Interesting LaTeX Packages – Bohr and Element – electronic orbits and atomic structure

One of the USPs of using LaTeX is the variety of packages that are available to get things done. Some packages will give you special environments to make your documents better, some will help in typesetting or some will help you create graphics or some just provide you with commands for specific symbols. Of course, all these can be done manually by creating your own command, but why reinvent the wheel? There are hundreds of packages at the Comprehensive TeX Archive Network. I have come across many packages that were useful via browsing the packages at CTAN. In this series of posts we will see some packages that are interesting and might be useful. This series of posts is also a sort of personal bookmarking scheme for me. It has happened in the past that I have discovered some interesting LaTeX package, only to forget its existence when I needed its functionality in a project.
In this first post, we will look at two related packages bohr and elements by Clemens Niederberger. The bohr package provides you with a simple functionality to draw the Bohr diagrams for different elements along with electronic configurations.
Load the bohr package by \usepackage{bohr} in the preamble
To use the package simple type the number of electrons and the element symbol. For example, Lithium \bohr{3}{Li} will simply give you

Similarly for other elements
Lithium \bohr{3}{Li}Oxygen \bohr{8}{O}Carbon \bohr{12}{C}Mercury \bohr{80}{Hg}

Now another very useful option in the vohr package is to print the shell-wise electronic configuration for a given element. For example Oxygen \bohr{8}{O} \elconf{O} will give you

This will be a very useful feature when you are writing chemistry or atomic physics texts. Of course you can change the way the shells look.
shell-options-add = dashed, shell-options-add = red, shell-dist = .75em, nucleus-options-set = {draw=black,fill=orange,opacity=0.5}, electron-options-set = {color=green}, insert-missing}

Mercury\bohr{80}{Hg} \elconf{Hg}

The insert-missing option will give you either the correct number of electrons when the element symbol is given, or  will give you the element symbol when the number of electrons is given. There are more options to explore in the documentation.
Now let us look at the elements package.

This package provides means for retrieving properties of chemical elements like atomic number, element symbol, element name, electron distribution or isotope number.

The package provides atomic number, symbol, name, main isotope and electronic configuration for elements upto 118. For example, just using the atomic number 35 I can get \elementname{35} \elementsymbol{35} \elconf{35}

Having the data accessible in the form of number can be very useful especially if you want to generate tables. The table below from the package documentation was generated by iteratively looping atomic number and invoking commands



Making the first letter decorative, large and capital in a text using LaTeX

In many of the old books we have the first letter as a large decorative capital. Many times very ornamental typefaces are used. Some examples

Petri Apiani Cosmographia, 1539

Johannes Hevelius Selenographia 1647

Johannes Hevelius  Machina celestis


A Letter from Hevelius on observations of a comet, 1683

Sphaera c. 1230 by Sacro Bosco (Ed. published by Peter Apianus, 1526)


example of drop caps from old books


Another style that is often employed with the large capital letter is that the rest of the word, or the sentence is in small caps. Now small caps are distinct than the regular caps. They are capitals, but with the x-height of small letters. And small caps usually have slightly larger spacing between the words than the regular one.


The Night Thoughts of a Classical Physicist McCormmach 1982

The Pleasure of Text Barthes 1975

Now, even in some of the modern books the same effect is used. So if you are looking for a way to achieve this effect using LaTex, then lettrine is the package you are looking for.

Drop caps

The name of this effect is drop caps. When I was searching for finding a solution for achieving this effect, the first block was that I didn’t know what it was called! After a bit of searching here and there I finally came to know about the name: drop caps. So if you are stuck as I was about what this large capital letter style is called, thence the descriptive and verbose title of post.
Now back to LaTeX implementation. lettering gives you several options for customising the drop caps. For the simplest case, we can use the default font of the document
\lettrine{W}{hile} overall the work is well informed, I did not like the (almost) condescending tone she uses when discussing anything “free”. 
\lettrine[lines=2,lhang=.1,loversize=0.1]{W}{hile} overall the work is well informed, I did not like the (almost) condescending tone she uses when discussing anything “free”. 
\lettrine{A}{nother} example is needed.
\lettrine[lines=1,lhang=1,loversize=0.5]{W}{hile} overall the work is well informed, I did not like the (almost) condescending tone she uses when discussing anything “free”. 
  \lettrine[lines=3,lhang=0.75,loversize=0.25]{F}{or} example, she (almost) claims only commercial fonts are well designed because
These examples produce the following output


Now we can also use fancy header fonts. Have a look at some of them here.



