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CommandList.txt
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Init: Collects data from file to create a molecule in code
INIT fileName fileType moleculeName
do not include any special characters except _ in moleculeName,
and no spaces. The moleculeName is arbitrary, but must remain
consistent. Only filetype available is xyz.
Example: INIT benzene.xyz xyz ben
----------------------------------------------------------------
Print: Prints out current coordinates of molecule in code
PRINT filename fileType moleculeName
The molecule name must be exactly the way it was Initiated
It is reccomended to choose a new file name to keep the original
geometry. fileTypes available are xyz and gamess
Example: INIT benzene.xyz xyz ben
----------------------------------------------------------------
Sort:
SORT moleculeName axis
Changes the order of atoms in code to be organized by spatial
arrangements. Very handy when a command triggers a display.
Example: SORT ben x
----------------------------------------------------------------
Align:
ALIGN moleculeName axis
Translates and rotates molecule until the first atom is 0,0,0
and the second atom intersects the desired axis. Triggers a
display, for additional input during program.
----------------------------------------------------------------
Device Switch:
DEVICE_SWITCH moleculeName angularDisplacement angularIncrement
Rotates a desired bond in the molecule for analysis of different
conformations. The angular Displacement represents how much the
is rotated in total, and the angular Increment is the difference
the dihedral angle changes with each molecule. This function
prints results without the PRINT command.
----------------------------------------------------------------
Electrode Family:
???_ELEC moleculeName
The ??? that preceeds _ELEC depends on the desired electrode.
Prefixes include: HR "Hydrogen Replaced", L "Linear",
TSQ "Tip SQuare", PYR "PYRamid".
This input type only requires the moleculeName, then requests
the additional input later.