| 265 |
|
} |
| 266 |
|
} |
| 267 |
|
myStatus = -1; |
| 268 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 268 |
> |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
| 269 |
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 270 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 271 |
|
} |
| 327 |
|
double pos[3]; // position place holders |
| 328 |
|
double vel[3]; // velocity placeholders |
| 329 |
|
double q[4]; // the quaternions |
| 330 |
< |
double jx, jy, jz; // angular velocity placeholders; |
| 330 |
> |
double ji[3]; // angular velocity placeholders; |
| 331 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 332 |
|
|
| 333 |
|
Atom **atoms = simnfo->atoms; |
| 490 |
|
c_in_name, n_atoms, atomIndex ); |
| 491 |
|
return strdup( painCave.errMsg ); |
| 492 |
|
} |
| 493 |
< |
jx = atof( foo ); |
| 493 |
> |
ji[0] = atof( foo ); |
| 494 |
|
|
| 495 |
|
foo = strtok(NULL, " ,;\t"); |
| 496 |
|
if(foo == NULL){ |
| 500 |
|
c_in_name, n_atoms, atomIndex ); |
| 501 |
|
return strdup( painCave.errMsg ); |
| 502 |
|
} |
| 503 |
< |
jy = atof(foo ); |
| 503 |
> |
ji[1] = atof(foo ); |
| 504 |
|
|
| 505 |
|
foo = strtok(NULL, " ,;\t"); |
| 506 |
|
if(foo == NULL){ |
| 510 |
|
c_in_name, n_atoms, atomIndex ); |
| 511 |
|
return strdup( painCave.errMsg ); |
| 512 |
|
} |
| 513 |
< |
jz = atof( foo ); |
| 513 |
> |
ji[2] = atof( foo ); |
| 514 |
|
|
| 515 |
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
| 516 |
|
|
| 528 |
|
|
| 529 |
|
// add the angular velocities |
| 530 |
|
|
| 531 |
< |
dAtom->setJx( jx ); |
| 532 |
< |
dAtom->setJy( jy ); |
| 533 |
< |
dAtom->setJz( jz ); |
| 531 |
> |
dAtom->setJ( ji ); |
| 532 |
|
} |
| 533 |
|
|
| 534 |
|
// add the positions and velocities to the atom |
| 585 |
|
entry_plug->setBoxM( theBoxMat3 ); |
| 586 |
|
|
| 587 |
|
//get chi and integralOfChidt, they should appear by pair |
| 590 |
– |
foo = strtok(NULL, " ,;\t\n"); |
| 591 |
– |
if(foo != NULL){ |
| 592 |
– |
chi = atof(foo); |
| 588 |
|
|
| 589 |
+ |
if( entry_plug->useInitXSstate ){ |
| 590 |
|
foo = strtok(NULL, " ,;\t\n"); |
| 591 |
< |
if(foo == NULL){ |
| 592 |
< |
sprintf( painCave.errMsg, |
| 593 |
< |
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
| 594 |
< |
return strdup( painCave.errMsg ); |
| 591 |
> |
if(foo != NULL){ |
| 592 |
> |
chi = atof(foo); |
| 593 |
> |
|
| 594 |
> |
foo = strtok(NULL, " ,;\t\n"); |
| 595 |
> |
if(foo == NULL){ |
| 596 |
> |
sprintf( painCave.errMsg, |
| 597 |
> |
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
| 598 |
> |
return strdup( painCave.errMsg ); |
| 599 |
> |
} |
| 600 |
> |
integralOfChidt = atof( foo ); |
| 601 |
> |
|
| 602 |
> |
//push chi and integralOfChidt into SimInfo::properties which can be |
| 603 |
> |
//retrieved by integrator later |
| 604 |
> |
DoubleData* chiValue = new DoubleData(); |
| 605 |
> |
