Sage for Physical Chemistry

[Gil Claudio]

Does anyone use sage for physical chemistry. I will teach a graduate level course in Chemical Thermodynamics, and I would like to use Sage as an integral aspect of the course. I'm still in the process of learning both Python and Sage, although I have used Mathematica before.

Thanks.

Gil

[Jonathan Gutow]

Gil,

I do.  I am also the person who has worked on the integration of 3-D plots with Jmol most recently.  I am in the process of integrating the javascript version at the moment (See http:trac.sagemath.org/16004).

Anyway, I use it for a number of exercises and for demonstrations/visualizations in class.  I have tried to adapt some of the other worksheets people have developed for Maple and Mathematica, but have only made limited progress (mostly because they don't quite fit my topic coverage/order of material and how much time I have).

We have Maple on our campus, but I much prefer the server for homework and the fact that my students do not have to pay to have an installation of their own if they wish.

If you have specific questions please ask.  We're wrapping up our semester, but if you remind me  in couple of weeks I will try to make available some of the worksheets I've developed.

regards,
Jonathan

[kcrisman]

On Thursday, May 8, 2014 10:45:30 AM UTC-4, Jonathan Gutow wrote:

Gil,

I do.  I am also the person who has worked on the integration of 3-D plots with Jmol most recently.  I am in the process of integrating the javascript version at the moment (See http:trac.sagemath.org/16004).

Anyway, I use it for a number of exercises and for demonstrations/visualizations in class.  I have tried to adapt some of the other worksheets people have developed for Maple and Mathematica, but have only made limited progress (mostly because they don't quite fit my topic coverage/order of material and how much time I have).

We have Maple on our campus, but I much prefer the server for homework and the fact that my students do not have to pay to have an installation of their own if they wish.

If you have specific questions please ask.  We're wrapping up our semester, but if you remind me  in couple of weeks I will try to make available some of the worksheets I've developed.

Our last few iterations of PChem have also used Sage (disclosure: I am not a chemist and don't teach it!) via a notebook server.  However, I checked and I think they did it mostly internally, without publishing a lot of sample worksheets etc.  Lots of multiple integrals and such.  It sounds like it is very doable for that.  I don't know the kinds of math that would show up in your course, though, so I couldn't say how many resources for that level there would be.

- kcrisman

[Karl Zachary]

I am teaching the two-semester undergraduate PChem sequence.  I have used Maple in the past and would like to switch to Sage.  I am hoping some of you will return to this group with brilliant tips!

Karl

[kcrisman]

I am teaching the two-semester undergraduate PChem sequence.  I have used Maple in the past and would like to switch to Sage.  I am hoping some of you will return to this group with brilliant tips!

Awesome!  I am not a chemist (cc:ing someone who is!) but I would say that the way that our students in pchem seemed to use it most effectively was as a "demo in class, modify for homework" strategy.  That is, the professor would show some sample computations for the in-class problems/demos, and then distribute the commands/share a worksheet/give to download/whatever distribution method they chose to students to use on homework, always assuming that most of the stuff would be similar enough they wouldn't need programming instruction or the like.

But that is my fairly uninformed opinion for chem.  There are lots of ideas for general math classes on this list...

[Jonathan Gutow]

I do teach p-chem and have used Sage instead of Maple for a number of years.  I have my own server set up, but would suggest using SageMathCloud as a starting place.  My first exercise with Sage is to have them practice using it for differentiation and integration (I basically have them do exercises out of Barrante's book).  I have them do it by hand and check themselves with Sage.  I have them save their work on the server and then I check that they did it.  They get a few points for doing it.  I provide almost all answers as screen shots of sage and encourage them to use sage for their homeworks, but do remind them that they still have to be able to do standard manipulations by hand on exams (you have to be clear about what they need to be able to do without the crutch).  I essentially am trying to get them to use Sage as an electronic version of the math tables. 

I do use it for lots of live in class demos, usually to show graphical information.  I ended my last second semester using sage in class to work our way through Gillespie's 1977 paper on stochastic kinetic modelling to write a program that did the technique.  I think it worked well.  Anything you've done with Maple should translate.  We use it for error propagation and other lab computations as well, although once the algebra is done we use a data analysis package like LoggerPro. Igor or Origin to process larger data sets.

I believe from discussions with him that Steve Singleton at COE college has converted some of the common Maple/Mathematica/Matlab worksheets into sage.  His web site is http://www.public.coe.edu/~ssinglet/.

Jonathan

[Karl Zachary]

Thanks for your replies -- this is very helpful.  My class is small so I'm going to start with SageMathCloud.  So far, I have found translating Maple sheets into Sage sheets to be pretty straightforward.

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[kcrisman]

Thanks, Jonathan!

