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gezelter |
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#include <math.h> |
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#include "RigidBody.hpp" |
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#include "DirectionalAtom.hpp" |
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#include "simError.h" |
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#include "MatVec3.h" |
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RigidBody::RigidBody() : StuntDouble() { |
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objType = OT_RIGIDBODY; |
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is_linear = false; |
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linear_axis = -1; |
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momIntTol = 1e-6; |
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} |
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RigidBody::~RigidBody() { |
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} |
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void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
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vec3 coords; |
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vec3 euler; |
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mat3x3 Atmp; |
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myAtoms.push_back(at); |
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if( !ats->havePosition() ){ |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tAtom %s does not have a position specified.\n" |
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"\tThis means RigidBody cannot set up reference coordinates.\n", |
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ats->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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coords[0] = ats->getPosX(); |
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coords[1] = ats->getPosY(); |
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coords[2] = ats->getPosZ(); |
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refCoords.push_back(coords); |
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if (at->isDirectional()) { |
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if( !ats->haveOrientation() ){ |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tAtom %s does not have an orientation specified.\n" |
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"\tThis means RigidBody cannot set up reference orientations.\n", |
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ats->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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euler[0] = ats->getEulerPhi(); |
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euler[1] = ats->getEulerTheta(); |
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euler[2] = ats->getEulerPsi(); |
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doEulerToRotMat(euler, Atmp); |
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refOrients.push_back(Atmp); |
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} |
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} |
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void RigidBody::getPos(double theP[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theP[i] = pos[i]; |
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} |
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void RigidBody::setPos(double theP[3]){ |
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for (int i = 0; i < 3 ; i++) |
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pos[i] = theP[i]; |
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} |
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void RigidBody::getVel(double theV[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theV[i] = vel[i]; |
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} |
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void RigidBody::setVel(double theV[3]){ |
