tim	2002
296	gezelter	2204	apos = pos + ref;
297	tim	2002
298	gezelter	2204	atoms_[i]->setPos(apos, frame);
299	tim	2002
300	gezelter	2204	if (atoms_[i]->isDirectional()) {
301	tim	2002
302	gezelter	2204	dAtom = (DirectionalAtom *) atoms_[i];
303	gezelter	2335	dAtom->setA(refOrients_[i] * a, frame);
304	gezelter	2204	}
305	tim	2002
306			}
307
308	gezelter	2204	}
309	tim	2002
310	gezelter	2204	void RigidBody::updateAtomVel() {
311	tim	2002	Mat3x3d skewMat;;
312
313			Vector3d ji = getJ();
314			Mat3x3d I = getI();
315
316			skewMat(0, 0) =0;
317			skewMat(0, 1) = ji[2] /I(2, 2);
318			skewMat(0, 2) = -ji[1] /I(1, 1);
319
320			skewMat(1, 0) = -ji[2] /I(2, 2);
321			skewMat(1, 1) = 0;
322			skewMat(1, 2) = ji[0]/I(0, 0);
323
324			skewMat(2, 0) =ji[1] /I(1, 1);
325			skewMat(2, 1) = -ji[0]/I(0, 0);
326			skewMat(2, 2) = 0;
327
328			Mat3x3d mat = (getA() * skewMat).transpose();
329			Vector3d rbVel = getVel();
330
331
332			Vector3d velRot;
333			for (int i =0 ; i < refCoords_.size(); ++i) {
334	gezelter	2204	atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
335	tim	2002	}
336
337	gezelter	2204	}
338	tim	2002
339	gezelter	2204	void RigidBody::updateAtomVel(int frame) {
340	tim	2002	Mat3x3d skewMat;;
341
342			Vector3d ji = getJ(frame);
343			Mat3x3d I = getI();
344
345			skewMat(0, 0) =0;
346			skewMat(0, 1) = ji[2] /I(2, 2);
347			skewMat(0, 2) = -ji[1] /I(1, 1);
348
349			skewMat(1, 0) = -ji[2] /I(2, 2);
350			skewMat(1, 1) = 0;
351			skewMat(1, 2) = ji[0]/I(0, 0);
352
353			skewMat(2, 0) =ji[1] /I(1, 1);
354			skewMat(2, 1) = -ji[0]/I(0, 0);
355			skewMat(2, 2) = 0;
356
357			Mat3x3d mat = (getA(frame) * skewMat).transpose();
358			Vector3d rbVel = getVel(frame);
359
360
361			Vector3d velRot;
362			for (int i =0 ; i < refCoords_.size(); ++i) {
363	gezelter	2204	atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
364	tim	2002	}
365
366	gezelter	2204	}
367	tim	2002
368
369
370	gezelter	2204	bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
371	gezelter	1930	if (index < atoms_.size()) {
372	gezelter	1490
373	gezelter	2204	Vector3d ref = body2Lab(refCoords_[index]);
374			pos = getPos() + ref;
375			return true;
376	gezelter	1930	} else {
377	gezelter	2204	std::cerr << index << " is an invalid index, current rigid body contains "
378			<< atoms_.size() << "atoms" << std::endl;
379			return false;
380	gezelter	1930	}
381	gezelter	2204	}
382	gezelter	1490
383	gezelter	2204	bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
384	gezelter	1930	std::vector<Atom*>::iterator i;
385			i = std::find(atoms_.begin(), atoms_.end(), atom);
386			if (i != atoms_.end()) {
387	gezelter	2204	//RigidBody class makes sure refCoords_ and atoms_ match each other
388			Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
389			pos = getPos() + ref;
390			return true;
391	gezelter	1930	} else {
392	gezelter	2204	std::cerr << "Atom " << atom->getGlobalIndex()
393			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
394			return false;
395	gezelter	1490	}
396	gezelter	2204	}
397			bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
398	gezelter	1490
399	gezelter	1930	//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
400	gezelter	1490
401	gezelter	1930	if (index < atoms_.size()) {
402	gezelter	1490
403	gezelter	2204	Vector3d velRot;
404			Mat3x3d skewMat;;
405			Vector3d ref = refCoords_[index];
406			Vector3d ji = getJ();
407			Mat3x3d I = getI();
408	gezelter	1490
409	gezelter	2204	skewMat(0, 0) =0;
410			skewMat(0, 1) = ji[2] /I(2, 2);
411			skewMat(0, 2) = -ji[1] /I(1, 1);
412	gezelter	1490
413	gezelter	2204	skewMat(1, 0) = -ji[2] /I(2, 2);
414			skewMat(1, 1) = 0;
415			skewMat(1, 2) = ji[0]/I(0, 0);
416	gezelter	1490
417	gezelter	2204	skewMat(2, 0) =ji[1] /I(1, 1);
