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methods_notes.tex
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methods_notes.tex
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Wed Jun 16 15:27:22 MDT 2021
In the 10.1002/cphc.201900793 paper it says that the highest ITIC transfer integral
is 16Mev. this motivates finding a morphology of itic that is well packed and
seeing if out TIs match this. in the transfer-qcc-pluck notebook im goin go
have it grab chromos that are near each other and give the TI for them.
I have conscripted gwen and cody to produce rdfs from /home/erjank_project/itic-project/workspace
to pick an educated guess of a nice morphology to begin with. that is, a non liquid or frozen one
at least.
the guts to achieve this are in the intramolecular notebook
Thu Jun 17 12:31:30 MDT 202
Going to get some benzene rings from mbuild in some oreintations and get transfer integrals
between them. I will call the notebook transfer-qcc-P3HT and i will build the benzenes in
new_molecule_test notebook
evans paper gives TI between .3 and 1 for various conditions ie bonded non-bonded, seperation
distance etcetera
instead of specifying the exact angles between thiophenes to compare to evans paper,
I am going to use fill_box from mbuild to give me a sudo random orientations of two
thiothenes in a box.
getting reasonable numbers for thiophenes in terms of homo humo and TI. jenny going to get
some more sceintifically shifted gsds.
Wed Jul 7 13:08:05 MDT 2021
Working through jennys modified workflow for morphct. Hole mobility is negative which I beleive
not good.
Thu Jul 8 13:06:52 MDT 2021
In our working example of p3ht mobility calculator, we are getting a negative mobility.
Sun Aug 22 19:54:41 MDT 2021
I thought the code was broken because I kept getting a nan for TI which resuted in a zero TI
but it wasnt broken. When a para meta two mer is relaxed in mbuild the meta and para have very different
homos whcih results in a negative number under a square root in the TI calc. But We get a .11 TI for an
unrelaxed para_meta. This is very different. a zero TI will result in no hop. Maybe we should use koopmans
aFri Jan 21 20:23:42 MST 2022pproximation to avoid this?
Mon Sep 20 11:30:00 MDT 2021
Digging into the mp going on in morphct I believe we can delete p.join() from
mobility_kmc. the purpose of it is two wait to execute the rest of the program
until all the children have finished. However, it was malfunctioning and I beleive
that using the connection pipe as Morphct the .recv() end of the pipe blocks the
program until the .send() end of the pipe sends somthing . This will achieve
a what p.join() was trying to do.
problem trying to get it going on fry. I dont know how to change the flow.
I am getting permission errors.
I tried to add an operation like this:
(https://github.com/mosdef-hub/reproducibility_study/blob/c54751f88739b16eb1c61174d88e48e7382cf699/reproducibility_project/src/engines/hoomd/project.py#L38-L45)
with a directive but I got operation function has no
attribute .with_directive .
Thu Sep 23 11:24:56 MDT 2021
I cant find any DFT or experimental numbers for PEKK mobility values. Is a time of flight o
pure peek and pekk something that southern miss can do?
Fri Jan 21 20:23:42 MST 2022
im going to run a script in fry that saves a pickle of the three large morphologies at at each step of the
process. That way any analyis I need to do I can pick it up at that pickle.
Thu Jan 27 11:51:27 MST 2022
I tried the see that the MSD would look like with life times at 10^-9 and 10^-6. But one carrier took 9
hours to stop hopping. LOL. My thought was if we took a linear fit from a time well past ballistic
transport and then a time way in the future we should get the true msd slope