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for (int i = 0; i < 3 ; i++) |
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vel[i] = theV[i]; |
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} |
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void RigidBody::getFrc(double theF[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theF[i] = frc[i]; |
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} |
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void RigidBody::addFrc(double theF[3]){ |
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for (int i = 0; i < 3 ; i++) |
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frc[i] += theF[i]; |
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} |
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void RigidBody::zeroForces() { |
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for (int i = 0; i < 3; i++) { |
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frc[i] = 0.0; |
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trq[i] = 0.0; |
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} |
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} |
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void RigidBody::setEuler( double phi, double theta, double psi ){ |
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A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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A[0][2] = sin(theta) * sin(psi); |
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A[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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A[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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A[1][2] = sin(theta) * cos(psi); |
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A[2][0] = sin(phi) * sin(theta); |
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A[2][1] = -cos(phi) * sin(theta); |
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A[2][2] = cos(theta); |
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} |
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void RigidBody::getQ( double q[4] ){ |
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double t, s; |
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double ad1, ad2, ad3; |
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t = A[0][0] + A[1][1] + A[2][2] + 1.0; |
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if( t > 0.0 ){ |
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s = 0.5 / sqrt( t ); |
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q[0] = 0.25 / s; |
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q[1] = (A[1][2] - A[2][1]) * s; |
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q[2] = (A[2][0] - A[0][2]) * s; |
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q[3] = (A[0][1] - A[1][0]) * s; |
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} |
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else{ |
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ad1 = fabs( A[0][0] ); |
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ad2 = fabs( A[1][1] ); |
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ad3 = fabs( A[2][2] ); |
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if( ad1 >= ad2 && ad1 >= ad3 ){ |
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s = 2.0 * sqrt( 1.0 + A[0][0] - A[1][1] - A[2][2] ); |
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q[0] = (A[1][2] + A[2][1]) / s; |
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q[1] = 0.5 / s; |
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q[2] = (A[0][1] + A[1][0]) / s; |
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q[3] = (A[0][2] + A[2][0]) / s; |
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} |
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else if( ad2 >= ad1 && ad2 >= ad3 ){ |
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s = sqrt( 1.0 + A[1][1] - A[0][0] - A[2][2] ) * 2.0; |
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q[0] = (A[0][2] + A[2][0]) / s; |
