| 307 |
|
|
| 308 |
|
|
| 309 |
|
if( simnfo->n_SRI ){ |
| 310 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
| 311 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
| 310 |
> |
Exclude::createArray(simnfo->n_SRI); |
| 311 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 312 |
|
simnfo->globalExcludes = new int; |
| 313 |
|
simnfo->n_exclude = tot_SRI; |
| 314 |
|
} |
| 315 |
|
else{ |
| 316 |
|
|
| 317 |
< |
the_excludes = new int[2]; |
| 318 |
< |
the_excludes[0] = 0; |
| 319 |
< |
the_excludes[1] = 0; |
| 317 |
> |
Exclude::createArray( 1 ); |
| 318 |
> |
the_excludes = new Exclude*; |
| 319 |
> |
the_excludes[0] = new Exclude(0); |
| 320 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 321 |
|
simnfo->globalExcludes = new int; |
| 322 |
|
simnfo->globalExcludes[0] = 0; |
| 323 |
< |
|
| 323 |
< |
simnfo->n_exclude = 1; |
| 323 |
> |
simnfo->n_exclude = 0; |
| 324 |
|
} |
| 325 |
|
|
| 326 |
|
// set the arrays into the SimInfo object |
| 674 |
|
|
| 675 |
|
void SimSetup::makeMolecules( void ){ |
| 676 |
|
|
| 677 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
| 677 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 678 |
|
molInit info; |
| 679 |
|
DirectionalAtom* dAtom; |
| 680 |
+ |
LinkedAssign* extras; |
| 681 |
+ |
LinkedAssign* current_extra; |
| 682 |
|
AtomStamp* currentAtom; |
| 683 |
|
BondStamp* currentBond; |
| 684 |
|
BendStamp* currentBend; |
| 692 |
|
// init the molecules |
| 693 |
|
|
| 694 |
|
atomOffset = 0; |
| 695 |
+ |
excludeOffset = 0; |
| 696 |
|
for(i=0; i<simnfo->n_mol; i++){ |
| 697 |
|
|
| 698 |
|
stampID = the_molecules[i].getStampID(); |
| 701 |
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 702 |
|
info.nBends = comp_stamps[stampID]->getNBends(); |
| 703 |
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 704 |
< |
|
| 704 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 705 |
> |
|
| 706 |
|
info.myAtoms = &the_atoms[atomOffset]; |
| 707 |
+ |
info.myExcludes = &the_excludes[excludeOffset]; |
| 708 |
|
info.myBonds = new Bond*[info.nBonds]; |
| 709 |
|
info.myBends = new Bend*[info.nBends]; |
| 710 |
|
info.myTorsions = new Torsions*[info.nTorsions]; |
| 752 |
|
} |
| 753 |
|
|
| 754 |
|
// make the bonds |
| 755 |
< |
for(j=0; j<nBonds; j++){ |
| 755 |
> |
for(j=0; j<info.nBonds; j++){ |
| 756 |
|
|
| 757 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
| 758 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
| 768 |
|
exJ = tempEx; |
| 769 |
|
} |
| 770 |
|
#ifdef IS_MPI |
| 771 |
+ |
tempEx = exI; |
| 772 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 773 |
+ |
tempEx = exJ; |
| 774 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 775 |
|
|
| 776 |
< |
the_excludes[index*2] = |
| 768 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 769 |
< |
the_excludes[index*2 + 1] = |
| 770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 771 |
< |
|
| 776 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 777 |
|
#else // isn't MPI |
| 778 |
< |
|
| 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 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 779 |
|
#endif //is_mpi |
| 780 |
< |
|
| 781 |
< |
} |
| 780 |
> |
} |
| 781 |
> |
excludeOffset += info.nBonds; |
| 782 |
|
|
| 783 |
< |
|
| 784 |
< |
|
| 785 |
< |
|
| 783 |
> |
//make the bends |
| 784 |
> |
for(j=0; j<info.nBends; j++){ |
| 785 |
> |
|
| 786 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 787 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 788 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 789 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 790 |
> |
|
| 791 |
> |
if( currentBend->haveExtras() ){ |
| 792 |
> |
|
| 793 |
> |
extras = current_bend->getExtras(); |
| 794 |
> |
current_extra = extras; |
| 795 |
> |
|
| 796 |
> |
while( current_extra != NULL ){ |
| 797 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 798 |
> |
|
| 799 |
> |
