Around the world in 80 months

A new year, a new job, a new continent...
Sounds like I've read that somewhere before. Now I'm going full circle. Starting at the West coast of the USA, in San Francisco, pretty much exactly 80 months ago, I embarked on a journey to Oxfordshire, UK, on to Canton Geneve, Suisse, then to 宮城県、日本。Starting in January 2015 I will be joining the staff of the Pacific Northwest National Laboratory. I am particularly pleased by the fact that I am cast as a physicist, not a particle physicist. Of course, I will stay involved in particle physics, but the lab has many interesting projects that I hope to contribute to. I look forward to proving that the training of a particle physicist enables one to have a positive impact on a variety of other subjects as well.  At the same time, I am confident that I can take advantage of the diverse capabilities at the lab for my research in particle physics, in particular for building an ILC detector that can deliver on the promise of precision physics in the Higgs and electroweak sector.

Now I will have to change my tag line. I have graduated from my journeyman days.

LaTeX style files

Prelude

Since nearly all funding for particle physics comes from tax payers around the globe, I am proud to say that particle physicist have been steadily improving at making their work public and open to all. Since the beginning of this year, a consortium sponsors open access to publications in particle physics. This funds the important peer-review process, which is how journals maintain the quality of their contributions. Of course, everybody is free to disseminate their opinion in blog articles, twitter messages, and to upload notes of their studies to online archives, but without verification by an independent reviewer, the quality of this information is questionable. The peer review process is of course no silver bullet, but it's the best method we have to qualify research as worthy of distribution to others, so that they can build upon the results.

Bibtex in particle physics

This long-winded introduction brings me to the crux of this post: We are submitting our current draft to EPJC. They provide LaTeX templates including a bibtex style file. (It would be great if they could arrive in this decade and allow biblatex, but most of them require natbib, which precludes the use of biblatex...) We usually cite references from various sources, so being able to use a bibtex database and a style file to get them all formatted consistently is a great bonus. The journals do a reasonable job of formatting their citations consistently, and they use the right fields for author, year, edition, pages, etc. Unfortunately for us, many contributions in the linear collider community did not go through a peer review, and the online repository we use for most of our work contains both, links to peer-reviewed journal articles, as well as private uploads of notes were not subject to the same scrutiny. This also means that the bibtex entries are somewhat inconsistent, to say the least. So some adjustment of the bibtex file (easy) and the bibtex style file (not easy) is needed.

Editing the style file

Adding fields from your bibtex database

As mentioned, most of our sources, peer-reviewed or not, can be found on the online archive, which gives them an "eprint" field in the bibtex database. Unfortunately, the style file distributed by EPJC ignores this field. The first course of action is to add an "eprint" field under the ENTRY section of the bst file (most likely near the top of the file).

Adding a document type

Bibtex allows to specify individual formatting rules for each document type: For a @book, you might want to mention editors and an ISBN, while for a published @article, the journal edition and page numbers are more relevant. For our current draft submission, I decided to format peer-reviewed articles differently from non peer-reviewed ones. Bibtex uses functions with the same names as the document type to specify formatting rules, so an @article is formatted by FUNCTION{article}{...}, while a book is formatted by FUNCTION{book}{...}. Unlike the formatting of individual fields, specifying a new document type does not need to be declared anywhere, other than writing a function for it.

I came up with this for formatting my new "arxiv" document type for articles uploaded to the online repository, but not published in a journal:

 FUNCTION {arxiv}  
 { output.bibitem  
  format.authors "author" output.check  
  add.comma  
  format.date "year" output.check  
  format.eprint "eprint" output.check  
  fin.entry  
 }  

Actually, each of these lines is a call to another FUNCTION. Most of these are defined by the style file already. I just had to write the format.eprint function, which looks like this:

 FUNCTION {format.eprint}  
 { eprint "eprint" bibinfo.check  
  duplicate$ empty$ 'skip$  
   {  
    new.block  
    "arXiv:" swap$ *   
   }  
  if$  
 }  

This prints the word "arXiv:" before the eprint entry of the bibtex database. I don't want to go into more detail about the different lines here. Mostly, because I don't understand every detail of the language used. Read the docs if you are interested.

Summary

This post assumes that you have at least cursory familiarity with bibtex and are faced with a somewhat constrained problem. As you can see, it's not a lot of code that needed writing, but finding out what to put where was somewhat time-consuming.
If you start from scratch, I suggest you follow the links in this post and only use the bibtex database to collect your references. Use biblatex rather than bibtex to format them.