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q[1] = (A[0][1] + A[1][0]) / s; |
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q[2] = 0.5 / s; |
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q[3] = (A[1][2] + A[2][1]) / s; |
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} |
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else{ |
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s = sqrt( 1.0 + A[2][2] - A[0][0] - A[1][1] ) * 2.0; |
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q[0] = (A[0][1] + A[1][0]) / s; |
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q[1] = (A[0][2] + A[2][0]) / s; |
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q[2] = (A[1][2] + A[2][1]) / s; |
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q[3] = 0.5 / s; |
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} |
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} |
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} |
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void RigidBody::setQ( double the_q[4] ){ |
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
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q0Sqr = the_q[0] * the_q[0]; |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
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q3Sqr = the_q[3] * the_q[3]; |
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A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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} |
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void RigidBody::getA( double the_A[3][3] ){ |
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for (int i = 0; i < 3; i++) |
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for (int j = 0; j < 3; j++) |
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the_A[i][j] = A[i][j]; |
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} |
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void RigidBody::setA( double the_A[3][3] ){ |
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for (int i = 0; i < 3; i++) |
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for (int j = 0; j < 3; j++) |
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A[i][j] = the_A[i][j]; |
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} |
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void RigidBody::getJ( double theJ[3] ){ |
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for (int i = 0; i < 3; i++) |
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theJ[i] = ji[i]; |
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} |
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void RigidBody::setJ( double theJ[3] ){ |
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for (int i = 0; i < 3; i++) |
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ji[i] = theJ[i]; |
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} |
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void RigidBody::getTrq(double theT[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theT[i] = trq[i]; |
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} |
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void RigidBody::addTrq(double theT[3]){ |
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for (int i = 0; i < 3 ; i++) |
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trq[i] += theT[i]; |
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} |
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void RigidBody::getI( double the_I[3][3] ){ |
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for (int i = 0; i < 3; i++) |
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for (int j = 0; j < 3; j++) |
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the_I[i][j] = I[i][j]; |
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} |
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void RigidBody::lab2Body( double r[3] ){ |
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double rl[3]; // the lab frame vector |
