July 2023

Saturday 8^th July

I haven’t written anything here for a while because I’ve just been working on my confirmation report. I got COVID again for the 7^th time on Tuesday which has really been a kick in the teeth while I’m cramming to get this report written.

I’ve finally sent it off to people today to get some feedback.

Sunday 9^th July

Katya just sent through some feedback last night which I have implemented and sent my report off! Now I can relax for today before I get started on the presentation tomorrow!

Monday 10^th July

I’m running on very little sleep today and I am pushing myself a bit too hard post COVID to make personal appointments, so I think since I worked through Saturday, I might call today my Sunday, since I worked through Saturday.

Tuesday-Friday 10/14^th July

Working on the presentation, but COVID has made me quite slow.

Monday 17^th July

Today I focused on getting my presentation done. I think it’s good enough for me to do a practice tomorrow to to group, and if they like it I’ll polish and practice with their feedback for Wednesday!

Tuesday 18^th July

Katya and the group liked my presentation, but thought it needed a bit more depth to show off all the work that I have actually done, so I spent my day making more slides, and putting together some fun figures to go with it!

Wednesday 19^th July

Smashed my confirmation! Tomorrow is group lunch, but otherwise I’mma take the rest of the week off, I think

Tuesday 25^th July

I got a couple of spectra done, and I got a couple of TCSPC histograms produced as well :)

Meeting notes:

• Moderation is a go for sem 2.
• People Movement
  • Two new PhDs for work with ML with Ralf.
  • Grant coming to work with Agilio.
  • Two potential honours students - currently research students.
• CHM3911 is probably not going to be revamped this year.
• Daniel Crawford will be coming while we’re teaching, so we’ll try to join after we’re done for drinks and possibly dinner.
• Dispersion paper
  • Trying to correlate electrostatics with dispersion to see where the trend becomes non-linear, using SAPT of non-charged, charge-neutral and charged clusters of organic, inorganic and metallic species.

Wednesday 26^th July

Rider training today, so no work.

Thursday 27^th July

I’m waiting for my bike to be delivered either today or tomorrow, so I’m wfh for the rest of the week.

I’m a bit sick of job maintenance though, so this is going to be a little bit tedious

Monday 31tst July

Teaching day. Also Daniel Crawford visit, so we’ll see how that goes

I’m a bit grumpy that the TCSPC is booked out all week (literally all day every day), so I won’t actually be able to collect any lifetimes.

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])

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;