I haven't fully finalized my formatting, yet, but this should give you an idea of how to change an existing bst file to suit your needs. I'll be sure to submit the revised version of the bst to the journal. If they just get rid of the natbib requirement and allow the use of biblatex, this will all become much easier. In the meantime, if you want to submit an article to a journal, and are faced with a similarly incomplete template, I hope this post is useful for you. 

Subversion to github

A big part of the daily routine of a particle physicist is writing code. Unfortunately, we're not particularly well trained for this, so new developments trickle through the system rather slowly. Recently a couple of colleagues and I chose to re-start development of a package that had seen only little activity in a while. The code was hosted on subversion, together with dozens of other packages. For our project, we chose to migrate to github.

So here's a little review on how we got on:

1. create github dir
2. checkout old code from svn
3. check new code into git
4. commit code
5. start applying some patches and start coding

At this point a colleague suggested that we should preserve the old commit history from subversion when importing the code. Terrific idea! But we already started coding... I'm lazy, so starting all over is clearly not an option. So here's what I did.

1. Import the code from subversion into github including the commit history and existing svn branches and tags
2. checkout the repository with our developments
3. git log #gives you the history, together with the sha for each commit
4. git format-patch -4 HEAD # to get patches for the last 4 commits. This creates 4 patch files
5. git checkout <new repo from github import>
6. cd <new repo from github import>
7. apply the patches from step 4 one by one. I think the "git am" command would do all of this in one step, so that may be a better solution. I will try that next time.

At one point, there was a conflict in the merge. I have simply copied the conflicting file over from the other repo. Again, "git am" looks like it would have worked better. I'm still on the upward path of the learning curve.

FPCCD Neutron Damage test at Tohoku CYRIC

From afar the ILC detectors are going to have a very similar look to the LHC detectors ATLAS and CMS. They are cylindrical objects, with different sub-detectors for measuring different properties of the high-energy particles that will be produced by the collisions of bunches of electrons and positrons. Closest to the interaction point in the center of the detector will be the vertex detector for the precise measurement of the decay point of long-lived particles. Next, a tracking detector measures the momenta of charged particles from their trajectories in a magnetic field. The calorimeters outside of the tracking detectors measure the energy of the particles.
Yet, at second glance, because of much cleaner environment of the ILC detectors, particularly the inner detectors look very different from their LHC counterparts. While for the LHC detectors the requirement of radiation hardness puts a serious constraint on the achievable precision, ILC vertex detectors hope to achieve about an order of magnitude better precision on momentum and impact parameter measurements. Nevertheless, radiation damage is also a concern for ILC detectors. The beams after the collision cannot be re-used for collisions. (But we can hopefully recover at least some of their energy.) The current plan is to safely dispose of them in a beam dump. Some of the neutrons produced there can travel back up the beam pipe and enter the detector. Their energy has been studied and roughly looks like this.

 

Expected Neutron energies from the ILC beam dump.
The first layer of a vertex detector at the ILC has to deal with
up to 10¹⁰ neutrons / cm² / year

Not a big problem compared to the factor of about 1,000 that the LHC detectors have to cope with, but nevertheless something we need to study. We have a facility at Tohoku University where we can get a neutron beam. The energy is close enough to what we would expect at the ILC.

Distribution of Neutron energies in the
Tohoku CYRIC facility. We still have to
evaluate our own measurements of
 neutron flux and energy.

After some intense preparation and frantic manufacture of beam profile monitor from scintillator bars, we now have pixel detectors with the equivalent of about 2.5 years equivalent of ILC neutron dose. Analysis of the data is underway, so I can't show anything yet. We are still not even done with the complete analysis of last year's data. Here are two plots to give you just a rough idea of what we are studying. I will try to go into more detail in some future blog posts.

Active area of the FPCCD chip. The red dot is a "hot pixel".
Similarly to a dead pixel in your LCD screen, this is bad.
In this case, we define a "hot pixel" as one that has a signal
significantly above the (blue) background.

We are measuring the number of pixels that was affected
by the neutron radiation. As you can see, measurements
at low temperatures are significantly less affected by the
damage, but the difference before and after irradiation is
obvious.

The ILC and time zones

A surprisingly big problem in a global collaboration is to find a meeting time that suits people in Asia, America and Europe equally badly well.
Usually this means getting up early at the west coast of the US, and being up late in Japan. The Europeans sacrifice their tea time or run into conflict with supper.

