Bryan Nicholson
Research Project:
Modeling low altitude, low mass eruption columns
Historically, modeling the largest of volcanic eruptions has been a primary focus of volcanologists. And rightly so, given the potential risk these eruptions pose on their surroundings. However, this focus has left a dearth of potent models for "small" eruption columns, where concern remains for aviation safety and populated areas proximal to volcanoes. The term "small" here is relative, as small eruptions can reach over 8 km into the atmosphere and even farther distances away from the vent. People and agriculture surrounding the immediate vicinity of a small eruption will still endure hazardous situations. Fine ash and glass deposits can wreck havoc on agriculture, especially grass feeding animals, while causing respiratory issues in both humans and animals alike. In a dry environment ash may linger in the area for an extended period and can become remobilized by wind where it will continue to pose a hazard. This project aims to step forward in providing a model(s) for small eruption columns. The difficulties lie in the differences between large and small eruptions where in smaller eruptions wind plays a more dynamic role by swiftly altering the shape and dispersal of the column and its ash contents.
Perhaps a useful analogy here would be that of comparing an aged tree having a trunk width of several feet reaching a height of 50 feet to that of a young tree with a width of about an inch reaching a height of 10 feet and considering the impact of a 50mph sustained wind. The larger tree would remain unyielding at it's trunk with it's leaves and smaller branches swaying appropriately with the wind. The smaller tree (assuming it's still rooted), however, would likely be bowed over with it's smaller branches near the top fluttering rapidly. One could image the increased complexities of modeling the smaller tree ("small" eruption column). Fortunately, a higher frequency of smaller eruptions allow us to compare our models to a multitude of observations.
Cleveland Volcano May 23, 2006
Image from http://earthobservatory.nasa.gov/IOTD/view.php?id=6592
Goals for MS program:
Develop an advanced problem solving skillset.
Critical analysis
Research experience from problem to conclusion
Become educated and fluent in modeling earth's dynamic systems
To further familiarize myself with academic literature.
Become knowledgeable in the utilization of computational models.
Expand my ability to write and communicate effectively to community level science.
Target skill sets applicable in career and industry (oil/gas, environmental, etc.)
Learn more geology!
Shockwave animation at Sakurajima Showa Crater, Dec. 2009
Image from http://earthquakes-mst.wikispaces.com/Sakurajima
Weekly research objectives:
Complete thesis draft: 3/20
Shannon edits: 3/23
Submit to committee (SKN, SG, GFR): 3/29
Activities for 3/15
Rough draft of complete thesis to SKN by 3/15
Runs/analyses done
timing of instability figures, separated by vent speed
" , separated by vent size
writing
uniform winds (10, 20, 30 m/s) for single vent speed
check on wind profile figs
Activities for 3/11:
Thesis due 3/29
Rough draft of complete thesis to SKN by 3/15
Runs/analyses done 3/11
finish cold/dry runs
do 2D runs - 6 runs completed 3 for each atmospheric profile
fill in MER gaps - Started runs with 250 m vent size for 10 and 15 m/s wind profiles
fill in 15 m/s gap - Started for both atmospheres
figure showing timing of partial instability
start runs for cold air with tall tropopause and vice versa (no wind and 10m/s) (rescale current atmospheric profiles to new altitudes)
{Return Intro/methods comments ASAP}
Activities for 3/4:
add two extra arrows for crossover events in plume tree (see photo)
use velocity vectors to determine fall vs flow along ground
do a couple runs with a steeper sided volcano to better distinguish fall vs flow (degree of partial instability)
finish cold/dry eruptions
finish 2D eruptions (may still be running at next meeting)
brief written analysis of warm/wet for various winds
- if time, also do cold/dry
- if more time, compare warm/wet to cold/dry
put points on plot of MER/wind showing stability
start runs for cold air with tall tropopause and vice versa (no wind and 10m/s) (rescale current atmospheric profiles to new altitudes)
submit for RM GSA
{Review new intro/methods content}
Activities for 2/12:
add arrows to plume tree
change colors to bottom row and connect to color coded photos
remove left column from Table 1 (epic table)
add Table 1 to results, plus extra columns (MER, stability)
add to methods: how you select ash threshold for visible edge, how simulations differ from real plumes
Check stability of completed runs
Prep images/slides for SG Friday
Activities for 2/5:
do 2D runs on laptop to match no-wind 3D outputs - I will run 2d on the cluster for a more complete comparison once 3d runs are completed.
