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June 2023

Thursday 1st June

Molecular sieves have come in today, but apart from drying some solvents and having a meeting about moderation, I’ve just been coding up pyqt guid like crazy.

Friday 2nd June

If I can pull myself away from my code for long enough, I think tomorrow might be a moderation day for me!

Monday 5th June

Big code day!

Tuesday 6th June

Another big code day!

Wednesday 7th June

This morning I went to 3MT to support a friend, but I’m really emotionally burned out, so I went to the office and spent the afternoon coding. I also fired off some failed jobs on the clusters for the first time in a while.

I think I’m going to take tomorrow off.

Thursday 8th June

Taking today off, though I did set up a spreadsheet to keep track of where each job is at in my computational pipeline.

Toby just sent me a call for abstracts for the Asian Photochemistry Conference to be held at MCEC in Nov/Dec this year, so I need to get something in for that. Abstract deadline is in the 14th

Friday - Wednesday 9-14th June

Marking… so much marking… Even through the weekend 😭

I did submit an abstract to APC 2023 though πŸ™‚

It’s fucking done! I’mma take a nap in the bath…

Thursday 15th June

Finally getting back to some science! I spent my day setting up a notebook for n-hexane/gas study and have all my plots in order. This also required a bit of fixing some old code from my main cluster handler that I never got to test.

I also fired off a bunch of jobs, including setting up a whole lot of wB97X-D and CAM-B3LYP single points at TZ instead of the usual DZ.

Friday 16th June

I submitted a few hundred very quick jobs last night, so this morning has been a lot of tedious updating of spreadsheets πŸ˜…

I’m mostly going to be running the JMSS immersion day day today, but BPA just came in and I’m going to grab spectra of it in nhex and ethanol before that! (I want to see what Ο†=1 looks like πŸ˜„)

Monday 19th June

  • Confirmation report needs to be done by the 12th
  • Submit confirmation report by the end of this week and the manuscript by the end of next.

Tuesday/Friday 20-23rd June

Focusing on getting my confirmation report out. I did spend a couple of hours doing some re-marking for CHM1011/51 exams though.

Confirmation report

  • Base structure
  • Lit review summary
  • Thesis plan
  • Aim/Progress/Plans
    • Mostly done
  • Deep dive (intro - manuscript to come later)
  • Conferences and publications
  • Gantt Chart

Sunday 25th June

Confirmation report first draft is done. I’ll start on the manuscript tomorrow.

Monday-Wednesday 16-28th June

So I did get a little bit done on Monday and Tuesday, but mostly on getting a latex template set up, building some figures and setting up notebooks. It’s Wednesday now, and I’m trying to focus on writing

Idea for freqs/deconv

What if instead of starting with a random guess, we make a function that has a fixed number of Gaussians at a fixed spacing from each other, and we fit them with an offset parameter. We could use the frequencies to dictate the distribution of the Gaussians and and only have the amplitude and sigma as free parameters

func(shift: float, amps: list[float], sigma: list[float] cen_FIXED: list[float])

To implement in code:

  • SVG visualisation for the fluorophores
  • Spectrum deconvolution
  • Rate limiting for spectraView

Important Questions:

  • Can we use the difference between TDDFT Eq and nEq energies to figure out the stokes correction to the 0-0 energy in abs and fluor
  • Can we use the shape of the Theoretical PES to determine what the width of the deconvoluting Gaussians should be for fitting?

Experimental work

Problematic spectra:

  • Collecting:
    • AZ lifetimes - all solvents. No solvatochromic shift on s2 → s0
    • DMSO with azulene seems to have issues, I’m guessing DMSO excites
  • Difficulty fitting
    • TCSPC
      • DAA/nhex
      • BSC/etoh

Experimental to-do:

  • Anisole series (sure/seal)
  • THF series (sure/seal)


nhex tol ans ether chcl3 thf dcm c80h etoh acn dmf dmso
nr βœ… βœ… βœ… βœ…
nda βœ… βœ… βœ… βœ…
r800 insol βœ… βœ… βœ…
c153 βœ… βœ… βœ… βœ…
bod493 βœ… βœ… βœ… βœ…
az βœ… βœ… βœ… βœ…
aaq βœ… βœ… βœ… βœ…
dapi insol βœ… βœ… βœ…
daa βœ… βœ… βœ… βœ…
bsc βœ… βœ… βœ… βœ…
fno βœ… βœ…
bpa βœ… βœ…
fat βœ… βœ… βœ… βœ…


nhex tol ans ether chcl3 thf dcm c80h etoh acn dmf dmso
nr βœ… βœ… βœ… βœ…
nda βœ… βœ… βœ… βœ…
r800 insol βœ… βœ… βœ…
c153 βœ… βœ… βœ… βœ…
bod493 βœ… βœ… βœ… βœ…
az - - - - - - - - - - - -
aaq βœ… βœ… βœ… βœ…
dapi insol βœ… βœ… βœ…
daa βœ… βœ… βœ… βœ…
bsc βœ… βœ… βœ… βœ…
fat βœ… βœ… βœ… βœ…

Job Matrix

CAS (M3)

State Active Spaces CASSCF/aug-cc-pvdz QD-NEVPT2/aug-cc-pvdz
s0 βœ…
s1+2 βœ…

DFT - Gas (MonARCH)

