Andy’s, like, whatever pages
ccGENIE.muffin EMIC
GENIE website (RIP)
got data?
Ocean observations [regridded, netCDF format]:
(1a) WOA2009 / worjh2 grid: NO3 O2 PO4 H4SiO4 temp sal
(1b) WOA2009 / worlg4 grid: NO3 O2 PO4 H4SiO4 temp sal
(2a) GLODAP / worjh2 grid: DIC ALK C14 CFC11 AnthCO2
(2b) GLODAP / worlg4 grid: DIC ALK C14 CFC11 AnthCO2
(3a) WOA2013 / worjh2 grid: NO3 O2 PO4 H4SiO4 temp sal
(3b) WOA2013 / worlg4 grid: NO3 O2 PO4 H4SiO4 temp sal
(4) OLD / worap2 grid: ALL
(5) Fe: worlg4 grid
(6) IO3-, I-: TBA
(7) Re-gridded PETM SST data from Dunkley Jones et al. [2013]: pre-PETM; peak-PETM
(8) Observations for ECOGEM
(9) Benthic d13C data for: late Holocene and LGM
got (the) runs?
mailing lists
(TBA)
muffin resources: DOCUMENTATION
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Current (cGENIE.)muffin documentation | |
| (cGENIE.)muffin combined user-manual and an introduction to Earth system modelling tutorials. (Also incorporating previous HOW-TO documentation.)
SEE: derpycode/muffindoc on GitHub for latex source. WARNING: Documentation in varying degrees of not updated-ness ... |
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| Various model experiment EXAMPLES, including example model configurations, experimental designs, and associated namelist parameter descriptions. | ||
| Namelist parameters in a separate and shocking incomplete/outdated Table. |
GEO266 -- Introduction to Earth system modelling
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GEO266 class guide (including syllabus and course overview) [CHECK BACK FOR UPDATES!]. | |
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GEO266 course text (the 'muffin manual'!) [CHECK BACK FOR UPDATES!]. | |
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GEO266 example (complete) class guide [old from 2019/20 and FYI only]. | |
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domino.ucr.edu cluster useage rules and account configuration instructions. | |
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Lectures: ... |
cGENIE resources: *legacy* (not current) documentation
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(1) Previous cGENIE.muffin documentation | |
| The soon-to-be infamous Quick-start Guide (also see platform-specific variant -- box on left)
plus the all important and vital READ-ME that you inevitably will not read ....
WARNING: Documentation in varying degrees of not updated-ness ... and there is no chance now of it ever being complete now either ... |
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| User manual, with details of the namelist parameters given in a separate and shocking incomplete/outdated Table. | ||
| Various model experiment EXAMPLES, including example model configurations, experimental designs, and associated namelist parameter descriptions. | ||
| The cGENIE HOW-TO - potted explanations of how to get useful stuff done, e.g., spinning up deep-sea sediment distributions. | ||
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(2) Original cGENIE branch documentation | |
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cGENIE (biogeochemistry focused) User manual.
Various model experiment EXAMPLES. The cGENIE HOW-TO. The soon-to-be infamous Quick-start Guide. |
SYR 2020 muffin (Earth system) modelling workshop
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2020 SYR muffin workshop guide. | |
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muffin model user manaul (and tutorials). | |
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domino.ucr.edu cluster useage rules and account configuration instructions (for reference only). |
LDEO 2020 muffin (Earth system) modelling workshop
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2020 LDEO muffin workshop guide. | |
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muffin model user manaul (and tutorials). | |
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domino.ucr.edu cluster useage rules and account configuration instructions (for reference only). |
GE290: Introduction to Earth system modelling (2019/20)
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GEO290 course guide *to-date* (including syllabus and course overview). | |
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The GEO290 course text (the 'muffin manual'!) [in revision]. | |
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domino.ucr.edu cluster useage rules and account configuration instructions. | |
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Lectures: 191002; 191004; 191016; 191023. |
cGENIE resources: WORKSHOPS -- UoB 2018
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Course Information: | |
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Workshop guide.
