Auxiliary Input Files
---------------------

XYZ Geometry Files
~~~~~~~~~~~~~~~~~~

In most cases, when the user wishes to perform calculations for a species and transition state for which no conformer exists, they can execute the `init_geom` and `find_ts` task, respectively, to seed the system via some guess method. (species generated from an InChI string via RDKit/OpenBabel, TS by our search methods).

There are certain problematic cases however, where the user must generate this information by hand. For these cases, we have implemented a procedure to have these conformer initialization tasks to use a geometry generated by hand. These hand-generated geometries can be given provided in a standard .xyz file.

There are no requirements for the name of the file, other than that the file must include
the .xyz extenstion. What is important is what is placed into the second line 
(usually reserved for comments)::

    <number of atoms>
    <name of species in species.csv file>
    <xyz coordinates>

Note that the second line requires the mechanism name of the species or transition state
that the geometry is associated with. As with other files, for a species, the name
should match the corresponding one from the .csv file. For transition states, use
the transition state name nomenclature scheme explained in <link>. These are examples:

Species Example (assuming C2H6 species defined in .csv)::
    
    6
    C2H6
    geom

Transition State Example (assuming C2H6+H H-abstraction TS on PES 1, SUBPES 1)::

    7
    ts_1_1_0
    geom


Active-Space Template Files
~~~~~~~~~~~~~~~~~~~~~~~~~~~

The ability to perform reliable multireference electronic-structure calculations
depends entirely on the ability to calculate initial guess multireference wavefunction
(usually CASSCF), in particular the assignment of a chemically representative orbitals
and electrons in the `active space`.

This is because it is not always clear what the active space should be to obtain
quantitative results for a given system. In addition, even when the orbitals are known, it is logistically difficult to build input files where the indices are appropriately chosen (often one is restricted to continuous ranges of energies, requiring orbital
rotations of wavefunction). This is particularly true for larger species.

This is disastrous from an automation standpoint. And unfortunately, while these issues are active areas of research, to our knowledge there is no robust
and reliable algorithm that can select and active space AND generate appropriate
program input to calculate the reference wavefunction.

For multireference calculations, we are able to automatically generate (2,2) active
spaces using the two highest energy singly-occupied orbitals. This provides a 
qualitative result for certain systems, but is by no means quantitative.

To allow for more complicated references, we allow the user to 
provide template files which provide all of the lines needed to calculate a reference
wavefunction.

File format::

    ! <species/transition state name>
    <rest of the wfn template>

The first line contains the name of the species and transition state similar to
the .xyz files. All of the remaining lines will be inserted in front of the
final CASSCF wavefunction calculation so that a quantitative multireference 
calculation can be performed

Currently, only Molpro is supported. However, we hope to expand these features to
other electronic structure codes which have implemented multireference methods. 

To show the template is used we provide an exmaple for a complicated system::
    <example with orbital rotations>