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#include <iostream> |
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|
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using namespace std; |
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|
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#include "simError.h" |
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#include "Atom.hpp" |
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|
8 |
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Atom::Atom(int theIndex) { |
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Atom::Atom(int theIndex, SimState* theConfig) { |
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|
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myConfig = theConfig; |
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hasCoords = false; |
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|
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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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offset = 0; |
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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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Axx = 0; |
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Axy = Axx+1; |
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Axz = Axx+2; |
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|
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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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void Atom::setCoords(void){ |
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|
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int nNew = nElements+nAdded; |
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if( myConfig->isAllocated() ){ |
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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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myConfig->getAtomPointers( index, |
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&pos, |
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&vel, |
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&frc, |
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&trq, |
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&Amat, |
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&mu, |
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&ul ); |
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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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else{ |
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sprintf( painCave.errMsg, |
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"Attempted to set Atom %d coordinates with an unallocated " |
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"SimState object.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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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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hasCoords = true; |
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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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// 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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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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// 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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// 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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// 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 = 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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// for(i = 0; i < 3*nAdded; i++) { |
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// j = i + 3*nElements; |
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// new_pos[j] = Apos[i]; |
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// new_vel[j] = Avel[i]; |
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// new_frc[j] = Afrc[i]; |
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// new_trq[j] = Atrq[i]; |
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// new_ul[j] = Aul[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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// for (i = 0; i < 9*nElements; i++) { |
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// new_Amat[i] = Amat[i]; |
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// } |
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|
|
103 |
< |
for(i = 9*(stopIndex + 1); i < 9*nElements; i++) { |
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j = i - 9*startIndex + 1; |
105 |
< |
new_Amat[j] = Amat[i]; |
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} |
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> |
// for(i = 0; i < 9*nAdded; i++) { |
104 |
> |
// j = i + 9*nElements; |
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> |
// new_Amat[j] = AAmat[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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> |
// for (i = 0; i < nElements; i++) { |
109 |
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// new_mu[i] = mu[i]; |
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// } |
111 |
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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] = Amu[i]; |
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// } |
116 |
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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; |
128 |
> |
// ul = new_ul; |
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// Amat = new_Amat; |
130 |
> |
// mu = new_mu; |
131 |
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|
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// nElements = nNew; |
133 |
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// } |
134 |
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|
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// void Atom::deleteAtom(int theIndex) { |
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// deleteRange(theIndex, theIndex); |
137 |
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// } |
138 |
> |
|
139 |
> |
// void Atom::deleteRange(int startIndex, int stopIndex) { |
140 |
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|
141 |
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// int nNew = nElements-(stopIndex-startIndex+1); |
142 |
> |
|
143 |
> |
// double* new_pos = new double[nNew*3]; |
144 |
> |
// double* new_vel = new double[nNew*3]; |
145 |
> |
// double* new_frc = new double[nNew*3]; |
146 |
> |
// double* new_trq = new double[nNew*3]; |
147 |
> |
// double* new_Amat = new double[nNew*9]; |
148 |
> |
// double* new_mu = new double[nNew]; |
149 |
> |
// double* new_ul = new double[nNew*3]; |
150 |
> |
// int i, j; |
151 |
> |
|
152 |
> |
// for (i = 0; i < 3*startIndex; i++) { |
153 |
> |
// new_pos[i] = pos[i]; |
154 |
> |
// new_vel[i] = vel[i]; |
155 |
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// new_frc[i] = frc[i]; |
156 |
> |
// new_trq[i] = trq[i]; |
157 |
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// new_ul[i] = ul[i]; |
158 |
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// } |
159 |
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|
160 |
> |
// for(i = 3*(stopIndex + 1); i < 3*nElements; i++) { |
161 |
> |
// j = i - 3*startIndex + 1; |
162 |
> |
// new_pos[j] = pos[i]; |
163 |
> |
// new_vel[j] = vel[i]; |
164 |
> |
// new_frc[j] = frc[i]; |
165 |
> |
// new_trq[j] = trq[i]; |
166 |
> |
// new_ul[j] = ul[i]; |
167 |
> |
// } |
168 |
> |
|
169 |
> |
// for (i = 0; i < 9*startIndex; i++) { |
170 |
> |
// new_Amat[i] = Amat[i]; |
171 |
> |
// } |
172 |
> |
|
173 |
> |
// for(i = 9*(stopIndex + 1); i < 9*nElements; i++) { |
174 |
> |
// j = i - 9*startIndex + 1; |
175 |
> |
// new_Amat[j] = Amat[i]; |
176 |
> |
// } |
177 |
> |
|
178 |
> |
// for (i = 0; i < startIndex; i++) { |
179 |
> |
// new_mu[i] = mu[i]; |
180 |
> |
// } |
181 |
> |
|
182 |
> |
// for(i = (stopIndex+1); i < nElements; i++) { |
183 |
> |
// j = i - startIndex + 1; |
184 |
> |
// new_mu[j] = mu[i]; |
185 |
> |
// } |
186 |
> |
|
187 |