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Course book (muffin manual).
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Additional resources and information: | |
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Basic use of the vi editor.
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Basic linux (MLP edition).
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Presentation
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cGENIE resources: GEO290
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Course Information | |
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Course guide.
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Course book.
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Individual course tutorials | |
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Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis. Lesson #2 == Ocean circulation and overturning stability. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification. Lesson #4 == Ocean biogeochemical cycles and the ‘biological pump’. Lesson x == Long-term regulation of atmospheric pCO2. |
cGENIE resources: WORKSHOPS [OLD -- AWI.2017]
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Course Introduction | |
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Boring presentation.
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Earth system modelling course | |
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Course program details.
Lab instructions [basic course]: Lesson #0 == cGENIE modelling basics Lesson #1 == Snowball Earth + experiments in climate hysteresis. Lesson #2 == Ocean circulation and overturning stability. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification. Lesson #4 == Engineering the carbon cycle and the ‘biological pump’. | ||
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Lab instructions [advanced]:
Lesson #5 (I) == Greenhouse climates of the past: the late Cretaceous. Lesson #5 (II) == Greenhouse climates of the past: early Eocene. |
cGENIE resources: WORKSHOPS [OLD -- UoB.2016]
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Course Introduction | |
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Boring presentation
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(1) Earth system modelling course | |
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Course details.
Lab instructions: Lesson #0 == cGENIE modelling basics Lesson #1 == Snowball Earth + experiments in climate hysteresis. Lesson #2 == Ocean circulation and overturning stability. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification. Lesson #4 == Engineering the carbon cycle and the ‘biological pump’. |
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(2) EcoGEnIE ecosystem modelling course | |
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Course details.
Lab instructions: Lesson 0.a == cGENIE modelling basics Lesson 0.b == Snowball Earth + experiments in climate hysteresis. Lesson 0.c == Ocean circulation and overturning stability. Lesson 0.d == The oceans biological pump. Lesson 1.a == Running EcoGEnIE and visualising output. Lesson 1.b == Ecosystem configuration. Lesson 2.0 == Increasing ecological complexity. Lesson 3.0 == Build it up, tear it down. Lesson 4.0 == Ecology in a paleo-ocean. |
cGENIE resources: WORKSHOPS [OLD -- Yale.2016]
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INFO:
Course details. | |
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Lab instructions:
Lesson #0 == cGENIE modelling basics Lesson #1 == Snowball Earth + experiments in climate hysteresis [ + optional ideas for further investigation -- Lesson #1b]. Lesson #2 == Ocean circulation and overturning stability [ + optional ideas for further investigation -- Lesson #2b]. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification [ + optional ideas for further investigation -- Lesson #3b]. Lesson x == Long-term regulation of atmospheric pCO2. |
cGENIE resources: WORKSHOPS [OLD -- UoB.2015]
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INFO:
Course details. Presentation. | |
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Lab instructions:
Lesson #0 == cGENIE modelling basics Lesson #1 == Snowball Earth + experiments in climate hysteresis. Lesson #2 == Ocean circulation and overturning stability. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification. Lesson #4 == Engineering the carbon cycle and the ‘biological pump’. |
cGENIE resources: WORKSHOPS [OLD -- AWI.2015]
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INFO:
Workshop outline. | |
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Lab instructions:
Lesson #0 == cGENIE modelling basics Lesson #1 == Snowball Earth + experiments in climate hysteresis. Lesson #2 == Ocean circulation and overturning stability. Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification. Lesson #4 == Engineering the carbon cycle and the ‘biological pump’. |
cGENIE resources: TEACHING LABS [OLD -- GEOGM1110 / GEOGM1404]
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INFO:
Course outline;
non-intimidating linux 101 (MLP version).
Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’ plus a supplement summerizing ocean acidification relevant results variables, and both together in a revised Session #0100 document // Session #0101: GEOGM1110 == Engineering the carbon cycle (GEOGM1110) // Session #0101: GEOGM1404 == Engineering the carbon cycle (GEOGM1404). INFO: Simple introduction to ocean acidiciation // and a slightly more in-depth guide with fuller referencing. Resources: potted references. Software (PC): SSH client; Current Panoply netCDF viewer, OR ... (old) version of Panoply; SCIntilla based Text Editor ['full download' under: 'Windows Executables']. |
cGENIE resources: WORKSHOPS [OLD -- Urbino.2013]
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INFO: Workshop outline. | Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’.
cGENIE resources: WORKSHOPS [OLD -- UoB.2013]
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INFO: Workshop outline. |
cGENIE resources: WORKSHOPS [OLD -- LifeAndThePlanet.2013]
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INFO: Workshop outline [REVISED]. |
cGENIE resources: WORKSHOPS [OLD -- AWI.2013]
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INFO:
Workshop outline [REVISED] (also:
Basic course flier,
Advanced course flier).
Lab instructions: Session #0000: cGENIE modelling basics + experiments in climate hysteresis; Session #0001: Ocean circulation and overturning stability; Session #0010: Greenhouse climates of the past: the late Cretaceous; Session #0100: Fossil fuel CO2 release and ‘ocean acidification’; Session #0101: Engineering the carbon cycle; Session #1000: How long is ‘forever’? -- The long tail of CO2 and other tales from the sediments. |
cGENIE resources: WORKSHOPS [OLD -- Caltech.2013]
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INFO:
Workshop outline.
Lab instructions: Session I+II: cGENIE modelling basics + experiments in climate hysteresis; Session III+IV README; Session III: Ocean circulation and overturning stability; Session IV: Consequences of fossil fuel CO2 release and ‘ocean acidification’, Session V: How long is ‘forever’? (role of deep-sea sediments in long-term carbon cycling), Session XX: 'Preformed nutrient' tracers of ocean biogeochemical cycling. |
cGENIE resources: TEACHING LABS [OLD -- GEOGM1110(EC4)/M1404]
cGENIE resources: WORKSHOPS [OLD -- UCSC2012]
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INFO:
Workshop outline.
Lab instructions: Session I+II: cGENIE modelling basics + experiments in climate hysteresis; Session III+IV README; Session III: Ocean circulation and overturning stability; Session IV: Consequences of fossil fuel CO2 release and ‘ocean acidification’; Session V: How long is ‘forever’?. Software (PC): SSH client; Panoply netCDF viewer (requires Java -- unzipping is only installation required); Freeware 'SciTE' text editor [direct link]. |
cGENIE resources: WORKSHOPS & TEACHING LABS [OLD -- MISC]
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*UoB2012* Presentations: Course introduction. | |
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*USSP2012* Handouts (main): Session I; Session II; Session IIIa; Session IIIb; Session IIIc. Software (PC): SSH client; Panoply netCDF viewer OR ... old Panoply (works better); SCIntilla based Text Editor. | |
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*Cardiff2012* Handouts (main): Session I; Session II; Session III; Session IV; Session Va; Session Vb; Session VI. | |
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*AWI2011* Handouts (main): Session I; Session II; Session III; Session IV; Session V; Handouts (additional): Session VI; Session VII; Re-starts: Basic re-start package (Labs I - V); 'glacial' re-start (VI + VII). | |
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*USSP2011* Handouts: Session I; Session II; Session III; (Session IV); Session V; (Session VI). Software (PC): SSH client; Panoply netCDF viewer; SCIntilla based Text Editor. |
Miscellaneous
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Project home page for the Grid Enabled Integrated Earth system model - GEnIE (a Grid-based, modular, distributed and scaleable Earth System Model for long-term and paleo-climate studies). Sounds good? Hell; that's because it is ;) | |
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Graphics resources (various project logos and GEnIE model schematics). | |
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Original marine carbon cycle 'tutorial' (including cb/s-goldstein user-manual), in html and PDF formats.This is actually something of a standard project joke, as it is well known that I rarely get around to finishing anything useful. Maybe I should get my finger out? You, the jury decide. Vote here. | |
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Miscellaneous model documentation such as descriptions of previous model versions and stuff. |