| 6 |
|
#include "Atom.hpp" |
| 7 |
|
|
| 8 |
|
Atom::Atom(int theIndex, SimState* theConfig) { |
| 9 |
< |
|
| 9 |
> |
|
| 10 |
> |
objType = OT_ATOM; |
| 11 |
|
myConfig = theConfig; |
| 12 |
|
hasCoords = false; |
| 13 |
< |
|
| 13 |
< |
c_n_hyd = 0; |
| 13 |
> |
|
| 14 |
|
has_dipole = 0; |
| 15 |
– |
is_VDW = 0; |
| 16 |
– |
is_LJ = 0; |
| 15 |
|
|
| 16 |
|
index = theIndex; |
| 17 |
|
offset = 0; |
| 52 |
|
else{ |
| 53 |
|
sprintf( painCave.errMsg, |
| 54 |
|
"Attempted to set Atom %d coordinates with an unallocated " |
| 55 |
< |
"SimState object.\n" ); |
| 55 |
> |
"SimState object.\n", index ); |
| 56 |
|
painCave.isFatal = 1; |
| 57 |
|
simError(); |
| 58 |
|
} |
| 59 |
< |
|
| 59 |
> |
|
| 60 |
|
hasCoords = true; |
| 61 |
< |
|
| 61 |
> |
|
| 62 |
|
} |
| 63 |
|
|
| 66 |
– |
// void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
| 67 |
– |
// double* Atrq, double* AAmat, double* Amu, |
| 68 |
– |
// double* Aul) { |
| 69 |
– |
|
| 70 |
– |
// int nNew = nElements+nAdded; |
| 71 |
– |
|
| 72 |
– |
// double* new_pos = new double[nNew*3]; |
| 73 |
– |
// double* new_vel = new double[nNew*3]; |
| 74 |
– |
// double* new_frc = new double[nNew*3]; |
| 75 |
– |
// double* new_trq = new double[nNew*3]; |
| 76 |
– |
// double* new_Amat = new double[nNew*9]; |
| 77 |
– |
// double* new_mu = new double[nNew]; |
| 78 |
– |
// double* new_ul = new double[nNew*3]; |
| 79 |
– |
// int i, j; |
| 80 |
– |
|
| 81 |
– |
// for (i = 0; i < 3*nElements; i++) { |
| 82 |
– |
// new_pos[i] = pos[i]; |
| 83 |
– |
// new_vel[i] = vel[i]; |
| 84 |
– |
// new_frc[i] = frc[i]; |
| 85 |
– |
// new_trq[i] = trq[i]; |
| 86 |
– |
// new_ul[i] = ul[i]; |
| 87 |
– |
// } |
| 88 |
– |
|
| 89 |
– |
// for(i = 0; i < 3*nAdded; i++) { |
| 90 |
– |
// j = i + 3*nElements; |
| 91 |
– |
// new_pos[j] = Apos[i]; |
| 92 |
– |
// new_vel[j] = Avel[i]; |
| 93 |
– |
// new_frc[j] = Afrc[i]; |
| 94 |
– |
// new_trq[j] = Atrq[i]; |
| 95 |
– |
// new_ul[j] = Aul[i]; |
| 96 |
– |
// } |
| 97 |
– |
|
| 98 |
– |
// for (i = 0; i < 9*nElements; i++) { |
| 99 |
– |
// new_Amat[i] = Amat[i]; |
| 100 |
– |
// } |
| 101 |
– |
|
| 102 |
– |
// for(i = 0; i < 9*nAdded; i++) { |
| 103 |
– |
// j = i + 9*nElements; |
| 104 |
– |
// new_Amat[j] = AAmat[i]; |
| 105 |
– |
// } |
| 106 |
– |
|
| 107 |
– |
// for (i = 0; i < nElements; i++) { |
| 108 |
– |
// new_mu[i] = mu[i]; |
| 109 |
– |
// } |
| 110 |
– |
|
| 111 |
– |
// for(i = 0; i < nAdded; i++) { |
| 112 |
– |
// j = i + nElements; |
| 113 |
– |
// new_mu[j] = Amu[i]; |
| 114 |
– |
// } |
| 115 |
– |
|
| 116 |
– |
// delete[] pos; |
| 117 |
– |
// delete[] vel; |
| 118 |
– |
// delete[] frc; |
| 119 |
– |
// delete[] trq; |
| 120 |
– |
// delete[] Amat; |
| 121 |
– |
// delete[] mu; |
| 122 |
– |
|
| 123 |
– |
// pos = new_pos; |
| 124 |
– |
// vel = new_vel; |
| 125 |
– |
// frc = new_frc; |
| 126 |
– |
// trq = new_trq; |
| 127 |
– |
// ul = new_ul; |
| 128 |
– |
// Amat = new_Amat; |
| 129 |
– |
// mu = new_mu; |
| 130 |
– |
|
| 131 |
– |
// nElements = nNew; |