The fact that Europe and the US cannot agree on a common start and end of daylight savings time, adds an additional dimension of complication, because - when do you change the time of the meeting: When daylight savings time ends in Europe, or in the US, or do you change it at all? Japan, after all, does not change the clocks.
This whole conundrum leads to much confusion and conflicts. Even more confusing is the fact that some of my venerable colleagues do not seem to understand the abbreviations of time zones. Here is something that helps:
http://www.timeanddate.com/time/zones

So here's a suggestion: Since the ILC will be built in Japan, the canonical time should be JST.
For all of you that don't know what time zone they are in (and there's a few of you, don't deny it), this may help:
http://www.timeanddate.com/time/map/

Finally, our default online agenda - indico - has support for displaying the meeting time in your favorite time zone.
So please, let's all specify the time zone when we announce a meeting. And let's not miss any more meetings because of time zone confusion.

LCWS14 Recap

Every year the Linear Collider community comes together for two large meetings. One is a regional meeting, usually held in spring. Every year this rotates between the three regions Asia, Europe and the Americas. The other meeting is the Linear Collider Workshop (LCWS), usually held in Fall. This is also hosted by one of the three regions in alternating fashion, and it's not the same region that holds the Spring meeting of the same year.
This year's event was in Belgrade.

View from the Fortress

The city still has not entirely recovered from the effects of the war over 15 years ago. As we were shuttled downtown for the summary sessions on the last day, we saw some derelict buildings with heavily damaged roofs at the outskirts of the city. Downtown, however, was very nice. There are plenty of options for dining, people were very friendly, and it was extremely easy to communicate in English.

The conference itself was held in two upscale hotels. Attendance was unfortunately not as good as previous workshops, but that did not stop the Serbian President from stopping by our little gathering. The sessions were a mix of plenaries and parallel group meetings. A notable item on the agenda was a session on how to make the ILC physics case. We were reminded on the first day that we should try to strengthen our presentation of the potential for discovery of new phenomena beyond the Standard Model. My colleagues and I believe we have a very strong case, so I guess we need to package it better. If you would like to contribute, post your video to the ILC communicators and let us know if you have suggestions how to present the ILC physics case.

In addition to politics we also did some real work. The reality of having a candidate site was very noticeable at the workshop. Both detectors have to agree on a common interface with the collider, which will lead to some changes in their design. And the design of the campus, including a computing center, is progressing as well. The work on estimating the computing requirements, both, for the proposed campus and off-site, unfortunately distracted me somewhat from carrying out my duties as a session convener. Thanks to my co-conveners, in particular Sophie Redford and Jerome Baudot, for picking up the slack.
The details of the computing will be the subject of a post once we have understood the details a bit better.

Goals for Detector Optimization: Mass resolution

We have several goals to optimize the ILC detectors to make the best use of the events that the machine will deliver. The physics case depends strongly on being able to deliver high precision and to cover as many new physics scenarios as possible that are still left after the LHC program. For this, we need to make sure the detectors meet our high performance standards. I have prepared an IPython Notebook that investigates the effect of the detector resolution on the reconstructed mass of gauge bosons. You can see that a seemingly small degradation in performance can have a big effect on the physics. We need to understand all of these subtleties when optimizing our detectors.

Newsline

This week my blog was syndicated on newsline.linearcollider.org. If this is how you found my blog, welcome, friend of the linear collider.
I hope you like what you find here.

The ILC site visits

In my role as the deputy LCC Detector R&D liaison, I have visited the recent workshops of the SiD detector and ILD detector collaborations in Tokyo and Oshu City, respectively. The purpose was to give an overview of where we are in the process of documenting and advertising technologies developed for the Linear Colliders.

While I generally enjoy my work, there was an even more fun aspect to these workshops. Both were coupled with a visit to the ILC candidate site in the Iwate prefecture. One started from Ichinoseki, the other one started from Oshu City. Both of these cities are candidates to host the ILC campus. From my home in Sendai, it's 34 minutes by Shinkansen to Ichinoseki, and another ~30 min by local train to Oshu City. That's pretty much commuting distance.

The local support for the ILC is very visible. There are ILC banners at the lamp posts in Ichinoseki, which you can see in Google Street View, for example, or, of course by just wandering down the streets physically rather than virtually.

Around the planned site there are several signs of support, like the two pictures to the left.

