Notebook 2 Functions

Below are the functions used for the geometry optimization, visualization, and electronic structure calculation of PAH molecules featured in Notebook 2.

NB2_functions.FF_optimization(molecule_num)	Performs a MMFF94 optimization of a PAH and displays 3D rendering of result.
NB2_functions.run_calculation(xyz_struc[, basis])	Performs a HF/STO-3G single-point calculation on a PAH structure.
NB2_functions.get_HL_gap(mf)	Finds HOMO-LUMO gap of molecule from HF/STO-3G calculation result.
NB2_functions.elec_properties(b)	Prints dipole moment, HL gap, and Mulliken charges from HF calculation result.
NB2_functions.mo_diagram(mf, show_diagram, ...)	Displays MO energy level diagram and dataframe.
NB2_functions.draw_orbital(label[, ...])	Renders isosurface of selected orbital from HF/STO-3G calculation.

NB2_functions.FF_optimization(molecule_num: int)

Performs a MMFF94 optimization of a PAH and displays 3D rendering of result.

Parameters:

molecule_num (int) – Number corresponding to a PAH from the menu.

PAH Options:

Table Index	PAH	Rings	Dimensions (Bohr)	pi electrons	Fuse-type
1	benzene	1	8 x 8 x 3	6	linear
2	naphthalene	2	12 x 8 x 3	10	linear
3	anthracene	3	16 x 8 x 3	14	linear
4	tetracene	4	20 x 8 x 3	18	linear
5	pentacene	5	24 x 8 x 3	22	linear
6	hexacene	6	28 x 8 x 3	26	linear
7	heptacene	7	32 x 8 x 3	30	linear
—	—	—	—	—	—
8	pyrene	4	16 x 12 x 3	16	non-linear
9	perylene	5	20 x 12 x 3	20	non-linear
10	coronene	7	20 x 16 x 3	24	non-linear

Example:

>>> # Perform a geometry optimization of heptacene
>>> FF_optimization(7)

NB2_functions.run_calculation(xyz_struc, basis='STO-3G')

Performs a HF/STO-3G single-point calculation on a PAH structure. Energy results are displayed in a Markdown table.

Parameters:

• xyz_struc (str) – geometry of PAH in xyz format

• basis (str) – basis set; see options: https://pyscf.org/_modules/pyscf/gto/basis.html

Heptacene Example:

NB2_functions.get_HL_gap(mf)

Finds HOMO-LUMO gap of molecule from HF/STO-3G calculation result.

Parameters:

mf (pyscf.scf.RHF) – pyscf HF calculation object

Returns:

Float representing HL gap in electron-volts.

NB2_functions.elec_properties(b)

Prints dipole moment, HL gap, and Mulliken charges from HF calculation result.

Parameters:

b – Button click

NB2_functions.mo_diagram(mf, show_diagram, show_table, savefig, filename)

Displays MO energy level diagram and dataframe.

Parameters:

• mf (pyscf.scf.RHF) – pyscf HF calculation object.

• show_diagram (bool) – Display matplotlib energy diagram.

• show_table (bool) – Display same data as Pandas dataframe.

• savefig (bool) – Save figure as .png file.

• filename (str) – filename to save .png file to (w/o file extension).

Example:

NB2_functions.get_orbital(i, label)

Saves a .cube file of orbital and prob. density from the above calculation.

Parameters:

• i (int) – index to iterate over in for loop

• label (str) – MO label, i.e. HOMO, HOMO-1, etc

NB2_functions.draw_orbital(label, psi_square=False, show_noninteractive_png=False)

Renders isosurface of selected orbital from HF/STO-3G calculation.

Parameters:

• label (str) – orbital designation, e.g. HOMO, HOMO-1, etc

• psi_square (bool) – show orbital (False) or probability density (True)

• show_noninteractive_png (bool) – render a static image (True) or interactive 3D display (False)

Example:

>>> # Display probability density of HOMO-3 orbital of heptacene (calculated in a previous cell)
>>> draw_orbital('HOMO-3', psi_square=True, show_noninteractive_png=False)