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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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|
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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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is_charged = 0; |
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|
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index = theIndex; |
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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 = 0; |
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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::setIndex(int theIndex) { |
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index = theIndex; |
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} |
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|
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void Atom::setCoords(void){ |
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|
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if( myConfig->isAllocated() ){ |
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|
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|
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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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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", index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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hasCoords = true; |
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|
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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] = 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*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] = AAmat[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] = Amu[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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// } |
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|
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|
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void Atom::getPos( double theP[3] ){ |
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|
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if( hasCoords ){ |
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theP[0] = pos[offsetX]; |
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theP[1] = pos[offsetY]; |
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theP[2] = pos[offsetZ]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get Pos for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::setPos( double theP[3] ){ |
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|
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if( hasCoords ){ |
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pos[offsetX] = theP[0]; |
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pos[offsetY] = theP[1]; |
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pos[offsetZ] = theP[2]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set Pos for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::getVel( double theV[3] ){ |
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|
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if( hasCoords ){ |
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theV[0] = vel[offsetX]; |
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theV[1] = vel[offsetY]; |
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theV[2] = vel[offsetZ]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get vel for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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void Atom::setVel( double theV[3] ){ |
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|
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if( hasCoords ){ |
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vel[offsetX] = theV[0]; |
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vel[offsetY] = theV[1]; |
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vel[offsetZ] = theV[2]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set vel for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::getFrc( double theF[3] ){ |
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|
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if( hasCoords ){ |
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theF[0] = frc[offsetX]; |
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theF[1] = frc[offsetY]; |
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theF[2] = frc[offsetZ]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::addFrc( double theF[3] ){ |
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|
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if( hasCoords ){ |
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frc[offsetX] += theF[0]; |
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frc[offsetY] += theF[1]; |
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frc[offsetZ] += theF[2]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to add frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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void GeneralAtom::zeroForces( void ){ |
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|
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|
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if( hasCoords ){ |
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frc[offsetX] = 0.0; |
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frc[offsetY] = 0.0; |
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frc[offsetZ] = 0.0; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to zero frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
