# | Line 354 | Line 354 | void SimSetup::createSim( void ){ | |
---|---|---|
354 | // set the arrays into the SimInfo object | |
355 | ||
356 | simnfo->atoms = the_atoms; | |
357 | + | simnfo->molecules = the_molecules; |
358 | simnfo->nGlobalExcludes = 0; | |
359 | simnfo->excludes = the_excludes; | |
360 | ||
# | Line 695 | Line 696 | void SimSetup::makeMolecules( void ){ | |
696 | BondStamp* currentBond; | |
697 | BendStamp* currentBend; | |
698 | TorsionStamp* currentTorsion; | |
699 | + | |
700 | + | bond_pair* theBonds; |
701 | + | bend_set* theBends; |
702 | + | torsion_set* theTorsions; |
703 | + | |
704 | ||
705 | //init the forceField paramters | |
706 | ||
707 | the_ff->readParams(); | |
708 | ||
709 | ||
710 | < | // init the molecules |
710 | > | // init the atoms |
711 | ||
712 | + | double ux, uy, uz, u, uSqr; |
713 | + | |
714 | atomOffset = 0; | |
715 | excludeOffset = 0; | |
716 | for(i=0; i<simnfo->n_mol; i++){ | |
# | Line 719 | Line 727 | void SimSetup::makeMolecules( void ){ | |
727 | info.myExcludes = &the_excludes[excludeOffset]; | |
728 | info.myBonds = new Bond*[info.nBonds]; | |
729 | info.myBends = new Bend*[info.nBends]; | |
730 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
730 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
731 | ||
732 | theBonds = new bond_pair[info.nBonds]; | |
733 | theBends = new bend_set[info.nBends]; | |
# | Line 729 | Line 737 | void SimSetup::makeMolecules( void ){ | |
737 | ||
738 | for(j=0; j<info.nAtoms; j++){ | |
739 | ||
740 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
740 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
741 | if( currentAtom->haveOrientation() ){ | |
742 | ||
743 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 802 | Line 810 | void SimSetup::makeMolecules( void ){ | |
810 | ||
811 | if( currentBend->haveExtras() ){ | |
812 | ||
813 | < | extras = current_bend->getExtras(); |
813 | > | extras = currentBend->getExtras(); |
814 | current_extra = extras; | |
815 | ||
816 | while( current_extra != NULL ){ | |
# | Line 919 | Line 927 | void SimSetup::makeMolecules( void ){ | |
927 | ||
928 | the_molecules[i].initialize( info ); | |
929 | atomOffset += info.nAtoms; | |
930 | + | delete[] theBonds; |
931 | + | delete[] theBends; |
932 | + | delete[] theTorsions; |
933 | } | |
934 | ||
935 | // clean up the forcefield |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |