a different method to answer FAQs?

in view of the increase of recurring questions on certain topics, i
want to throw an idea that i saw on some other mailing list in the air
and see if it sticks.

for some questions, a traditional mailing list is not effective and
maintaining a FAQ is laborious and people that have to write them are
not always good at determining what is a good answer.

how about having a suitable "MD with LAMMPS" or even a "general MD and
Stat Mech" project on a website similar to stackoverflow.com ?

over the years i have learned that the up/downvoting system plus
moderation that removes topics that are not suitable or not well put
results in an invaluable resource for programming problems. perhaps
this could work for MD as well.

the hoster, stackexchange.com provides quite a long list of similar
sites on different topics. it should be useful to make an effort to
make this an effort that transcends different MD codes, since the
problems are often the same.

comments are welcome

axel.

This is a good idea but I foresee problems with enough users. I wonder if the topic is too narrow to warrant a whole stackexchange site. Do you envision hosting the website on their platform (go through Area 51)? If so, there are already sites for physics (launched) and another one for “computational science” (year and a half in beta). Unless there is collaboration with the other MD codes (and possibly MC) I don’t see how the site can get out of beta. Perhaps initially, veteran users would have to post questions and answers to get the site going.

There would also need to be a shift in the function of this mailing list. Mainly addressing bugs, feature requests, and announcing new releases. Other types of questions would be redirected to the stackexchange site.

If you decide to move forward I will be glad to participate.

Salomon

Some data that may help determine if the above is appropriate. I looked at my email list load for the past month. This includes CCL, dl_poly, lammps, mmtk, hoomd-blue, vmd mailing lists. I have 404 messages which is more than I thought. Many of these are not stackexchange material (like the bugs and feature requests). Most of the email comes from CCL and lammps it seems.

Salo

This is a good idea but I foresee problems with enough users. I wonder if
the topic is too narrow to warrant a whole stackexchange site. Do you
envision hosting the website on their platform (go through Area 51)? If so,
there are already sites for physics (launched) and another one for
"computational science" (year and a half in beta). Unless there is
collaboration with the other MD codes (and possibly MC) I don't see how the
site can get out of beta. Perhaps initially, veteran users would have to
post questions and answers to get the site going.

i share the concern about having not enough participation. unlike for
software development, scientific computing communities don't really
have much more a culture of competition than of cooperation. too many
people are lurkers (eager to wait for somebody else to ask the
questions they would like to get answered, but too timid) and the
questions that don't belong here are often from people that lack the
experience to tell the difference between a generic problem and a
LAMMPS specific problem.

There would also need to be a shift in the function of this mailing list.
Mainly addressing bugs, feature requests, and announcing new releases. Other
types of questions would be redirected to the stackexchange site.

yeah, ultimately we need to find a way to answer "how do i xxxx?"
questions in a way that more people can participate in answering them
and in a way that good and useful answers are more visible and people
answering get credit for it.

on the other hand, a mailing list is little overhead and it is very
convenient to have all communications consolidated in an e-mail
client. i only wish people would not cc: anybody on their original
post to the list and remember to reply to the list or to all in their
answers, as that messes up mail list filters and leads to incomplete
conversations in the archives.

in a different life when i was working on a DFT MD code, i would
occasionally download the mail list archives and edit it into a "best
questions and answers" list. perhaps we just need a "user support
group" that meets once a 1-2 weeks via IM and reviews the most
useful/interesting questions of the last 1-2 weeks and edits them
collaboratively into some kind of wiki. if everybody takes care of one
or two questions, say, one that has been answered well and a second
that would need a little research to answer properly there should be
fairly quickly some kind of "knowledge base".

the useful thing about stackoverflow is that through its scoring
system it is primarily the *readers* that determine what is helping
them and thus provide a feedback that we usually don't have and
particularly help *others* in a similar situation to find a good
answer. searching the mailing list archives is often too daunting and
assembling the whole answer from an e-mail exchange can be confusing.

If you decide to move forward I will be glad to participate.

i mainly put this out there to start a discussion. a lot of things are
"a good idea(tm)", but many of them don't work for various reasons. we
do need (more) tutorials more "howto" documents for LAMMPS, we need
some way to make information more accessible, but we also need to
avoid dissipating effort and - ideally - making it easier for people
to participate on all levels.

axel.

It is probable that other MD softwares won’t be willing to change functionality of their mailing lists but a bot could be developed to scan mailing lists and post questions (along with their answers) with a specific keyword in subject (e.g. StackExchange) on StackExchange site and the answers there back on mailing list. Then ask users to put that keyword in subject if they want their questions to be asked on StackExchange site too or a moderator can mark such e-mails for the bot. I’d be happy to help.

Hi Morteza,
I dont think it would be needed. All it would take is for moderators in other forums to redirect appropriate questions to the stackexchange site, if that is the way to go.

I think Axel’s second suggestion is less ambitious and could help this mailing list faster in the short term. It fits within a set of changes that would help the lammps beginner. I mean, LAMMPS already has a FAQ! Currently the homepage, as thorough as it is, has a lot of redundant information in different places. 31 links to get anyone started can become overwhelming. Where should someone start?

I clarify that my intention is not to criticize but to critique in hopes that as a community we can improve the current home page.

There are two different how to sections: in the manual and in the how-tos submissions, which as of now just contains redirections to the manual how tos. There are also the tutorials and the FAQ. The tutorial page does not contain any tutorials but a link to an off-site tutorial page. That is four different locations to find a how-to that may not exist.

About visualization there are many locations that currently address the issue. There is the FAQ, the visualization link in related tools, and there is a section in the manual. Consolidation of this into the FAQ may be useful. Is there a desire to keep the answers in the FAQ short?

Talking about the FAQ. We just need to organize it an expand it. Is it wrong to have a FAQ such as cygwin.com/faq/faq-nochunks.html? I dont know what people think about this topic.

The User Scripts link in the home page should be very prominent. I think a lot of people miss it among the link sea. Should this be consolidated with the tutorials page somehow? Also regarding tutorials. The documentation currently has Restrictions, Related commands, and Default sections at the bottom. I think adding a tutorials or example scripts section at the bottom with links would help people find what they are looking for faster. That is, if the tutorials/user script sections ever takes off.

The wish list and contributing to lammps sections may be merged somehow. The wish list could be extensive. We wish to have a tutorial on shaking bonds, we wish to have a tutorial on setting up npt. We wish to have a tutorial on depositing a film or on uniaxial extension (we have this for solids, at least on an external site)

Apologies re. the long email. Just got away from me brainstorming.

Salomon

All of these are good suggestions by various folks. I'm open to any
improvements
others wish to make if they are willing to do the work. I have little
time for things beyond what I'm already doing (new features, bug fixes,
answer emails, keep the manual up-to-date). It's important to
realize that everything else about the WWW site is fully automated,
so anything you are willing to do needs to fit into that framework.

For example:

a) If someone wants to upgrade/update the FAQ that's great.
But you need to do that by editing the FAQ.txt file in the format
it's in (so it can be auto-converted to HTML) and giving it back to me.
Ditto for any other LAMMPS web site pages you want to re-organize.

b) The mail list itself is handled by SourceForge. I agree that having
the mail archive organized by topic to make it easier for people to find/search
for postings they are interested in would be great. But that will
only happen if someone is willing to assign-by-hand the various
threads into topics. Having meetings to do that won't work. It
needs to be done by one person who knows LAMMPS and MD and is willing
to do it on a continuing basis. The volume is about 200 threads per month.

In addition there is some scripting software that would need to
be put into place, which someone else will need to write.

The way that this page is auto-generated:
http://lammps.sandia.gov/threads/threads.html
is as follows. Note that there is a by-date version. A by-topic
version could also be auto-generated.

I have a script that downloads the entire message archive from SForge,
as a single file (few 100 Mb). I have another script that breaks it
into messages
and threads, and that then creates the 1000s of WWW pages (as text files)
for http://lammps.sandia.gov/threads/threads.html and its sub-pages
(one per message).

It would not be hard to modify that script to create a 3rd kind of by-topic
page. Someone would have to design the format of that page as a text
file, like the other LAMMPS WWW pages. But that script would require
a file as input
that assigned each thread to a topic.

So there would need to be another script that someone runs periodically and
which prompts you to assign each new thread to a list of topics, and then writes
out that file. I imagine a list of 20-30 such topics that would cover
most of the LAMMPS mail topics.

What would also be nice would be if there was a way to search within each
topic for keywords in messages. I don't know how to do that. I
imagine it would
require some pre-scanning to create an index of words for the sub-corpus
of messages. It seems like there should be Python software out there that
does something like that. All the searching we have now for the LAMMPS web
pages or mail messages is a Google tool, which is fairly imprecise. The search
facility on the SourceForge WWW page for the mail archive is better.

c) If someone wants to host LAMMPS-related content on their own WWW site,
that's also great. E.g. a Wiki, or repository of scripts, etc. We'll publicize
it on the LAMMPS WWW site. But you have to do the work to generate content
and maintain it, the LAMMPS developers like me are not likely to contribute.

Steve

All of these are good suggestions by various folks. I'm open to any
improvements
others wish to make if they are willing to do the work. I have little
time for things beyond what I'm already doing (new features, bug fixes,
answer emails, keep the manual up-to-date). It's important to
realize that everything else about the WWW site is fully automated,
so anything you are willing to do needs to fit into that framework.

For example:

a) If someone wants to upgrade/update the FAQ that's great.
But you need to do that by editing the FAQ.txt file in the format
it's in (so it can be auto-converted to HTML) and giving it back to me.
Ditto for any other LAMMPS web site pages you want to re-organize.

Regarding the FAQ, as far as I can tell, FAQ.txt is not in the repository
(GIT). Can we add it to it? Also, does the txt to html conversion mean that
no images are allowed in the FAQ?

None of the WWW pages are in the public repo. There's several
Gb of content there. Instead, think of the web server as the
repo. If you do:
% wget lammps.sandia.gov/FAQ.txt
you have the page.

Steve

Re: images - the FAQ.txt page can include them
like other top-level WWW pages do (e.g. Pictures),
by pulling them from the images sub-dir of the WWW site.

Steve

Thanks Steve. Is the markup used in the txt files something you developed or some available language? Everything seems straightforward. In order to augment the FAQ and to make it useful for common problems that people try to address through the mailing list I thought we could crowd-source some of the typical questions. A few I remember seeing a couple of times:

*My pressure/temperature is fluctuating too much! What is going on? This can have complex answers depending on situation but we can address the basics. I can compile previous answers to this questions in the mailing list and consolidate for the FAQ.

*Why can’t I shake the entire molecule? I know this is performance related and explained in the documentation to some degree. A link might be enough to answer.

*When using shake my energy is not conserved! Why? Again, many things can happen but a common mistake is not to use enough shake precision here

*Where is the WCA potential? Steve has answered this previously and I can add it to the FAQ.

*How do I do Lees-Edwards BCs? Lammps doesn’t do quite this but does equivalent things with fix deform etc. I can get the standard answer from Steve and write something up.

Salo

The markup tool is here:

http://www.sandia.gov/~sjplimp/download.html#txt2html

Steve