Restart 3D ATHAM as soon as cluster comes back online - Running models again, encountering larger queue times though.
New figure for methods: (may be 1 or 2) tree of possible eruption outcomes, names, images, descriptions (if 2, use color coding)
Methods: add table showing intended simulations -The simulations table is now in methods and results, where the results table has a stability and a MER column.
Methods: add section on 2D vs. 3D - 2D vs 3D comparisons are written throughout the section.
results: (revised together) start working on figures, tables
{FINISH REVIEW!!!!}
Activities for 1/29:
Keep running 3D atham, fill in charts
compare 3D no wind to 2D no wind
finish first complete draft of methods
{SKN: finish edits on Ch2}
write outline (structure-level) of Results
email SKN and SG to set up committee meeting, get initial possible dates for defense
Activities for 10/16:
finish Background updates
try running atham on falcon using AVE's input files
{SKN: install own copy of atham on falcon using BN's updates, look for stability error}
fix stabilization problem
do search in code for error message, track to trigger
Activities for 9/18:
{SKN: read Intro}
Continue on Ch2 -Still working through edits, most of the time was spent working to get atham set-up
Unzip and install new atham copy - Unzipped and on the cluster, just trying to install it. - It is compiled and 'running' but coming up against runtime errors, I'm attempting to adjust inputs to fix it.
- note: switch extension to .tgz
check velocities during eruption - I need to get the new atham version up and running to start these
for dry profiles, use same as wet but decrease humidity (use actual dry climate profiles as a guide for reasonable values and rate of change)
Activities for 9/11:
finalize Intro -Completed and Sent
edits on Ch2 -Still working through it
{dig up old, clean atham copy for B}
{Continue to check in with MH}
install new/old atham copy to check for output gaps (DO NOT DELETE CURRENT WORK) -Will do asap, just need to extract the new Herzog file and make it.
run current atham for wind conditions, plotting at low (optical opaque) concentration
- looking for stability fields, filling in existing plot
- treat high and low latitudes separately (high vs. low, humid vs. dry) -So we want a high latitude wet & dry profile and a low latitude wet & dry profile? I'm working on getting these 4 profiles ready to go and nicely documented so we know where they are from and of what time frame (one snap shot or average of month or year?) I am thinking of using a Venezuela area profile for the warm & wet profile and Alaska (maybe near the Aleutians where is it probably wetter) for the cold & wet. But I'm not sure if I should pick dry profiles from the same locations (where it is more dry) or go somewhere across the globe?
Also, is the only input to adjust for wind located within the profile?
Figure out how user defined init_vel turns into real vent_vel -Missing vent from output, can't get reading on vertical velocity at vent or density for MER calc. Hopefully it's fixed in the new Atham code from Herzog. But from previous work I remember that it is roughly half of the input velocity, e.g., 200 m/s translates to ~90 m/s at vent. This may explain why I have never been able to have an eruption complete successfully when using ~100 m/s or lower; the code would usually end with a "cfl number too large" statement. I think it is because at the low input velocities, the eruption would put out material but it wouldn't go very far very fast and so the near vent area would accumulate and become dense with ash (in air) and it is too much for the code to work through.
---Break----
Activities for 5/14:
keep working with print statements (add myid equivalent) to find stall point
retry 36 procs with npx, npy updated
make isosurfaces in paraview with existing data
move icenter, jcenter to middle to see if that fixes the cut-off error
edits on Ch 1&2
Activities for 5/7:
Play with ATHAM output for different number of time slice outputs: is that where the completeness problem appears?
Try ATHAM output for 6x6 procs (36 total) - Used 36 procs, got immediate error
use print statements to find stalling part in output
in output file writing code: remove icenter, jcenter, etc., and replace with i, j, etc. - Complete, finally have good output
Activities for 4/30:
make isosurfaces in Paraview
run atham with wind
compare 3D heights to 2D heights -> compile into table/fig
continue with Ch 1/2 updates
finish parallel project
Activities for 4/23:
find where procs cropping in combination to solve viz issue
work on updates to CH 1&2
keep running 3D...
