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qzhu2017 / XRD

X-ray diffraction calculations
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VXRD: Forms #22

Closed sabaronett closed 4 years ago

sabaronett commented 4 years ago

Tasks

Reference

sabaronett commented 4 years ago

@qzhu2017 @sayred1 I saw with 354fc09ef24980ed3b4dd74c118f16c29c6c3fa2 that the get_profile() function now takes a res argument, as in below:

xrd.get_profile(res=0.01)

Before (when it used to be N), we wanted the default to be 10000. I'm assuming we now want this res argument to default to 0.01? Also, what do you guys want to set for min/max values?

Thanks.

qzhu2017 commented 4 years ago

@sabaronett let use 0.01 as the default, min=1e-3, max=1.

qzhu2017 commented 4 years ago

@sabaronett

image

It is not urgent. But I think you need to rearrange the menus later. For instance, it is more convenient to put theta_max and min in the same line.

qzhu2017 commented 4 years ago

@sabaronett I just tried to load NaCl.cif, but it output the following

image
sabaronett commented 4 years ago

@qzhu2017 I'll add menu-rearrangements to the task list. I'm currently rendering a quick_form in the HTML template for simplicity (one line), but once we've finalized the form fields and functionality I can build the layout from scratch. We should meet to sketch and finalize the layout when we get there.

As for the error, can you try one of the working test files I've put in /flask/instance/uploads (here)? I had to disable validation on the uploads so there are issues with some of the "bad" files in the /dataset directory.

Also, did you pull /flask/.flaskenv (here)? You should only be getting that error page if debug-mode is off, and I've forced it on in that file when you run flask run.

qzhu2017 commented 4 years ago

@qzhu2017 I'll add menu-rearrangements to the task list. I'm currently rendering a quick_form in the HTML template for simplicity (one line), but once we've finalized the form fields and functionality I can build the layout from scratch. We should meet to sketch and finalize the layout when we get there.

As for the error, can you try one of the working test files I've put in /flask/instance/uploads (here)? I had to disable validation on the uploads so there are issues with some of the "bad" files in the /dataset directory.

Also, did you pull /flask/.flaskenv (here)? You should only be getting that error page if debug-mode is off, and I've forced it on in that file when you run flask run.

Just realized that I used a new PC to run this app. After I installed the required python packages, the problem is gone!

sabaronett commented 4 years ago

Hahaha. Whew, you had me worried!

sabaronett commented 4 years ago

@qzhu2017 @sayred1 Is there a min/max value you'd like to set for the pseudo-Voigt V parameter?

Also, here are the results of the different profiling methods implemented with their default parameter values:

Gaussian

gaussian

Lorentzian

lorentzian

Pseudo-Voigt

pseudo_voigt

sabaronett commented 4 years ago

In order to get the profile-specific params working, I had to add arguments to the following lines: https://github.com/qzhu2017/XRD/blob/58355bde56655843c936711da8bf4bb0007fe563/pyxtal_xrd/XRD.py#L51-L52

You'll have to rerun python setup.py install after you pull 58355bde56655843c936711da8bf4bb0007fe563, otherwise flask/app/routes.py will encounter an error when you try to submit.

Seems to be working. Here's an example NaCl lorentzian profile with FWHM=0.5: fwhm_0 5

qzhu2017 commented 4 years ago

@sabaronett @sayred1 Are you guying coming to school tomorrow?

Can we have a meeting at my office regarding the following items

I want to

sayred1 commented 4 years ago

@qzhu2017 @sabaronett, I will be free after 12.

On Mon, Feb 17, 2020 at 4:43 PM Qiang Zhu notifications@github.com wrote:

@sabaronett https://github.com/sabaronett @sayred1 https://github.com/sayred1 Are you guying coming to school tomorrow?

Can we have a meeting at my office regarding the following items

  • Set min/max for V (pseudo-Voigt)
  • Finalize form layout (sketch)
    • Put 2θ min/max fields on same line.
  • Dynamic sub-form for gaussian/lorentzian vs. pseudo_voigt params
  • Implement final form layout

I want to

  • finalize the sketch of layout
  • clarify the profile function applied to PXRD computation.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/qzhu2017/XRD/issues/22?email_source=notifications&email_token=AIPGLD6PBLI5YITV4HF2NXDRDMVJVA5CNFSM4KOB7HB2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMADUAA#issuecomment-587217408, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIPGLD6TPSADE5TLGJRHCEDRDMVJVANCNFSM4KOB7HBQ .

sabaronett commented 4 years ago

@qzhu2017 @sayred1 I finish class at 12:45 PM, so I can meet at your office by 1:00 PM.

sabaronett commented 4 years ago

Final layout sketch from today's meeting.

layout

qzhu2017 commented 4 years ago

@sabaronett What is the progress?

Final layout sketch from today's meeting.

layout

@s

sabaronett commented 4 years ago

@qzhu2017, sorry, I've been busy with my research so no progress, but I can spend some time this weekend or maybe sooner. I'll let you know.

sabaronett commented 4 years ago

@qzhu2017, aside from adding JSmol, the layout with the dynamic JS toggling of the profiling sub-forms is done in 7d966a2c5c366d22ffddff9401dbc6af063886f1. However, there's kind of a bug where the sub-form defaults to FWHM after pseudo-Voight is submitted. It only re-updates with a profile "'double" change. I've added this bug to my task list.

qzhu2017 commented 4 years ago

@sabaronett I see. After you fix this, let me know if you need any help on JSmol. I may be able to help on that.

sabaronett commented 4 years ago

@qzhu2017 Fixed it! c118a957a7edb70f5caabc874a9c483dfae32570 😀 And I learned something new in the process: jQuery. I had seen the name before, but never knew what it was, as it wasn't developed until after I learned web development back in high school.

I don't have class tomorrow (Wednesday), so I should be able to spend a lot of time on this project and hopefully get the JSmol working and more.

By the way, is there a preferred min/max value for V (pseudo-Voigt) parameter? It's currently defaulted to -0.00167383

qzhu2017 commented 4 years ago

@sabaronett Thanks for fixing the bug. For V parameter, let's just leave as it is. I don't think there will be a need to change this parameter.

sabaronett commented 4 years ago

@qzhu2017, I meant there's currently no validation protection for that field, so the user can enter any nonsense float and potentially cause an error. If it should remain fixed then maybe we don't offer it as a field. Otherwise, make the validation range something like [-0.002, -0.001 ]?

Let me know what you think. Thanks.

qzhu2017 commented 4 years ago

@sabaronett Yes, you can put some range between [-0.002, -0.001]

sabaronett commented 4 years ago

Task list as of 3/16/2020 complete.

Closing issue.