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  • Sep 18 20:17

    bocklund on weighting-selection

    Remove xarray in ZPF data hot p… FIX: squeeze plot output to acc… Equilibrium hessians (pycalphad… and 3 more (compare)

  • Sep 12 08:11
    duxiaoxian opened #108
  • Aug 06 10:46
    duxiaoxian closed #106
  • Aug 06 10:46
    duxiaoxian commented #106
  • Jul 31 16:14
    richardotis commented #107
  • Jul 31 12:56
    bocklund opened #107
  • Jul 17 17:37
    bocklund commented #106
  • Jul 17 17:37
    bocklund commented #106
  • Jul 17 17:37
    bocklund commented #106
  • Jul 10 15:23
    duxiaoxian commented #106
  • Jul 08 21:16
    bocklund commented #106
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    bocklund commented #106
  • Jul 04 03:16
    duxiaoxian commented #106
  • Jul 03 17:40
    bocklund commented #106
  • Jul 02 04:26
    duxiaoxian opened #106
  • Jun 12 20:51
    bocklund closed #94
  • Jun 12 20:51
    bocklund commented #94
  • Jun 12 20:49
    bocklund demilestoned #98
  • Jun 12 20:48
    bocklund milestoned #99
  • Jun 12 20:48
    bocklund demilestoned #99
Brandon Bocklund
@bocklund
Some in the POSCAR format are available here for some simple phases: http://www.phases.psu.edu/?page_id=77
zhanghaihui
@zhanghaihui_gitlab
@bocklund Wow, very detailed. Thanks a million. I really appreciate it.
zhanghaihui
@zhanghaihui_gitlab
@bocklund Hi, Brandon, in the calculation of Ag-Cu phase diagram, I use Ag3Cu,AgCu and AgCu3 solid solution structure for phonopy calculation, that is, replace one or more copper atoms in the FCC cell, which are all fcc-A1 phases. May I ask how to configure HM,SM with temperature variation in the input file? In my opinion, sublattice_site_ratios are [1, 1], so how to distinguish Ag3Cu,AgCu and AgCu3 solid solution structure when the variable is T?
zhanghaihui
@zhanghaihui_gitlab
For example, for this diagram, my input file is as follows
image.png
image.png
Is this correct? If I use phonopy to calculate HM,SM,CPM as a function of temperature, what is the format of the input file when the variable is just T?
zhanghaihui
@zhanghaihui_gitlab
I have recently used the latest version of espei = 0.7.2 and I always get an error, but I used espei = 0.6 and it works fine.
image.png
My current computer can't use espei = 0.6 again, so I don't know which version to use, I don't know what went wrong.
image.png
I always get MPI errors when I use espei = 0.6
Richard Otis
@richardotis
Can you check which version of pycalphad you are running?
That error looks like an old bug
conda list is probably the easiest way
You should be running pycalphad 0.8
Richard Otis
@richardotis
Can you open an issue on GitHub about this? And can you upload the Python and JSON files you're using for the plot? If it used to work in an old version of ESPEI, it could be a regression (in either ESPEI or pycalphad)
zhanghaihui
@zhanghaihui_gitlab
My pycalphad is 0.8, ESPEI is 0.7.2
zhanghaihui
@zhanghaihui_gitlab
Can anyone help me?😭I have opened an issue on GitHub.
Richard Otis
@richardotis
The next few days are a holiday in the US, you may not get a response right away.
duxiaoxian
@duxiaoxian
Oh oh oh....Bad news😭
Richard Otis
@richardotis
@npaulson You (and others) may find this new MCMC package interesting: https://pymcmcstat.readthedocs.io/en/latest/
zhanghaihui
@zhanghaihui_gitlab
@bocklund I found that the input data for Ni3Al on github is different from the refence of "Shunli DFT calculations (2010)". Is the reference "First-principles thermodynamics from phonon and Debye model: Application to Ni and Ni3Al"? The HM, SM, CPM data obtained from Fig7 and 8 are not the same as the data on github. For example, the HM value at 1615K, github is 39428.25, while in the literature is 157430.
What is the cause? Do you need a numerical conversion?
Noah Paulson
@npaulson
@bocklund @richardotis I've been working on PDUQ (https://github.com/npaulson/pduq) a bit and I believe it is finally in pretty good shape (including documentation, https://pduq.readthedocs.io/en/latest/index.html). If you have the chance, take a look and perhaps even try installing/doing some analyses. Any feedback would be fantastic before I do an official release.
