Writing a Paper¶
Here we document some relevant information for writing a paper.
Typesetting with Latex¶
Most of the papers that we write are submitted to the Physical Review, and the primary means of typesetting is
latex. APS has their own custom set of macros that are used to make the document look the way they want it to,
and these are called Revtex. A sample tex file is here tex.
Latex will always be used to write our papers unless there is some extreme exception.
If you prefer a GUI based experience, there is a rather amazing GUI called lyx, which is free, open source, and avaiable on all modern OS’s. To install in Ubunut:
sudo apt install lyx
Lyx can also be helpful if you are typsetting extremely complex equations, as it is easy to see what is happening. Lyx saves files as plain text using their own markup language, which can then be directly edited, and this can be convenient for performing intricate search and replace with standard utilities. The output can also be exported to raw latex.
Overleaf¶
We will often be collaborating and writing papers with people that are not familiar with latex, which can be a huge barrier. There have been a variety of small companies over the years that have been developing web based solutions. Finally, Overleaf seems to have crossed a major threshold, as they will allow you to pull the project as a git repository, and interact purely in that manner. Others can still simultaneously use the web based interface. So far, we have done this without and issues.
In order to make your project accessible as a git repository, you need to pay for a certain level of membership (though in the past it was free, and perhaps students still have some free capabilities). I did pay for a membership, so I can always create a project and then give full access. I have asked Columbia to purchase a site license, but that could take time.
One annoyance is that overleaf will not let you use ssh keys. While there are a variety of solutions, , the simplest is to enter you password manually and have git store it in memory:
git config --global credential.helper "cache --timeout=86400"
where timeout specifies the time in seconds to store the password, with the above being 1 day. I am not sure what the upper limit is, but hundreds of days is apparently fine. For more details on the command see this and for more general details see this.
Version Control¶
We will use git for version control when writing our papers, and this will allow us to collaborate in an efficient fashion.
When we begin to write a paper, please send me the location of your remote git repository such that I can clone it. Please host this on grandcentral or some other machine that can easily be reached from outside our network. If you are unfamiliar on how to do this, please so our git tutorial. A few pointers:
Please do not commit unecessary files, including files ending in log, aux, dvi, etc. If seeing these files in your git status bothers you, just create a file called .gitignore and add these names and they will be ignored.
You do not need to include the main pdf file that is generated upon running pdflatex, but you may if you wish. If you do, please only commit when necessary as repeatedly doing this will make the repository very large.
Please include the scripts and data that were used to generate the figures. Everyone has there own way of doing this, and that is fine. However, please use some convention that can be followed by another human being. For example, some people make one subdirectory for each figure in the paper. Other people have separate data and script directories which are clearly labeleled. Whatever makes you happy is fine, but I need to be able to track things down if necessary.
Please do your best not to include massively large files in the repository. I know that there can be cases where a large data set was used when generating the figures and it really needs to be there, but otherwise please do not do this.
Grant Acknowledgements¶
Whenever a publish a paper we absolutely most acknowledge who funded the research. Below I will list the proper citations for our various grants. If you have a government fellowship, this should also be properly acknowledged.
The authors acknowledge support from the National Science Foundation (Grant No. CMMI-1150795).
This is the grant focussed on strained monolayers (`link`__).
This material is based upon work supported by the NSF MRSEC program through Columbia in the Center for Precision Assembly of Superstratic and Superatomic Solids (DMR-1420634).
This is the MRSEC.
The authors acknowledge support from FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.
This work was supported by the grant DE-SC0016507 funded by the U.S. Department of Energy, Office of Science.
This research was supported by the Center for Thermal Energy Transport Under Irradiation (TETI), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.
Every paper should also acknowledge supercomputing resources if any where used. Our NERSC allocation should be referenced as follows:
This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
PRL Justification Box¶
Directly address the four criteria in this link: http://prl.aps.org/edannounce/PhysRevLett.111.180001 (2013) as explicitly as possible.
These criteria are: (i) substantially advances a particular field; or (ii) opens a significant new area of research; or (iii) solves a critical outstanding problem, or makes a significant step toward solving such a problem; or (iv) is of great general interest, based, for example, on scientific aesthetics.
Chanul found that this text must be less than 50 words. We did not see this requirement written anywhere, but violating it will block submission.
Checking status of papers in Physical Review¶
You can check the access of a paper using this link.