Introducing molecular dynamics tutorial

[joaander]

Description

Add the introductory MD tutorial for the HOOMD v3 API.

Review request

Reviewers, in addition to detailed comments, I'd like you to think about and comment on the following:

• Are the concepts presented clearly, with no fluid representations and reasonable assumptions for prior knowledge?
• Are there any core MD concepts that this tutorial is missing?
• Does the tutorial get sidetracked and go into too much detail on concepts that are not critical to understanding MD simulations with HOOMD?
• Remember, this is the introduction tutorial aimed at first time HOOMD users. There will be separate tutorial that cover additional topics like Logging, bonds, etc...

The concept map ppt will be included in the PR if you want to check it out.

Note: There are a few TODOs already marked (especially in section 2) on things I already plan to change.

Checklist:

• [x] I have reviewed the Contributor Guidelines.
• [x] I agree with the terms of the HOOMD-blue Contributor Agreement.
• [x] My name is on the list of authors.

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b-butler commented on 2020-09-23T20:42:10Z ----------------------------------------------------------------

I might mention in a # comment that the from_box method is used to copy the box.

joaander commented on 2020-09-24T12:40:59Z ----------------------------------------------------------------

Should we enable support for Python's copy.copy to make this more explicit?

review-notebook-app[bot] commented 3 years ago

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b-butler commented on 2020-09-23T20:42:11Z ----------------------------------------------------------------

While I think all 3 methods are useful to know, we are providing multiple ways to do the same thing (although they all have different use case for which they are optimal). I know we are trying to avoid fluid representations with ways to do things. I personally don't mind it here, but I thought it worth mentioning.

joaander commented on 2020-09-24T12:43:23Z ----------------------------------------------------------------

You are correct, we should show only one method here. We covered triggers in the intro tutorial so let's show only the remove method here.

joaander commented 3 years ago

Should we enable support for Python's copy.copy to make this more explicit?

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joaander commented 3 years ago

You are correct, we should show only one method here. We covered triggers in the intro tutorial so let's show only the remove method here.

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b-butler commented on 2020-09-23T20:42:11Z ----------------------------------------------------------------

While I think all 3 methods are useful to know, we are providing multiple ways to do the same thing (although they all have different use case for which they are optimal). I know we are trying to avoid fluid representations with ways to do things. I personally don't mind it here, but I thought it worth mentioning.

joaander commented on 2020-09-24T12:43:23Z ----------------------------------------------------------------

You are correct, we should show only one method here. We covered triggers in the intro tutorial so let's show only the remove method here.

joaander commented 3 years ago

Should we enable support for Python's copy.copy to make this more explicit?

---

View entire conversation on ReviewNB

joaander commented 3 years ago

You are correct, we should show only one method here. We covered triggers in the intro tutorial so let's show only the remove method here.

---

View entire conversation on ReviewNB

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[joaander]

Should we enable support for Python's copy.copy to make this more explicit?

---

View entire conversation on ReviewNB

[joaander]

You are correct, we should show only one method here. We covered triggers in the intro tutorial so let's show only the remove method here.

---

View entire conversation on ReviewNB