sorry, this should work for the documentation: https://pduq.readthedocs.io/en/latest/
Richard Otis
@richardotis
Writing docs is a lot of work. This looks great.
Care to comment on what's going on in this figure? https://pduq.readthedocs.io/en/latest/_images/phase-fraction_1000K.png
Noah Paulson
@npaulson
Thanks, it was definitely a bit of effort
Richard Otis
@richardotis
Is that the UQ reflecting the fact that you aren't sure about the stability of Laves, so you're seeing a metastable liquidus showing up
Noah Paulson
@npaulson
I think it makes some sense when looking at this figure at the same time: https://pduq.readthedocs.io/en/latest/_images/phase-diagram_superimposed.png
It's because we are right at 1000K around the invariant
so there's huge uncertainty in the stability of liquid, Laves and CuMg2
Richard Otis
@richardotis
Very cool
Noah Paulson
@npaulson
I should definitely comment on that a bit in the docs
It totally looks wrong at first glance, but I think it's real
Richard Otis
@richardotis
Agreed on both. Looks wrong at first, but it makes sense
I have a use case for this, but I need to get some new functionality implemented in pycalphad first. I want to look at uncertainty for a liquidus temperature versus chemical potential plot
Noah Paulson
@npaulson
Interesting, we can talk about how to implement that when you are ready. If PDUQ starts getting users I'm sure people will start asking for analyses I haven't thought of yet
Brandon Bocklund
@bocklund
This is great. I'm going to work some links into the ESPEI docs that point people towards PDUQ for UQ. Does this follow exactly the Cu-Mg example on espei.org (particularly the espei-datasets data)? Most people who have come across ESPEI and attempted to use it have followed the example, so having continuity where they can verify their plots and diagnostics match the website would be good.
Brandon Bocklund
@bocklund
Another thing I think we have seen in pycalphad and ESPEI is that the literate programming notebook style is very informative, but copy-pasting code chunks are how people tend to use the examples. That spawned ESPEI's Recipes page, which collects the useful code to produce one output into one pastable chunk that you can link to when people ask "how do I plot the thermodynamic properties with my data", etc. The recipes I have up there now are commented, but don't have much explanation, since those chunks and pieces are distributed through the example
Noah Paulson
@npaulson
I don't think that my trace files will be exactly identical to yours unless we happened to use the exact same weights for the various datasets. I had done some messing around to ensure that I was getting good convergence. That said, the code examples should work "out of the box" with those traces
Maybe we can think about converging the examples so they are actually identical
I think similarly to ESPEI, the code chunks in PDUQ should be readily useable
Brandon Bocklund
@bocklund
The datasets in the espei.org example haven't been updated since we added the weighting feature last year, so it needs to be redone. If you want to share the datasets you've weighted with me or a make a PR against https://github.com/PhasesResearchLab/ESPEI-datasets, I can rerun the example to produce consistent output
Noah Paulson
@npaulson
what do you think would be easiest? I can even share the traces directly with you so you don't have to re-run anything. These would be identical results to our UQ paper on Cu-Mg
Brandon Bocklund
@bocklund
No problem, you can edit the messages with the three dots on the right hand side or by hitting the up arrow from the blank Gitter text box to cycle through your previous messages. I do it all the time haha
Noah Paulson
@npaulson
haha, very handy - thanks
Brandon Bocklund
@bocklund
I'm fine rerunning it locally, just to make sure it's all consistent. Eventually I'd like to have some kind of CI system that runs the examples automatically as it becomes more computationally tractable
Noah Paulson
@npaulson
okay, I'll go about collecting all of the relevant input files so you can reproduce the paper results