[petsc-dev] Request for comments on paper on PETSc TS

[Smith, Barry F.]

  Karl,

     Thanks for the corrections and suggestions.

   Barry


> On Feb 21, 2018, at 8:49 PM, Karl Rupp <rupp at iue.tuwien.ac.at> wrote:
> 
> Hi,
> 
> thanks, that's a nice manuscript! I like the general setup and flow of discussion. Here are a couple of further comments; feel free to consider or ignore as you see fit:
> 
> Page 1: The references to MATLAB and NAG are incomplete, as they only show the year. Instead of "MATLAB [2014]" it should be something like "MATLAB [MATLAB 2014]" in order to be consistent with other references. Compare also with the chemkin reference on page 25.
> 
> Page 2: Consider removing the sentence "The document is organized as follows."
> 
> Page 3: Finish item "XXXSetUp(...) ... to be used" with a dot like for the other items in the list.
> 
> Page 4: (shift) is a somewhat ugly notation, because the parentheses are also used for mathematical expressions. Consider "[shift]" as an alternative.
> 
> Page 4: Swap order of the expressions (shift)F_{\dot u^n}(...) and F_{u^n}(...) in order to match the order used in the first line of the page: F_u + (shift)F_{\dot u}
> 
> Page 4: The sentence "For example, the backward Euler method \dot{u}^n = (u^n - u^{n-1})/\Delta t." is not a complete sentence.
> 
> Page 5/6: The code listing may benefit from more explanations, especially for readers who are not familiar with PETSc.
> 
> Page 7: The opening sentence "Oregonator: stiff ..." is not a full sentence.
> 
> Page 7/8: Again, a discussion of the code example is desirable.
> 
> Page 11: The table heading for Table 2 is too generic and does not properly explain the table content. Also, a table header like for Table 1 should be added.
> 
> Page 12: Consider rotating Table 3 by 90 degrees and make it a full page table. This way the columns "Embed.", "Dense Output" and "Remarks" can be integrated. Also, prssp2 should have an entry in column 'SA'.
> 
> Page 14: Consider the same tweaks to Table 4 as for Table 3.
> 
> Page 13-16: The code listing is fairly heavy. Consider a reduction to the relevant parts. More importantly: Explain what is going on: Which PDE is solved ("a reaction-diffusion equation" is too vague), how are things discretized, etc.
> 
> Page 17: Replace "... registered vis the PETSc API." by "... registered via the PETSc API."
> 
> Page 17: Add blank after "estimation" in Table 5.
> 
> Page 18: Replace "... with adjoint method" by "... with the adjoint method".
> 
> Page 18: Replace "The features of PETSc adjoint solver" by "The features of the PETSc adjoint solver"
> 
> Page 19: "The paper [Marin et al. 2017] contains ..." is not a very elegant formulation. Consider to reformulate the sentence to something like "Details on using the infrastructure discussed here for solving PDE-constrained optimization problems utilizing the spectral element method can be found in the literature [Marin et al. 2017]."
> 
> Page 20: 'TSSetCostIntegrand()' is not formatted correctly.
> 
> Page 20: "apporach" -> "approach"
> 
> Page 21: "Figure 4 presents ..." should be supplemented by further explanations of the bouncing ball example, e.g.: Where does the event-handling kick in? What would happen without proper event handling? How much effort is required to set this up?
> This would also convert an unpleasant one-sentence paragraph into a more pleasant multi-sentence paragraph.
> 
> Page 22: Consider rephrasing "Often users of ODE solver packages do not know ..." into "Users of ODE solver packages often do not know ..."
> 
> Page 22: Replace "... by the PETSc libraries" by "... by PETSc."
> 
> Page 23: Explain the TSView() output.
> 
> Page 25: Here I noticed the spelling "time-step". In earlier parts of the paper it was spelled "timestep". Please unify.
> 
> Page 26: Explain the code listing.
> 
> Page 26: A conclusion should be added, summarizing the paper and outlining the potential impact of having TS available for tacking problems in CSE.
> 
> References: Some entries contain full first names, others only the first letter. Please unify. Similarly, check for consistent capitalization of titles, e.g. "Using PETSc to Develop Scalable Applications ..." vs. "Evaluation of overlapping restricted additive ..."
> 
> Best regards,
> Karli
> 
> 
> 
> 
> On 02/19/2018 10:49 PM, Smith, Barry F. wrote:
>>    PETSc developers,
>>      We have recently completed a draft manuscript on the PETSc TS component, that includes discussion of adjoints and forward sensitivities. It is attached. We'd appreciate any feed back on the manuscript.
>>     Thanks
>>      Barry