\section{GRAPE:  Generalizable Replaceable Atomic Position Engine File List}
Here is a list of all files with brief descriptions:\begin{CompactList}
\item\contentsline{section}{{\bf abbrev.h} }{\pageref{abbrev_h}}{}
\item\contentsline{section}{{\bf abitset.C} }{\pageref{abitset_C}}{}
\item\contentsline{section}{{\bf abitset.h} }{\pageref{abitset_h}}{}
\item\contentsline{section}{{\bf ajiobin.h} }{\pageref{ajiobin_h}}{}
\item\contentsline{section}{{\bf amatrix.h} }{\pageref{amatrix_h}}{}
\item\contentsline{section}{{\bf amatrix.inc} }{\pageref{amatrix_inc}}{}
\item\contentsline{section}{{\bf atom.h} }{\pageref{atom_h}}{}
\item\contentsline{section}{{\bf atom\_\-buildup.C} }{\pageref{atom_buildup_C}}{}
\item\contentsline{section}{{\bf atom\_\-buildup.h} }{\pageref{atom_buildup_h}}{}
\item\contentsline{section}{{\bf atom\_\-constraint.C} }{\pageref{atom_constraint_C}}{}
\item\contentsline{section}{{\bf atom\_\-constraint.h} }{\pageref{atom_constraint_h}}{}
\item\contentsline{section}{{\bf atom\_\-registry.C} }{\pageref{atom_registry_C}}{}
\item\contentsline{section}{{\bf atom\_\-registry.h} }{\pageref{atom_registry_h}}{}
\item\contentsline{section}{{\bf bin\_\-envelope\_\-constraint.C} }{\pageref{bin_envelope_constraint_C}}{}
\item\contentsline{section}{{\bf bin\_\-envelope\_\-constraint.h} }{\pageref{bin_envelope_constraint_h}}{}
\item\contentsline{section}{{\bf bits.h} }{\pageref{bits_h}}{}
\item\contentsline{section}{{\bf compoper.h} }{\pageref{compoper_h}}{}
\item\contentsline{section}{{\bf constraint.C} }{\pageref{constraint_C}}{}
\item\contentsline{section}{{\bf constraint.h} }{\pageref{constraint_h}}{}
\item\contentsline{section}{{\bf constraint\_\-manager.C} }{\pageref{constraint_manager_C}}{}
\item\contentsline{section}{{\bf constraint\_\-manager.h} }{\pageref{constraint_manager_h}}{}
\item\contentsline{section}{{\bf constraint\_\-registry.C} }{\pageref{constraint_registry_C}}{}
\item\contentsline{section}{{\bf constraint\_\-registry.h} }{\pageref{constraint_registry_h}}{}
\item\contentsline{section}{{\bf cycle\_\-all.C} }{\pageref{cycle_all_C}}{}
\item\contentsline{section}{{\bf cycle\_\-all.h} }{\pageref{cycle_all_h}}{}
\item\contentsline{section}{{\bf ddgraph.h} }{\pageref{ddgraph_h}}{}
\item\contentsline{section}{{\bf ddgraph.inc} }{\pageref{ddgraph_inc}}{}
\item\contentsline{section}{{\bf ddvertex.h} }{\pageref{ddvertex_h}}{}
\item\contentsline{section}{{\bf ddvertex.inc} }{\pageref{ddvertex_inc}}{}
\item\contentsline{section}{{\bf dens-trans.C} }{\pageref{dens-trans_C}}{}
\item\contentsline{section}{{\bf dist.C} }{\pageref{dist_C}}{}
\item\contentsline{section}{{\bf distance\_\-constraint.C} }{\pageref{distance_constraint_C}}{}
\item\contentsline{section}{{\bf distance\_\-constraint.h} }{\pageref{distance_constraint_h}}{}
\item\contentsline{section}{{\bf dllist.h} }{\pageref{dllist_h}}{}
\item\contentsline{section}{{\bf dllist.inc} }{\pageref{dllist_inc}}{}
\item\contentsline{section}{{\bf dlliter.inc} }{\pageref{dlliter_inc}}{}
\item\contentsline{section}{{\bf dsiter.inc} }{\pageref{dsiter_inc}}{}