You will need to play with the parameters for different fonts to find a better fit for your document.
Now how to add colour?
\lettrine{\color{green}W}{hile} overall the work is well informed, I did not like the (almost) condescending tone she uses when discussing anything “free”. 
\lettrine[lines=2,lhang=.1,loversize=0.1]{\color{blue}W}{hile} overall the work is well informed, I did not like the (almost) condescending tone she uses when discussing anything “free”.

Happy typesetting!

Forever Free Fonts

There are fonts and there are fonts. One of my earliest recollections of cognising that there are different “fonts” is from a typewritten letter I saw in my childhood (perhaps in the early-mid 90s). Though I didn’t know the term “font” then. Now I had seen typewritten materials earlier, as our exam papers were typewritten. But this said letter was somehow “different”. I didn’t know exactly what was different, but that letter and the typewritten text felt so elegant and aesthetic (again these words I didn’t know then, but trying to reconstruct my feelings from that time) as compared to the other typewritten documents that I had seen. The fact that I still remember that letter implies that it must have had some impact on my mind at that time. After that the printed “text” was never the same. I always tried to “see” the shapes of the text that I would read. Hence I “discovered” that the “fonts” in my school textbooks, and other books are different. I also discovered sans and serif in this way, but didn’t know the terms for them till a few years later. Thus began the journey to look at fonts keenly. Even with my handwriting, I developed 3-4 different scripts. None were cursive. I would play with the slant, then height of the letters, and my fountain pens did play the capable tools. With the computers came in plethora of fonts, more than you could count and keep track of. In the various image editing programmes the fonts achieve prime importance. A good font can make or break a document. It can render something mundane or render it to aesthetic appeal.
A good scientific question to think about is how does our cognitive system recognise that it is the same letter even if it is written in different fonts? Everyone’s handwriting is different even then (if they are legible) we can read and understand what they have written. This would imply that our cognitive system for recognising font faces as particular characters of language must be very very flexible. Any rigidity and we would not communicate. Douglas Hofstadter considers this very question in one of his essays Variations on a Theme as the Crux of Creativity in the Metamagical Themas (an anagram of “Mathematical Games”  by Martin Gardner whose columns Hofstadter replaced) column in Scientific American. The compilation of the columns was later published as a book in 1985.

FIGURE 12-3. 56 As in different styles, all drawn from a recent Letraset catalogue. The names of their respective typefaces are given on the facing page. To native readers of the Latin alphabet, it is an almost immediate visual experience to recognize how any one of them is an ‘A’. No conscious processing is required. A couple of these seem far-fetched, but the rest are quite obvious. The most canonical of all 56 is probably Univers (D-3). Note that no single feature, such as having a pointed top or a horizontal crossbar (or even a crossbar at all!) is reliable. Even being open at the bottom is unreliable. What is going on here? p. 243

Hence we have more and more fonts. Some very legible and some not so much.
Though I never somehow liked Times New Roman or Arial, which arguably might be the most popular fonts in documents (how do you find out the most used font?). Might be because they are default fonts on MS Word. One of my earliest, serious documents that I had to prepare on the computer was the project report of my bachelors programme. I did use MS Word, but the font used was Bookman Old Style. And the document did look different than the rest.

I did have a lot of fonts at that point. I installed all fonts that I could get my hands on. Remember this is early 2000, finding free resources on the internet was not easy, and downloading and getting them to your computer was even a bigger an issue (particularly large files). I owe to Viktor Juliet Papa most of my computer knowledge. Because of his mentoring I could muster guts to take out my HDD to cafe where he was the manager, to get downloaded stuff back. (Again only, portable data transfer devices were 3.5 inch floppy drives with 1.44 MB memory. Good luck with transferring 100s of MBs!, my main disk was 8G for reference) So much to risk, but no risk no gain.
Then in that summer during my internship at the University, I discovered LaTeX. And Computer Modern. It looked sooo elegant compared to TNR or Arial. And it had all the mathematical symbols too. At that point, you had to edit the tex file separately, and then compile it via terminal. It would produce a dvi file, which you would convert to postscript via dvi2ps, and then to pdf via ps2pdf. But it was all worth it! The output was divine compared to plebian MS Word. They say LaTeX doesn’t work well for people who have sold their souls! So my report for masters just two years later was in LaTeX. And I never switched back for most serious documents.

