Talk:Constraint (computational chemistry)

Minor errors

Some (minor) errors seem to be present in formulas within the Lagrange multipliers section: I suppose that, instead of
This implies solving a system of n non-linear equations

$\sigma _{j}^{(t+\Delta t)}:=\left\|{\hat {\mathbf {x} }}_{j\alpha }^{(t+\Delta t)}-{\hat {\mathbf {x} }}_{j\beta }^{(t+\Delta t)}+\sum _{k=1}^{n}\lambda _{k}\left[{\frac {\partial \sigma _{k}^{(t)}}{\partial \mathbf {x} _{j\alpha }}}m_{j\alpha }^{-1}-{\frac {\partial \sigma _{k}^{(t)}}{\partial \mathbf {x} _{j\beta }}}m_{j\beta }^{-1}\right]\right\|_{2}^{2}-d_{j}^{2}=0,\quad j=1\dots n$ "
it should be
"This implies solving a system of n non-linear equations

$\sigma _{j}^{(t+\Delta t)}:=\left\|{\hat {\mathbf {x} }}_{j\alpha }^{(t+\Delta t)}-{\hat {\mathbf {x} }}_{j\beta }^{(t+\Delta t)}+\sum _{k=1}^{n}\lambda _{k}\left[{\frac {\partial \sigma _{k}^{(t)}}{\partial \mathbf {x} _{j\alpha }}}m_{j\alpha }^{-1}-{\frac {\partial \sigma _{k}^{(t)}}{\partial \mathbf {x} _{j\beta }}}m_{j\beta }^{-1}\right]\left(\Delta t\right)^{2}\right\|^{2}-d_{j}^{2}=0,\quad j=1\dots n$ "

Al2bec (talk) 12:02, 22 April 2009 (UTC)

That is correct, the $(\Delta t)^{2}$ is missing. Good catch! Since it does not depend on the individual constraints, we could even move it out before the sum. In practice, it is usually left out since this constant scaling is absorbed by the individual $\lambda _{k}$.

Cheers, pedrito - talk - 22.04.2009 12:11

GA Review

This review is transcluded from Talk:Constraint algorithm/GA1. The edit link for this section can be used to add comments to the review.

Hi: I'll be reviewing this article. It might take a couple of days - this is just an initial note. Best, Ray^Talk 17:02, 6 May 2009 (UTC)

Hi Ray,

Thanks for the heads-up! This is my first GA, so there may be a few things to fix... In any case, I'm looking forward to your comments. Cheers and thanks, pedrito - talk - 07.05.2009 08:34

Hi -- apologies, I was out of town and it dropped my mind, and then things have been a little crazy over here in real life. Anyhow, a checklist, followed by some general comments.

GA review (see here for criteria)

1. It is reasonably well written.

   a (prose): b (MoS):

2. It is factually accurate and verifiable.

   a (references): b (citations to reliable sources): c (OR):

3. It is broad in its coverage.

   a (major aspects): b (focused):

4. It follows the neutral point of view policy.

   Fair representation without bias:

5. It is stable.

   No edit wars etc.:

6. It is illustrated by images, where possible and appropriate.

   a (images are tagged and non-free images have fair use rationales): b (appropriate use with suitable captions):

7. Overall:

   Pass/Fail:

This was, in general, a very nice article. Technically clear, well organized, with plenty of links and references for the interested reader. A few points follow.

• In the section on mathematical background, you explain why external explicit constraint forces are not preferred. This section could use more references -- I'm sure it's elementary knowledge to anybody working in the field, but the general reader might not be in the field -- indeed, he might come here specifically to get an idea of what some elementary references on the subject are. This is the nitpick on 2a.

• Is the use of the term "constraint algorithm" common in mechanics generally, or is it restricted to simulations of molecular dynamics using classical physics? All the references seem to point to the latter, but the lead seems to suggest differently. That's the reason for the nitpick on 2c.

• You allude at various points to considerations of computational complexity, or other advantages and disadvantages to particular methods. Might it be possible to get a table, or some such, of advantages versus disadvantages for each type of method? This might make it easier for the reader. This is not required as part of the GA review, just to be clear -- it's just a suggestion that would make reading the article easier.

It was a pleasure to read, and increased my knowledge a good bit. It's been a while since I was a physics student, but it does bring back memories. Ray^Talk 22:09, 10 June 2009 (UTC)

Hi Ray!

Thanks for the detailed feedback. I've had a busy few weeks and couldn't work on fixing the issues yet. Can we keep this on hold until next week?

