fixes. colors. links.

Author: sbryngelson

docs/assets/extra.css

@@ -1,3 +1,5 @@
+@import url('https://fonts.googleapis.com/css2?family=IBM+Plex+Sans:wght@400;500;600&display=swap');
+
 :root {
   --md-primary-fg-color: #262829;
   --md-primary-fg-color--light: #343a40;
@@ -11,11 +13,15 @@
   --md-default-bg-color--light: #282a2a;
   --md-default-bg-color--lighter: #313333;
   --md-default-bg-color--lightest: #3a3c3c;
+  --md-code-bg-color: #1e2b38;
+  --md-code-fg-color: #d0dde8;
 }
 
 .md-header {
-  background-color: #262829;
+  background-color: #242627;
   color: #fff;
+  border-bottom: 1px solid #333637;
+  box-shadow: 0 1px 12px rgba(0, 0, 0, 0.35);
 }
 
 .md-header a,
@@ -33,11 +39,16 @@ a {
   color: #c0995e;
 }
 
+a:visited {
+  color: #c0995e;
+}
+
 a:hover {
   color: #d4b07a;
 }
 
 .md-nav__link--active,
+.md-nav__link:visited,
 .md-nav__link:hover {
   color: #c0995e;
 }
@@ -52,10 +63,25 @@ a:hover {
   color: #c0995e;
 }
 
+.md-typeset a:visited {
+  color: #c0995e;
+}
+
 .md-typeset a:hover {
   color: #d4b07a;
 }
 
+.md-typeset a code,
+.md-typeset a:visited code {
+  color: #c0995e;
+  background-color: transparent;
+  border-color: rgba(192, 153, 94, 0.3);
+}
+
+.md-typeset a:hover code {
+  color: #d4b07a;
+}
+
 .md-header__button.md-logo {
   display: none;
 }
@@ -64,58 +90,106 @@ a:hover {
   display: none;
 }
 
-/* Top navbar matching comp-physics.group Bootstrap navbar */
+/* Top navbar — mirrors comp-physics.group Bootstrap navbar exactly */
 .md-banner {
-  background-color: #262829 !important;
-  padding: 0 1rem;
+  background-color: #242627 !important;
+  border-bottom: 1px solid #333637;
+  box-shadow: 0 1px 12px rgba(0, 0, 0, 0.35);
+  padding: 0;
+}
+
+/* Material wraps announce content in .md-banner__inner.md-grid.md-typeset —
+   bust out of its max-width and padding so our navbar controls its own layout.
+   Also reset font-size to 16px so rem units inside resolve correctly. */
+.md-banner__inner {
+  max-width: 100% !important;
+  padding: 0 1rem !important;
+  margin: 0 !important;
+  font-size: 16px !important;
 }
 
+/* max-width container centred inside the full-width banner, brand left then links */
 .cp-navbar {
   display: flex;
   align-items: center;
-  justify-content: center;
-  width: 100%;
-  height: 3.5rem;
-  gap: 2rem;
+  max-width: 1000px;
+  margin: 0 auto;
+  padding: 0.55rem 0;
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
 }
 
 .cp-navbar-brand {
   display: flex;
   align-items: center;
-  gap: 0.5rem;
-  color: #fff !important;
+  padding: 0.25rem 0;
+  margin-right: 1.25rem;
+  color: #cec6bc !important;
   text-decoration: none !important;
-  font-size: 1rem;
+  font-family: "IBM Plex Sans", sans-serif;
+  font-size: 17.6px !important;
+  font-weight: 600;
   white-space: nowrap;
+  word-break: normal;
+  overflow-wrap: normal;
+  flex-shrink: 0;
+  transition: color 0.18s ease;
 }
 
 .cp-navbar-brand:hover {
-  color: rgba(255,255,255,0.75) !important;
+  color: #fff !important;
+  text-decoration: none !important;
 }
 
 .cp-navbar-brand img {
+  margin-right: 5px;
   border-radius: 3px;
 }
 
 .cp-navbar-links {
   display: flex;
   align-items: center;
-  gap: 0.25rem;
 }
 
 .cp-navbar-links a {
   color: #c0995e !important;
   text-decoration: none !important;
-  font-size: 1rem;
-  padding: 0.4rem 0.75rem;
-  border-radius: 4px;
-  transition: color 0.15s;
+  font-family: "IBM Plex Sans", sans-serif;
+  font-size: 16.8px !important;
+  font-weight: 500;
+  padding: 0.4rem 0.85rem;
+  white-space: nowrap;
+  word-break: normal;
+  overflow-wrap: normal;
+  transition: color 0.18s ease;
+  position: relative;
+}
+
+.cp-navbar-links a::after {
+  content: '';
+  position: absolute;
+  bottom: 0;
+  left: 0.85rem;
+  right: 0.85rem;
+  height: 2px;
+  background: #c0995e;
+  transform: scaleX(0);
+  transition: transform 0.2s ease;
+  border-radius: 1px;
+}
+
+.cp-navbar-links a:hover,
+.cp-navbar-links a:focus {
+  color: #d4b07c !important;
+  text-decoration: none !important;
 }
 
-.cp-navbar-links a:hover {
-  color: #d4b07a !important;
+.cp-navbar-links a:hover::after,
+.cp-navbar-links a:focus::after,
+.cp-navbar-links a.cp-navbar-active::after {
+  transform: scaleX(1);
 }
 
 .cp-navbar-active {
-  color: #d4b07a !important;
+  color: #d4b07c !important;
 }

docs/group-syllabus/doing-research.md

@@ -56,7 +56,7 @@ This is important for your sense of progress, as the more challenging work might
 This is also important to get exposure for you and your ideas in wider venues.
 
 3. Concurrently, try to be a supporting author on at least one other project.
-This isn't your core work; it's someone else-led.
+This isn't your core work; it's led by someone else.
 It should take less than 1/2-1/3 of a day of your time per week.
 But you have something to offer and will be listed in a supporting author position.
 Also, of the lower-risk, lower-reward variety.
@@ -106,7 +106,7 @@ For example, the authors' methods, the way they asked their research questions,
 * When you read a good paper in your research area, ask yourself what should come next.
 What assumptions do they make?
 What would make this even better?
-What are the authors missing that is not an immediate "future work"  for that scholar's arc?
+What are the authors missing that is not an immediate "future work" for that scholar's arc?
 Identifying papers like that can impact your research directions over time.
 
 * Many phenomena we see online and around technology are not, strictly speaking, new.
@@ -134,7 +134,7 @@ If the student is not excited and motivated about a research direction, the outc
 Similarly, students can pursue a project that I am less interested in, making me less engaged and less helpful as an advisor.
 The process of coming up with ideas, research questions, and project decisions thus naturally gravitates towards mutually interesting directions that overlap with existing or potential funding.
 
-At the same time, "interest splits" happen, and students often pursue questions and directions.
+At the same time, "interest splits" happen, and students often pursue questions and directions independently.
 If there's no overlap, one option is to switch advisors.
 I have had students leave me to work with other advisors as it became clear that their pursuit and intellectual passion do not overlap with mine.
 This is normal and healthy.

docs/group-syllabus/faq.md

@@ -11,7 +11,7 @@ If your question isn't answered here, please reach out to Spencer or other membe
 Our group focuses on developing computational models and numerical methods for physics problems.
 We accompany our methods with algorithms crafted to make efficient use of the latest exascale machines and computer architectures, including AMD GPUs, Arm/RISC CPUs, and quantum computers.
 We develop open-source software for these methods that scales to the world's largest supercomputers.
-Our work pushes applications forward in areas jet and rocket design, defense broadly, medical therapies and physiology, and the energy sector.
+Our work pushes applications forward in areas of jet and rocket design, defense broadly, medical therapies and physiology, and the energy sector.
 
 ### How do I join the group?
 
@@ -32,8 +32,8 @@ It ebbs and flows, depending on the interest of the students.
 
 ### What software/programming languages should I know?
 
-Proficiency in one high-level and one-level language is important.
-We often use Fortran (free-form) as a low-level language, but new projects may be more ammenable to C/C++.
+Proficiency in one high-level and one low-level language is important.
+We often use Fortran (free-form) as a low-level language, but new projects may be more amenable to C/C++.
 High-level languages are mostly up to you, though I prefer you use Python to maximize the reach of your software.
 Our group develops widely used open-source software like MFC, an exascale multi-phase flow solver.
 
@@ -82,6 +82,6 @@ See [When and where of working](when-where-working.md) for more details.
 
 Yes, taking breaks is important for maintaining productivity and mental health (at least for most folks).
 Typically, students take 2-3 weeks of vacation per year, plus university holidays.
-This is flexible, so just talk to Spencer and coordinate with Spencer in advance, especially for longer absences.
+This is flexible, so just talk to Spencer and coordinate in advance, especially for longer absences.
 You may find yourself taking semi-vacations, where you aren't in town but find yourself doing some side-work for fun anyway.
 This is up to you.

docs/group-syllabus/figures.md

@@ -131,7 +131,7 @@ Common guidelines are
   * A violation would be using such a color scheme for data that varies from 0 to 1
   * In 2D settings, Paraview uses, by default, a lighting scheme that modifies the colors, including making white appear sand colored. Alleviate this by going to `View -> Light inspector` and deselect `Light Kit`.
   * Adjust the RGB values of the color bar to let the unique/special value be exactly white if the data is centered at the unique/special value.
-* Using a monochromatic color scheme (e.g., from white to black) for data that vary uniformly as above, say from 0 to 1.
+* Use a monochromatic color scheme (e.g., from white to black) for data that vary uniformly as above, say from 0 to 1.
 * Use a tri-color scheme that centers the color at black or white, e.g., the Paraview default red-white-blue for nominally centered data at a special or reference value, like 0 or 1.
 
 ## Coordinate direction arrow triad.
@@ -205,7 +205,7 @@ __An exception__ to the above is if the figure contains no text or equations, li
 
 **Rule:** Use vector graphic formats (PDF, please) for all plots that involve text or equations.
 
-**Rule:** Use the same color palette for all of your figures (not including flow visualizations) and your main text (see [formatting](formatting.md)]).
+**Rule:** Use the same color palette for all of your figures (not including flow visualizations) and your main text (see [formatting](formatting.md)).
 
 An excerpt from [Formatting your work](formatting.md).
 

docs/group-syllabus/formatting.md

@@ -19,7 +19,7 @@ From [here](https://www.annaclemens.com/blog/figure-graph-data-vizualisation-plo
 
 * Use LaTeX for all of your documents.
 * Make sure your documents _do not_ compile with errors, especially if you are using Overleaf!
-* If you have warnings, understand where they warnings come from. They may be signaling something important!
+* If you have warnings, understand where those warnings come from. They may be signaling something important!
 * On my local computer, I like using `latexmk` for compilation.
 * __Put each sentence on one line of source `.tex` code__
 
@@ -136,9 +136,10 @@ Some examples and common errors:
     * Not like this: _A Gaussian Moment Method and its Augmentation via LSTM Recurrent Neural Networks for the Statistics of Cavitating Bubble Populations_
     * And definitely not like this: _A gaussian moment method and its augmentation via lstm recurrent neural networks for the statistics of cavitating bubble populations_
     * Accomplish this via the `.bib` entry, like this
-    ```tex
-    title = {A {G}aussian moment method and its augmentation via {LSTM} recurrent neural networks for the statistics of cavitating bubble populations},
-    ```
+
+        ```tex
+        title = {A {G}aussian moment method and its augmentation via {LSTM} recurrent neural networks for the statistics of cavitating bubble populations},
+        ```
 
 * Book titles are usually capitalized as you enter them verbatim (capitalization and all) in the `.bib` file. So, be consistent when citing book titles!
     * Like this:
@@ -168,11 +169,14 @@ __Note__ the use of `\citep{ref}` and `\citet{ref}` here.
 Text `\citet{ref}` instances can be used as nouns but parenthetical references _cannot_.
 
 * This is OK (via `\citet{ref}`):
+
     > So and so [1] did this awesome thing.
+
 * This is not (via `\citep{ref}`):
+
     > [1] did this awesome thing.
 
-Always prevent line-breaks via tides `~` between a parenthetical reference and the text before it.
+Always prevent line-breaks via tildes `~` between a parenthetical reference and the text before it.
 For example:
 
 * This is correct: `The algorithm is fast, but not as fast as possible~\citep{ref}.`
@@ -181,17 +185,22 @@ For example:
 We generally want our references at the end of sentences unless they are part of a long list.
 
 * Incorrect:
+
     > The LBM method [1] is not as accurate as the finite volume method [2].
+
 * Correct:
-    > The LBM method is described in So and So [1]. However, is not as accurate as the finite volume method [2].
+
+    > The LBM method is described in So and So [1]. However, it is not as accurate as the finite volume method [2].
+
 * And this is also acceptable
+
     > Cavitation is seen in many engineering applications, including submarines [1], pumps [2], and medical devices [3].
 
 ## Creating your bibliography
 
 * Use `bibtool` to remove unused entries from your bibliography (`.bib`) file
     * Remove all unused bibliography entries from your `.bib` file. To do this,
-        * Make sure you have `bibtool` installed your your system
+        * Make sure you have `bibtool` installed on your system
         * Copy a `bibtool.config` file to your document path, mine is located [here](https://github.com/comp-physics/group-docs/blob/master/templates/paper/bibtool.config)
         * Compile your document (I prefer `latexmk` for this, but a combination of `pdflatex` and `bibtex` also works).
         * Use the command `bibtool -r bibtool.config -x main.aux > test.bib`
@@ -254,7 +263,7 @@ First, labeling them appropriately as
     \label{e:lineareqn}
 \end{gather}
 ```
-and then reference then via `cleveref`! As `\cref{e:lineareqn}`.
+and then reference them via `cleveref`! As `\cref{e:lineareqn}`.
 
 Treat your equations as nouns, and never use the abbreviation "eqn." before it.
 

docs/group-syllabus/funding.md

@@ -12,7 +12,7 @@ You also do not pay to attend conferences, this is covered via research funds.
 It is my role to make sure that you are supported by an RA, TA, or fellowship for as much of your Ph.D. as possible.
 Your Ph.D. program will require some (typically two) semesters of TA during your Ph.D., though you could be asked to do more of them.
 
-RAs generally means some sort of grant or research award supports your work.
+RAs generally mean some sort of grant or research award supports your work.
 Again, it is my role to raise this money to support your research, or to fit your research into funding that I already have.
 It is also possible that later in the Ph.D. I will ask you (or you will initiate) for your help in writing a grant proposal in your area.
 This is good practice for you as a future scientist.

docs/group-syllabus/going-to-conferences.md

@@ -85,7 +85,7 @@ Spencer is rather busy and does not have time to help you with your slides in th
 3. Prepare a nice visual slideshow/poster that keeps your audience engaged and interested in your work.
 Your goal is to make everyone read your papers and consider using your methods.
 Practice your presentation multiple times; I recommend at least 10 practice talks with yourself.
-__Don't wait until the last minute to do this:__ The conference is a time for listening to other people's presentations and making connections, not for practicing your  presentation or doing homework.
+__Don't wait until the last minute to do this:__ The conference is a time for listening to other people's presentations and making connections, not for practicing your presentation or doing homework.
 
 4. Before you go to the conference, check the session schedule and decide which ones you want to attend.
 Look for interesting papers and authors.

docs/group-syllabus/improving-your-writing.md