switch( current_extra->getType() ){ |
| 800 |
> |
|
| 801 |
> |
case 0: |
| 802 |
> |
theBends[j].ghost = |
| 803 |
> |
current_extra->getInt() + atomOffset; |
| 804 |
> |
theBends[j].isGhost = 1; |
| 805 |
> |
break; |
| 806 |
> |
|
| 807 |
> |
case 1: |
| 808 |
> |
theBends[j].ghost = |
| 809 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 810 |
> |
theBends[j].isGhost = 1; |
| 811 |
> |
break; |
| 812 |
> |
|
| 813 |
> |
default: |
| 814 |
> |
sprintf( painCave.errMsg, |
| 815 |
> |
"SimSetup Error: ghostVectorSource was neiter a " |
| 816 |
> |
"double nor an int.\n" |
| 817 |
> |
"-->Bend[%d] in %s\n", |
| 818 |
> |
j, comp_stamps[stampID]->getID() ); |
| 819 |
> |
painCave.isFatal = 1; |
| 820 |
> |
simError(); |
| 821 |
> |
} |
| 822 |
> |
} |
| 823 |
> |
|
| 824 |
> |
else{ |
| 825 |
> |
|
| 826 |
> |
sprintf( painCave.errMsg, |
| 827 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 828 |
> |
" -->%s in Bend[%d] in %s\n", |
| 829 |
> |
current_extra->getlhs(), |
| 830 |
> |
j, comp_stamps[stampID]->getID() ); |
| 831 |
> |
painCave.isFatal = 1; |
| 832 |
> |
simError(); |
| 833 |
> |
} |
| 834 |
> |
|
| 835 |
> |
current_extra = current_extra->getNext(); |
| 836 |
> |
} |
| 837 |
> |
} |
| 838 |
> |
|
| 839 |
> |
if( !theBends[j].isGhost ){ |
| 840 |
> |
|
| 841 |
> |
exI = theBends[j].a; |
| 842 |
> |
exJ = theBends[j].c; |
| 843 |
> |
} |
| 844 |
> |
else{ |
| 845 |
> |
|
| 846 |
> |
exI = theBends[j].a; |
| 847 |
> |
exJ = theBends[j].b; |
| 848 |
> |
} |
| 849 |
> |
|
| 850 |
> |
// exclude_I must always be the smaller of the pair |
| 851 |
> |
if( exI > exJ ){ |
| 852 |
> |
tempEx = exI; |
| 853 |
> |
exI = exJ; |
| 854 |
> |
exJ = tempEx; |
| 855 |
> |
} |
| 856 |
> |
#ifdef IS_MPI |
| 857 |
> |
tempEx = exI; |
| 858 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 859 |
> |
tempEx = exJ; |
| 860 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 861 |
> |
|
| 862 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 863 |
> |
#else // isn't MPI |
| 864 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 865 |
> |
#endif //is_mpi |
| 866 |
> |
} |
| 867 |
> |
excludeOffset += info.nBends; |
| 868 |
|
|
| 869 |
+ |
for(j=0; j<info.nTorsions; j++){ |
| 870 |
+ |
|
| 871 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 872 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 873 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 874 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 875 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 876 |
+ |
|
| 877 |
+ |
exI = theTorsions[j].a; |
| 878 |
+ |
exJ = theTorsions[j].d; |
| 879 |
|
|
| 880 |
+ |
// exclude_I must always be the smaller of the pair |
| 881 |
+ |
if( exI > exJ ){ |
| 882 |
+ |
tempEx = exI; |
| 883 |
+ |
exI = exJ; |
| 884 |
+ |
exJ = tempEx; |
| 885 |
+ |
} |
| 886 |
+ |
#ifdef IS_MPI |
| 887 |
+ |
tempEx = exI; |
| 888 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 889 |
+ |
tempEx = exJ; |
| 890 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 891 |
+ |
|
| 892 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 893 |
+ |
#else // isn't MPI |
| 894 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 895 |
+ |
#endif //is_mpi |
| 896 |
+ |
} |
| 897 |
+ |
excludeOffset += info.nTorsions; |
| 898 |
|
|
| 899 |
+ |
|
| 900 |
+ |
// send the arrays off to the forceField for init. |
| 901 |
|
|
| 902 |
+ |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 903 |
+ |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 904 |
+ |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 905 |
+ |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 906 |
|
|
| 907 |
|
|
| 908 |
+ |
the_molecules[i].initialize( info ); |
| 909 |
+ |
atomOffset += info.nAtoms; |
| 910 |
+ |
} |
| 911 |
|
|
| 912 |
+ |
// clean up the forcefield |
| 913 |
|
|
| 914 |
+ |
the_ff->cleanMe(); |
| 915 |
+ |
} |
| 916 |
|
|
| 917 |
|
|
| 918 |
|
|