State Functional Opt Freq Pol Ex/Em ESD
s0 Ο‰B97X-D πŸƒ πŸƒ βœ… πŸƒ
s1+2 Ο‰B97X-D πŸƒ πŸƒ πŸƒ
s0 CAM-B3LYP βœ… βœ… N/A
s1+2 CAM-B3LYP βœ… πŸƒ N/A

DFT - solv (MonARCH)

State Functional Opt Freq Pol SS VEM ESD
s0 Ο‰B97X-D βœ… πŸƒ
s1+2 Ο‰B97X-D βœ… πŸƒ
s1+2 CAM-B3LYP

To do:

  • Jobs to figure out
    • Test QChem to figure out how to do VEM/cLR/LR/IBSF emission
  • Code
    • Write energy extractors
      • pullQChem_Freq
        • \(\Delta E_{ZPVE}\)
        • \(\Delta E_{elec}\)
        • Number of -ve freqs
        • Extend and test for CASSCF
      • Q-chem ex/em extractors
        • ss-ex
        • ss-em
        • lr-ex
        • lr-em


    dateFormat D/M/YY
    title Adrea's PhD Plan
    %%excludes    weekends

    section Preparation
    Preliminary reading                     :active,                    5/4/22,     10/2/23
    Method "Play"                               :done,                      5/4/22,     10/6/22
    Software comparisons                    :done,                      10/6/22,    13/7/22
    Preliminary benchmarking            :done,                      12/7/22,    27/10/22
    Christmas break                             :crit,                      22/12/22,   3/1/23
    Dataset design                              :active,                    12/7/22,    18/12/22
    Experimental design                     :active,                    28/11/22,   27/1/23

    section Chapter 2
    Data collection                             :dc,                            23/2/23,    16/8/23
    Data processing                             :                                   23/2/23,    23/8/23
    Writeup                                             :w,               after dc, 8w
  R&R break                                         :crit,            after w,  2w

    section Chapter 3
  Computation & Analysis                :comp,                      1/10/22,      58w
  Writeup                                               :                 after comp,   10w
  Christmas break                               :crit,                      22/12/23,   3w

  section Chapter 4
  Computation & Analysis                :c4,                            26/2/24,    20w
  Writeup                                               :w4,                            after c4, 6w
  R&R break                                         :crit,                      after w4,   2w

  section Chapter 5
  Computation & Analysis                :c5,                            after w4, 20w
  Christmas break                               :crit,                      20/12/24,   2w
  Writeup                                               :w5,                            after c5, 6w

    section Milestones and Thesis
    IPR writeup                   :ipr,                         19/12/22, 10/2/23
    IPR                           :milestone, ipr,  23/2/23,    0d

    Confirmation writeup                    :                                   19/6/23,    11/7/23
    Confirmation                                    :crit, milestone, 19/7/23,  0d

  Progress review writeup               :                                   23/4/24,    9/5/24
    Progress review                             :milestone,             23/5/24,    0d

    Final review writeup                    :                                   28/3/25,    9/5/25
    Final review                                    :milestone,             23/5/25,    0d

    Drop everyhting for thesis      :                                   25/4/25,    25/7/25
    Thesis submission                           :crit, milestone,   22/8/25,    0d

    section Conferences
    APC 2023                      :                 27/11/23, 1/12/23
    APATCC-11 Kobe                :                 01/09/24, 30/11/24
    WATOC Oslo                    :                 22/6/25,  6d

Code Object Structure

flowchart LR
    subgraph Legend
    5[/Data Types/]
    6[Hidden Code\n12000+ lines]:::backend
    7[User Facing Code\n3000+ lines]:::ui

    classDef backend fill:#bfbdbd;
    classDef ui fill:#fa4ba0;
    classDef db fill:#00f2ff;
flowchart TD
    a -- Output Files --> g
    g -- SLURM Scripts -->  
    a((HPC Clusters))
    subgraph Backend Code
    s[/Spectrum Object/]:::backend
    o[/PCM Models/]:::backend
    q[/Basis Sets/]:::backend
    s & m & n & o & p & r & q -.-> l[[Data Types]]:::backend -.- w
    g[[HPC Manager]]:::backend -.- w
    w[[Resources module]]:::backend

    c <-- Job Status --> v
    c -- QM Properties --> k

    subgraph Databases
    j[DB Manager]:::ui -.- b & e & k
    e[(Ξ”E/Ξ»/Ξ¦/Ο„ DB)]:::backend
    b[(Spectra DB)]:::backend 
    k[(Computational Results DB)]:::backend
    v[(Computational Progress DB)]:::backend
    v <--> j

    subgraph Experiment
    h[Spectra Importer]:::ui 
    i[Spectra Analyser/Plotter]:::ui
    t -- .txt files --> h
    d -- .csv files --> h

    c[Job Manager]:::ui 
    b <-- Fitted spectra --> i

    h -.- i -- Spectral Features --> e
    b <-- Fitted spectra --> h

    w -. Jobs -.- c
    w -.- j

    k & e --> u[Stats Scripts]:::ui

    classDef backend fill:#bfbdbd;
    classDef ui fill:#fa4ba0;
    classDef db fill:#00f2ff;