@@ -58,7 +58,7 @@ Such mistakes are a quick way for an editor or reviewer to perceive your work as
 
 One should keep styles consistent within a manuscript.
 You might be forgiven for even poor style choices if you are consistent.
-Please look at the [these](formatting.md) documents for more.
+Please look at [these](formatting.md) documents for more.
 Note that this consistency extends to the level of detail throughout the paper.
 A detailed introduction is best matched with a results section that achieves a similar level of detail.
 
@@ -105,7 +105,7 @@ You can consult replacement lists for common mistakes:
 These lists help me realize, "Hey, I write wordy phrases like this all the time!"
 Use the lists to learn the general ways one ends up with low information-density writing.
 You can then identify similar phrases in your writing.
-Often, eliminating them is relatively easy, but noticing them is (at first).
+Often, eliminating them is relatively easy, but noticing them is hard (at first).
 
 Conciseness can be viewed in a broader sense.
 For example, you should structure your paragraphs such that you aren't repeating information.
@@ -148,7 +148,7 @@ See, for example, the first figure in my paper, "Fast Macroscopic Forcing Method
 * Avoid redundancy. For example, use "investigate" instead of "conduct an investigation of".
 * Use active voice. Although not always possible, most text should be in an active voice.
 * Avoid inappropriate language. Keep words like "really, actually, pretty much" for social networks.
-* Avoid rare words and latinisms. Non credo all readers know the meaning.
+* Avoid rare words and latinisms. Not all readers know the meaning.
 * Keep abbreviations to a minimum. Abbreviations are hard to read, consider just spelling it out.
 * Beware of zombie nouns. Utilization of nominalization is the causation of distraction.
 
@@ -174,7 +174,7 @@ See, for example, the first figure in my paper, "Fast Macroscopic Forcing Method
     * Never use a foreign phrase, a scientific word, or a jargon word if you can think of an everyday English equivalent.
     * Break any of these rules sooner than say anything outright barbarous.
 
-* Kill your darlings. Sometimes, you'll write a so elegant and well-crafted phrase that it jars with the rest of your writing and pulls the reader out of the flow. So cut it. As Stephen King once put it: _'Kill your darlings, kill your darlings, even when it breaks your egocentric little scribbler's heart, kill your darlings.'_
+* Kill your darlings. Sometimes, you'll write such an elegant and well-crafted phrase that it jars with the rest of your writing and pulls the reader out of the flow. So cut it. As Stephen King once put it: _'Kill your darlings, kill your darlings, even when it breaks your egocentric little scribbler's heart, kill your darlings.'_
 
 * If you want to describe a figure/table in the results text, it can help to imagine you're giving a seminar. What features would you draw your audience's attention to? What would you tell people about during coffee break?
 
@@ -228,5 +228,5 @@ Over the years, I found the documents below helpful for improving my writing:
 * [Writing a science paper some dos and don'ts](https://www.elsevier.com/connect/writing-a-science-paper-some-dos-and-donts)
 * [Experimental Biosciences writing science](http://www.ruf.rice.edu/~bioslabs/tools/report/reportform.html)
 * [11 steps to structuring a science paper editors will take seriously](https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take-seriously)
-* [Strunk and Write](https://www.amazon.com/Elements-Style-Fourth-William-Strunk/dp/020530902X) is a classical book that describes common writing gaffs and style particulars.
+* [Strunk and White](https://www.amazon.com/Elements-Style-Fourth-William-Strunk/dp/020530902X) is a classical book that describes common writing gaffs and style particulars.
 * [Move over Strunk and White: My all-time favorite books on writing](https://clauswilke.com/blog/2017/11/12/move-over-strunk-and-white/)