Uranus-Viewmol

Uranus-Titania.py

Uranus-Titania is the current final version of the program, which processes .xyz files in the cluster. However, if everything is working, you usually don't call Uranus-Titania directly.

Use

python3 Uranus-Titania.py [name_of_xyz_file] (-args)

Args frequently used

• -c lets you customize the process, to run only what you want.
• -away send all process to the cluster, so you can shut down your computer and the whole calculation will continue.
• -n [name] lets you to put the name directly and thus disable every input.

What it can do:

Output files	Used for
geom.xyz	Optimized geometry
Homo/Lumo cub files	yes
mos.in	A hundred or so calculated orbital densities
mos_cut.in	Twenty orbitals densities around the homo/lumo
freq.in	Vibration vector matrix in a wide range of wavelengths
exspectrum/convolution.csv	Exited orbitals informations (energy, occupancy, wavelength)
panama_files	First exited orbitals calculated densities

I believe this program is also flexible, and new operations can be added in the launch_job() function.

What it can't do

• Use turbomole files already calculated, or start from a previous calculation. Actually, it can do that, but not in -away mode, which is the mode used for every long calculation.
• In -away mode, if an operation fails-but-not-too-much, the program will try to continue anyway, thus creating weird results. This is not the case in normal mode, the mode that nobody will use, which happens to have a nice gui.
• It can't process molecules with an impair number of electrons. Actually, it will do it, but it will fail.

to_dtb.py

to_dtb.py can be put anywhere in the cluster.

It is used for :

• Starting the process of .xyz files that are in z_calc/to_be_made/ with to_dtb.py -p [NUMBER OF FILES TO BE PROCESSED]
• Sorting the processed files into xDatabase/ with to_dtb.py -s

retrieve.py

retrieve.py can be put anywhere in your local computer.

It is used for:

• Retrieving final files that were processed in the cluster with retrieve.py -r. It will get every file from your remote xDatabase/ and put them in a temporary folder, then create the needed file tree in static/data/
• Sending waiting files in files_from_users to the cluster, with retrieve.py -s [NUMBER OF FILE TO SENT]. It will put these files in xDatabase/to_be_made

Hard-code

• The location of my modified program of PANAMA is hard-coded in Uranus-Titania.py. The normal version of panama doesn't work for some processes, so my modified version should be downloaded.
• The location of spyctrum is hard-coded.
• /home/barres/ is hard-coded in Uranus-Titania.py, need to be replaced with current user of the cluster.
• The first variables of retrieve.py and to-dtb.py are hard-coded paths, they must be changed according to the instructions that are near them.
• scp frontale: is hard-coded in retrieve.py, it must be changed to the ssh address.

Neptune-draw

Arguments	Effects
-yz, -xz	Change visible axis, which are by default xy
-fx	Flip the x axis
-s	Save the picture in a pics/ folder
-wh	Give input for length and height

Neptune-draw.py

Draw distances of thecoord files in the current directory, color them by quartiles.

Arguments	Effects
-showv	Show values
-diff [MAIN DIR]	Plot the difference of distance between the two coord files, found in the directories given in input.
-p	Show atom labels

Neptune-draw+.py

Draw the molecule structure with double and simple bonds, from the Gaussian output file.

Neptune-draw-gimic.py

Draw from the OUTPUT.OUT and coord file generated respectively from gimicall.py and turbomole.

Show properties corresponding to the -iwant parameter:

-iwant [int]	Property
0	Induced current (sum of positive and negative)
1	Positive contribution
2	Negative contribution

Utilities

triangle.py

Find the center of each triangle of points given in input, and repeat the operation for each cycle given.

Then, write these coordinates to the coord file, as q phantom atoms.

truc.py

Create the first 50 structures from the Gaussian output, by calling Neptune-draw+.py.

Neptune.py

Automatize the process of:

Argument	Effect
-o	Basic optimization
-x	escf calculation
-ox	Optimisation of first excited state
-p	Electronic density of the first excitation

gimicall.py

Need

• An input.txt file in which is written every atom bond that has to be examined, one bond per line.
• Change the fixpoint of gimic.inp to an hydrogen atom so that it can't fail during the process.

It will write every output in the OUTPUT.OUT file, appending to it.