In the earliest days, there were very limited fonts in LaTeX. But with packages like XeLaTeX and LuaLaTeX you can use any system fonts in your documents, including non-Roman scripts also. Now there are native packages also which have a variety of fonts. So in my PhD I used Linux Libertine as the main font and associated Linux Biolinum as the Sans font. Wikipedia logo uses Linux Libertine.

Now with libertinus package you can use it with pdfLaTeX, no need to use XeLaTeX/LuaLaTeX (though some might find this step regressive). The font  comes with full math support, so that you can write the documents seamlessly.

Another nice set of fonts with full math support are kpfonts. Though I do not personally like the default sans that is bundled with it.

And one of the more elegant math fonts is urw-garamond, garamondx with mathdesign. Though this set has licensing restrictions that you may not like.

A sans math variant, that I have used occasionally is the GFS Neohellenic from the Greek Font Society.

These days for most of my Office documents (including google docs) I use EB Garamond for serif. It is too good.

And Quattracento Sans. For monofonts, particularly to be used in text editors (Emacs, I still use Linux Biolinum

in TeXShop I use Average Mono.

Some of the other sans fonts that I do use often are
GeoSans Light, Comfortaa and Josefin Sans.
For fixed width fonts, Latin Modern and Inconsolata, TeX Gyre Cursor are used. See the programming fonts in the list below

For handwriting effect there are several nice fonts that I have used. The best ones are Purisa, Comili

Amatic SC is a very elegant font for titles

New fonts will be continually developed. And for me fonts being free  (as in freedom) is the most significant aspect. Given this there is a large number of fonts which have been released under GPL, OFL and similar open licenses. Fonts released GPL license come with the font exception. Below is a partial list of free (as in freedom) fonts which you can browse to get the font for your needs (though some might have non-free content). The listing is alphabetical
Arkandis Digital Foundry  Not updated since 2015, but has nice fonts

Font Library (a largish list of Free Fonts with various licenses)

Google Fonts  Several nice fonts, in different scripts too.

LaTeX Font Catalog contains OTF and TTF files as well, my go to site for choosing LaTeX fonts

Lesser Known Programming Fonts
Programming Fonts (check individual licenses)
Let me know any other links to font databases which have free (as in freedom) fonts.
Happy typesetting!

Color and underline text in LaTeX

For a particular project, I had a requirement that the text be coloured as well as underlined. Now making text underlined in LaTeX has a default support in the form of \underline{text}, which simply produces an underlined text.

But what if you want to customise the underlining, for example, change the thickness of the underline, or its distance from the text baseline. Or simply you might want to have a different colour for the underline. There are several packages which allow you to customise this exact requirement.

For the present post I will choose the soul package which has some other goodies for typesetting as well. You can load the package with \usepackage{soul} Along with underlining, you have have strikeout and highlight. To setup the underline, soul package gives three options, underline depth, underline thickness and underline colour (page 12-13 of the package documentation).

You can set this in the preamble

\setul{⟨underline depth⟩}{⟨underline thickness⟩}

It is recommended that the units of these lengths are in ex, so that they are relative to the font size. For example,


To use it in the document \ul{underlined text} will produce

Another option is to set the colour of the underline. This can be done with


With this option, the above code will look like

The color option can be changed anywhere in the document, so you can have change of colours as required. Defining in the preamble has a universal effect.

So far so good. Now in this case I wanted the underlined text to be of different colour. For this one can define a newcommand with text colour option.


I am also using the svgnames option from the xcolor package for calling colours by names.


In the main text, you can use it as \ublue{coloured and underlined text} to produce the required result. Will produce 



Positive and Negative thin spaces in LaTeX

At times in LaTeX you want to introduce a small space between words. This is especially important in mathematical typesetting. Just adding a little bit of space hairspace, can alter the aesthetic look of the equation or mathematical entity substantially. For example consider this expression:


This produces the following
Screenshot 2020-04-04 at 15.47.51
The | braces are too close to the character “a”. To create a better version of this we introduce a small hairspace between the two. The code for hairspace is \,.
This produces a much nicer looking expression.
Screenshot 2020-04-04 at 15.47.55
This feature of hairspace was known to me for some time. But the problem came when I had to create a negative space. Take for example this expression:
 $F_{eff} = kx$
The result of this is not so nice looking as you can see:
Screenshot 2020-04-04 at 16.06.38
But then I came to know about a negative hairspace. The code for it is \!. Now let us introduce this in the above expression
$F_{e\!f\!\!f} = kx$
The result is much better visually:
Screenshot 2020-04-04 at 16.10.33