The area around the planned site is very rural. During the visits, several references were made to the nature and to the peaceful and quiet environment. The construction of the ILC will certainly change that, but hopefully, the operations phase after construction won't be too intrusive. The exact location of the campus and the sizes of the site campus and the science city are still under discussion. While some people might enjoy living close to the site in rural Iwate, others will prefer the proximity to shops and businesses of the science city. Or, like me, to live in Sendai.   

Japanese Culture Week

Japan is known for its rich culture. Food is a big part of it, and I am thoroughly enjoying sampling my way through the whole range of culinary offerings so far.

The last week of April, however, took my cultural education to the next step.
I was invited to a traditional Japanese tea ceremony of the type "Shogo-no-Chaji". The whole course took about 5 hours. (Usually it's only 4, but the host was giving us special treatment.) I cannot possibly describe it in words. Suffice it to say that it was a great honor. If you ever have the opportunity to participate in such an event, do not miss it! Sorry, no pictures. There wasn't really a good moment to pull out my cell phone and aim it randomly at objects and people...

The other very Japanese event is hanami - the cherry blossom viewing.

Every year the particle physics group celebrates the beginning of spring with a barbecue. If you've never had yakisoba at a barbecue, you don't know what you're missing.

Snow on the Horizon

The view from my bus stop on Saturday,

As part of my new job, I was trying to attend the AIDA Horizon2020 workshop at CERN next week. It's a good opportunity to network with the groups who are active in detector development, and to get a good overview of the field. Not really a short trip from Sendai, but such is the life of a particle physicist.

Well, it looks like Frau Holle had something against my travel plans. After my flight from Sendai to Narita got canceled on Saturday, I spend a significant fraction of my day on the phone to get the flight changed to Sunday. It's not as easy to get the airline to accept they are responsible for taking care of their passengers as you might think. And apparently the travel agents can't always call the airline support numbers from outside of the country. A little after midnight everything was sorted and I had my new itinerary.

The view from my browser window on Sunday.

Unfortunately, the flight got canceled again. Notice the missing arrival time next to the flights expected at 08:55 in NRT.
So now I am trying to get a refund. It seems to be completely normal for the airlines to fly for 20 hrs. from Japan to Switzerland, arrive in the evening, spend the night in Switzerland and fly back the next morning. I'm trying to convince that a) I was trying to attend a meeting that will be over by the time they propose to get me there, and b) spending less time on the ground than in the air is something I would rather avoid in any case.

There are again some lessons to take away from this:

• Online travel agencies are worth their money.
• When it looks like it's going to take forever for the agent to get back to you, or if they put you on hold repeatedly, have them call you back. Most agents will happily do that. It took me a while to learn that, and I am honestly a bit nervous about my next phone bill.
• If you cancel or change an inbound flight, and you would like to keep your outbound flight, make sure the airline knows about this change. Most airlines will cancel your whole itinerary including your return trip if you don't show up on an inbound flight. The airlines are supposed to notify the operators of your connecting flights of any cancellations, but apparently you cannot rely on this. 
• Trips with several different carriers cause significant headaches to change.
• The airline that cancels the flight should be held responsible for the follow-up with the connecting flights and possibly re-booking those, even if they are code-share flights operated by other airlines. I had to call offices in Japan, Switzerland, and in the UK to find this out. After insisting that the operator of the canceled flight should take responsibility, the agent became suddenly quite helpful.

Safe travels.

The first month in review

The first month in Sendai has certainly been rather eventful. The excitement of the new environment hasn't worn off, yet, but fortunately I'm starting to become more productive. I still don't have my household, yet; apparently that will take another month. On the other hand, I do have:

• registered myself at the ward office (if you live east of Sendai Station, your ward office is surprisingly far away from the station).
• opened a bank account. This took about two hours, but it was rather straightforward (given the fact that my wife speaks Japanese). Unfortunately, I don't have a Japanese credit card, yet.
• met (most of) the graduate students. Seems to be a great bunch. I look forward to working with them.
• introduced myself a number of times to different groups. I find myself sharing different bits of information each time, just to prevent myself from getting bored.
• bought a six-months bus pass. I'm not an avid driver.
• signed up for a new cell phone plan with a data flat rate. This helped me survive several weeks without a laptop. See also my previous post.
• registered with a new certification authority (KEK) for a grid certificate. Apparently, moving between different certification authorities is not foreseen on the grid. I can currently not delete my old files.
• started to get involved with some of the different research projects that we work on at Tohoku University. I plan to post a bit about each in turn in the coming episodes.
• accepted the job of deputy Linear Collider Detector R&D liaison. This task will most certainly provide material for future blog posts as well. My responsibility is mostly to facilitate communication. To ensure the best achievable performance and cost-effectiveness of the detectors it's important to encourage the widest possible participation in building them. The Detector Baseline Documents for ILD and SiD have been written, but the detector collaborations are still in the process of being formed. Now is the time to get involved with the detector concepts and help shape the face of these collaborations. If you work on particle physics detectors and care about Linear Colliders, please make yourself known.
• not really studied as much Japanese as I had planned. Back to work.

