| 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 |
– |
info->the_integrator = this; |
| 28 |
|
|
| 29 |
|
nAtoms = info->n_atoms; |
| 30 |
|
|
| 146 |
|
|
| 147 |
|
|
| 148 |
|
template<typename T> void Integrator<T>::integrate(void){ |
| 150 |
– |
int i, j; // loop counters |
| 149 |
|
|
| 150 |
|
double runTime = info->run_time; |
| 151 |
|
double sampleTime = info->sampleTime; |
| 158 |
|
double currThermal; |
| 159 |
|
double currStatus; |
| 160 |
|
double currReset; |
| 161 |
< |
|
| 161 |
> |
|
| 162 |
|
int calcPot, calcStress; |
| 165 |
– |
int isError; |
| 163 |
|
|
| 164 |
|
tStats = new Thermo(info); |
| 165 |
|
statOut = new StatWriter(info); |
| 166 |
|
dumpOut = new DumpWriter(info); |
| 167 |
|
|
| 168 |
|
atoms = info->atoms; |
| 172 |
– |
DirectionalAtom* dAtom; |
| 169 |
|
|
| 170 |
|
dt = info->dt; |
| 171 |
|
dt2 = 0.5 * dt; |
| 172 |
|
|
| 173 |
+ |
readyCheck(); |
| 174 |
+ |
|
| 175 |
|
// initialize the forces before the first step |
| 176 |
|
|
| 177 |
|
calcForce(1, 1); |
| 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 |
|
} |
| 197 |
|
dumpOut->writeDump(info->getTime()); |
| 198 |
|
statOut->writeStat(info->getTime()); |
| 199 |
|
|
| 202 |
– |
readyCheck(); |
| 200 |
|
|
| 201 |
+ |
|
| 202 |
|
#ifdef IS_MPI |
| 203 |
|
strcpy(checkPointMsg, "The integrator is ready to go."); |
| 204 |
|
MPIcheckPoint(); |
| 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){ |
| 246 |
|
#endif // is_mpi |
| 247 |
|
} |
| 248 |
|
|
| 249 |
< |
dumpOut->writeFinal(info->getTime()); |
| 249 |
> |
|
| 250 |
> |
// write the last frame |
| 251 |
> |
dumpOut->writeDump(info->getTime()); |
| 252 |
|
|
| 253 |
|
delete dumpOut; |
| 254 |
|
delete statOut; |
| 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); |
| 404 |
|
} |
| 405 |
|
|
| 406 |
|
template<typename T> void Integrator<T>::constrainA(){ |
| 407 |
< |
int i, j, k; |
| 407 |
> |
int i, j; |
| 408 |
|
int done; |
| 409 |
|
double posA[3], posB[3]; |
| 410 |
|
double velA[3], velB[3]; |
| 548 |
|
} |
| 549 |
|
|
| 550 |
|
template<typename T> void Integrator<T>::constrainB(void){ |
| 551 |
< |
int i, j, k; |
| 551 |
> |
int i, j; |
| 552 |
|
int done; |
| 553 |
|
double posA[3], posB[3]; |
| 554 |
|
double velA[3], velB[3]; |
| 557 |
|
int a, b, ax, ay, az, bx, by, bz; |
| 558 |
|
double rma, rmb; |
| 559 |
|
double dx, dy, dz; |
| 560 |
< |
double rabsq, pabsq, rvab; |
| 561 |
< |
double diffsq; |
| 560 |
> |
double rvab; |
| 561 |
|
double gab; |
| 562 |
|
int iteration; |
| 563 |
|
|
| 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 |
+ |
} |