Cheers and thanks, pedrito - talk - 07:39 19.06.2009

Sure. There's no hurry. Ray^Talk 07:45, 19 June 2009 (UTC)

Still no work done since May. Wizardman 17:27, 8 August 2009 (UTC)

There have been no updates to this review since June, and no significant edits to the article itself since May. The on hold is now being removed and the article not listed at WP:GA. Please address the concerns raised by the reviewer. Once they are addressed, and the article meets the Good Article criteria, it can be renominated at WP:GAN for another review. Thank you. Dr. Cash (talk) 21:41, 13 August 2009 (UTC)

Some new developments

I think the recent articles that detail the effecient implementation of matrix inversion methods for linear and ring topologies

"Efficient constraint dynamics using MILC SHAKE" Journal of Computational Physics, Volume 227 , Issue 20 (October 2008) Pages 8949-8959

And a hybrid scheme for more general problems

MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes Journal of Computational Chemistry Volume 30 Issue 15 (2009) , Pages 2485 - 2493

should be mentioned —Preceding unsigned comment added by Cplowe1 (talk • contribs) 19:00, 16 December 2009 (UTC)

Summary is too general and not expository

I recently, changed the word mechanics in the first line of the summary to Physical Chemistry but, that is still too general. Also, there is no information linking this article to the constraints one is dealing with to give this article context. The summary says that contraint algorithms are to satisfy constraints. I think this is enough to remove the article altogether, as it has no link to other articles in wiktionary. The article on "contraint" will lead right back here from it's disambiguation page. Kckid (talk) 00:11, 15 September 2013 (UTC)

Missing mass term?

This article on the whole was quite well written. However, in working through the equations in the Lagrange section, I wonder if there is a missing mass term at the end of the section...

${\hat {\mathbf {x} }}_{i}(t+\Delta t)\leftarrow {\hat {\mathbf {x} }}_{i}(t+\Delta t)+\sum _{k=1}^{n}\lambda _{k}{\frac {\partial \sigma _{k}}{\partial \mathbf {x} _{i}}}$.

... should this be ....?

${\hat {\mathbf {x} }}_{i}(t+\Delta t)\leftarrow {\hat {\mathbf {x} }}_{i}(t+\Delta t)+\sum _{k=1}^{n}\lambda _{k}{\frac {\partial \sigma _{k}}{\partial \mathbf {x} _{i}}}m_{i}^{-1}$.

I'm not a maths expert, and I'm not fully sure if this is the correct solution, but without some sort of mass term in this final equation, then the same constraint acting on two different mass particles will result in the same movement of both particles, as if they were the same mass. Juggles82 (talk) 11:40, 25 December 2014 (UTC)

Requested move 7 February 2018

The following is a closed discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. Editors desiring to contest the closing decision should consider a move review. No further edits should be made to this section.

The result of the move request was: page moved. TonyBallioni (talk) 17:17, 14 February 2018 (UTC)

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Constraint algorithm → Constraint (computational chemistry) – May I suggest this article be renamed to "Constraint (computational chemistry)". That way the focus could be on the concept of a constraint with a section dedicated to various algorithms used to implement them. EvilxFish (talk) 14:31, 7 February 2018

• Support, and with a bit more lay-language introduction (focusing on the idea not the specific applications). If we don't have an article about the whole topic, demonstrating notability of it (and I do think it's notable), I have trouble supporting having an article hosting a collection of ideas that are presented solely in the context of a non-notable idea. DMacks (talk) 16:54, 7 February 2018 (UTC)
• Comment We also have a Constraint (classical mechanics) stub that is a bit of a mess IMO. DMacks (talk) 16:57, 7 February 2018 (UTC)
• Comment Whereas I agree with the previous and would be happy to take a look at Constraint (classical mechanics) I think it is important to remember that there are unique features of constraints in the context of computational chemistry. For example the position of each particle is dependent on the position of other particles in the system (you can't keep a hydrogen atom in the same place if the carbon it is bonded to moves) and a discussion of how forces are modified to incorporate constraints. An explanation of why constraints are important and regularly employed in molecular dynamics simulations would be good. I would argue the notability of this subject is well established, it has a whole subsection in Leach's "Molecular modelling principles and applications" on pages 368-374 as well as pages 113-120 in the most recent edition of "Computer simulation of liquids". I know you acknowledge the notability I just wanted to make sure all other readers do as well. EvilxFish (talk) 09:30, 8 February 2018 (UTC)

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The above discussion is preserved as an archive of a requested move. Please do not modify it. Subsequent comments should be made in a new section on this talk page or in a move review. No further edits should be made to this section.