Activities for 4/18:
{read, review Background (Thesis_background_renew_stability1.doc)}
{read/review Intro}
visualize 3D run (play with script option; if all else fails, write short code concatenate files, remove duplicates, and plot from ASCII grid in paraview)
keep running 3D...
Activities for 4/9:
{read, review Background (Thesis_background_renew_stability1.doc)}
{read/review Intro}
visualize 3D run (play with script option; if all else fails, write short code concatenate files, remove duplicates, and plot from ASCII grid in paraview)
keep running 3D...
parallel HW4
Activities for 4/2:
{read, review Background (Thesis_background_renew_stability1.doc)}
read Overview section in workbook, use to guide Intro chapter development
Finish Intro draft
Use port connection to speed up file transfer from falcon (or check globus)
keep running 3D
try file conversion for paraview input from 3D
follow-up email to Carrie
follow up with Cody about submitting to Monsanto
Activities for 3/26:
Complete 1st draft of new Background
Outline Intro; all categories/subcategories with brief explanation/text in each to make intent clear
3D atham: run no-wind 3D versions of 2D that we have, compare to 2D stability and plume heights
play with file conversion code to get output into Paraview input style
Activities for 3/19:
continue to work with Ben about netcdf link problem
run ATHAM in 3D - start by re-creating 2D eruptions
continue to update Background
Activities for 3/12:
continue to work with Ben about netcdf link problem
run ATHAM in 3D - start by re-creating 2D eruptions
{Review slides}
edit slides, practice talk
Activities for 3/5:
email Ben Nickell about netcdf on falcon
complete tropical collection - Completed 4 runs (100-400 m/s) under tropical conditions
continue to update Background - No updates this week, I've spent most of my time on prepping colloquium talk and on programming exam
prep colloquium talk; bring draft slides - Draft available, need feedback
MER vs. col height: Woods (1988), plus things that reference it. Specific examples in Encyc. of Volcanoes p 265 - Searching yielded no results for recent MER vs height.
Activities for 2/26:
1 p addendum summarizing goal changes, progress
continue with faux polar - Completed, working on tropical eruptions now
find references for MER vs. column height, evaluate against current output
redo on temperate/tropical plumes, to get MER
try to update paths on falcon - Just need location of netcdf, unable to find it using 'module avail' or 'module spider netcdf'
continue Background updates
Activities for 2/19:
If no response from SG by Monday, resend with cc SKN - SG Responded with grammatical edits, is looking forward to seeing prospectus addendum with updated schedule and progress thus far.
run model for faux polar tropopause and polar tropopause - Runs with true polar profile are complete, running faux polar profile now.
calculare MER - Completed for available runs
continue to play with file transfer - ATHAM transferred!! Now the paths in Makefile.COMPILE need updated.
{SKN forward INL email to BN}
continue Background updates
Activities for 2/12:
check in with SG after 2/6 Sent email, awaiting response
{SKN: tropo text; follow up with MH}
Finish minor updates to Dispatch
ATHAM - run model for restricted vent to compare to existing suite; pay attention to stability and fingering deposition
transfer atham code to Falcon - Tried, failed. Got errors involving path names during attempts.
calculate MER for runs (add output for density at top of crater, use velocity to top of crater, area of crater) - Do I use vent velocity from initial conditions or wnew at each grid point as an average?
update Background for morphology theme switch
post the paper summaries file in dropbox, add 2 more
read up on movies in Paraview
Activities for 2/4:
(remember to check back in with SG after 2/6)
write van Eaton Dispatch draft (bring text, figures, links, keyword suggestions)
Continue with collapse identification; run eruption through full length of simulations (at least 1 hr), always use same time step; make word doc showing peak image and concentration ratio
read & write brief (2 line?) summaries of key points for 3-4 papers
look up Tupper paper Got it, placed it into dropbox/papers/Column_Collapse1
update Background for morphology theme switch
{reply to MH; read/review tropo sensitivity}
Activities for 1/28:
email SG gentle reminder. Include attachment of prospectus.