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rl[0] = r[0]; |
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rl[1] = r[1]; |
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rl[2] = r[2]; |
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r[0] = (A[0][0] * rl[0]) + (A[0][1] * rl[1]) + (A[0][2] * rl[2]); |
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r[1] = (A[1][0] * rl[0]) + (A[1][1] * rl[1]) + (A[1][2] * rl[2]); |
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r[2] = (A[2][0] * rl[0]) + (A[2][1] * rl[1]) + (A[2][2] * rl[2]); |
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} |
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void RigidBody::body2Lab( double r[3] ){ |
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double rb[3]; // the body frame vector |
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rb[0] = r[0]; |
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rb[1] = r[1]; |
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rb[2] = r[2]; |
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r[0] = (A[0][0] * rb[0]) + (A[1][0] * rb[1]) + (A[2][0] * rb[2]); |
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r[1] = (A[0][1] * rb[0]) + (A[1][1] * rb[1]) + (A[2][1] * rb[2]); |
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r[2] = (A[0][2] * rb[0]) + (A[1][2] * rb[1]) + (A[2][2] * rb[2]); |
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} |
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double RigidBody::getZangle( ){ |
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return zAngle; |
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} |
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void RigidBody::setZangle( double zAng ){ |
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zAngle = zAng; |
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} |
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void RigidBody::addZangle( double zAng ){ |
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zAngle += zAng; |
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} |
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void RigidBody::calcRefCoords( ) { |
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int i,j,k, it, n_linear_coords; |
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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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// First, find the center of mass: |
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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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for (i = 0; i < myAtoms.size(); i++) { |
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mtmp = myAtoms[i]->getMass(); |
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mass += mtmp; |
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apos = refCoords[i]; |
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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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for(j = 0; j < 3; j++) |
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refCOM[j] /= mass; |
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// Next, move the origin of the reference coordinate system to the COM: |
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for (i = 0; i < myAtoms.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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// Moment of Inertia calculation |
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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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for (it = 0; it < myAtoms.size(); it++) { |
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mtmp = myAtoms[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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for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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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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diagonalize3x3(Itmp, evals, sU); |
