Hello,
Any updates? It would be helpful if someone can help me with this.
Thanks,
Aditya Jain
Undergrad – 3rd year
IIIT- H , India
ᐧ
On Fri, Mar 13, 2015 at 9:52 PM, aditya jain <[email protected]>
wrote:
> Hello,
>
> Thank you for the detailed instructions. I have listed my understanding on
> the various subtopics related to the project along with my
> suggestions/comments on the same in the same document :
>
>
> https://docs.google.com/document/d/1rGqABpdIOaIcIUCID9nsz3neMwPmbMoyhvaGwT0gjvM/edit?usp=sharing
>
> I request you to kindly read the same and comment if you find anything
> inappropriate with my thoughts or claims. If possible, please direct me to
> an existing bug which is related to the analysing part of ASCEND, which
> will help me understand the existing code in a better way. Lastly, I have
> listed some broad level doubts and would be obliged if you can help me
> clear them.
>
> Thanking you,
> Aditya Jain
> Undergrad – 3rd year
> IIIT- H , India
>
>
> On Thu, Mar 12, 2015 at 9:23 AM, John Pye <[email protected]> wrote:
>
>> Hi Aditya
>>
>> Thanks for your careful thoughts and good comments on this problem.
>>
>> Regarding the suggested implementation, I would suggest that you look at
>> the ida_analyse.c file in solvers/integrators. Also look at
>> ascend/integrator for the API specific to integrators. We are trying to use
>> the Integrator API for all dynamic solvers, whereas the Solver API is used
>> for steady-state (NLA and NLP) problems. So I don't think that slv_presolve
>> is the right place for the code you are proposing.
>>
>> I understand your comment about not having to include index reduction in
>> order for this algorithm to work. Perhaps as a first step, we could use
>> this algorithm to *alert* the user about the likely need for index
>> reduction in their problem, even if we don't actually implement it yet?
>>
>> You mention that the algorithm is O(n²). Is "n" the number of variables
>> in this case, or the number of variable-relation edges? Does the sparsity
>> of the incidence matrix of problem come into play?
>>
>> You had some doubts filed in your document:
>>
>> - Regarding the point where flat vars/equations are
>> created/accessible, check out the "anaylsis" info at
>> http://ascend4.org/Integrator_API#Analysis and also
>> http://ascend4.org/Developer%27s_Manual#Analyser. Sorry for the
>> inconsistency of US/GB spelling here!
>> - I think that if you look at the ida_analyse stuff, and also
>> possibly the ascend/integrator stuff, you may be able to identify a
>> solver-independent place to put this proposed debugging code for dynamic
>> (integrator) systems. It will need some careful thought though. Definitely
>> our preference would be for this debugging to be separate from the
>> numerical code for the solver itself if possible.
>>
>> Regarding your second suggestion about meaningful error messages etc,
>> that's definitely what we're aiming for. We're not there yet; I hope you
>> will help us. We have implemented various useful tools for steady-state
>> solvers, etc "Show fixable variables" and "Check" button; ideally we could
>> construct the GUI in such a way that these functions are
>> replaced/supplemented with suitable alternatives in the case that the use
>> is attempting to solve a dynamic problem. Note that sometimes a user will
>> want to switch between dynamic/steady solvers, however, so GUI design is a
>> bit tricky.
>> Finally, note that Ksenija wrote the recent 'ksenija2' branch, which
>> implements the functionality for switching behaviour in dynamic models.
>> That greatly complicated the debugging process. You should consider that,
>> and come up with a strategy for eventually supporting debugging of models
>> with boundary-switching. My suggestion would be to allow the user to turn
>> on the debugging function after *every* boundary event. It would be slow,
>> but safe.
>>
>> Cheers
>> JP
>>
>>
>> On 11/03/15 06:52, aditya jain wrote:
>>
>> Hi,
>>
>> Thank you for the detailed response. I have done the required reading
>> and have documented my understanding of the various aspects of the project
>> in the following document :
>>
>> https://docs.google.com/document/d/1rGqABpdIOaIcIUCID9nsz3neMwPmbMoyhvaGwT0gjvM/edit?usp=sharing
>>
>> I have answered the two specific questions under the "Suggestions"
>> heading of the document. I have also worked out two examples explicitly as
>> suggested. I have a couple of doubts regarding the project which I have
>> mentioned under the "Doubts" heading in the above document. I would be
>> obliged if anyone could help clear those doubts or provide a direction
>> towards a better understanding of those issues. Please feel free to comment
>> if you have any suggestion with respect to any part of the document.