{read/comment on Background}
fix Background citations (add as necessary, compile complete full ref list) Updated, only a few questions/comments remain
check RSA token for instructions, let SKN know (forward)
Finish tropopause sensitivity text Draft complete, see document for comments -BN
write first draft of VanEaton et al. Dispatch Not completed, paper has been read & highlighted
{re-email for code updates}
Going through existing runs: sort by which collapse, which partially collapse, which rise (make rule for partial vs. stable based on summation of mass in max plume time slice) Started, need feedback on calculation method
put together list of at least 5-10 papers we should review on collapse regimes {make sure SKN has access, too} Placed folder (named: Column_Collapse) in 'papers'.
Activities for 1/14:
follow up with SG re: prospectus Awaiting Response / signature - BN
finish Background updates The Final draft is ....finalized, needs references sorted out. Needs final edits from SKN.
submit INL form Account set up (received an emailed response), waiting for dongle to arrive in mail.
plot clasts to check PDC vs plume transport Using ParaView to plot these now, Excel can't handle the number of data points (>1 Million). ParaView is incredibly slow with this, however. - BN
Write section on sensitivity to tropopause height (2 week effort, bring copy to demonstrate effort to next meeting)
Select next Dispatch topic (look for Van Eaton) (consider emailing her to ask for copies of slides) Emailed and responded back to, forwarded to this site: https://avaneaton.wordpress.com/projects/modeling/ Need to figure out how (assuming we can) to use UNIDATA IDV to display data (Grads binary grid files?) - BN
Start on table of eruption/ambient conditions for ATHAM 3D Started, trying to determine the values to have constant throughout different eruptions - BN
Activities for 12/11:
complete, final poster due to SKN no later than 11am Monday
finish projects/exams
make a list of goals for over break
Activities for 12/4:
complete and finished draft of poster
study for exams; finish class projects
Activities for 11/20:
revise poster statements
{SKN send 3D imagery}
revise Dispatch per notes
finish last sections of Background per discussion
add id to clast tracking output file
plot trajectories for various clasts per eruption (think about this for poster) (use grep line from discussion)
continue to play with eruption vent sizes, velocities
check Carazzo et al. for eruption ranges
email Carrie about GIS internship position
Activities for 11/13:
poster: 1 sentence central idea, 3 sentences support/explanation
confirm access to Illustrator
finish Dispatch edits
finish Background draft
try increasing vent size for really big eruptions to look for impact on col height
figure out if clasts from PDC eruption were in PDC or the plume portion (need to check trajectories)
Activities for 11/5:
Confirm travel dates with Nick, Doug, and Chris before finalizing travel paperwork
- finish travel forms
finish Dispatch edits
finish Background draft
try increasing vent size for really big eruptions to look for impact on col height
figure out if clasts from PDC eruption were in PDC or the plume portion (need to check trajectories)
start AGU poster - get layout and sections started, check with Diana on height restrictions
Activities for 10/30:
{transfer/test code for new computer}
why isn't paraview point-query displaying conc?
to nomogram-basis table: add vent size, vent velocity
decrease ash tracer densities; try to hit bigger/smaller events
1) finish prospectus edits
convert at least 1 atm profile to vectors
2) more Background updates
3) Dispatch edits
AGU travel forms
Activities for 10/23:
(1) plot heights vs velocities (nomogram) (check that color ramp is the same)
(1) drop copy of SG's comments off to SKN
(3) establish rainy vs dry conditions, compile appropriate atmospheric profiles for prehistoric events -- be prepared to justify decisions
(1) continue prospectus edits
(2) Background edits (address current comments, add minimum 4 pages)
(1) test azimuth conversion equations for all quadrants
(hold till next week on Dispatch edits)
{follow up with minerve vs. minerve2 issue}
Activities for 10/7:
continue running atham with full output for excel vs paraview picks
get Background up to min 5 clean pages (can use holders for some refs, etc.)
