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/* |
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* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project |
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* |
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* Contact: gezelter@openscience.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include "primitives/RigidBody.hpp" |
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|
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namespace OpenMD { |
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|
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData){ |
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|
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} |
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|
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void RigidBody::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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((snapshotMan_->getPrevSnapshot())->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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|
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std::vector<Atom*>::iterator i; |
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for (i = atoms_.begin(); i != atoms_.end(); ++i) { |
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if ((*i)->isDirectional()) { |
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(*i)->setPrevA(a * (*i)->getPrevA()); |
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} |
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} |
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|
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} |
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|
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|
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void RigidBody::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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((snapshotMan_->getCurrentSnapshot())->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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|
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std::vector<Atom*>::iterator i; |
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for (i = atoms_.begin(); i != atoms_.end(); ++i) { |
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if ((*i)->isDirectional()) { |
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(*i)->setA(a * (*i)->getA()); |
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} |
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} |
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} |
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|
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void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).unitVector[localIndex_] = a.inverse() * sU_.getColumn(2); |
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|
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std::vector<Atom*>::iterator i; |
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for (i = atoms_.begin(); i != atoms_.end(); ++i) { |
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if ((*i)->isDirectional()) { |
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(*i)->setA(a * (*i)->getA(snapshotNo), snapshotNo); |
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} |
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} |
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|
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} |
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|
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void DirectionalAtom::setUnitFrameFromEuler(double phi, double theta, double psi) { |
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sU_.setupRotMat(phi,theta,psi); |
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} |
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|
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Mat3x3d RigidBody::getI() { |
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return inertiaTensor_; |
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} |
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|
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std::vector<double> RigidBody::getGrad() { |
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vector<double> grad(6, 0.0); |
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Vector3d force; |
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Vector3d torque; |
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Vector3d myEuler; |
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double phi, theta, psi; |
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double cphi, sphi, ctheta, stheta; |
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Vector3d ephi; |
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Vector3d etheta; |
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Vector3d epsi; |
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|
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force = getFrc(); |
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torque =getTrq(); |
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myEuler = getA().toEulerAngles(); |
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|
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phi = myEuler[0]; |
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theta = myEuler[1]; |
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psi = myEuler[2]; |
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|
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cphi = cos(phi); |
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sphi = sin(phi); |
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ctheta = cos(theta); |
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stheta = sin(theta); |
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|
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// get unit vectors along the phi, theta and psi rotation axes |
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|
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ephi[0] = 0.0; |
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ephi[1] = 0.0; |
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ephi[2] = 1.0; |
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|
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etheta[0] = cphi; |
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etheta[1] = sphi; |
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etheta[2] = 0.0; |
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|
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epsi[0] = stheta * cphi; |
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epsi[1] = stheta * sphi; |
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epsi[2] = ctheta; |
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|
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//gradient is equal to -force |
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for (int j = 0 ; j<3; j++) |
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grad[j] = -force[j]; |
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|
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for (int j = 0; j < 3; j++ ) { |
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|
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grad[3] += torque[j]*ephi[j]; |
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grad[4] += torque[j]*etheta[j]; |
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grad[5] += torque[j]*epsi[j]; |
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|
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} |
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|
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return grad; |
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} |
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|
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void RigidBody::accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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|
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void RigidBody::calcRefCoords() { |
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/* |
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double mtmp; |
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vec3 apos; |
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double refCOM[3]; |
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vec3 ptmp; |
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double Itmp[3][3]; |
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double evals[3]; |
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double evects[3][3]; |
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double r, r2, len; |
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|
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// First, find the center of mass: |
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|
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mass = 0.0; |
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for (j=0; j<3; j++) |
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refCOM[j] = 0.0; |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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mtmp = atoms_[i]->getMass(); |
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mass += mtmp; |
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|
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apos = refCoords[i]; |
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|
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for(j = 0; j < 3; j++) { |
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refCOM[j] += apos[j]*mtmp; |
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} |
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} |
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|
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for(j = 0; j < 3; j++) |
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refCOM[j] /= mass; |
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|
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// Next, move the origin of the reference coordinate system to the COM: |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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apos = refCoords[i]; |
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for (j=0; j < 3; j++) { |
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apos[j] = apos[j] - refCOM[j]; |
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} |
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refCoords[i] = apos; |
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} |
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|
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// Moment of Inertia calculation |
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|
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for (i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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Itmp[i][j] = 0.0; |
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|
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for (it = 0; it < atoms_.size(); it++) { |
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|
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mtmp = atoms_[it]->getMass(); |
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ptmp = refCoords[it]; |
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r= norm3(ptmp.vec); |
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r2 = r*r; |
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|
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for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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|
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if (i==j) Itmp[i][j] += mtmp * r2; |
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Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j]; |
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} |
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} |
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} |
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|
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diagonalize3x3(Itmp, evals, sU); |
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|
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// zero out I and then fill the diagonals with the moments of inertia: |
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|
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n_linear_coords = 0; |
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|
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for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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I[i][j] = 0.0; |
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} |
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I[i][i] = evals[i]; |
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|
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if (fabs(evals[i]) < momIntTol) { |
