88 |
|
|
89 |
|
|
90 |
|
|
91 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
91 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 |
|
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 |
|
else{ |
94 |
|
sprintf( painCave.errMsg, |
652 |
|
|
653 |
|
// new AllLong( simnfo ); |
654 |
|
|
657 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
658 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
655 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
656 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
657 |
|
|
695 |
|
BondStamp* currentBond; |
696 |
|
BendStamp* currentBend; |
697 |
|
TorsionStamp* currentTorsion; |
698 |
+ |
|
699 |
+ |
bond_pair* theBonds; |
700 |
+ |
bend_set* theBends; |
701 |
+ |
torsion_set* theTorsions; |
702 |
+ |
|
703 |
|
|
704 |
|
//init the forceField paramters |
705 |
|
|
706 |
|
the_ff->readParams(); |
707 |
|
|
708 |
|
|
709 |
< |
// init the molecules |
709 |
> |
// init the atoms |
710 |
|
|
711 |
+ |
double ux, uy, uz, u, uSqr; |
712 |
+ |
|
713 |
|
atomOffset = 0; |
714 |
|
excludeOffset = 0; |
715 |
|
for(i=0; i<simnfo->n_mol; i++){ |
726 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
727 |
|
info.myBonds = new Bond*[info.nBonds]; |
728 |
|
info.myBends = new Bend*[info.nBends]; |
729 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
729 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
730 |
|
|
731 |
|
theBonds = new bond_pair[info.nBonds]; |
732 |
|
theBends = new bend_set[info.nBends]; |
736 |
|
|
737 |
|
for(j=0; j<info.nAtoms; j++){ |
738 |
|
|
739 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
739 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
740 |
|
if( currentAtom->haveOrientation() ){ |
741 |
|
|
742 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
809 |
|
|
810 |
|
if( currentBend->haveExtras() ){ |
811 |
|
|
812 |
< |
extras = current_bend->getExtras(); |
812 |
> |
extras = currentBend->getExtras(); |
813 |
|
current_extra = extras; |
814 |
|
|
815 |
|
while( current_extra != NULL ){ |
926 |
|
|
927 |
|
the_molecules[i].initialize( info ); |
928 |
|
atomOffset += info.nAtoms; |
929 |
+ |
delete[] theBonds; |
930 |
+ |
delete[] theBends; |
931 |
+ |
delete[] theTorsions; |
932 |
|
} |
933 |
|
|
934 |
|
// clean up the forcefield |