> |
// delete[] pos; |
188 |
> |
// delete[] vel; |
189 |
> |
// delete[] frc; |
190 |
> |
// delete[] trq; |
191 |
> |
// delete[] Amat; |
192 |
> |
// delete[] mu; |
193 |
> |
|
194 |
> |
// pos = new_pos; |
195 |
> |
// vel = new_vel; |
196 |
> |
// frc = new_frc; |
197 |
> |
// trq = new_trq; |
198 |
> |
// ul = new_ul; |
199 |
> |
// Amat = new_Amat; |
200 |
> |
// mu = new_mu; |
201 |
> |
|
202 |
> |
// nElements = nNew; |
203 |
> |
// } |
204 |
> |
|
205 |
> |
|
206 |
> |
void Atom::getPos( double theP[3] ){ |
207 |
> |
|
208 |
> |
if( hasCoords ){ |
209 |
> |
theP[0] = pos[offsetX]; |
210 |
> |
theP[1] = pos[offsetY]; |
211 |
> |
theP[2] = pos[offsetZ]; |
212 |
|
} |
213 |
+ |
else{ |
214 |
|
|
215 |
< |
for(i = (stopIndex+1); i < nElements; i++) { |
216 |
< |
j = i - startIndex + 1; |
217 |
< |
new_mu[j] = mu[i]; |
215 |
> |
sprintf( painCave.errMsg, |
216 |
> |
"Attempt to get Pos for atom %d before coords set.\n", |
217 |
> |
index ); |
218 |
> |
painCave.isFatal = 1; |
219 |
> |
simError(); |
220 |
|
} |
221 |
+ |
} |
222 |
|
|
223 |
< |
delete[] pos; |
224 |
< |
delete[] vel; |
225 |
< |
delete[] frc; |
226 |
< |
delete[] trq; |
227 |
< |
delete[] Amat; |
228 |
< |
delete[] mu; |
223 |
> |
void Atom::setPos( double theP[3] ){ |
224 |
> |
|
225 |
> |
if( hasCoords ){ |
226 |
> |
pos[offsetX] = theP[0]; |
227 |
> |
pos[offsetY] = theP[1]; |
228 |
> |
pos[offsetZ] = theP[2]; |
229 |
> |
} |
230 |
> |
else{ |
231 |
|
|
232 |
< |
pos = new_pos; |
233 |
< |
vel = new_vel; |
234 |
< |
frc = new_frc; |
235 |
< |
trq = new_trq; |
236 |
< |
ul = new_ul; |
237 |
< |
Amat = new_Amat; |
238 |
< |
mu = new_mu; |
232 |
> |
sprintf( painCave.errMsg, |
233 |
> |
"Attempt to set Pos for atom %d before coords set.\n", |
234 |
> |
index ); |
235 |
> |
painCave.isFatal = 1; |
236 |
> |
simError(); |
237 |
> |
} |
238 |
> |
} |
239 |
|
|
240 |
< |
nElements = nNew; |
240 |
> |
void Atom::getVel( double theV[3] ){ |
241 |
> |
|
242 |
> |
if( hasCoords ){ |
243 |
> |
theV[0] = vel[offsetX]; |
244 |
> |
theV[1] = vel[offsetY]; |
245 |
> |
theV[2] = vel[offsetZ]; |
246 |
> |
} |
247 |
> |
else{ |
248 |
> |
|
249 |
> |
sprintf( painCave.errMsg, |
250 |
> |
"Attempt to get vel for atom %d before coords set.\n", |
251 |
> |
index ); |
252 |
> |
painCave.isFatal = 1; |
253 |
> |
simError(); |
254 |
> |
} |
255 |
> |
|
256 |
|
} |
257 |
+ |
|
258 |
+ |
void Atom::setVel( double theV[3] ){ |
259 |
+ |
|
260 |
+ |
if( hasCoords ){ |
261 |
+ |
vel[offsetX] = theV[0]; |
262 |
+ |
vel[offsetY] = theV[1]; |
263 |
+ |
vel[offsetZ] = theV[2]; |
264 |
+ |
} |
265 |
+ |
else{ |
266 |
+ |
|
267 |
+ |
sprintf( painCave.errMsg, |
268 |
+ |
"Attempt to set vel for atom %d before coords set.\n", |
269 |
+ |
index ); |
270 |
+ |
painCave.isFatal = 1; |
271 |
+ |
simError(); |
272 |
+ |
} |
273 |
+ |
} |
274 |
+ |
|
275 |
+ |
void Atom::getFrc( double theF[3] ){ |
276 |
+ |
|
277 |
+ |
if( hasCoords ){ |
278 |
+ |
theF[0] = frc[offsetX]; |
279 |
+ |
theF[1] = frc[offsetY]; |
280 |
+ |
theF[2] = frc[offsetZ]; |
281 |
+ |
} |
282 |
+ |
else{ |
283 |
+ |
|
284 |
+ |
sprintf( painCave.errMsg, |
285 |
+ |
"Attempt to get frc for atom %d before coords set.\n", |
286 |
+ |
index ); |
287 |
+ |
painCave.isFatal = 1; |
288 |
+ |
simError(); |
289 |
+ |
} |
290 |
+ |
} |
291 |
+ |
|
292 |
+ |
void Atom::addFrc( double theF[3] ){ |
293 |
+ |
|
294 |
+ |
if( hasCoords ){ |
295 |
+ |
frc[offsetX] += theF[0]; |
296 |
+ |
frc[offsetY] += theF[1]; |
297 |
+ |
frc[offsetZ] += theF[2]; |
298 |
+ |
} |
299 |
+ |
else{ |
300 |
+ |
|
301 |
+ |
sprintf( painCave.errMsg, |
302 |
+ |
"Attempt to add frc for atom %d before coords set.\n", |
303 |
+ |
index ); |
304 |
+ |
painCave.isFatal = 1; |
305 |
+ |
simError(); |
306 |
+ |
} |
307 |
+ |
} |
308 |
+ |
|
309 |
+ |
|
310 |
+ |
void GeneralAtom::zeroForces( void ){ |
311 |
+ |
|
312 |
+ |
|
313 |
+ |
if( hasCoords ){ |
314 |
+ |
frc[offsetX] = 0.0; |
315 |
+ |
frc[offsetY] = 0.0; |
316 |
+ |
frc[offsetZ] = 0.0; |
317 |
+ |
} |
318 |
+ |
else{ |
319 |
+ |
|
320 |
+ |
sprintf( painCave.errMsg, |
321 |
+ |
"Attempt to zero frc for atom %d before coords set.\n", |
322 |
+ |
index ); |
323 |
+ |
painCave.isFatal = 1; |
324 |
+ |
simError(); |
325 |
+ |
} |
326 |
+ |
} |