| 670 |
|
MPIcheckPoint(); |
| 671 |
|
#endif // is_mpi |
| 672 |
|
} |
| 673 |
+ |
|
| 674 |
+ |
|
| 675 |
+ |
void SimSetup::makeMolecules( void ){ |
| 676 |
+ |
|
| 677 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
| 678 |
+ |
molInit info; |
| 679 |
+ |
DirectionalAtom* dAtom; |
| 680 |
+ |
AtomStamp* currentAtom; |
| 681 |
+ |
BondStamp* currentBond; |
| 682 |
+ |
BendStamp* currentBend; |
| 683 |
+ |
TorsionStamp* currentTorsion; |
| 684 |
+ |
|
| 685 |
+ |
//init the forceField paramters |
| 686 |
+ |
|
| 687 |
+ |
the_ff->readParams(); |
| 688 |
+ |
|
| 689 |
+ |
|
| 690 |
+ |
// init the molecules |
| 691 |
+ |
|
| 692 |
+ |
atomOffset = 0; |
| 693 |
+ |
for(i=0; i<simnfo->n_mol; i++){ |
| 694 |
+ |
|
| 695 |
+ |
stampID = the_molecules[i].getStampID(); |
| 696 |
+ |
|
| 697 |
+ |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 698 |
+ |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 699 |
+ |
info.nBends = comp_stamps[stampID]->getNBends(); |
| 700 |
+ |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 701 |
+ |
|
| 702 |
+ |
info.myAtoms = &the_atoms[atomOffset]; |
| 703 |
+ |
info.myBonds = new Bond*[info.nBonds]; |
| 704 |
+ |
info.myBends = new Bend*[info.nBends]; |
| 705 |
+ |
info.myTorsions = new Torsions*[info.nTorsions]; |
| 706 |
+ |
|
| 707 |
+ |
theBonds = new bond_pair[info.nBonds]; |
| 708 |
+ |
theBends = new bend_set[info.nBends]; |
| 709 |
+ |
theTorsions = new torsion_set[info.nTorsions]; |
| 710 |
+ |
|
| 711 |
+ |
// make the Atoms |
| 712 |
+ |
|
| 713 |
+ |
for(j=0; j<info.nAtoms; j++){ |
| 714 |
+ |
|
| 715 |
+ |
currentAtom = theComponents[stampID]->getAtom( j ); |
| 716 |
+ |
if( currentAtom->haveOrientation() ){ |
| 717 |
+ |
|
| 718 |
+ |
dAtom = new DirectionalAtom(j + atomOffset); |
| 719 |
+ |
simnfo->n_oriented++; |
| 720 |
+ |
info.myAtoms[j] = dAtom; |
| 721 |
+ |
|
| 722 |
+ |
ux = currentAtom->getOrntX(); |
| 723 |
+ |
uy = currentAtom->getOrntY(); |
| 724 |
+ |
uz = currentAtom->getOrntZ(); |
| 725 |
+ |
|
| 726 |
+ |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 727 |
+ |
|
| 728 |
+ |
u = sqrt( uSqr ); |
| 729 |
+ |
ux = ux / u; |
| 730 |
+ |
uy = uy / u; |
| 731 |
+ |
uz = uz / u; |
| 732 |
+ |
|
| 733 |
+ |
dAtom->setSUx( ux ); |
| 734 |
+ |
dAtom->setSUy( uy ); |
| 735 |
+ |
dAtom->setSUz( uz ); |
| 736 |
+ |
} |
| 737 |
+ |
else{ |
| 738 |
+ |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 739 |
+ |
} |
| 740 |
+ |
info.myAtoms[j]->setType( currentAtom->getType() ); |
| 741 |
+ |
|
| 742 |
+ |
#ifdef IS_MPI |
| 743 |
+ |
|
| 744 |
+ |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 745 |
+ |
|
| 746 |
+ |
#endif // is_mpi |
| 747 |
+ |
} |
| 748 |
+ |
|
| 749 |
+ |
// make the bonds |
| 750 |
+ |
for(j=0; j<nBonds; j++){ |
| 751 |
+ |
|
| 752 |
+ |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 753 |
+ |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 754 |
+ |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 755 |
+ |
|
| 756 |
+ |
exI = theBonds[i].a; |
| 757 |
+ |
exJ = theBonds[i].b; |
| 758 |
+ |
|
| 759 |
+ |
// exclude_I must always be the smaller of the pair |
| 760 |
+ |
if( exI > exJ ){ |
| 761 |
+ |
tempEx = exI; |
| 762 |
+ |
exI = exJ; |
| 763 |
+ |
exJ = tempEx; |
| 764 |
+ |
} |
| 765 |
+ |
#ifdef IS_MPI |
| 766 |
+ |
|
| 767 |
+ |
the_excludes[index*2] = |
| 768 |
+ |
the_atoms[exI]->getGlobalIndex() + 1; |
| 769 |
+ |
the_excludes[index*2 + 1] = |
| 770 |
+ |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 771 |
+ |
|
| 772 |
+ |
#else // isn't MPI |
| 773 |
+ |
|
| 774 |
+ |
the_excludes[index*2] = exI + 1; |
| 775 |
+ |
the_excludes[index*2 + 1] = exJ + 1; |
| 776 |
+ |
// fortran index from 1 (hence the +1 in the indexing) |
| 777 |
|
|
| 778 |
+ |
#endif //is_mpi |
| 779 |
+ |
|
| 780 |
+ |
} |
| 781 |
+ |
|
| 782 |
+ |
|
| 783 |
+ |
|
| 784 |
+ |
|
| 785 |
+ |
|
| 786 |
+ |
|
| 787 |
+ |
|
| 788 |
+ |
|
| 789 |
+ |
|
| 790 |
+ |
|
| 791 |
+ |
|
| 792 |
+ |
|
| 793 |
+ |
|
| 794 |
+ |
|
| 795 |
+ |
|
| 796 |
|
void SimSetup::makeAtoms( void ){ |
| 797 |
|
|
| 798 |
|
int i, j, k, index; |
