| 335 |
|
|
| 336 |
|
|
| 337 |
|
if( simnfo->n_SRI ){ |
| 338 |
+ |
|
| 339 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
| 340 |
+ |
|
| 341 |
|
Exclude::createArray(simnfo->n_SRI); |
| 342 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 343 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 344 |
|
simnfo->globalExcludes = new int; |
| 345 |
|
simnfo->n_exclude = tot_SRI; |
| 346 |
|
} |
| 358 |
|
// set the arrays into the SimInfo object |
| 359 |
|
|
| 360 |
|
simnfo->atoms = the_atoms; |
| 361 |
+ |
simnfo->molecules = the_molecules; |
| 362 |
|
simnfo->nGlobalExcludes = 0; |
| 363 |
|
simnfo->excludes = the_excludes; |
| 364 |
|
|
| 700 |
|
BondStamp* currentBond; |
| 701 |
|
BendStamp* currentBend; |
| 702 |
|
TorsionStamp* currentTorsion; |
| 703 |
+ |
|
| 704 |
+ |
bond_pair* theBonds; |
| 705 |
+ |
bend_set* theBends; |
| 706 |
+ |
torsion_set* theTorsions; |
| 707 |
+ |
|
| 708 |
|
|
| 709 |
|
//init the forceField paramters |
| 710 |
|
|
| 711 |
|
the_ff->readParams(); |
| 712 |
|
|
| 713 |
|
|
| 714 |
< |
// init the molecules |
| 714 |
> |
// init the atoms |
| 715 |
|
|
| 716 |
+ |
double ux, uy, uz, u, uSqr; |
| 717 |
+ |
|
| 718 |
|
atomOffset = 0; |
| 719 |
|
excludeOffset = 0; |
| 720 |
|
for(i=0; i<simnfo->n_mol; i++){ |
| 731 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
| 732 |
|
info.myBonds = new Bond*[info.nBonds]; |
| 733 |
|
info.myBends = new Bend*[info.nBends]; |
| 734 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
| 734 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 735 |
|
|
| 736 |
|
theBonds = new bond_pair[info.nBonds]; |
| 737 |
|
theBends = new bend_set[info.nBends]; |
| 741 |
|
|
| 742 |
|
for(j=0; j<info.nAtoms; j++){ |
| 743 |
|
|
| 744 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
| 744 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 745 |
|
if( currentAtom->haveOrientation() ){ |
| 746 |
|
|
| 747 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
| 814 |
|
|
| 815 |
|
if( currentBend->haveExtras() ){ |
| 816 |
|
|
| 817 |
< |
extras = current_bend->getExtras(); |
| 817 |
> |
extras = currentBend->getExtras(); |
| 818 |
|
current_extra = extras; |
| 819 |
|
|
| 820 |
|
while( current_extra != NULL ){ |
| 931 |
|
|
| 932 |
|
the_molecules[i].initialize( info ); |
| 933 |
|
atomOffset += info.nAtoms; |
| 934 |
+ |
delete[] theBonds; |
| 935 |
+ |
delete[] theBends; |
| 936 |
+ |
delete[] theTorsions; |
| 937 |
|
} |
| 938 |
|
|
| 939 |
|
// clean up the forcefield |
