# | Line 88 | Line 88 | void SimSetup::createSim( void ){ | |
---|---|---|
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, | |
# | Line 337 | Line 335 | void SimSetup::createSim( void ){ | |
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 | } | |
# | Line 356 | Line 358 | void SimSetup::createSim( void ){ | |
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 | ||
# | Line 654 | Line 657 | void SimSetup::createSim( void ){ | |
657 | ||
658 | // new AllLong( simnfo ); | |
659 | ||
657 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
658 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
660 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); | |
661 | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); | |
662 | ||
# | Line 699 | Line 700 | void SimSetup::makeMolecules( void ){ | |
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++){ | |
# | Line 723 | Line 731 | void SimSetup::makeMolecules( void ){ | |
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]; | |
# | Line 733 | Line 741 | void SimSetup::makeMolecules( void ){ | |
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); | |
# | Line 806 | Line 814 | void SimSetup::makeMolecules( void ){ | |
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 ){ | |
# | Line 923 | Line 931 | void SimSetup::makeMolecules( void ){ | |
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 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |