| 25 |
|
if (info->the_integrator != NULL){ |
| 26 |
|
delete info->the_integrator; |
| 27 |
|
} |
| 28 |
< |
|
| 28 |
> |
|
| 29 |
|
nAtoms = info->n_atoms; |
| 30 |
|
|
| 31 |
|
// check for constraints |
| 158 |
|
double currThermal; |
| 159 |
|
double currStatus; |
| 160 |
|
double currReset; |
| 161 |
< |
|
| 161 |
> |
|
| 162 |
|
int calcPot, calcStress; |
| 163 |
|
|
| 164 |
|
tStats = new Thermo(info); |
| 174 |
|
|
| 175 |
|
// initialize the forces before the first step |
| 176 |
|
|
| 177 |
+ |
std::cerr << "Before initial Force calc\n"; |
| 178 |
+ |
|
| 179 |
|
calcForce(1, 1); |
| 180 |
|
|
| 181 |
|
if (nConstrained){ |
| 182 |
|
preMove(); |
| 183 |
|
constrainA(); |
| 184 |
< |
calcForce(1, 1); |
| 184 |
> |
calcForce(1, 1); |
| 185 |
|
constrainB(); |
| 186 |
+ |
std::cerr << "premove done\n"; |
| 187 |
|
} |
| 188 |
< |
|
| 188 |
> |
|
| 189 |
> |
|
| 190 |
> |
|
| 191 |
|
if (info->setTemp){ |
| 192 |
|
thermalize(); |
| 193 |
|
} |
| 232 |
|
} |
| 233 |
|
|
| 234 |
|
if (info->getTime() >= currStatus){ |
| 235 |
< |
statOut->writeStat(info->getTime()); |
| 236 |
< |
calcPot = 0; |
| 235 |
> |
statOut->writeStat(info->getTime()); |
| 236 |
> |
calcPot = 0; |
| 237 |
|
calcStress = 0; |
| 238 |
|
currStatus += statusTime; |
| 239 |
< |
} |
| 239 |
> |
} |
| 240 |
|
|
| 241 |
|
if (info->resetIntegrator){ |
| 242 |
|
if (info->getTime() >= currReset){ |
| 245 |
|
} |
| 246 |
|
} |
| 247 |
|
|
| 248 |
+ |
std::cerr << "done with time = " << info->getTime() << "\n"; |
| 249 |
+ |
|
| 250 |
|
#ifdef IS_MPI |
| 251 |
|
strcpy(checkPointMsg, "successfully took a time step."); |
| 252 |
|
MPIcheckPoint(); |
| 373 |
|
if (atoms[i]->isDirectional()){ |
| 374 |
|
dAtom = (DirectionalAtom *) atoms[i]; |
| 375 |
|
|
| 376 |
< |
// get and convert the torque to body frame |
| 376 |
> |
// get and convert the torque to body frame |
| 377 |
|
|
| 378 |
|
dAtom->getTrq(Tb); |
| 379 |
|
dAtom->lab2Body(Tb); |
| 665 |
|
|
| 666 |
|
dAtom->getA(A); |
| 667 |
|
dAtom->getI(I); |
| 668 |
< |
|
| 669 |
< |
// rotate about the x-axis |
| 668 |
> |
|
| 669 |
> |
// rotate about the x-axis |
| 670 |
|
angle = dt2 * ji[0] / I[0][0]; |
| 671 |
< |
this->rotate( 1, 2, angle, ji, A ); |
| 672 |
< |
|
| 671 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 672 |
> |
|
| 673 |
|
// rotate about the y-axis |
| 674 |
|
angle = dt2 * ji[1] / I[1][1]; |
| 675 |
|
this->rotate( 2, 0, angle, ji, A ); |
| 676 |
< |
|
| 676 |
> |
|
| 677 |
|
// rotate about the z-axis |
| 678 |
|
angle = dt * ji[2] / I[2][2]; |
| 679 |
|
this->rotate( 0, 1, angle, ji, A); |
| 680 |
< |
|
| 680 |
> |
|
| 681 |
|
// rotate about the y-axis |
| 682 |
|
angle = dt2 * ji[1] / I[1][1]; |
| 683 |
|
this->rotate( 2, 0, angle, ji, A ); |
| 684 |
< |
|
| 684 |
> |
|
| 685 |
|
// rotate about the x-axis |
| 686 |
|
angle = dt2 * ji[0] / I[0][0]; |
| 687 |
|
this->rotate( 1, 2, angle, ji, A ); |
| 688 |
< |
|
| 689 |
< |
dAtom->setA( A ); |
| 688 |
> |
|
| 689 |
> |
dAtom->setA( A ); |
| 690 |
|
} |
| 691 |
|
|
| 692 |
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
| 754 |
|
} |
| 755 |
|
} |
| 756 |
|
|
| 757 |
< |
// rotate the Rotation matrix acording to: |
| 757 |
> |
// rotate the Rotation matrix acording to: |
| 758 |
|
// A[][] = A[][] * transpose(rot[][]) |
| 759 |
|
|
| 760 |
|
|
| 783 |
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
| 784 |
|
return tStats->getTotalE(); |
| 785 |
|
} |
| 786 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
| 787 |
+ |
//By default, return a null string |
| 788 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
| 789 |
+ |
//return a pointer point to local variable which might cause problem |
| 790 |
+ |
return string(); |
| 791 |
+ |
} |