establish rainy vs dry conditions, compile appropriate atmospheric profiles for prehistoric events -- be prepared to justify decisions
text velocity conversions to make sure facing correct directions
update prospectus
write draft of Dispatch (MMC)
Activities for 10/2:
compare Paraview height picks to Excel picks (make table)
start converting Background to text; min 5 pages
establish rainy vs dry conditions, compile appropriate atmospheric profiles for prehistoric events -- be prepared to justify decisions
convert wind from knots/degrees to U and V velocities
keep fingers crossed for minerve memory update
{Intro!!!!!}
start updating prospectus
(for next time: Dispatch)
Activities for 9/25:
finish paraview tutorial suite
use tutorial info to contour/colorize 2D ATHAM output (slice)
{read/edit Intro}
flesh out Background outline down to paragraph-level bullets; eschew meta-ness
get atmospheric data for eruption suite; vent diameter and depth; median and stdev of grain sizes
meet with SG and/or CB about Arc interpolation problems
email MF about getting Matlab code for flowfield generation (vectors)
Activities for 9/18:
continue work thru tutorial (paraview)
continue on Intro
Background - firm up next level of sub-headers
input folders (see below)
updates to Dispatch
{continue compiler issues}
Activities for 9/11:
go through ParaView tutorial using sample data
ping SG
more Intro updates
detailed outline (section/subsection headers) of Background (Ch2)
organize input folders for each of the target eruptions (vent width, height, atmosphere, grain size dist., etc.) Keep notes on refs.
during week, send Dispatch draft to SKN
Activities for 9/4:
sort out paraview contouring problem
make updates from SG, if applicable
make updates on Intro
cross-check model classifications in lit review draft
identify 3-5 well-documented deposits for model training
finish Dispatch rough draft
Activities 8/28:
figure out how to plot points with color designations in Paraview (like in Arc)
update prospectus, send to SG for comments
send Intro to SKN
{edit Intro}
Expand on Lit Review
Flow chart methods
{contact Jonathan again about compiler build -- done?}
rough draft Dispatch (MMC)
Activities for 8/21:
plot 2 and 3D images in paraview - use user's manual and online documentation
practice making new files of extracted output using grep and >
follow up with Diana and/or Carrie/Lori about Vulcan license issue
{read new prospectus draft}
with approval, send prosp. to SG for comments
Intro chapter - how to place problem statement and hypothesis in first 2 pages of text, with italics (see Polun; Statement of Problem; Scope of Work; Significance)
standby for cluster updates from Shannon/Jonathan
plot atham 2D outputs to see if getting PDCs is causing lower heights for faster ejections
Activities for 7/15:
re-run new heights using centered icenter, see if that changes strange acceleration patterns on centerline
write out and plot 2D slice of ash and velocity (wnew)
keep playing with Vulcan
download/install Paraview, check on data format requirements
{SKN: continue atham fight on clusters; read/edit outlines and drafts}
work on fleshing out Intro
start abstract for AGU
<field work>
Activities for 7/8:
run with corrected sim times to compare wind-derived height to ash conc. derived height
withdraw workshop registration
plot and display sample data in Vulcan
edit prospectus
write 1st draft of introduction
outline of lit review chapter
outline of methods
{atham wars}
Activities for 7/1:
send SKN prospectus
{edit prospectus}
move col height output code into gradspic zone, don't cut off with ash concentration (will give 1 W-wind profile, at final time step)
- check new output against ash-based plume top calculations
update atham compilation file if we get word back from J
submit proposed travel budget to SKN for Vulcan (dates, travel, food, lodging)
<break due to end-o-semester, travels>
Activities for 4/30:
add code to output vertical velocity and ash concentration above vent, use to identify plume top
re-run current models to check change
read MMC paper
Activities for 4/23:
change current location of maxH calculation in code to remove from loops
rerun current 3.2 and 6.4 models, identical to before, to see if max height is reproducible
Continue war on ATHAM -- compiler issue?? Try on luna
read Herzog et al. (98)
Dispatch recent MMC paper
Activities for 4/9:
compare nx120 zoom50 and zoom100 to other models for col height.
based on preferred fit, complete diagonals for that # grid points and zoom
resend message to CoSETech via geohelp email
play with connecting netcdf options (use "locate netcdf" to get started)
Sims: PDAC (2D or 3D), Darcy Ogden, SuKo07
Activities for 4/2:
put together new diagonals 30zoom and 50zoom
finish Connor & Volentik for bestiary
contact CoSETech about compiler error, why emacs won't open files
compile ATHAM on minerve
pick next Dispatch topic
Activities for 3/19:
update nomogram diagonal positions for sparse-output entries (continue playing)
notes on schedule: need to pick 2 non-dept classes, currently assuming intro python and advanced programming
for bestiary: look up Connor and/or Volentik stuff on tephra model
edit Dispatch
transfer ATHAM to cluster; check for netcdf; check for compiler
Activities for 3/12:
play with nreps vs. periodt in code.
check problematic outlier values in current nomogram lines
for other vars constant, how does zoom impact col height? How does turb length scale effect?