418			skewMat(2, 1) = -ji[0]/I(0, 0);
419			skewMat(2, 2) = 0;
420	gezelter	1490
421	gezelter	2204	velRot = (getA() * skewMat).transpose() * ref;
422	gezelter	1490
423	gezelter	2204	vel =getVel() + velRot;
424			return true;
425	gezelter	1930
426			} else {
427	gezelter	2204	std::cerr << index << " is an invalid index, current rigid body contains "
428			<< atoms_.size() << "atoms" << std::endl;
429			return false;
430	gezelter	1490	}
431	gezelter	2204	}
432	gezelter	1490
433	gezelter	2204	bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
434	gezelter	1490
435	gezelter	1930	std::vector<Atom*>::iterator i;
436			i = std::find(atoms_.begin(), atoms_.end(), atom);
437			if (i != atoms_.end()) {
438	gezelter	2204	return getAtomVel(vel, i - atoms_.begin());
439	gezelter	1930	} else {
440	gezelter	2204	std::cerr << "Atom " << atom->getGlobalIndex()
441			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
442			return false;
443	gezelter	1930	}
444	gezelter	2204	}
445	gezelter	1490
446	gezelter	2204	bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
447	gezelter	1930	if (index < atoms_.size()) {
448
449	gezelter	2204	coor = refCoords_[index];
450			return true;
451	gezelter	1930	} else {
452	gezelter	2204	std::cerr << index << " is an invalid index, current rigid body contains "
453			<< atoms_.size() << "atoms" << std::endl;
454			return false;
455	gezelter	1490	}
456
457	gezelter	2204	}
458	gezelter	1490
459	gezelter	2204	bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
460	gezelter	1930	std::vector<Atom*>::iterator i;
461			i = std::find(atoms_.begin(), atoms_.end(), atom);
462			if (i != atoms_.end()) {
463	gezelter	2204	//RigidBody class makes sure refCoords_ and atoms_ match each other
464			coor = refCoords_[i - atoms_.begin()];
465			return true;
466	gezelter	1930	} else {
467	gezelter	2204	std::cerr << "Atom " << atom->getGlobalIndex()
468			<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
469			return false;
470	gezelter	1930	}
471	gezelter	1490
472	gezelter	2204	}
473	gezelter	1490
474
475	gezelter	2204	void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
476	gezelter	1490
477	gezelter	2204	Vector3d coords;
478			Vector3d euler;
479	gezelter	1490
480
481	gezelter	2204	atoms_.push_back(at);
482	gezelter	1930
483	gezelter	2204	if( !ats->havePosition() ){
484			sprintf( painCave.errMsg,
485			"RigidBody error.\n"
486			"\tAtom %s does not have a position specified.\n"
487			"\tThis means RigidBody cannot set up reference coordinates.\n",
488			ats->getType() );
489			painCave.isFatal = 1;
490			simError();
491			}
492	gezelter	1490
493	gezelter	2204	coords[0] = ats->getPosX();
494			coords[1] = ats->getPosY();
495			coords[2] = ats->getPosZ();
496	gezelter	1490
497	gezelter	2204	refCoords_.push_back(coords);
498	gezelter	1490
499	gezelter	2204	RotMat3x3d identMat = RotMat3x3d::identity();
500	gezelter	1490
501	gezelter	2204	if (at->isDirectional()) {
502	gezelter	1490
503	gezelter	2204	if( !ats->haveOrientation() ){
504			sprintf( painCave.errMsg,
505			"RigidBody error.\n"
506			"\tAtom %s does not have an orientation specified.\n"
507			"\tThis means RigidBody cannot set up reference orientations.\n",
508			ats->getType() );
509			painCave.isFatal = 1;
510			simError();
511			}
512	gezelter	1930
513	gezelter	2204	euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
514			euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
515			euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
516	gezelter	1490
517	gezelter	2204	RotMat3x3d Atmp(euler);
518			refOrients_.push_back(Atmp);
519	gezelter	1490
520	gezelter	2204	}else {
521			refOrients_.push_back(identMat);
522			}
523	gezelter	1490
524
525	gezelter	2204	}
526	gezelter	1490
527			}
528