\item\contentsline{section}{{\bf dynstring.C} }{\pageref{dynstring_C}}{}
\item\contentsline{section}{{\bf dynstring.h} }{\pageref{dynstring_h}}{}
\item\contentsline{section}{{\bf env\_\-diff.C} }{\pageref{env_diff_C}}{}
\item\contentsline{section}{{\bf envelope.C} }{\pageref{envelope_C}}{}
\item\contentsline{section}{{\bf envelope.h} }{\pageref{envelope_h}}{}
\item\contentsline{section}{{\bf envelope\_\-constraint.C} }{\pageref{envelope_constraint_C}}{}
\item\contentsline{section}{{\bf envelope\_\-constraint.h} }{\pageref{envelope_constraint_h}}{}
\item\contentsline{section}{{\bf err\_\-eval.C} }{\pageref{err_eval_C}}{}
\item\contentsline{section}{{\bf error\_\-handler.h} }{\pageref{error_handler_h}}{}
\item\contentsline{section}{{\bf globals.C} }{\pageref{globals_C}}{}
\item\contentsline{section}{{\bf globals.h} }{\pageref{globals_h}}{}
\item\contentsline{section}{{\bf grape.C} }{\pageref{grape_C}}{}
\item\contentsline{section}{{\bf graph\_\-weights.h} }{\pageref{graph_weights_h}}{}
\item\contentsline{section}{{\bf grid.C} }{\pageref{grid_C}}{}
\item\contentsline{section}{{\bf grid.h} }{\pageref{grid_h}}{}
\item\contentsline{section}{{\bf gw\_\-numerics.C} }{\pageref{gw_numerics_C}}{}
\item\contentsline{section}{{\bf gw\_\-numerics.h} }{\pageref{gw_numerics_h}}{}
\item\contentsline{section}{{\bf gw\_\-relax\_\-atom.C} }{\pageref{gw_relax_atom_C}}{}
\item\contentsline{section}{{\bf gw\_\-relax\_\-atom.h} }{\pageref{gw_relax_atom_h}}{}
\item\contentsline{section}{{\bf idgen.h} }{\pageref{idgen_h}}{}
\item\contentsline{section}{{\bf intvec.C} }{\pageref{intvec_C}}{}
\item\contentsline{section}{{\bf intvec.h} }{\pageref{intvec_h}}{}
\item\contentsline{section}{{\bf intvec.inc} }{\pageref{intvec_inc}}{}
\item\contentsline{section}{{\bf ipqueue.h} }{\pageref{ipqueue_h}}{}
\item\contentsline{section}{{\bf ipqueue.inc} }{\pageref{ipqueue_inc}}{}
\item\contentsline{section}{{\bf jd\_\-anim\_\-frame.C} }{\pageref{jd_anim_frame_C}}{}
\item\contentsline{section}{{\bf jd\_\-anim\_\-frame.h} }{\pageref{jd_anim_frame_h}}{}
\item\contentsline{section}{{\bf jd\_\-err\_\-eval.C} }{\pageref{jd_err_eval_C}}{}
\item\contentsline{section}{{\bf jd\_\-err\_\-eval.h} }{\pageref{jd_err_eval_h}}{}
\item\contentsline{section}{{\bf jd\_\-iterator.C} }{\pageref{jd_iterator_C}}{}
\item\contentsline{section}{{\bf jd\_\-iterator.h} }{\pageref{jd_iterator_h}}{}
\item\contentsline{section}{{\bf jd\_\-occ\_\-count.C} }{\pageref{jd_occ_count_C}}{}
\item\contentsline{section}{{\bf jd\_\-occ\_\-count.h} }{\pageref{jd_occ_count_h}}{}
\item\contentsline{section}{{\bf jd\_\-rand\_\-eval.C} }{\pageref{jd_rand_eval_C}}{}
\item\contentsline{section}{{\bf jd\_\-rand\_\-eval.h} }{\pageref{jd_rand_eval_h}}{}
\item\contentsline{section}{{\bf jd\_\-relax\_\-subset.C} }{\pageref{jd_relax_subset_C}}{}
\item\contentsline{section}{{\bf jd\_\-relax\_\-subset.h} }{\pageref{jd_relax_subset_h}}{}
\item\contentsline{section}{{\bf jd\_\-stop\_\-eval.C} }{\pageref{jd_stop_eval_C}}{}
\item\contentsline{section}{{\bf jd\_\-stop\_\-eval.h} }{\pageref{jd_stop_eval_h}}{}
\item\contentsline{section}{{\bf jsmisc.h} }{\pageref{jsmisc_h}}{}
\item\contentsline{section}{{\bf jvector.C} }{\pageref{jvector_C}}{}
\item\contentsline{section}{{\bf jvector.h} }{\pageref{jvector_h}}{}
\item\contentsline{section}{{\bf kadjmat.h} }{\pageref{kadjmat_h}}{}
\item\contentsline{section}{{\bf Leak\-Tracer/Makefile} }{\pageref{LeakTracer_Makefile}}{}
\item\contentsline{section}{{\bf lib/Makefile} }{\pageref{lib_Makefile}}{}
\item\contentsline{section}{{\bf Makefile} }{\pageref{Makefile}}{}
\item\contentsline{section}{{\bf src/aux/Makefile} }{\pageref{src_aux_Makefile}}{}
\item\contentsline{section}{{\bf src/Makefile} }{\pageref{src_Makefile}}{}
\item\contentsline{section}{{\bf matrix.C} }{\pageref{matrix_C}}{}
\item\contentsline{section}{{\bf matrix.h} }{\pageref{matrix_h}}{}
\item\contentsline{section}{{\bf molecule.C} }{\pageref{molecule_C}}{}
\item\contentsline{section}{{\bf molecule.h} }{\pageref{molecule_h}}{}
\item\contentsline{section}{{\bf molio.C} }{\pageref{molio_C}}{}
\item\contentsline{section}{{\bf ocount.C} }{\pageref{ocount_C}}{}
\item\contentsline{section}{{\bf position\_\-constraint.C} }{\pageref{position_constraint_C}}{}
\item\contentsline{section}{{\bf position\_\-constraint.h} }{\pageref{position_constraint_h}}{}
\item\contentsline{section}{{\bf process.C} }{\pageref{process_C}}{}
\item\contentsline{section}{{\bf process.h} }{\pageref{process_h}}{}
\item\contentsline{section}{{\bf queue.h} }{\pageref{queue_h}}{}
\item\contentsline{section}{{\bf rand\_\-eval.C} }{\pageref{rand_eval_C}}{}
\item\contentsline{section}{{\bf randomgenerator.C} }{\pageref{randomgenerator_C}}{}
\item\contentsline{section}{{\bf randomgenerator.h} }{\pageref{randomgenerator_h}}{}
\item\contentsline{section}{{\bf refrep.h} }{\pageref{refrep_h}}{}
\item\contentsline{section}{{\bf residue.C} }{\pageref{residue_C}}{}
\item\contentsline{section}{{\bf residue.h} }{\pageref{residue_h}}{}
\item\contentsline{section}{{\bf residue\_\-registry.h} }{\pageref{residue_registry_h}}{}
\item\contentsline{section}{{\bf satisfy\_\-molecule.h} }{\pageref{satisfy_molecule_h}}{}
\item\contentsline{section}{{\bf sdgalg.inc} }{\pageref{sdgalg_inc}}{}
\item\contentsline{section}{{\bf sdgiter.inc} }{\pageref{sdgiter_inc}}{}
\item\contentsline{section}{{\bf sdgraph.h} }{\pageref{sdgraph_h}}{}
\item\contentsline{section}{{\bf sdgraph.inc} }{\pageref{sdgraph_inc}}{}
\item\contentsline{section}{{\bf sdvertex.h} }{\pageref{sdvertex_h}}{}
\item\contentsline{section}{{\bf sdvertex.inc} }{\pageref{sdvertex_inc}}{}
\item\contentsline{section}{{\bf search-sort.h} }{\pageref{search-sort_h}}{}
\item\contentsline{section}{{\bf segments.inc} }{\pageref{segments_inc}}{}
\item\contentsline{section}{{\bf stack.h} }{\pageref{stack_h}}{}
\item\contentsline{section}{{\bf streamoper.h} }{\pageref{streamoper_h}}{}
\item\contentsline{section}{{\bf top\_\-process.h} }{\pageref{top_process_h}}{}
\item\contentsline{section}{{\bf utils.C} }{\pageref{utils_C}}{}
\item\contentsline{section}{{\bf utils.h} }{\pageref{utils_h}}{}
\end{CompactList}
