The em from geoscixyz

short titles for navigation bar?

The long titles don't look very good on the navbar. We might be able to assign an abbreviated title?

Transient Electric Dipole

Pages that need to be filled in:

Located in

maxwell1_fundamentals/
   maxwells_equations/
      maxwells_equations_in_homogeneous_media/
         time_domain/
            dipole_sources/
              electric_dipole/

See attached notes:

transient_electric_dipole.pdf

http://em.geosci.xyz/en/latest/_images/LenzsLawDiagram.png is not properly referenced, and with the copyright stamp on it, it doesn't look like we have permission to reproduce it. Wikimedia commons has a pretty good database of figures (https://commons.wikimedia.org/wiki/Main_Page), and the licensing attached to them is pretty transparent, so that is a good place to look. Otherwise, this figure should be re-created by us

Maxwell IV: TDEM

Similar structure to #101

Geophysical Surveys / Fundamentals

MIM #2

http://em.geosci.xyz/content/case_histories/mt_isa/data.html
The writing is pretty terse. Anything more to be added? Also why is one IP pseudosection truncated and the other not? We were unable to fit the long off-set IP data and hence they were winnowed in the inversion. The paper talks about this. Expand as you can and I'll try to fill in the blanks. Your images are great but they will have more impact if there is extra dialogue/learning associated with them.

http://em.geosci.xyz/content/case_histories/mt_isa/processing.html
Extra comments about the individual 2D inversions on p-dp or dp-p?

_A resistive domain on the western edge of the survey, marked by a steeply dipping contact near location 11,300 m, which may correspond to the Surprise Creek Formation
      Hard to locate 11,300 on the image.


      The synthetic geology model is complicated and the initial paper was never interpreted in terms of that complexity. I think the essential geology is from east to west

(a) eastern volcanic zone (resistive)
(b) native Bee which houses breakaway shales and norvit
(c) potential western Surprise Creek (which is resistive) It may be that the Moondarra is not be a significant unit. The western side is thus Surprise Creek and Eastern Volcanics
(d) between (b) and (c) there might be another resistive and slightly conductive zone (moondarra and Eastern Creek volcanics quarzites) but we can't distinguish between the quartzites and surprise creek and also between moondarra and native Bee. Trying to tie our inversion images to all of these elements means were a likely over interpreting, and in process, making things complicated.

A narrow, steeply dipping conductor near 12,300 m, adjacent to a more resistive unit, possibly the conductive Breakaway Shale within a resistive Native Bee Siltstone._

My story, and the one laid out in the paper, is consistent with
(a) resistor in the west
(b) a background low conductivity unit that includes a mid-sized conductor (novit) and a large conductor (black shale)
(c) and for the southern half: a resistive unit to east and indication of a conductor.

If we can simplify our geology to that general model then we can be in step with the images and geologic interpretation presented in the case history.

Fig 89: Is this the final figure? I thought the max conductivity was 0.4 S/m for the contaminating block on the west.

http://em.geosci.xyz/content/case_histories/mt_isa/processing.html
2D IP inversion: What happened to some of the northern lines?
Is there a story that can be attached? Something to be learned by the reader?

http://em.geosci.xyz/content/case_histories/mt_isa/processing.html
The 3D IP inversion is very complicated. By changing the iso-surface limits can we get something that looks like Fig 4b in the initial paper?
Also, as per the initial paper (Fig 4a, Fig 4b) can we put on a line for the Breakaway shale and the Mt. Novit horizon?
(c)

Need to say something about the large conductor on the west

http://em.geosci.xyz/content/case_histories/mt_isa/interpretation.html
Let's talk about this. I worry that we are over-interpreting. See my comments above.

http://em.geosci.xyz/content/case_histories/mt_isa/interpretation.html
Again, we should discuss. My suggestion is
(a) keep the intepretation simple. If we can reach the same general conclusions as the initial paper then we will make an impact.
In this regard, you have some movies, but can we make exactly the same movie as Roman did. Le'ts look at it and see what we think. That movie, although simple, had a huge impact on the audience and it made important statements visually without the need for dialogue.

(b) Perhaps more intricate discussion and geologic interpretation can be put into a second "lessons worth highlighting" There we can discuss all of the items of concern and the potential for more intricate intepretation.

http://em.geosci.xyz/content/case_histories/mt_isa/synthesis.html
Synthesis should recap the ability for DC and IP to delineate between the two conductive and chargeable units and the benefits of looking for two physical properties. Do the best you can and we can discuss.

Geophysical Surveys: Example?