Survival Tactics of a Road Warrior

As a particle physicist, I am extremely dependent on a computer for my daily work. But not only for work, I am increasingly relying on mails and text messages for communication. In particular, calls on my mobile from Japan to Europe are not a particular economically sustainable option. So here's how I survived eight weeks without a proper computer.

Move to the cloud. While I haven't found a good solution for larges quantities of pics and videos, yet, here are some suggestions for migrating the rest of your data.

• Music: I am getting my music from Spotify. The subscription rate for one year is less than getting a new hard drive, plus I get the latest music. I hope they start their service in Japan soon.
• Code: Your source code should of course live in a repository under version control somewhere. CERN, for example provides access to svn and git servers to their users.
• Documents: The lingua franca of scientific documents is LaTeX. Allows you to change Operating Systems easily. See code.
• EMail: Tricky. I use gmail, which provides me with all the services I need. If you have privacy concerns, you need a hard disk. But then you need to make sure you get the same operating system for your new computer.
• Calendar: Provided by gmail for me. Use the Provider for Google Calendar add-on for integration into Thunderbird, a cross-platform solution for communication.
• Contacts: Again, gmail has what I need. Integration into Thunderbird via the gContactSync add-on seems to work for me, but I've just started using it, so the verdict is still out.
• To-Do List: I use ToDoist. Has nice integration with the rest of my eco-system.
• Notes: Springpad is a great solution to jot down quick notes, upload images or plots for a project you work on, or upload some files (like bash configs, or the like).
• Editor: If you spend a large fraction of your time writing code (or documents), do yourself a favor and learn how to type. I learned the Colemak layout and I'm not going back. In addition, learn keyboard shortcuts for your editor. Which means that you want to use one that is cross-platform, so you don't have to re-learn everything when you borrow a laptop from somebody. I like Sublime Text. For my purposes it's as powerful as Emacs, plus it looks pretty.
• FTP client: My tool of choice is Cyberduck. Works on Mac and Windows and integrates with Sublime Text for editing of remote files. Make sure you donate. On Linux, of course the default file browsers for KDE and Gnome support browsing remote file systems.

Once you reduced your dependence on a physical hard drive, you can get quite far with a modern smartphone and a data flat-rate. It's quite impressive, really. I've survived the last 2 weeks almost exclusively on such a device.

But now that I have my new laptop, and everything's set up the way I like it again, it's back to work.

Thoughts about Nigel Lockyer's editorial in Nature

Deciding on the future of particle physics is a complicated process, due to the size of the projects that are being proposed. Nigel Lockyer, director of Fermilab has written an editorial that was recently published in Nature. He outlines some of the questions that our field is facing. As director of the larges particle physics laboratory in the US he should be familiar with large projects.

Unfortunately, this editorial contains a rather indifferent enumeration of  projects that have been proposed at one point in time and ought to be classified rather differently in terms of time scale and scientific merit.
An important consideration that Nigel forgets to mention completely is that each large project comes with its own window of opportunity that depends on a number of factors other than physics. This puts the argument of waiting for results of the upgraded LHC to make a decision on the ILC in a completely different light. There is no ideal point in time to take a decision on the ILC if the LHC finds nothing. Particle physicists will gradually move on to other projects, politicians' focus will shift away from particle physics after years of waiting for news.

This is not a situation we need to get ourselves into. Physicists have worked hard over the past decade and more to put all the pieces in place to take a decision on the ILC in the next couple years. It's quite hard to come up with a scenario in which an LHC discovery in the next five years would invalidate the case for the ILC.
Particle physicists will continue to come up with projects that can be considered at the next step. We will not be short on ideas for future experiments. They will require a foundation that can be laid by the ILC now.

Japanese Identity

Here in Japan you prove your identity on official documents not with your signature, but with a hanko.

This is a quick shout out to a hanko shop 判子屋　near nihombashi station D1 exit in Tokyo that worked extra hours to get us our hanko before the holiday break. If you need a hanko or some other writing material, I recommended you pay them a visit. Turn right at the exit and then right again after the bridge.