O.K. Hughes' lab notebook

I'm a computational atmospheric scientist at the University of Michigan who is most interested in the computational fluid models called Dynamical Cores (Dycores) that lie at the heart of climate and weather models.

I had the idea of putting my lab notebooks online for all to see. This isn't a particularly useful idea in and of itself, but I could see a number of future projects that might be able to build on this.

Posts

• FV3 Dycore Posts
  • Trying out the SHIELD container
  • Creating a laplacian sponge layer mechanism
  • Identifying problems with dycore
• MPAS tutorials
  • Adding a variable resolution grid to CAM via CIME
  • Porting the deep atmosphere version of MPAS to CAM-MPAS
  • Creating a Made to Measure MPAS grid.
• Installing Dycores
  • Installing HOMME on Cheyenne
  • Installing HOMME
  • Installing MPAS on GreatLakes
    • mpas.def
• LeatGrakes
  • Hosts
  • Login
  • setting up nfs
  • setting up raid
• Moonshot Ideas
  • Native SVD for SE?
  • barcode tracers
  • Parametric Held Suarez
  • Test case based on held+soden
  • Uncertainty Tracer
• NCL Script Documentation
  • NCL Fundamentals Cheat Sheet
  • NCL Interpolation Cookbook
  • NCL IO Cheat Sheet
  • Installing NCL on greatlakes (03/22/2023)
  • NCL Plotting Cheat Sheet
• Todo
  • Todo 05 18 2022
  • Todo 2023.09.xx
• AMR Research
• Transport Algorithms
  • finite volume transport on a regular grid
• Climate 451 Final Project
  • Outline for final presentation
• Climate 589
  • Make deep atmosphere aquaplanet
  • Make shallow atmosphere aquaplanet
  • Project 1
  • Project 4
• Main Glass Post
  • fishy tangent
  • Outline of MPM strategy
    • Rewriting the equations
  • Code outline
  • viscoelastic treatment
  • Continuum mechanics
  • Firedrake test
  • Mathematical quantities
  • Python prototype
  • Working up to NS
• Grad School Applications
  • AIM
• My experience writing a GRFP application
• What the DOE looks for in a CSGF application
• clever steady state
• Scientific Computing
  • A quick to set up trash alias for bash
  • Defensive Bash Boilerplate
  • Some slurm hacks
  • An Easy-to-implement Numerical Recipe for Computing Spherical Harmonics
  • Efficiently allocating resources in sbatch scripts
  • Using Globus to access locker on GreatLakes
• Conference posters
  • AGU 2024 Poster
  • CESM Workshop 2023 Poster
  • CESM Workshop 2024 Poster
  • EESM Workshop 2024 Poster
• Directories
• The two-mountain gravity wave
  • Using the CAM Eulerian dynamical core to explore the 2MGW
  • Deriving a minimal model of the topography-induced lamb wave
  • Testing the hypothesis that it's a lamb wave
  • Lamb Waves and Gravity
  • Parametric Lamb Waves
  • Turning this phenomenon into a paper
• Science Communication
  • Creating an online lab notebook.
  • Responsible Doohickey Ownership
  • WebGPU spectral transform shallow water model.
• scratch
  • E3SM 2.0 install notes
  • config_machines.xml
  • Little math puzzle
  • Scratch for aniket
  • Scratch for Joe vis a vis tracer concentration
• climate411
  • Final paper 411
  • Final project 411
• eecs587
  • final project 587
  • hw_2
  • hw_3
• E3SM
  • Installing E3SM 2.0 on Greatlakes using my jank MPAS dependencies
    • config_compilers.xml
    • config_machines.xml
  • Debuggin potential vorticity in E3SM
  • Adding PV and PT as dynamical tracers to E3SM
  • Where to find files for modifying the shallow water core in the HOMME dynamical core.
  • Potential vorticity in E3SM
  • Singularity Container
    • e3sm.def
    • bash.source
    • config_compilers.xml
    • config_machines.xml
    • singularity_create_aquaplanet.sh
    • submit.sh
• AEROSP 567
  • Exponential families and linear models
  • Sampling and Monte Carlo
• Community Earth System Model lifehacks
  • 2022/05/05 CAM FV3 install on UM GreatLakes system
    • Case creation script
  • CAM devel install on UM GreatLakes system
  • Adding new namelist options
  • Average regridding
  • Cheyenne Submission Script
  • Installing Locally in Containerized form
  • Getting started with NetCDF4 and Python.
  • Manually regridding
  • A singularity container for CESM
• CLaSP 586
  • Notes 2023.09.01
  • Notes 2023.09.11
  • Notes 2023.09.25
  • Notes 2023.09.29
  • Presentation
• DCMIP 2024
  • Idealized eta coordinates
• math
  • Quasi-rigorous Calculus of Variations
  • Differential geometry
  • How does the Hilbert transform work?
• Building and running the MPAS shallow water core
• Physics Dynamics Coupling
  • Method of manufactured solutions
  • Can moist theta, PV be a P-D coupling test case?
• SEAS 577
• STATS 700
  • Lecture 01
  • Lecture 02
• Papers
  • Baroclinic Wave Test Case with Topography
    • updates 01 21
    • BW Scratch notes
    • SE_NE60L30_evolution.ncl
    • Scratch for derived omega in hybrid coordinates
    • BW Topo figures document
    • How does mpas do vertical velocity?
    • BW Topo outline
    • Scratch 09 21
    • Todo 07_17
• Deep Atmosphere HOMME
  • Code modifications
  • Doing the hamiltonian myself
  • Plan June 2023
  • Plan March 2023
  • Bulk Mass Coordinates
  • Final init
  • Hybrid Coordinates
  • eta-to-eta initialization
  • efficient IMEX
  • Non-local initialization
  • jan 12
  • matsuno gill
  • Benchmarking the first functional checkpoint
  • Porting DA HOMME to C++
  • Thermo forcing
  • Optimizing IMEX convergence
  • Running Held-suarez on a reduced-radius earth
  • Storylines?
  • Semi-deep UMJS
• Causality