| 559 |
|
std::copy(globalMolMembership.begin(), globalMolMembership.end(), |
| 560 |
|
info->getGlobalMolMembershipPointer()); |
| 561 |
|
#endif |
| 562 |
– |
|
| 563 |
– |
} |
| 564 |
– |
|
| 565 |
– |
|
| 566 |
– |
void SimCreator::initFortran(SimInfo* info) { |
| 567 |
– |
|
| 568 |
– |
//setup fortran simulation (Actually, in parallel version it will initialze the parallel part of fortran first) |
| 569 |
– |
info->update(); |
| 562 |
|
|
| 571 |
– |
//notify fortran whether reaction field is used or not |
| 572 |
– |
//deprecated |
| 573 |
– |
int isError; |
| 574 |
– |
isError = 0; |
| 575 |
– |
initFortranFF( &useReactionField, &isError ); |
| 576 |
– |
|
| 577 |
– |
if(isError){ |
| 578 |
– |
sprintf( painCave.errMsg, |
| 579 |
– |
"SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" ); |
| 580 |
– |
painCave.isFatal = 1; |
| 581 |
– |
simError(); |
| 582 |
– |
} |
| 583 |
– |
|
| 584 |
– |
//figure out the cutoff radius and pass it to fortran |
| 585 |
– |
setCutoff(info); |
| 563 |
|
} |
| 564 |
|
|
| 588 |
– |
void SimCreator::setCutoff(SimInfo* info) { |
| 589 |
– |
Globals* globals = info->getGlobals(); |
| 590 |
– |
double rcut; //cutoff radius |
| 591 |
– |
double rsw; //switching radius |
| 592 |
– |
|
| 593 |
– |
simtype* st = info->getSimType(); |
| 594 |
– |
|
| 595 |
– |
if (st->SIM_uses_Charges | st->SIM_uses_Dipoles | st->SIM_uses_RF) { |
| 596 |
– |
|
| 597 |
– |
if (!globals->haveRcut()){ |
| 598 |
– |
sprintf(painCave.errMsg, |
| 599 |
– |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
| 600 |
– |
"\tOOPSE will use a default value of 15.0 angstroms" |
| 601 |
– |
"\tfor the cutoffRadius.\n"); |
| 602 |
– |
painCave.isFatal = 0; |
| 603 |
– |
simError(); |
| 604 |
– |
rcut = 15.0; |
| 605 |
– |
} else{ |
| 606 |
– |
rcut = globals->getRcut(); |
| 607 |
– |
} |
| 608 |
– |
|
| 609 |
– |
if (!globals->haveRsw()){ |
| 610 |
– |
sprintf(painCave.errMsg, |
| 611 |
– |
"SimCreator Warning: No value was set for switchingRadius.\n" |
| 612 |
– |
"\tOOPSE will use a default value of\n" |
| 613 |
– |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
| 614 |
– |
painCave.isFatal = 0; |
| 615 |
– |
simError(); |
| 616 |
– |
rsw = 0.95 * rcut; |
| 617 |
– |
} else{ |
| 618 |
– |
rsw = globals->getRsw(); |
| 619 |
– |
} |
| 620 |
– |
|
| 621 |
– |
} else { |
| 622 |
– |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
| 623 |
– |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 624 |
– |
|
| 625 |
– |
if (globals->haveRcut()) { |
| 626 |
– |
rcut = globals->getRcut(); |
| 627 |
– |
} else { |
| 628 |
– |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 629 |
– |
rcut = info->calcMaxCutoffRadius(); |
| 630 |
– |
} |
| 631 |
– |
|
| 632 |
– |
if (globals->haveRsw()) { |
| 633 |
– |
rsw = globals->getRsw() |
| 634 |
– |
} else { |
| 635 |
– |
rsw = rcut; |
| 636 |
– |
} |
| 637 |
– |
|
| 638 |
– |
} |
| 639 |
– |
|
| 640 |
– |
//store them into Siminfo |
| 641 |
– |
info->setRcut(rcut); |
| 642 |
– |
info->setRsw(rsw); |
| 643 |
– |
|
| 644 |
– |
double rnblist = rcut + 1; // skin of neighbor list |
| 645 |
– |
|
| 646 |
– |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 647 |
– |
notifyFortranCutoffs(&rcut, &rsw, &rnblist); |
| 648 |
– |
} |
| 649 |
– |
|
| 565 |
|
void SimCreator::loadCoordinates(SimInfo* info) { |
| 566 |
|
Globals* globals; |
| 567 |
|
globals = info->getGlobals(); |