 

I believe from discussions with him that Steve Singleton at COE college has converted some of the common Maple/Mathematica/Matlab worksheets into sage.  His web site is http://www.public.coe.edu/~ssinglet/.

And I believe he has some interest in the notebook as well. 

[ssin...@coe.edu]

Hello,

I'm late to the thread, but happy to learn of others interested in using sage in chemistry. Several people asked for more information about sage at the recent BCCE meeting (I saw Jonathon Gutow), so it sounds like I need to get serious about sharing more stuff.

Echoing or adding to things mentioned earlier in the thread:

I started by translating a lot of T. Zielinski's and J Noggle's MathCAD stuff to mma, and then to sage which I've used the past couple years. I've also adapted or written pogil-like activities that utilize sage. All of this hopefully gets students playing with quantum and thermo concepts like eigenvalues, orthonormality, data fitting/analysis, some group theory, etc. The goal was/is to go beyond trivial examples that can be solved by hand and use 'real' tools for 'real' problems.

SMC (sage math cloud) is a great way to get going quickly and efficiently...no setup problems. I used it almost exclusively last year, and my students *did* use it exclusively. SMC is a full-blown unix env. with dozens of tools if you or your students are interested in other areas of technical computing.

I'm still figuring out the best work flow for assigning and collecting homework with SMC, but William Stein is adding new functionality that will likely make this smoother.

I keep a local sagenb server running for occasional uses:

- sharing older worksheets; SMC doesn't have a "publish worksheet" system yet (I understand it will), but you can distribute sagews files via transfer (git, cp, email, etc) or shared projects. SMC can import sws files if you find useful materials on other sagenb servers that pop up in web searches.

- visualizations requiring 3D. Effort has gone into beefing up the 3D capabilities in SMC, but I haven't figured out how to do several things that "just work" with jmol and sagenb. There are only a few exercises (e.g., orbitals, ESP, cube files) that are impacted, so I just show these in class with either sagenb or IPython notebooks running on my laptop. (I've promoted the use of contour plots over volume rendering...not really a bad thing since nobody uses topo maps any more.)

If there is interest among even this small group, I'm can spend some time cleaning up worksheets, seek distribution permission for the translated work, and put the stuff on github or elsewhere. Might be nice to have a library of materials so we aren't building from scratch.

And thanks to Jonathon and Karl-Dieter for reminding me about an ancient web page in dire need of attention! Another stale project...

Thanks,
Steve

[William Stein]

I spent all day working hard on exactly that. I hope to make a first
release of something for testing tomorrow, if all goes well.

>
> I keep a local sagenb server running for occasional uses:
>
> - sharing older worksheets; SMC doesn't have a "publish worksheet" system
> yet (I understand it will), but you can distribute sagews files via transfer
> (git, cp, email, etc) or shared projects. SMC can import sws files if you
> find useful materials on other sagenb servers that pop up in web searches.
>
> - visualizations requiring 3D. Effort has gone into beefing up the 3D
> capabilities in SMC, but I haven't figured out how to do several things that
> "just work" with jmol and sagenb. There are only a few exercises (e.g.,
> orbitals, ESP, cube files) that are impacted, so I just show these in class
> with either sagenb or IPython notebooks running on my laptop. (I've promoted
> the use of contour plots over volume rendering...not really a bad thing
> since nobody uses topo maps any more.)
>
> If there is interest among even this small group, I'm can spend some time
> cleaning up worksheets, seek distribution permission for the translated
> work, and put the stuff on github or elsewhere. Might be nice to have a
> library of materials so we aren't building from scratch.
>
> And thanks to Jonathon and Karl-Dieter for reminding me about an ancient web
> page in dire need of attention! Another stale project...
>
> Thanks,
> Steve
>

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--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

[Karl Zachary]

Since I see William Stein here, this seems like a good time to say "thank you!"  Coming from Maple, I've been working with sage for a few weeks now and am extremely happy with it.  I installed it on my home linux box but plan on using SMC this year.  My campus is very windows-centric and there's only so much class time.  Limited availability is probably the biggest single factor that finally turned me off of Maple so  SMC is a huge. 

And yes, Steve, I'll be cheering on whatever you have time to share!

One of my main goals in the thermodynamics section of PChem is getting students working with more powerful equations of state.  Typically what trips them up is the algebra that follows the differentiation.  It's just more laborious than what they are used to so it bogs down class/homework time and the ideas get lost.

By the time we get to quantum, I'm hoping they have enough facility with this that can work with some python.

Karl

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[Melissa Reeves]

I'm also considering adopting SAGE for the undergraduate and graduate Pchem classes I teach.  The cloud is a plus, although I think my students might use the iPad app more.  

On Thursday, May 8, 2014 2:48:35 AM UTC-5, Gil Claudio wrote: