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#include "Atom.hpp" |
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|
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Atom::Atom(int theIndex) { |
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c_n_hyd = 0; |
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has_dipole = 0; |
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is_VDW = 0; |
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is_LJ = 0; |
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|
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index = theIndex; |
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offset = 3 * index; |
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offsetX = offset; |
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offsetY = offset+1; |
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offsetZ = offset+2; |
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|
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Axx = index*9; |
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Axy = Axx+1; |
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Axz = Axx+2; |
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|
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Ayx = Axx+3; |
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Ayy = Axx+4; |
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Ayz = Axx+5; |
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|
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Azx = Axx+6; |
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Azy = Axx+7; |
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Azz = Axx+8; |
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} |
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|
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void Atom::createArrays (int nElements) { |
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int i; |
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|
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pos = new double[nElements*3]; |
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vel = new double[nElements*3]; |
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frc = new double[nElements*3]; |
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trq = new double[nElements*3]; |
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Amat = new double[nElements*9]; |
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mu = new double[nElements]; |
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ul = new double[nElements*3]; |
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|
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// init directional values to zero |
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|
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for( i=0; i<nElements; i++){ |
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trq[i] = 0.0; |
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trq[i+1] = 0.0; |
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trq[i+2] = 0.0; |
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|
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Amat[i] = 1.0; |
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Amat[i+1] = 0.0; |
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Amat[i+2] = 0.0; |
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|
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Amat[i+3] = 0.0; |
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Amat[i+4] = 1.0; |
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Amat[i+5] = 0.0; |
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|
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Amat[i+6] = 0.0; |
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Amat[i+7] = 0.0; |
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Amat[i+8] = 1.0; |
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|
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mu[i] = 0.0; |
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|
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ul[i] = 1.0; |
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ul[i+1] = 0.0; |
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ul[i+2] = 0.0; |
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} |
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} |
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|
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void Atom::destroyArrays(void) { |
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delete[] pos; |
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delete[] vel; |
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delete[] frc; |
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delete[] trq; |
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delete[] Amat; |
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delete[] mu; |
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} |
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|
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void Atom::setIndex(int theIndex) { |
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index = theIndex; |
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offset = index*3; |
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offsetX = offset; |
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offsetY = offset+1; |
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offsetZ = offset+2; |
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|
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Axx = index*9; |
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Axy = Axx+1; |
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Axz = Axx+2; |
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|
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Ayx = Axx+3; |
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Ayy = Axx+4; |
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Ayz = Axx+5; |
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|
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Azx = Axx+6; |
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Azy = Axx+7; |
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Azz = Axx+8; |
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} |
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|
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void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
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double* Atrq, double* AAmat, double* Amu, |
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double* Aul) { |
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|
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int nNew = nElements+nAdded; |
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|
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double* new_pos = new double[nNew*3]; |
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double* new_vel = new double[nNew*3]; |
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double* new_frc = new double[nNew*3]; |
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double* new_trq = new double[nNew*3]; |
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double* new_Amat = new double[nNew*9]; |
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double* new_mu = new double[nNew]; |
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double* new_ul = new double[nNew*3]; |
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int i, j; |
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|
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for (i = 0; i < 3*nElements; i++) { |
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new_pos[i] = pos[i]; |
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new_vel[i] = vel[i]; |
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new_frc[i] = frc[i]; |
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new_trq[i] = trq[i]; |
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new_ul[i] = ul[i]; |
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} |
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|
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for(i = 0; i < 3*nAdded; i++) { |
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j = i + 3*nElements; |
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new_pos[j] = pos[i]; |
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new_vel[j] = vel[i]; |
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new_frc[j] = frc[i]; |
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new_trq[j] = trq[i]; |
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new_ul[j] = ul[i]; |
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} |
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|
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for (i = 0; i < 9*nElements; i++) { |
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new_Amat[i] = Amat[i]; |
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} |
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|
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for(i = 0; i < 9*nAdded; i++) { |
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j = i + 9*nElements; |
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new_Amat[j] = Amat[i]; |
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} |
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|
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for (i = 0; i < nElements; i++) { |
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new_mu[i] = mu[i]; |
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} |
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|
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for(i = 0; i < nAdded; i++) { |
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j = i + nElements; |
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new_mu[j] = mu[i]; |
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} |
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|
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delete[] pos; |
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delete[] vel; |
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delete[] frc; |
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delete[] trq; |
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delete[] Amat; |
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delete[] mu; |
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|
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pos = new_pos; |
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vel = new_vel; |
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frc = new_frc; |
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trq = new_trq; |
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ul = new_ul; |
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Amat = new_Amat; |
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mu = new_mu; |
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|
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nElements = nNew; |
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} |
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|
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void Atom::deleteAtom(int theIndex) { |
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deleteRange(theIndex, theIndex); |
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} |
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|
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void Atom::deleteRange(int startIndex, int stopIndex) { |
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|
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int nNew = nElements-(stopIndex-startIndex+1); |
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|
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double* new_pos = new double[nNew*3]; |
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double* new_vel = new double[nNew*3]; |
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double* new_frc = new double[nNew*3]; |
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double* new_trq = new double[nNew*3]; |
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double* new_Amat = new double[nNew*9]; |
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double* new_mu = new double[nNew]; |
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double* new_ul = new double[nNew*3]; |
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int i, j; |
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|
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for (i = 0; i < 3*startIndex; i++) { |
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new_pos[i] = pos[i]; |
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new_vel[i] = vel[i]; |
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new_frc[i] = frc[i]; |
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new_trq[i] = trq[i]; |
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new_ul[i] = ul[i]; |
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} |
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|
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for(i = 3*(stopIndex + 1); i < 3*nElements; i++) { |
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j = i - 3*startIndex + 1; |
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new_pos[j] = pos[i]; |
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new_vel[j] = vel[i]; |
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new_frc[j] = frc[i]; |
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new_trq[j] = trq[i]; |
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new_ul[j] = ul[i]; |
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} |
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|
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for (i = 0; i < 9*startIndex; i++) { |
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new_Amat[i] = Amat[i]; |
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} |
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|
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for(i = 9*(stopIndex + 1); i < 9*nElements; i++) { |
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j = i - 9*startIndex + 1; |
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new_Amat[j] = Amat[i]; |
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} |
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|
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for (i = 0; i < startIndex; i++) { |
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new_mu[i] = mu[i]; |
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} |
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|
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for(i = (stopIndex+1); i < nElements; i++) { |
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j = i - startIndex + 1; |
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new_mu[j] = mu[i]; |
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} |
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|
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delete[] pos; |
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delete[] vel; |
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delete[] frc; |
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delete[] trq; |
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delete[] Amat; |
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delete[] mu; |
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|
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pos = new_pos; |
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vel = new_vel; |
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frc = new_frc; |
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trq = new_trq; |
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ul = new_ul; |
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Amat = new_Amat; |
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mu = new_mu; |
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|
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nElements = nNew; |
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} |