| 132 |
– |
// } |
| 133 |
– |
|
| 134 |
– |
// void Atom::deleteAtom(int theIndex) { |
| 135 |
– |
// deleteRange(theIndex, theIndex); |
| 136 |
– |
// } |
| 137 |
– |
|
| 138 |
– |
// void Atom::deleteRange(int startIndex, int stopIndex) { |
| 139 |
– |
|
| 140 |
– |
// int nNew = nElements-(stopIndex-startIndex+1); |
| 141 |
– |
|
| 142 |
– |
// double* new_pos = new double[nNew*3]; |
| 143 |
– |
// double* new_vel = new double[nNew*3]; |
| 144 |
– |
// double* new_frc = new double[nNew*3]; |
| 145 |
– |
// double* new_trq = new double[nNew*3]; |
| 146 |
– |
// double* new_Amat = new double[nNew*9]; |
| 147 |
– |
// double* new_mu = new double[nNew]; |
| 148 |
– |
// double* new_ul = new double[nNew*3]; |
| 149 |
– |
// int i, j; |
| 150 |
– |
|
| 151 |
– |
// for (i = 0; i < 3*startIndex; i++) { |
| 152 |
– |
// new_pos[i] = pos[i]; |
| 153 |
– |
// new_vel[i] = vel[i]; |
| 154 |
– |
// new_frc[i] = frc[i]; |
| 155 |
– |
// new_trq[i] = trq[i]; |
| 156 |
– |
// new_ul[i] = ul[i]; |
| 157 |
– |
// } |
| 158 |
– |
|
| 159 |
– |
// for(i = 3*(stopIndex + 1); i < 3*nElements; i++) { |
| 160 |
– |
// j = i - 3*startIndex + 1; |
| 161 |
– |
// new_pos[j] = pos[i]; |
| 162 |
– |
// new_vel[j] = vel[i]; |
| 163 |
– |
// new_frc[j] = frc[i]; |
| 164 |
– |
// new_trq[j] = trq[i]; |
| 165 |
– |
// new_ul[j] = ul[i]; |
| 166 |
– |
// } |
| 167 |
– |
|
| 168 |
– |
// for (i = 0; i < 9*startIndex; i++) { |
| 169 |
– |
// new_Amat[i] = Amat[i]; |
| 170 |
– |
// } |
| 171 |
– |
|
| 172 |
– |
// for(i = 9*(stopIndex + 1); i < 9*nElements; i++) { |
| 173 |
– |
// j = i - 9*startIndex + 1; |
| 174 |
– |
// new_Amat[j] = Amat[i]; |
| 175 |
– |
// } |
| 176 |
– |
|
| 177 |
– |
// for (i = 0; i < startIndex; i++) { |
| 178 |
– |
// new_mu[i] = mu[i]; |
| 179 |
– |
// } |
| 180 |
– |
|
| 181 |
– |
// for(i = (stopIndex+1); i < nElements; i++) { |
| 182 |
– |
// j = i - startIndex + 1; |
| 183 |
– |
// new_mu[j] = mu[i]; |
| 184 |
– |
// } |
| 185 |
– |
|
| 186 |
– |
// delete[] pos; |
| 187 |
– |
// delete[] vel; |
| 188 |
– |
// delete[] frc; |
| 189 |
– |
// delete[] trq; |
| 190 |
– |
// delete[] Amat; |
| 191 |
– |
// delete[] mu; |
| 192 |
– |
|
| 193 |
– |
// pos = new_pos; |
| 194 |
– |
// vel = new_vel; |
| 195 |
– |
// frc = new_frc; |
| 196 |
– |
// trq = new_trq; |
| 197 |
– |
// ul = new_ul; |
| 198 |
– |
// Amat = new_Amat; |
| 199 |
– |
// mu = new_mu; |
| 200 |
– |
|
| 201 |
– |
// nElements = nNew; |
| 202 |
– |
// } |
| 203 |
– |
|
| 204 |
– |
|
| 64 |
|
void Atom::getPos( double theP[3] ){ |
| 65 |
|
|
| 66 |
|
if( hasCoords ){ |
| 79 |
|
} |
| 80 |
|
|
| 81 |
|
void Atom::setPos( double theP[3] ){ |
| 82 |
< |
|
| 82 |
> |
|
| 83 |
|
if( hasCoords ){ |
| 84 |
|
pos[offsetX] = theP[0]; |
| 85 |
|
pos[offsetY] = theP[1]; |
| 165 |
|
} |
| 166 |
|
|
| 167 |
|
|
| 168 |
< |
void GeneralAtom::zeroForces( void ){ |
| 168 |
> |
void Atom::zeroForces( void ){ |
| 169 |
|
|
| 311 |
– |
|
| 170 |
|
if( hasCoords ){ |
| 171 |
|
frc[offsetX] = 0.0; |
| 172 |
|
frc[offsetY] = 0.0; |