Example is not very inviting / motivating

"Motivation"
"Motivating Example"
"There and back again"

- ...

Harmonic Electric Dipole

Content for Frequency Domain electric dipole

Pages that need to be filled in:

Located in

maxwell1_fundamentals/
   maxwells_equations/
      maxwells_equations_in_homogeneous_media/
         frequency_domain/
            dipole_sources/
              electric_dipole/

See attached notes:

harmonic_electric_dipole.pdf

Geophysical Surveys / Airborne TDEM

Purpose!

For all topics, there should be a purpose! See how to highlight it using a .. topic:: box in the wiki: https://github.com/ubcgif/em/wiki/Development-Notes

Transient Magnetic Dipole

Content for time domain magnetic dipole

Pages that need to be filled in:

Located in

maxwell1_fundamentals/
   maxwells_equations/
      maxwells_equations_in_homogeneous_media/
         time_domain/
            dipole_sources/
              magnetic_dipole/

See attached notes:

transient_magnetic_dipole.pdf

end youtube videos on blank screen or initial image

https://developers.google.com/youtube/iframe_api_reference

permittivity

\varepsilon or \epsilon ??

broken link

The link to the video: http://video.mit.edu/watch/physics-demo-lenzs-law-with-copper-pipe-10268/ on the page em/content/maxwell1_fundamentals/fundamental_laws/lenz.rst is no longer playing :(

So we should find a new one or remove it for the time being.

If you happen to find a video on youtube we can embed it using: https://pypi.python.org/pypi/sphinxcontrib.youtube

@micmitch , @sgkang , @dccowan : can you help out here??

Google App engine site

The site is now too large to build through read the docs, so we could...

write it to a google app engine site (http://emgeosci.appspot.com)
replace subdomain with app engine site
set up analytics
ideally, we do this from travis instead of a manual deployment on updates to master

Technical House-keeping on Gauss-Electric

Looking good! These are just a couple minor technical house-keeping items:

after each new environment is finished (ie .. math::, after a table or an itemized list) a new line needs to be included (it signals the end of the environment and makes the build more stable)
->>fixed (Dom)
need to attribute / cite the gif (unless it is something you made??)
->>New figure from us (Dom) --> Very cool!!
for equations you can make the brackets look better when there are large symbols using \left( \right) (ie. equation after 7)
->>Fixed (Dom)
divergence should be \mathbf{\nabla} b/c it is a vector operator
->> Is it me or \mathbf{\nable} doesn't do anything? I did a \boldsymbol{\nabla} instead (Dom)

@fourndo , @lacmajedrez , @focus-shift, @DanielBild-Enkin

TODOs motivated from Bookpuronong

Skin depth and Diffusion distance (to explain depth information; where do we put?)
Dipole moment (needs to explain Tx moment; where do we put? @lheagy )
Footprint of a system (how do we compute this? any ideas?)
Resistive and Inductive limits (possibly from 3 loops)
Scaling with induction number (? not sure what do you mean @yangdikun)
Frequency to Time transform (where do we put? @dougoldenburg )

Online Binders are broken: SimPeG.Examples not found

Biot Savart Law

The Biot-Savart Law is not an independent law but is derivable from others. Nevertheless it plays an important role in much of our analysis so we have an entry under "fundamental laws".
Also, currently Biot Savart is brought into Gauss's law for magnetics but without any indication of what it is.

Math formulas do not display well

Some maths formulas do not display well in the new outfit:

http://em.geosci.xyz/content/maxwell2_dc/fields_from_grounded_sources_dcr/electrostatic_sphere.html

other example on http://em.geosci.xyz/content/maxwell2_dc/governing_equations/interface_conditions.html?highlight=interface%20condition

Useful Math Appendix

@dccowan suggested an appendix containing derivations, useful math that also contains scripts / resources for using these. Please add topics here!

fourier transform
...

TODOs: List of simple background theory pages (needed for sphere)

Theory of Frequency to Time domain transforms (inverse Fourier, inverse Laplace, inverse sine/cosine)
Self-demagnetization page
Frequency-dependent wave attenuation
The field from a magnetic dipole

Maxwell II: DC

Wavenumber page not in toctree

#67 introduced the wavenumber page (wave_number.rst) inside of /Users/lindseyjh/git/geosci/em/content/maxwell1_fundamentals/physical_principles/maxwells_equations_in_homogeneous_media that is not currently in a table of contents tree.