chiValue->setID(CHIVALUE_ID); |
| 606 |
> |
chiValue->setData(chi); |
| 607 |
> |
entry_plug->addProperty(chiValue); |
| 608 |
> |
|
| 609 |
> |
DoubleData* integralOfChidtValue = new DoubleData(); |
| 610 |
> |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
| 611 |
> |
integralOfChidtValue->setData(integralOfChidt); |
| 612 |
> |
entry_plug->addProperty(integralOfChidtValue); |
| 613 |
> |
|
| 614 |
|
} |
| 615 |
< |
integralOfChidt = atof( foo ); |
| 616 |
< |
|
| 617 |
< |
//push chi and integralOfChidt into SimInfo::properties which can be |
| 615 |
> |
else |
| 616 |
> |
return NULL; |
| 617 |
> |
|
| 618 |
> |
//get eta |
| 619 |
> |
foo = strtok(NULL, " ,;\t\n"); |
| 620 |
> |
if(foo != NULL ){ |
| 621 |
> |
|
| 622 |
> |
for(int i = 0 ; i < 9; i++){ |
| 623 |
> |
|
| 624 |
> |
if(foo == NULL){ |
| 625 |
> |
sprintf( painCave.errMsg, |
| 626 |
> |
"error in reading eta[%d] from %s\n", i, c_in_name ); |
| 627 |
> |
return strdup( painCave.errMsg ); |
| 628 |
> |
} |
| 629 |
> |
eta[i] = atof( foo ); |
| 630 |
> |
foo = strtok(NULL, " ,;\t\n"); |
| 631 |
> |
} |
| 632 |
> |
} |
| 633 |
> |
else |
| 634 |
> |
return NULL; |
| 635 |
> |
|
| 636 |
> |
//push eta into SimInfo::properties which can be |
| 637 |
|
//retrieved by integrator later |
| 638 |
< |
DoubleData* chiValue = new DoubleData(); |
| 639 |
< |
chiValue->setID(CHIVALUE_ID); |
| 640 |
< |
chiValue->setData(chi); |
| 641 |
< |
entry_plug->addProperty(chiValue); |
| 642 |
< |
|
| 609 |
< |
DoubleData* integralOfChidtValue = new DoubleData(); |
| 610 |
< |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
| 611 |
< |
integralOfChidtValue->setData(integralOfChidt); |
| 612 |
< |
entry_plug->addProperty(integralOfChidtValue); |
| 613 |
< |
|
| 638 |
> |
//entry_plug->setBoxM( theBoxMat3 ); |
| 639 |
> |
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 640 |
> |
etaValue->setID(ETAVALUE_ID); |
| 641 |
> |
etaValue->setData(eta, 9); |
| 642 |
> |
entry_plug->addProperty(etaValue); |
| 643 |
|
} |
| 615 |
– |
else |
| 616 |
– |
return NULL; |
| 644 |
|
|
| 618 |
– |
//get eta |
| 619 |
– |
for(int i = 0 ; i < 9; i++){ |
| 620 |
– |
foo = strtok(NULL, " ,;\t"); |
| 621 |
– |
if(foo == NULL){ |
| 622 |
– |
sprintf( painCave.errMsg, |
| 623 |
– |
"error in reading eta[%d] from %s\n", i, c_in_name ); |
| 624 |
– |
return strdup( painCave.errMsg ); |
| 625 |
– |
} |
| 626 |
– |
eta[i] = atof( foo ); |
| 627 |
– |
} |
| 628 |
– |
|
| 629 |
– |
//push eta into SimInfo::properties which can be |
| 630 |
– |
//retrieved by integrator later |
| 631 |
– |
//entry_plug->setBoxM( theBoxMat3 ); |
| 632 |
– |
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 633 |
– |
etaValue->setID(ETAVALUE_ID); |
| 634 |
– |
etaValue->setData(eta, 9); |
| 635 |
– |
entry_plug->addProperty(etaValue); |
| 636 |
– |
|
| 637 |
– |
|
| 645 |
|
return NULL; |
| 646 |
|
} |
| 647 |
|
|