>>
>> Thanking you,
>> Aditya Jain
>> Undergrad – 3rd year
>> IIIT- H , India
>>
>>
>>
>> On Sun, Mar 8, 2015 at 4:52 AM, John Pye <[email protected]> wrote:
>>
>>> Hi Aditya
>>>
>>> Welcome to ASCEND! I'm pleased that you're interested in becoming
>>> involved.
>>>
>>> For the project you are proposing I suggest that you should probably
>>> start with the code in the 'ksenija2' branch of our repository, which has
>>> our 'state of the art' ODE/DAE modelling code. Ksenija previously worked on
>>> event handling and boundary traversal in that solver, and we want to build
>>> on that code rather than start something new in parallel. There's a fair
>>> bit you to read and absorb, starting with the underlying IDA solver (check
>>> out the SUNDIALS documentation for that) then our Developers Manual on the
>>> wiki which will give you an overview of the ASCEND architecture.
>>>
>>> A couple of open questions for your consideration:
>>>
>>> - how feasible is it for us to add support for the Soares and Secchi
>>> algorithm, including support for index reduction (I believe it's a
>>> necessary part of their algorithm -- please check that for me) in ASCEND?
>>> what would be the best approach?
>>> - what can we do to make dynamic models in IDA easier to use and
>>> easier to debug?
>>>
>>> For the first one, I suggest you read the code and consider the options.
>>> In the second, I suggest you also make sure you've built up your own
>>> dynamic model from scratch, and gone through all the steps of debugging it
>>> yourself.
>>> Before we proceed with index reduction and the Soares/Secchi approach,
>>> we will need to discuss and agree on an approach. I suggest you open a
>>> discussion on our mailing list once you have done the necessary reading.
>>>
>>> Cheers
>>> JP
>>>
>>>
>>> On 08/03/15 08:26, aditya jain wrote:
>>>
>>> Dear Dr John PYE,
>>>
>>> I am Aditya Jain, a 3rd year undergraduate student from International
>>> Institute of Information Technology, Hyderabad (IIIT-H), India. I am
>>> currently pursuing a 5 year dual degree course comprising of B Tech in
>>> Computer Science and MS (by research) in Computational Natural Sciences. I
>>> have been involved with both programming and study of Chemistry since my
>>> freshman year. I recently came across the project entitled "*Debugging
>>> tools for DAE modelling*". on the Student projects
>>> <http://ascend4.org/Student_projects#Reaction_kinetics_data_support> page
>>> for ASCEND and wish to contribute to the same.
>>>
>>> This project appealed to me because it stands at the confluence of my
>>> areas of interest which include Programming, Mathematics (specifically
>>> Graph Theory) and Physical Chemistry. I have gone through the research
>>> paper entitled "*Debugging for Equation-Oriented CAPE Tools*" and
>>> discovered that the algorithms are implementable with ease. Having taken
>>> courses like 'Topics in Physical Chemistry', 'Optimization Methods' and
>>> 'Computational Natural Sciences Lab', and served as a Teaching Assistant
>>> for 'Mathematics I (Discrete Mathematics)' , I believe that I have the
>>> required expertise for this project. I have used a number of simulation
>>> tools during these courses and always had the desire to contribute to the
>>> designing of one. I am comfortable with programming in both Python and C
>>> since I have been doing it since my freshman year and have done some
>>> projects in both of them.
>>>
>>> I realize that the demands of the project overlaps to a large extent
>>> with what I am looking to work on in my summer project. I shall be highly
>>> obliged, if given the opportunity, to contribute to ASCEND.I request you to
>>> please guide me with some directions in which I can proceed so as to get
>>> started with the same. I have also attached a copy of my CV for your kind
>>> perusal and look forward to hearing from you soon.
>>>
>>> Thanking you in advance,
>>> Aditya Jain
>>> Undergrad – 3rd year
>>> IIIT- H , India
>>>
>>> ᐧ
>>>
>>>
>>>
>>
>>
>
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