The content should be included, as relevant, to the wave propagation in free space (topic of the pull request #58) @sdevriese, you may want to take a look at this file and see if the content @micmitch generated meshes with what you have done

MIM issues #1

Mt. Isa: opening page: paper does not come up

http://em.geosci.xyz/content/case_histories/mt_isa/setup.html
color codes on the synthetic??; Mt Novit Horizon in the circle should have its own color; it'shosted either by Native Bee or Moondarra Siltstone if we go by the text; For this diagram Mt. Novit is hosted by Native Bee (background blue) and Moondarra siltstone is on the east. Let's stick with that.

http://em.geosci.xyz/content/case_histories/mt_isa/properties.html
The Moondara siltstone and Native Bee are indistinguishable cousins from our perpsective. They are both moderately resistivity (10-15 ohm-m); The Mt Novit horizon, when mineralized will be more conductive than these hosts. (0.7 ohm-m for 4.8% Cu). The Breakaway shale is conductive
Maybe we should provide numbers:
Low: rho>> 15 ohm-m
Med rho ~ 10-15 ohm-m
High rho << 10 ohm-m
this would mesh with the text and also help us out later when we think of Mt.Novit horizon having a "moderate conductivity: bigger than background siltstone but less than the Breakaway shales)

What is justification for Moondarra unit being chargeable? Also, why are Eastern Creek Volcanics listed as chargeable?

http://em.geosci.xyz/content/case_histories/mt_isa/survey.html
Does the pseudo-section fill out? I don't think the current plot is overly informative.

"The unit of interest is the Mt. Novit Horizon which is conductive compared to the host Moondarra Siltsone. We also expect a large conductive contrast between the Breakaway Shale unit and the Native Bee siltstone, which may also be a host for mineralization. "

In our diagram earlier we had the Mt. Novit horizon in the Native Bee.

In the Survey Design: This is a nice section that goes from currents, to pseudo-sections to inversions.
The current density and figures are interesting but can you provide some reasons for what to look for and what information can be cleaned? Although it lengthens the presentation, having the plot with and without the conductor would be informative. Then we can state that we notice how the conductor draws in the currents.etc... Also, that meshes with the pseudo-section plots given next.

Adding show / hide options (?)

I guess this will be a useful for making concise documents.

http://stackoverflow.com/questions/2454577/sphinx-restructuredtext-show-hide-code-snippets

Geophysical Surveys / Airborne FDEM

We need reference bank ...

Maxwell III: FDEM

MIM figures

if it is easy to re-create, there are a couple figures with overlapping text and colorbars. This can be solved with plt.tight_layout() at the end of the plotting instructions in python

Fix Latex Build

inline math
add pdf build to travis testing

move code and examples

the repo https://github.com/ubcgif/em_examples has been created to hold notebook examples. This is hooked up with binders so that the examples can be run on the web without requiring python or dependencies be installed.

migrate code to em_examples repo
integrate examples with SimPEG examples
allow site to compile locally without running all of the examples (if statement in the sphinx build)

Harmonic Magnetic Dipole

Content for frequency domain magnetic dipole

Pages that need to be filled in:

Located in

maxwell1_fundamentals/
   maxwells_equations/
      maxwells_equations_in_homogeneous_media/
         frequency_domain/
            dipole_sources/
              magnetic_dipole/

See attached notes:

harmonic_magnetic_dipole.pdf

Attribution

to provide attribution for contributors!
who page with info on each author (connects to github for picture)
page level attribution with authors and reviewers.

Figure placeholders in Bookpurnong case history

Figures in "setup" and "properties" need to be remade.

Formula sheet

add a table with equation names, equations and how to include in the introduction of geosci em

DC Forward Modelling Image has spell check red underline

on the page: http://em.geosci.xyz/en/latest/content/maxwell2_steady_state/Forward_Modelling.html

MIM overview

Updated interpretation discussion

Remove circle/background from pseudo-sections (Fig 101)
Remove true model from background and add it to a third vertical panel (Figure 102).
Add larger chifact for individual 2D IP inversions - 2 northernmost lines only

change stacked 2D inversion figure (Fig 107)
Fig 104: steeper angle from meshTools so the gap does not show between line 1 and 2
Write description for a/b in Figure 107
Fig 106/108 -> update Figures (parameters are already done) (these images will also go onto interpretation with annotations)

Synthesis: old versus new (plan view) with DC and IP

Site layout and user interaction

Geophysical Surveys / DCR

Spell Check in testing

We can add a spell checker on the text through - http://sphinxcontrib-spelling.readthedocs.io/en/latest/customize.html. It looks reasonably flexible, so we can add words to our own dictionary, etc.