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// zero out I and then fill the diagonals with the moments of inertia: |
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n_linear_coords = 0; |
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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]; |
| 353 |
|
|
|
| 354 |
|
|
if (fabs(evals[i]) < momIntTol) { |
| 355 |
|
|
is_linear = true; |
| 356 |
|
|
n_linear_coords++; |
| 357 |
|
|
linear_axis = i; |
| 358 |
|
|
} |
| 359 |
|
|
} |
| 360 |
|
|
|
| 361 |
|
|
if (n_linear_coords > 1) { |
| 362 |
|
|
sprintf( painCave.errMsg, |
| 363 |
|
|
"RigidBody error.\n" |
| 364 |
|
|
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 365 |
|
|
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 366 |
|
|
"\t 1) Only one atom was specified, or \n" |
| 367 |
|
|
"\t 2) All atoms were specified at the same location, or\n" |
| 368 |
|
|
"\t 3) The programmers did something stupid.\n" |
| 369 |
|
|
"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
| 370 |
|
|
); |
| 371 |
|
|
painCave.isFatal = 1; |
| 372 |
|
|
simError(); |
| 373 |
|
|
} |
| 374 |
|
|
|
| 375 |
|
|
// renormalize column vectors: |
| 376 |
|
|
|
| 377 |
|
|
for (i=0; i < 3; i++) { |
| 378 |
|
|
len = 0.0; |
| 379 |
|
|
for (j = 0; j < 3; j++) { |
| 380 |
|
|
len += sU[i][j]*sU[i][j]; |
| 381 |
|
|
} |
| 382 |
|
|
len = sqrt(len); |
| 383 |
|
|
for (j = 0; j < 3; j++) { |
| 384 |
|
|
sU[i][j] /= len; |
| 385 |
|
|
} |
| 386 |
|
|
} |
| 387 |
|
|
} |
| 388 |
|
|
|
| 389 |
|
|
void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){ |
| 390 |
|
|
|
| 391 |
|
|
double phi, theta, psi; |
| 392 |
|
|
|
| 393 |
|
|
phi = euler[0]; |
| 394 |
|
|
theta = euler[1]; |
| 395 |
|
|
psi = euler[2]; |
| 396 |
|
|
|
| 397 |
|
|
myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 398 |
|
|
myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 399 |
|
|
myA[0][2] = sin(theta) * sin(psi); |
| 400 |
|
|
|
| 401 |
|
|
myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 402 |
|
|
myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 403 |
|
|
myA[1][2] = sin(theta) * cos(psi); |
| 404 |
|
|
|
| 405 |
|
|
myA[2][0] = sin(phi) * sin(theta); |
| 406 |
|
|
myA[2][1] = -cos(phi) * sin(theta); |
| 407 |
|
|
myA[2][2] = cos(theta); |
| 408 |
|
|
|
| 409 |
|
|
} |
| 410 |
|
|
|
| 411 |
|
|
void RigidBody::calcForcesAndTorques() { |
| 412 |
|
|
|
| 413 |
|
|
// Convert Atomic forces and torques to total forces and torques: |
| 414 |
|
|
int i, j; |
| 415 |
|
|
double apos[3]; |
| 416 |
|
|
double afrc[3]; |
| 417 |
|
|
double atrq[3]; |
| 418 |
|
|
double rpos[3]; |
| 419 |
|
|
|
| 420 |
|
|
zeroForces(); |
| 421 |
|
|
|
| 422 |
|
|
for (i = 0; i < myAtoms.size(); i++) { |
| 423 |
|
|
|
| 424 |
|
|
myAtoms[i]->getPos(apos); |
| 425 |
|
|
myAtoms[i]->getFrc(afrc); |
| 426 |
|
|
|
| 427 |
|
|
for (j=0; j<3; j++) { |
| 428 |
|
|
rpos[j] = apos[j] - pos[j]; |
| 429 |
|
|
frc[j] += afrc[j]; |
| 430 |
|
|
} |
| 431 |
|
|
|
| 432 |
|
|
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 433 |
|
|
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 434 |
|
|
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 435 |
|
|
|
| 436 |
|
|
// If the atom has a torque associated with it, then we also need to |
| 437 |
|
|
// migrate the torques onto the center of mass: |
| 438 |
|
|
|
| 439 |
|
|
if (myAtoms[i]->isDirectional()) { |
| 440 |
|
|
|
| 441 |
|
|
myAtoms[i]->getTrq(atrq); |
| 442 |
|
|
|
| 443 |
|
|
for (j=0; j<3; j++) |
| 444 |
|
|
trq[j] += atrq[j]; |
| 445 |
|
|
} |
| 446 |
|
|
} |
| 447 |
|
|
|
| 448 |
|
|
// Convert Torque to Body-fixed coordinates: |
| 449 |
|
|
// (Actually, on second thought, don't. Integrator does this now.) |
| 450 |
|
|
// lab2Body(trq); |
| 451 |
|
|
|
| 452 |
|
|
} |
| 453 |
|
|
|
| 454 |
|
|
void RigidBody::updateAtoms() { |
| 455 |
|
|
int i, j; |
| 456 |
|
|
vec3 ref; |
| 457 |
|
|
double apos[3]; |
| 458 |
|
|
DirectionalAtom* dAtom; |
| 459 |
|
|
|
| 460 |
|
|
for (i = 0; i < myAtoms.size(); i++) { |
| 461 |
|
|
|
| 462 |
|
|
ref = refCoords[i]; |
