1 |
|
#include <iostream> |
2 |
< |
#include <cstdlib> |
3 |
< |
#include <cmath> |
2 |
> |
#include <stdlib.h> |
3 |
> |
#include <math.h> |
4 |
|
|
5 |
|
#ifdef IS_MPI |
6 |
|
#include "mpiSimulation.hpp" |
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); |
179 |
|
if (nConstrained){ |
180 |
|
preMove(); |
181 |
|
constrainA(); |
182 |
< |
calcForce(1, 1); |
182 |
> |
calcForce(1, 1); |
183 |
|
constrainB(); |
184 |
|
} |
185 |
< |
|
185 |
> |
|
186 |
|
if (info->setTemp){ |
187 |
|
thermalize(); |
188 |
|
} |
227 |
|
} |
228 |
|
|
229 |
|
if (info->getTime() >= currStatus){ |
230 |
< |
statOut->writeStat(info->getTime()); |
231 |
< |
calcPot = 0; |
230 |
> |
statOut->writeStat(info->getTime()); |
231 |
> |
calcPot = 0; |
232 |
|
calcStress = 0; |
233 |
|
currStatus += statusTime; |
234 |
< |
} |
234 |
> |
} |
235 |
|
|
236 |
|
if (info->resetIntegrator){ |
237 |
|
if (info->getTime() >= currReset){ |
366 |
|
if (atoms[i]->isDirectional()){ |
367 |
|
dAtom = (DirectionalAtom *) atoms[i]; |
368 |
|
|
369 |
< |
// get and convert the torque to body frame |
369 |
> |
// get and convert the torque to body frame |
370 |
|
|
371 |
|
dAtom->getTrq(Tb); |
372 |
|
dAtom->lab2Body(Tb); |
658 |
|
|
659 |
|
dAtom->getA(A); |
660 |
|
dAtom->getI(I); |
661 |
< |
|
662 |
< |
// rotate about the x-axis |
661 |
> |
|
662 |
> |
// rotate about the x-axis |
663 |
|
angle = dt2 * ji[0] / I[0][0]; |
664 |
< |
this->rotate( 1, 2, angle, ji, A ); |
665 |
< |
|
664 |
> |
this->rotate( 1, 2, angle, ji, A ); |
665 |
> |
|
666 |
|
// rotate about the y-axis |
667 |
|
angle = dt2 * ji[1] / I[1][1]; |
668 |
|
this->rotate( 2, 0, angle, ji, A ); |
669 |
< |
|
669 |
> |
|
670 |
|
// rotate about the z-axis |
671 |
|
angle = dt * ji[2] / I[2][2]; |
672 |
|
this->rotate( 0, 1, angle, ji, A); |
673 |
< |
|
673 |
> |
|
674 |
|
// rotate about the y-axis |
675 |
|
angle = dt2 * ji[1] / I[1][1]; |
676 |
|
this->rotate( 2, 0, angle, ji, A ); |
677 |
< |
|
677 |
> |
|
678 |
|
// rotate about the x-axis |
679 |
|
angle = dt2 * ji[0] / I[0][0]; |
680 |
|
this->rotate( 1, 2, angle, ji, A ); |
681 |
< |
|
682 |
< |
dAtom->setA( A ); |
681 |
> |
|
682 |
> |
dAtom->setA( A ); |
683 |
|
} |
684 |
|
|
685 |
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
747 |
|
} |
748 |
|
} |
749 |
|
|
750 |
< |
// rotate the Rotation matrix acording to: |
750 |
> |
// rotate the Rotation matrix acording to: |
751 |
|
// A[][] = A[][] * transpose(rot[][]) |
752 |
|
|
753 |
|
|
776 |
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
777 |
|
return tStats->getTotalE(); |
778 |
|
} |
779 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
780 |
+ |
//By default, return a null string |
781 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
782 |
+ |
//return a pointer point to local variable which might cause problem |
783 |
+ |
return string(); |
784 |
+ |
} |