Script for automated workflow

[Misty-W]

Fixes #75 and #77.

Create a script to

• Load input files
• Call functions to slice the density and find the locations of water molecules
• Save the output

[DanieleQubit]

Testing docker + automated script for analog emulation: WIP

[Misty-W]

@DanieleQubit please make sure you update your clone to the latest commit on this branch, since I just reverted a change I made yesterday, experimenting with grid scaling in slicing.

[DanieleQubit]

Hi, here my first test, which results in a python error message (see later in this message):

1. 3DRISM density used attached here inside the .zip
   2a15_ph4.zip
2. the analog parameter file (in the zip too):

"7 7.3585242543498035 124.66370614359172 3000
10 30
poisson-disk 0 0 4 6 5
filter gaussian-laplace 0.5
crop 4.70 -12.0 5.0 5.0
2.702 -11.26 -9.197 3.202 -11.260 -9.197 2.702 -10.76 -9.197
2.702 -11.26 -9.697 3.202 -11.260 -9.697 2.702 -10.76 -9.697"

3. the automated flow .py modified is in the zip too.

I have this error:

in the same screenshot you can also see the command I used to run the simulation:
"docker exec aquapointer_test /bin/bash -c 'python ./aquapointer/analog/automated_flow.py'"

[Misty-W]

@DanieleQubit @darcangelomauro I fixed the error Daniele reported and the one I subsequently encountered (ordering of the slicing planes), but now there are issues when creating the lattice from the density slices.
The first and third examples from Daniele "hang" at the lattice creation step but run through without errors when I remove the cropping line from the settings file. On Daniele's second example (minus the cropping line), I get this error:

Traceback (most recent call last):
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/analog/automated_flow.py", line 6, in
from aquapointer.slicing import density_file_to_grid, density_slices_by_planes
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/init.py", line 8, in
from aquapointer.analog import analog, automated_flow, density_mapping, qubo_solution, utils
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/analog/automated_flow.py", line 132, in
locations = rism_to_locations(
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/analog/automated_flow.py", line 65, in rism_to_locations
[c.set_poisson_disk_lattice(spacing) for c in canvases]
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/analog/automated_flow.py", line 65, in
[c.set_poisson_disk_lattice(spacing) for c in canvases]
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/density_canvas/DensityCanvas.py", line 349, in set_poisson_disk_lattice
lattice = Lattice.poisson_disk(
File "/Users/mistywahl/Documents/GitHub/aquapointer/aquapointer/density_canvas/Lattice.py", line 135, in poisson_disk
ref_radius = radius_density[_index_from_position(ref_point)]
IndexError: index 82 is out of bounds for axis 0 with size 79

I've set up a call for tomorrow to discuss and will continue to troubleshoot in the meantime.