Dispatch draft
Reading: go back to family tree of models. add 2 more entries. add info on later papers using it.
bring list of classes (incl. #'s) completed
Activities for 3/5:
in volc models using Morton, Taylor, Turner (195x?) entrainment, does coefficient value increase with height?
keep working on diagonal line start for nomograms
try various zooms to test stability and run duration
pick a paper for abstract (let SKN know)
pick next DIspatch topic
Activities for 2/26:
edit Dispatch per discussion
complete ATHAM deposition plots
modify output from ATHAM to include vertical flow (for plume top calculation)
run for even smaller vent speeds
Abstract SuKo05.pdf
Activities for 2/19:
make ATHAM deposition plots like we discussed in meeting for rho = 2500, 500. Do for "small" and "large" eruptions
make figure illustrating 2D solution relationship between eruption column height and grain size distribution
edit Dispatch based on discussion
abstract OgWo08
Activities for 2/7:
Try random number seeding to change Random_Toy.f90
abstract Johari (2006)
write dispatch 1st draft on one of papers we talked about
keep running atham 2d
Activities for 1/29:
read & abstract Johari (2006), Bursik et al. (2012)
work out file access b/w virtual machine and regular box
plot tephra: in air and deposited
read atham_dep.F90
pick a topic for next dispatch
Activities for 1/22:
try grads 1.6 (or so) for qview; if that fails try switch to windows version
run ATHAM with deposition: change clast sizes & distribution, change eruption conditions, NO WIND. plot output to check distances
read
Activities for 11/20:
install grads (follow INSTALL directions)
try to see something in qview
play with atham inputs
read abstract 1 family tree paper, plus Burden et al.
work on internship apps
SC13!
Activities for 11/13:
rebuild netcdf with proper links b/w gfortran and gcc
atham (??)
read/abstract 2 papers suggested by Family Tree, fill in as appropriate (BuPh)
register (check w/ CB re: geostats)
look into summer internship opportunities
Activities for 11/6:
check $PATH for netcdf build; chat with BN about netcdf3.inc mystery
once netcdf sorted out, celebrate... and run ATHAM
edit Dispatch
put together family tree of ash fall models, including majors refs
Activities for 10/30:
{SKN: get some version of ATHAM running on shasta}
new draft for Dispatch
abstract a Fall3D paper (Folch, Costa, etc.), find online
stay in contact with COSE Tech; contact about expanding VPN authorization to shasta
Activities for 10/9:
continue work on Dispatch
add necessary files for cgg installation
install gcc
install g95
abstract paper Papale and Rosi (1993)
Activities for 10/2:
dispatch article
abstract paper Herzog et al. (1998)
continue the good fight (compiler, atham)
Activities for 9/25:
install/build g95 in Linux
try running atham ("make clean" "make" "make run" from directory holding source, input, output, etc.)
abstract Tanaka; Searcy et al. (1998)
send Susquehanna to Sh
{post Susq}
find another recent paper of interest for Dispatches
Activities for 9/11:
read/abstract BuKo09, ObHe98
install linux on virtual box, move ATHAM files and other stuff over to linux side
fix atham Makefile.COMPILE addresses
try running atham ("make clean" "make" "make run" from directory holding source, input, output, etc.)
derive Eqn 3 from Bu01 using earlier eqns and Ue = kW (Morton, Taylor, Turner, 1956)
Activities for 9/4:
revise Susquehanna
read/abstract 2 papers: Bu01.pdf and Woods (1988)
scan Woods(88) (return hard copy to Sh)
bring laptop Friday to install ATHAM
after Friday, run ATHAM (try not to crash too often)
Activities for 8/12:
email Sh revised comm article
pack and move! (Welcome to Poky!!!)
Activities for 8/7:
edit website, find cool photo (?)
abstract 2 papers (see email)
find one 2013 publication that interests you and write community translation, find photo to go with it, include link to source, a possible title, and suggested tags (send original to Sh)
SC application
Activities for 7/10:
read/abstract BoPh05 (see email)
populate website
{SH - go through code/report}
Activities for 7/3:
Read and abstract Veitch and Woods (2001)
F90 code for sin wave, I/O
