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#include <math.h> |
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#include <iostream> |
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#include "RigidBody.hpp" |
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#include "VDWAtom.hpp" |
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#include "MatVec3.h" |
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void RigidBody::calcRefCoords( ) { |
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int i, j, it, n_linear_coords; |
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int i, j, it, n_linear_coords, pAxis, maxAxis, midAxis; |
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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 pAxisMat[3][3], pAxisRotMat[3][3]; |
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double evals[3]; |
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double r, r2, len; |
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double iMat[3][3]; |
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double test[3]; |
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// First, find the center of mass: |
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mass = 0.0; |
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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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if (n_linear_coords > 1) { |
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printf( |
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"RigidBody error.\n" |
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"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
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"\tSHAPES 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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); |
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exit(-1); |
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} |
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// renormalize column vectors: |
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for (i=0; i < 3; i++) { |
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sU[i][j] /= len; |
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} |
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} |
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//sort and reorder the moment axes |
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// The only problem below is for molecules like C60 with 3 nearly identical |
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// non-zero moments of inertia. In this case it doesn't really matter which is |
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// the principal axis, so they get assigned nearly randomly depending on the |
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// floating point comparison between eigenvalues |
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if (! is_linear) { |
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pAxis = 0; |
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maxAxis = 0; |
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for (i = 0; i < 3; i++) { |
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if (evals[i] < evals[pAxis]) pAxis = i; |
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if (evals[i] > evals[maxAxis]) maxAxis = i; |
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} |
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midAxis = 0; |
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for (i=0; i < 3; i++) { |
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if (pAxis != i && maxAxis != i) midAxis = i; |
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} |
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} else { |
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pAxis = linear_axis; |
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// linear molecules have one zero moment of inertia and two identical |
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// moments of inertia. In this case, it doesn't matter which is chosen |
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// as mid and which is max, so just permute from the pAxis: |
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midAxis = (pAxis + 1)%3; |
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maxAxis = (pAxis + 2)%3; |
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} |
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//let z be the smallest and x be the largest eigenvalue axes |
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for (i=0; i<3; i++){ |
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pAxisMat[i][2] = sU[i][pAxis]; |
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pAxisMat[i][1] = sU[i][midAxis]; |
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pAxisMat[i][0] = sU[i][maxAxis]; |
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} |
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//calculate the proper rotation matrix |
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transposeMat3(pAxisMat, pAxisRotMat); |
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//rotate the rigid body to the principle axis frame |
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for (i = 0; i < myAtoms.size(); i++) { |
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matVecMul3(pAxisRotMat, refCoords[i].vec, refCoords[i].vec); |
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myAtoms[i]->setPos(refCoords[i].vec); |
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} |
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identityMat3(iMat); |
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setA(iMat); |
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} |
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void RigidBody::doEulerToRotMat(double euler[3], double myA[3][3] ){ |
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pos[2] = ref[2]; |
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} |
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double RigidBody::getAtomRpar(int index){ |
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return myAtoms[index]->getRpar(); |
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} |
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double RigidBody::getAtomEps(int index){ |
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return myAtoms[index]->getEps(); |
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} |