Sidenotes and label in LaTeX

Recently I have been using the sidenotes package in LaTeX. It provides many options which I find aesthetically pleasing. For example, instead of footnotes, it gives sidenotes. This particular typesetting has been used beautifully by Tufte in his books. But even before Tufte’s books this option has been used, for example, see the beautifully designed book The Evolution of Culture in Animals by John. T. Bonner.
Not the recent reprint, some idiots at Princeton University Press have completely killed the aesthetically pleasing landscaped typesetting to portrait one (and a not very good one)! In general Bonner’s book are a visual treat in terms of designing and of course the content as well. His meticulous detail to the images, and use of log-scales to depict biological scale in time and space it something that I have not seen very often.
The Evolution of Culture in Animals uses a landscape mode with sidenotes and figures in margins extensively. This is the exact functionality that the sidenotes package provides. Even the tufte-book and tufte-handout classes use this package in a modified manner.
When using sidenotes package, I found that the marginfigure and margintable environments worked without a problem when using a label and referring them to in the document. But when it came to the sidecaption option for wider figures and tables, somehow I could not get the referencing to work. The hyperref showed the correct page and even the captions had the correct numbers for tables and figures. But the label and \ref{} to it didn’t work.
For example, if a figure was created as such:

\sidecaption[][1cm]{This is an eagle.}

The first [] controls the text that appears in the List of Figures, while the second [] controls the vertical placement of the caption.
Now when I referred to this figure in the document using Figure~\ref{eagle1}, it gave an error and typeset it as Figure ??, instead of Figure 1.1 or something similar. The same problem was there for a sidecaption used for tables as well. A common mistake which usually causes this error is placing the label before the caption. So the golden rule seems to be:

Always place your \label{} after the \caption{}.

But it was not the case in my example. A bit of digging in the log file showed this error:

Package caption Warning: \label without proper reference on input line xxx.
See the caption package documentation for explanation.

LaTeX Warning: Reference `eagle1′ on page 7 undefined on input line 415.

Now back to caption package documentation, it had this explanation for this error (page 44):

\label without proper \caption
Regarding \label the floating environments behave differently than its non-floating counter-parts: The internal reference will not be generated at the beginning of the environment, but at \caption instead. So you have to place the \label command either just after or inside the caption text (mandatory argument of \caption).

So that was it. You have to place the \label{} inside the \caption{} environment and the issue was solved. Placing it just after the caption did not work for me.
\sidecaption[][1cm]{This is an eagle.\label{eagle1}}

Multiple citations, biblatex and APA

Issues with multiple citations of an author and biblatex-apa
Recently I had to refer an author multiple times in a document. I had recently shifted to biber and biblatex. The American Psychological Association (APA) style was the recommended style.
And in the final references
The author name was, let us, was Wilbur-Markus Rowland, and he had about 10-11 articles. The author had many co-authors, in some cases this author was the first author in other cases he was the second or even third one.
Now the issue that I was facing was this: The same author name was getting cited differently at different places.
For example, in some cases it appeared like
W.-M. Rowland, in other cases Wilbur-Markus Rowland, and in some cases even as Rowland. This was very confusing. And on top of all that the final references had entries like
Rowland W.-M. (W. M.)
Rowland W.-M. (Wilbur-Markus)
Rowland W. M. (Wilbur-Markus)
Rowland W. M. (W.-M.)
I checked and rechecked the bibtex entries in hope of finding some error but it was not to be found. I must have done a Clean All a dozen times, after editing the bib file.. I tried adding same name entries for Rowland as first author to be the same, but it didn’t work. This was really frustrating.
Similarly a couple of references with two different authors with a common surname were giving intials in the main text. For example, D. R. Cook and M. P. Cook. Now all other refernces (except the Rowland one) were coming as per the APA requirement, which is (Author, Year), so ideally they should have been (Cook & Weston, 1999) and (Cook, 2004). But rather they were being displayed as (D. R. Cook & Weston, 1999) and (M. P. Cook, 2004). Now no change in the bib file was changing any of this. I thought there was some issue with the bib entries. I deleted the entries and entered them again manually, but no avail.
Then I chanced upon this link

 even though the year of publication differs in the two Campbell (Cook in our case) references, the lead author’s initials should be included in all text citations, regardless of how often they appear.

So the Cook mystery was solved. biblatex was compiling correctly as per the APA guidelines, the initials for the two different Cook entries must be there. This is because

 Including the initials helps the reader avoid confusion within the text and locate the entry in the reference list.