| 463 |
|
|
|
| 464 |
|
|
body2Lab(ref.vec); |
| 465 |
|
|
|
| 466 |
|
|
for (j = 0; j<3; j++) |
| 467 |
|
|
apos[j] = pos[j] + ref.vec[j]; |
| 468 |
|
|
|
| 469 |
|
|
myAtoms[i]->setPos(apos); |
| 470 |
|
|
|
| 471 |
|
|
if (myAtoms[i]->isDirectional()) { |
| 472 |
|
|
|
| 473 |
|
|
dAtom = (DirectionalAtom *) myAtoms[i]; |
| 474 |
|
|
dAtom->rotateBy( A ); |
| 475 |
|
|
|
| 476 |
|
|
} |
| 477 |
|
|
} |
| 478 |
|
|
} |
| 479 |
|
|
|
| 480 |
|
|
void RigidBody::getGrad( double grad[6] ) { |
| 481 |
|
|
|
| 482 |
|
|
double myEuler[3]; |
| 483 |
|
|
double phi, theta, psi; |
| 484 |
|
|
double cphi, sphi, ctheta, stheta; |
| 485 |
|
|
double ephi[3]; |
| 486 |
|
|
double etheta[3]; |
| 487 |
|
|
double epsi[3]; |
| 488 |
|
|
|
| 489 |
|
|
this->getEulerAngles(myEuler); |
| 490 |
|
|
|
| 491 |
|
|
phi = myEuler[0]; |
| 492 |
|
|
theta = myEuler[1]; |
| 493 |
|
|
psi = myEuler[2]; |
| 494 |
|
|
|
| 495 |
|
|
cphi = cos(phi); |
| 496 |
|
|
sphi = sin(phi); |
| 497 |
|
|
ctheta = cos(theta); |
| 498 |
|
|
stheta = sin(theta); |
| 499 |
|
|
|
| 500 |
|
|
// get unit vectors along the phi, theta and psi rotation axes |
| 501 |
|
|
|
| 502 |
|
|
ephi[0] = 0.0; |
| 503 |
|
|
ephi[1] = 0.0; |
| 504 |
|
|
ephi[2] = 1.0; |
| 505 |
|
|
|
| 506 |
|
|
etheta[0] = cphi; |
| 507 |
|
|
etheta[1] = sphi; |
| 508 |
|
|
etheta[2] = 0.0; |
| 509 |
|
|
|
| 510 |
|
|
epsi[0] = stheta * cphi; |
| 511 |
|
|
epsi[1] = stheta * sphi; |
| 512 |
|
|
epsi[2] = ctheta; |
| 513 |
|
|
|
| 514 |
|
|
for (int j = 0 ; j<3; j++) |
| 515 |
|
|
grad[j] = frc[j]; |
| 516 |
|
|
|
| 517 |
|
|
grad[3] = 0.0; |
| 518 |
|
|
grad[4] = 0.0; |
| 519 |
|
|
grad[5] = 0.0; |
| 520 |
|
|
|
| 521 |
|
|
for (int j = 0; j < 3; j++ ) { |
| 522 |
|
|
|
| 523 |
|
|
grad[3] += trq[j]*ephi[j]; |
| 524 |
|
|
grad[4] += trq[j]*etheta[j]; |
| 525 |
|
|
grad[5] += trq[j]*epsi[j]; |
| 526 |
|
|
|
| 527 |
|
|
} |
| 528 |
|
|
|
| 529 |
|
|
} |
| 530 |
|
|
|
| 531 |
|
|
/** |
| 532 |
|
|
* getEulerAngles computes a set of Euler angle values consistent |
| 533 |
|
|
* with an input rotation matrix. They are returned in the following |
| 534 |
|
|
* order: |
| 535 |
|
|
* myEuler[0] = phi; |
| 536 |
|
|
* myEuler[1] = theta; |
| 537 |
|
|
* myEuler[2] = psi; |
| 538 |
|
|
*/ |
| 539 |
|
|
void RigidBody::getEulerAngles(double myEuler[3]) { |
| 540 |
|
|
|
| 541 |
|
|
// We use so-called "x-convention", which is the most common |
| 542 |
|
|
// definition. In this convention, the rotation given by Euler |
| 543 |
|
|
// angles (phi, theta, psi), where the first rotation is by an angle |
| 544 |
|
|
// phi about the z-axis, the second is by an angle theta (0 <= theta |
| 545 |
|
|
// <= 180) about the x-axis, and the third is by an angle psi about |
| 546 |
|
|
// the z-axis (again). |
| 547 |
|
|
|
| 548 |
|
|
|
| 549 |
|
|
double phi,theta,psi,eps; |
| 550 |
|
|
double pi; |
| 551 |
|
|
double cphi,ctheta,cpsi; |
| 552 |
|
|
double sphi,stheta,spsi; |
| 553 |
|
|
double b[3]; |
| 554 |
|
|
int flip[3]; |
| 555 |
|
|
|
| 556 |
|
|
// set the tolerance for Euler angles and rotation elements |
| 557 |
|
|
|
| 558 |
|
|
eps = 1.0e-8; |
| 559 |
|
|
|
| 560 |
|
|
theta = acos(min(1.0,max(-1.0,A[2][2]))); |
| 561 |
|
|
ctheta = A[2][2]; |
| 562 |
|
|
stheta = sqrt(1.0 - ctheta * ctheta); |
| 563 |
|
|
|
| 564 |
|
|
// when sin(theta) is close to 0, we need to consider the |
| 565 |
|
|
// possibility of a singularity. In this case, we can assign an |
| 566 |
|
|
// arbitary value to phi (or psi), and then determine the psi (or |
| 567 |
|
|
// phi) or vice-versa. We'll assume that phi always gets the |
| 568 |
|
|
// rotation, and psi is 0 in cases of singularity. we use atan2 |
| 569 |
|
|
// instead of atan, since atan2 will give us -Pi to Pi. Since 0 <= |
| 570 |
|
|
// theta <= 180, sin(theta) will be always non-negative. Therefore, |
| 571 |
|
|
// it never changes the sign of both of the parameters passed to |
| 572 |
|
|
// atan2. |
| 573 |
|
|
|
| 574 |
|
|
if (fabs(stheta) <= eps){ |
| 575 |
|
|
psi = 0.0; |
| 576 |
|
|
phi = atan2(-A[1][0], A[0][0]); |
| 577 |
|
|
} |
| 578 |
|
|
// we only have one unique solution |
| 579 |
|
|
else{ |
| 580 |
|
|
phi = atan2(A[2][0], -A[2][1]); |
| 581 |
|
|
psi = atan2(A[0][2], A[1][2]); |
| 582 |
|
|
} |
| 583 |
|
|
|
| 584 |
|
|
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
| 585 |
|
|
//if (phi < 0) |
| 586 |
|
|
// phi += M_PI; |
| 587 |
|
|
|
| 588 |
|
|
//if (psi < 0) |
| 589 |
|
|
// psi += M_PI; |
| 590 |
|
|
|
| 591 |
|
|
myEuler[0] = phi; |
| 592 |
|
|
myEuler[1] = theta; |
| 593 |
|
|
myEuler[2] = psi; |
| 594 |
|
|
|
| 595 |
|
|
return; |
| 596 |
|
|
} |
| 597 |
|
|
|
| 598 |
|
|
double RigidBody::max(double x, double y) { |
| 599 |
|
|
return (x > y) ? x : y; |
| 600 |
|
|
} |
| 601 |
|
|
|
| 602 |
|
|
double RigidBody::min(double x, double y) { |
| 603 |
|
|
return (x > y) ? y : x; |
| 604 |
|
|
} |
| 605 |
|
|
|
| 606 |
|
|
void RigidBody::findCOM() { |
| 607 |
|
|
|
| 608 |
|
|
size_t i; |
| 609 |
|
|
int j; |
| 610 |
|
|
double mtmp; |
| 611 |
|
|
double ptmp[3]; |
| 612 |
|
|
double vtmp[3]; |
| 613 |
|
|
|
| 614 |
|
|
for(j = 0; j < 3; j++) { |
| 615 |
|
|
pos[j] = 0.0; |
| 616 |
|
|
vel[j] = 0.0; |
| 617 |
|
|
} |
| 618 |
|
|
mass = 0.0; |
| 619 |
|
|
|
| 620 |
|
|
for (i = 0; i < myAtoms.size(); i++) { |
| 621 |
|
|
|
| 622 |
|
|
mtmp = myAtoms[i]->getMass(); |
| 623 |
|
|
myAtoms[i]->getPos(ptmp); |
| 624 |
|
|
myAtoms[i]->getVel(vtmp); |
| 625 |
|
|
|
| 626 |
|
|
mass += mtmp; |
| 627 |
|
|
|
| 628 |
|
|
for(j = 0; j < 3; j++) { |
| 629 |
|
|
pos[j] += ptmp[j]*mtmp; |
| 630 |
|
|
vel[j] += vtmp[j]*mtmp; |
| 631 |
|
|
} |
| 632 |
|
|
|
| 633 |
|
|
} |
| 634 |
|
|
|
| 635 |
|
|
for(j = 0; j < 3; j++) { |
| 636 |
|
|
pos[j] /= mass; |
| 637 |
|
|
vel[j] /= mass; |
| 638 |
|
|
} |
| 639 |
|
|
|
| 640 |
|
|
} |
| 641 |
|
|
|
| 642 |
|
|
void RigidBody::accept(BaseVisitor* v){ |
| 643 |
|
|
vector<Atom*>::iterator atomIter; |
| 644 |
|
|
v->visit(this); |
| 645 |
|
|
|
| 646 |
|
|
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
| 647 |
|
|
// (*atomIter)->accept(v); |
| 648 |
|
|
} |
| 649 |
|
|
void RigidBody::getAtomRefCoor(double pos[3], int index){ |
| 650 |
|
|
vec3 ref; |
| 651 |
|
|
|
| 652 |
|
|
ref = refCoords[index]; |
| 653 |
|
|
pos[0] = ref[0]; |
| 654 |
|
|
pos[1] = ref[1]; |
| 655 |
|
|
pos[2] = ref[2]; |
| 656 |
|
|
|
| 657 |
|
|
} |
| 658 |
|
|
|
| 659 |
|
|
|
| 660 |
|
|
void RigidBody::getAtomPos(double theP[3], int index){ |
| 661 |
|
|
vec3 ref; |
| 662 |
|
|
|
| 663 |
|
|
if (index >= myAtoms.size()) |
| 664 |
|
|
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
| 665 |
|
|
|
| 666 |
|
|
ref = refCoords[index]; |
| 667 |
|
|
body2Lab(ref.vec); |
| 668 |
|
|
|
| 669 |
|
|
theP[0] = pos[0] + ref[0]; |
| 670 |
|
|
theP[1] = pos[1] + ref[1]; |
| 671 |
|
|
theP[2] = pos[2] + ref[2]; |
| 672 |
|
|
} |
| 673 |
|
|
|
| 674 |
|
|
|
| 675 |
|
|
void RigidBody::getAtomVel(double theV[3], int index){ |
| 676 |
|
|
vec3 ref; |
| 677 |
|
|
double velRot[3]; |
| 678 |
|
|
double skewMat[3][3]; |
| 679 |
|
|
double aSkewMat[3][3]; |
| 680 |
|
|
double aSkewTransMat[3][3]; |
| 681 |
|
|
|
| 682 |
|
|
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
| 683 |
|
|
|
| 684 |
|
|
if (index >= myAtoms.size()) |
| 685 |
|
|
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
| 686 |
|
|
|
| 687 |
|
|
ref = refCoords[index]; |
| 688 |
|
|
|
| 689 |
|
|
skewMat[0][0] =0; |
| 690 |
|
|
skewMat[0][1] = ji[2] /I[2][2]; |
| 691 |
|
|
skewMat[0][2] = -ji[1] /I[1][1]; |
| 692 |
|
|
|
| 693 |
|
|
skewMat[1][0] = -ji[2] /I[2][2]; |
| 694 |
|
|
skewMat[1][1] = 0; |
| 695 |
|
|
skewMat[1][2] = ji[0]/I[0][0]; |
| 696 |
|
|
|
| 697 |
|
|
skewMat[2][0] =ji[1] /I[1][1]; |
| 698 |
|
|
skewMat[2][1] = -ji[0]/I[0][0]; |
| 699 |
|
|
skewMat[2][2] = 0; |
| 700 |
|
|
|
| 701 |
|
|
matMul3(A, skewMat, aSkewMat); |
| 702 |
|
|
|
| 703 |
|
|
transposeMat3(aSkewMat, aSkewTransMat); |
| 704 |
|
|
|
| 705 |
|
|
matVecMul3(aSkewTransMat, ref.vec, velRot); |
| 706 |
|
|
theV[0] = vel[0] + velRot[0]; |
| 707 |
|
|
theV[1] = vel[1] + velRot[1]; |
| 708 |
|
|
theV[2] = vel[2] + velRot[2]; |
| 709 |
|
|
} |
| 710 |
|
|
|
| 711 |
|
|
|
