Allow setting user box dimensions to a multidimensional array.

[hmacdope]

Is your feature request related to a problem?

You should be able to set the box size manually over your whole trajectory. Related to #2691, however the fix in #3175 (NOTE: currently pending merge) only sets the box dimensions to a constant [a, b, c,alpha, beta, gamma].

Describe the solution you'd like

This can be done easily with a multidimensional array of shape timesteps, [a, b, c,alpha, beta, gamma] and something like the below:

def set_traj_dimensions(input_dims, u):
    for i, ts in  enumerate(u.trajectory):
		ts.dimensions = input_dims[i,:] 

Describe alternatives you've considered

Additional context

You cannot work on this issue until #3175 is merged.

[lilyminium]

You’d probably want an OTF transformation like PR #3175, as changes to ts.dimensions won’t persist throughout the loop.

…

On 5 Apr 2021, at 5:18 pm, Hugo MacDermott-Opeskin ***@***.***> wrote: Is your feature request related to a problem? You should be able to set the box size manually over your whole trajectory. Related to #2691 <#2691>, however the fix in #3175 <#3175> (NOTE: currently pending merge) only sets the box dimensions to a constant [a, b, c,alpha, beta, gamma]. Describe the solution you'd like This can be done easily with a multidimensional array of shape timesteps, [a, b, c,alpha, beta, gamma] and something like the below: def set_traj_dimensions(input_dims, u): for i, ts in enumerate(u.trajectory): ts.dimensions = input_dims[i,:] Describe alternatives you've considered Additional context You cannot work on this issue until #3175 <#3175> is merged. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3217>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHNMOXNZISF3MZVC6AWGVELTHJHOVANCNFSM42NV2EOQ>.

[yizhuang1]

Hi, is this thread still available for GSoC? I'd like to make a contribution. Thanks!

[hmacdope]

@yizhuang1 yes it! Go ahead and make a PR. :)

[nancyalaswad90]

Hi everyone 😊

Please advise me on how we distinguish between the active or close issues?

[orbeckst]

As @ljwoods2 correctly pointed out in #4400 , the current implementation

mdanalysis/package/MDAnalysis/transformations/boxdimensions.py

Line 37 in 734314b

class set_dimensions(TransformationBase):

already allows setting the box dimension from an array for all frames of the trajectory. This behavior was added in f50a097 as part of PR #4258 .