June 2023

Thursday 1^st 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 2^nd June

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

Monday 5^th June

Big code day!

Tuesday 6^th June

Another big code day!

Wednesday 7^th 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 8^th 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 14^th

Friday - Wednesday 9-14^th June

Marking… so much marking… Even through the weekend

I did submit an abstract to APC 2023 though

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

Thursday 15^th 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 16^th June

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

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 φ=1 looks like )

Monday 19^th June

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

Tuesday/Friday 20-23^rd 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 25^th June

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

Monday-Wednesday 16-28^th 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)

UV/FL

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

TCSPC

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

Job Matrix

CAS (M3)

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

DFT - Gas (MonARCH)

State	Functional	Opt	Freq	Pol	Ex/Em	ESD
s0	ωB97X-D
s1+2	ωB97X-D
s0	CAM-B3LYP			N/A
s1+2	CAM-B3LYP			N/A

DFT - solv (MonARCH)

State	Functional	Opt	Freq	Pol	SS	VEM	ESD
s0	ωB97X-D
s1+2	ωB97X-D
s0	CAM-B3LYP
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

GANTT Chart

gantt
    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
    1((Entity))
    3[[module]]
    4[(database)]
    5[/Data Types/]
    6[Hidden Code\n12000+ lines]:::backend
    7[User Facing Code\n3000+ lines]:::ui
    end

    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
    m[/Fluorophores/]:::backend
    n[/Solvents/]:::backend
    o[/PCM Models/]:::backend
    p[/Software/]:::backend
    r[/Methods/]:::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
    end

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

    subgraph Databases
    j[DB Manager]:::ui -.- b & e & k
    e[(ΔE/λ/Φ/τ DB)]:::backend
    b[(Spectra DB)]:::backend 
    k[(Computational Results DB)]:::backend
    v[(Computational Progress DB)]:::backend
    v <--> j
    end

    subgraph Experiment
    h[Spectra Importer]:::ui 
    i[Spectra Analyser/Plotter]:::ui
    t -- .txt files --> h
    d -- .csv files --> h
  t((TCSPC))
    d((UV-Vis/Fl)) 
    end


    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;