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is_linear = true; |
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n_linear_coords++; |
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linear_axis = i; |
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} |
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} |
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if (n_linear_coords > 1) { |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
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"\tmoment of inertia. This can happen in one of three ways:\n" |
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"\t 1) Only one atom was specified, or \n" |
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"\t 2) All atoms were specified at the same location, or\n" |
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"\t 3) The programmers did something stupid.\n" |
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"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// renormalize column vectors: |
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|
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for (i=0; i < 3; i++) { |
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len = 0.0; |
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for (j = 0; j < 3; j++) { |
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len += sU[i][j]*sU[i][j]; |
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} |
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len = sqrt(len); |
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for (j = 0; j < 3; j++) { |
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sU[i][j] /= len; |
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} |
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} |
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*/ |
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} |
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|
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void RigidBody::calcForcesAndTorques() { |
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unsigned int i; |
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unsigned int j; |
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//Vector3d apos; |
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Vector3d afrc; |
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Vector3d atrq; |
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Vector3d rpos; |
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Vector3d frc; |
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Vector3d trq; |
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//Vector3d pos; |
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|
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zeroForces(); |
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|
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//pos = getPos(); |
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frc = getFrc(); |
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trq = getTrq(); |
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for (i = 0; i < atoms_.size(); i++) { |
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|
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afrc = atoms_[i]->getFrc(); |
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|
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//apos = atoms_[i]->getPos(apos); |
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//rpos = apos - pos; |
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rpos = refCoords_[i]; |
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|
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frc += afrc; |
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|
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trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
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trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
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trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
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|
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// If the atom has a torque associated with it, then we also need to |
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// migrate the torques onto the center of mass: |
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|
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if (atoms_[i]->isDirectional()) { |
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atrq = atoms_[i]->getTrq(); |
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trq += atrq; |
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} |
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|
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} |
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|
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setFrc(frc); |
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setTrq(trq); |
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|
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} |
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|
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void RigidBody::updateAtoms() { |
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unsigned int i; |
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unsigned int j; |
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Vector3d ref; |
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Vector3d apos; |
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DirectionalAtom* dAtom; |
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Vector3d pos = getPos(); |
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RotMat3x3d A = getA(); |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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|
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ref = body2Lab(refCoords_[i]); |
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|
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apos = pos + ref; |
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|
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atoms_[i]->setPos(apos); |
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|
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if (atoms_[i]->isDirectional()) { |
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|
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dAtom = (DirectionalAtom *) atoms_[i]; |
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dAtom->rotateBy( A ); |
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} |
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|
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} |
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|
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} |
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|
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|
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bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
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if (index < atoms_.size()) { |
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|
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Vector3d ref = body2Lab(refCoords_[index]); |
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pos = getPos() + ref; |
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return true; |
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { |
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std::vector<Atom*>::iterator i; |
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i = find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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//RigidBody class makes sure refCoords_ and atoms_ match each other |
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Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); |
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pos = getPos() + ref; |
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return true; |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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} |
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bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { |
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|
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//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
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|
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if (index < atoms_.size()) { |
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|
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Vector3d velRot; |
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Mat3x3d skewMat;; |
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Vector3d ref = refCoords_[index]; |
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Vector3d ji = getJ(); |
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Mat3x3d I = getI(); |
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|
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skewMat(0, 0) =0; |
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skewMat(0, 1) = ji[2] /I(2, 2); |
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skewMat(0, 2) = -ji[1] /I(1, 1); |
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|
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skewMat(1, 0) = -ji[2] /I(2, 2); |
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skewMat(1, 1) = 0; |
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skewMat(1, 2) = ji[0]/I(0, 0); |
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|
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skewMat(2, 0) =ji[1] /I(1, 1); |
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skewMat(2, 1) = -ji[0]/I(0, 0); |
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skewMat(2, 2) = 0; |
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|
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velRot = (getA() * skewMat).transpose() * ref; |
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|
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vel =getVel() + velRot; |
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return true; |
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|
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { |
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|
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std::vector<Atom*>::iterator i; |
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i = find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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return getAtomVel(vel, i - atoms_.begin()); |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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} |
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|
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bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { |
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if (index < atoms_.size()) { |
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|
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coor = refCoords_[index]; |
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return true; |
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} else { |
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std::cerr << index << " is an invalid index, current rigid body contains " |
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<< atoms_.size() << "atoms" << std::endl; |
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return false; |
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} |
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|
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} |
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|
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bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { |
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std::vector<Atom*>::iterator i; |
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i = find(atoms_.begin(), atoms_.end(), atom); |
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if (i != atoms_.end()) { |
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//RigidBody class makes sure refCoords_ and atoms_ match each other |
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coor = refCoords_[i - atoms_.begin()]; |
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return true; |
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} else { |
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std::cerr << "Atom " << atom->getGlobalIndex() |
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<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
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return false; |
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} |
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|
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} |
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|
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} |
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|