Now for the Rowland entry, the next part of the blog gave me a hint towards the possible problem:

Although this rule seems straightforward, one thing that trips up some writers is how to proceed when different lead authors with the same surname are also listed in other references in which they are not the lead author.

After this I checked the entries where Rowland was second or third author. These entries differed from the entries where he was the lead author. And this was causing the problem. For each different entry style of his name, biblatex was considering him as a separate author. Hence the initials and the different references entries with names in brackets. Once all the entries for Rowland were made consistent the problem disappeared. Phew!
This issue bugged me for almost a couple of working days, to find the cause and subsequent addressing was most rewarding.
Note that the bibtex references that I had were taken from google scholar, hence differing styles in author name. Please make them consistent. This is a warning for future me and others who are reading this post.

Lists with LaTeX

While writing documents one needs lists. Usually the lists are either numbered or with bullet. The standard enumerate option in LaTeX by default provides Arabic-Hindu numbers for the list.
The standard syntax is as under:

\item First item
\item Second item

This will produce a list with Arabic-Hindu numbers with the items at each head.
In case one wanted a list with bullets, we can use the itemize environment.

\item First item
\item Second item

This will produce a list with with bullets
There is yet another environment description which can take user supplied options for list headings.
For example:

\item[First] First item
\item[Second] Second item

In this case the descriptors in square brackets after the \item will be used as the item titles. So when I required any alphabetical list, I used to make list in the description environment and put the alphabets/ descriptors manually.
So far so good.
Recently I had to make a list with Roman numerals instead of Arabic ones. The list was fairly long so manual option seemed to be a very un-LaTeX kind of thing to do. Just a little googling and I found a treasury of options that can be used with the standard enumerate environment. This was the enumitem package.
The package provides various options for the enumerate environment like label and its formatting, style, alignment,  indent, vertical and horizontal spacing etc.
The label options that are available are \alph, \Alph, \arabic, \roman and \Roman,
These can be intialised by using
After this the regular \item will produce list with alphabets, numbers or roman numerals.
Please see the documentation for more details.
Suppose you have a list which is split in many parts. You can use resume function to continue with numbering left off in the last part of the list. The resume function can be named and you can have different lists to resume.

Citation inside a Caption – LaTeX

Recently while writing my thesis, I came across a strange error while compiling with LaTeX. The problem arose when I gave a cite command inside a caption environment. The caption was for a figure. For example
\caption{This is the caption for a figure. From  \cite{friend2005}}
This gave the following error:

! Argument of \Hy@tempa has an extra }.
<inserted text>
l.89 ...sity estimate. From  \cite{friend2005}}

Runaway argument?
\@captype {\@firstoftwo {\@ifstar {\HAR@acite }{\HAR@fcite }}}\def \reserved@b
! Paragraph ended before \Hy@tempa was complete.
<to be read again>
l.89 …sity estimate. From  \cite{friend2005}}
A little googling around I found this site which solved the problem in a second.
So the command should read like:

\caption{This is the caption for a figure. From  \protect\cite{friend2005}}

And the problem is solved. In case you are wondering what \protect does look here.

Latex Tufte class in org-mode

Edward Tufte is known for graphical excellence in his famous books. Some enthusiasts combined his design principles into LaTeX and you have the tufte-book and tufte-handout classes for excellence in typesetting. This has support for sidenotes, margin figures, full width figures etc.
Now, since I have shifted to org-mode on Emacs for most of my writing work including that of LaTeX, it was but natural to take this in org-mode output.
For this a small addition to your .emacs file and you are done. Of course after installing the dependencies. I also came to know about another nice package nicefrac for using in the documents.
For Fedora #yum install texlive-tufte-latex should do the job. Also some font problems may arise which can be solved by running updmap and enabling the needed font.

 ;; tufte-book class for writing classy books
(require 'org-latex)
(add-to-list 'org-export-latex-classes
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 ;; tufte-handout class for writing classy handouts and papers
(require 'org-latex)
(add-to-list 'org-export-latex-classes
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))

Once you have added these to .emacs, in the org-mode you have to define #LaTeX_CLASS: tuftehandout or #LaTeX_CLASS: tuftebook to invoke this style in the tex output.
Enjoy the Tuftesque typesetting in your own work! Some snippets from my work in progress, no figures so far.

Title Page

tufte-latex-book-2Table of contents

tufte-latex-book-3Main text