wmd-group / macrodensity Goto Github PK

The lattice_constant setting is the most difficult to understand. Generate a tutorial page and references to the origin of the technique.

Hello,

When trying attempting to analyze my LOCPOT file, after running macrodensity.py and PlanarAverage.py, I get the following error:

Traceback (most recent call last):
File "/home/eww9/bin/AvgCharg", line 16, in
vasp_pot, NGX, NGY, NGZ, Lattice = md.read_vasp_density(input_file)
File "/gpfs/home/eww9/bin/macrodensity.py", line 306, in read_vasp_density
Potential[k + m] = inp[m]
IndexError: index 1741825 is out of bounds for axis 0 with size 1741824

I attempted to set NGX, NGY and NGZ in my INCAR file and did a single point calculation (NSW=0) with a converged WAVECAR but this didn't fix the issue. Has anyone else had this issue and resolved it??

When the font size is < 11 the vacuum level tickmark goes to the centre of the band alignment diagram.

Try to write a routine to correct potentials with an electric field, by applying a dipole correction.

Hi,

When I tried using the code OnSitePotential.py it didn't work. It gave the error atom has no attribute get_symbol().

I had to modify the code slightly to make it run. I used get_chemical_symbols instead. The following is the modified code

coords = ase.io.vasp.read_vasp(coordinate_file)
scaled_coords = coords.get_scaled_positions()
symbols = coords.get_chemical_symbols()
ox_coords = []
i = -1

for atom in coords:
i = i + 1
if symbols[i] == species:
print symbols[i]
ox_coords.append(scaled_coords[i])

Hope this helps anyone trying to use it.

Hello, I am trying to plot the macroscopic average potential using the PlanarAverage.py script but I am not getting the correct average. For instance, the planar average will oscillate and after running the PlanarAverage.py that oscillation will be replaced by a flat line. Could anyone help me with this?

I am trying to create the plot in https://github.com/Anower120/MacroDensity/blob/master/tutorials/HeteroJunction/HeteroJunction.ipynb
with the Planar and Macroscopic averages.

The MacroDensity package takes a long time to download. This is primarily due to large LOCPOT files for the examples.

Generate smaller example LOCPOTs to do the same thing with less overhead.

Thanks for developing this package!
I have a question regarding the "Ionisation potential of a bulk material" part: in the slab calculation, should we relax the slab structure, or keep it the same as bulk structure? Might be helpful to clarify in the Tutorial.

1. Guidelines for unscripted testing are available here: http://www.mantidproject.org/Unscripted_Manual_Testing
2. Comment against this ticket the OS environment you are testing against.
3. Don't spend more than a few hours on the testing; fatigue will kick in!
4. If you find errors in the (possibly scant) documentation, please correct them.
5. Close the this issue once you are done.
   If you find bugs:

• Search to see if an issue already exists
• create an issue if it is new
• Urgent bugs or crashes should by against the current release, and assigned to a developer, then go and talk to the developer if possible.
• Less urgent bugs should be against a subsequent release, and assigned if the correct developer is known.

Specific Notes:

test stuff

There are not many style rules observed in the code. It would be nice to tidy this up before a submission to JOSS.

ToDo: run the source code through and try to check for style conventions, imports of unused functions etc.

I am using a MAC OS and with the following command
pip3 install git+git://github.com/WMD-group/MacroDensity.git
I get this error:
Collecting git+git://github.com/WMD-group/MacroDensity.git
Cloning git://github.com/WMD-group/MacroDensity.git to /private/var/folders/m7/7c68by855bq5bn4p89v0jj880000gp/T/pip-req-build-227v2sb0
ERROR: Command errored out with exit status 128: git clone -q git://github.com/WMD-group/MacroDensity.git /private/var/folders/m7/7c68by855bq5bn4p89v0jj880000gp/T/pip-req-build-227v2sb0 Check the logs for full command output.

I was trying to plot electric field in an arbitrary plane. I am getting the error messege
module 'macrodensity' has no attribute 'points_2_plane' when I am running the code PlaneField.py.
Can anybody help me to overcome this issue?

Build a test suite.

Hi

Your plot of HJ.png is so coool! Could you please tell me how to plot that? Thanks!

I got error by "pip install git+git://github.com/WMD-group/MacroDensity.git".

I solved it by installing with "pip install git+https://github.com/WMD-group/MacroDensity.git"

Please introduce Hank's constant to the full release.