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  • Dec 31 2020 03:13
    erh3cq opened #5
  • Dec 29 2020 23:23

    cophus on master

    Delete autosave matlab file (compare)

  • Dec 29 2020 23:22

    cophus on master

    Fix markdown 02 (compare)

  • Dec 29 2020 23:22

    cophus on master

    Fix markdown (compare)

  • Dec 29 2020 23:12

    cophus on master

    Fixing example and defaults Ch… (compare)

  • Nov 23 2020 19:22
    Angel-Ranger commented on 96c1474
  • Sep 15 2019 18:21
    cophus commented #2
  • Sep 15 2019 18:18
    cophus commented #4
  • Sep 04 2019 21:20
    thomasaarholt opened #4
  • Aug 29 2019 08:21
    thomasaarholt closed #1
  • Aug 29 2019 08:21
    thomasaarholt commented #1
  • Aug 29 2019 08:20
    thomasaarholt commented #2
  • Aug 29 2019 08:06
    thomasaarholt closed #3
  • Aug 29 2019 08:06
    thomasaarholt commented #3
  • Aug 29 2019 08:06
    thomasaarholt commented #3
  • Aug 28 2019 17:18
    cophus commented #2
  • Aug 28 2019 17:13
    cophus commented #1
  • Aug 28 2019 17:05
    cophus commented #3
  • Aug 27 2019 07:32
    thomasaarholt opened #3
Tara Prasad Mishra
@Quantumstud
It seems there are a lot of updates recently in the Prism-em package. I think it would be important to update the website?
Luis RD
@lerandc
@Quantumstud yes indeed! once all these new changes make their way through some testing and to the main repository, they'll be released together as an update and the website will be updated accordingly (as well as fixing all the things that currently need updating already)
Carter Francis
@CSSFrancis
Hello all, I was just running some simulations where I was looking at a system as a function of the Debye Waller factor. What I found was that it seems like any factor under 1.0 doesn't seem to change the simulation and at 1.0 suddenly the thermal effects are included. After looking at the source code
if (pars.meta.includeThermalEffects)
    { // apply random perturbations
    X = round((x[atom_num] + randn(de) * sigma[atom_num]) / pars.pixelSize[1]);
    Y = round((y[atom_num] + randn(de) * sigma[atom_num]) / pars.pixelSize[0]);
    }
Carter Francis
@CSSFrancis
This seems to suggest that if sigma is less than 1 it is just rounded back to the original position? Maybe I am misunderstanding this and there is another parameter I need to change. The code is from prismatic/src/PRISM01_calcPotential.cpp lines 171-175
Carter Francis
@CSSFrancis
Is it possible that pars.pixelSize is stuck at 1 in the new release? I know there are some changes with the addition of the realSpacePixelSize variable. I can run some more tests a little bit later, but just wondering if anyone with more familiarity could comment.
Luis RD
@lerandc

@CSSFrancis the round is applied the quantity (x[atom_num] + randn(de) * sigma[atom_num]) / pars.pixelSize[1], this rounds the atomic position + displacement to the nearest pixel for the 2D potentials so it can be placed

it should be having an effect below 1, though-- what commit version of the source are you using? the prism-em/master branch was updated with a quick string parsing fix earlier this year. if you don't have that fix, the parser might be dropping the last character in each line, so if you have DW factors 0.1, 0.2, etc., they would be read as 0

the pixelSize shouldn't be stuck at 1
the fix for the above w/o recompiling would be just to add a trailing 0 to each of your DW factors
Carter Francis
@CSSFrancis
@lerandc I was using version 1.2 so that's probably the issue. Thanks for the tip! I'll look into it a bit more but hopefully everything that sorts everything out
deRemarkable
@De_REMARKABLE_twitter
Hello all, I'm new here in terms of Prismatic. Would anyone be kindly enough to tell me if Prismatic could do simple plane wave TEM simulations (rather than STEM)?
ahinroy
@ahinroy
Hello all, I have been trying to read 4D-STEM simulation data generated by Prismatic using py4DSTEM. But, the output HDF5 file from Prismatic is not being recognized by py4DSTEM. As I understand, the EMD attributes are necessary in the Prismatic output HDF5 file to be compatible to py4DSTEM input. Is there a way to write the proper attributes to the output HDF5 through input simulation parameters in Prismatic?
Thomas Aarholt
@thomasaarholt
@ahinroy, I believe @ericpre added prismatic support in the latest master of hyperspy. I don't know if py4DSTEM directly relies on hyperspy for that import, but you can try.
Luis RD
@lerandc
@ahinroy I just checked against the most recently updated version of py4DSTEM and am hitting the same import issues-- looks like it's related on my end to the top group being named "4DSTEM_simulation" instead of "4DSTEM_experiment". there used to be a check in the repository for this very issue but it may have gotten lost in some recent updates (py4DSTEM went through a decent overhaul in its file IO module in the past months)
does your error log report something at this at the end of the stack trace when you try to the open the file? KeyError: "Unable to open object (object '4DSTEM_experiment' doesn't exist)
@De_REMARKABLE_twitter with version 1.2 of Prismatic, plane wave simulations are currently not possible; however, the functionality is mostly through the development pipeline and will certainly be a part of the next release!
ahinroy
@ahinroy
@lerandc I changed the topgroup through h5_py to "4DSTEM_experiment", even then the file is not readable by py4DSTEM. The only difference between the Prismatic output (after renaming the "4DSTEM_simulation" to "4DSTEM_experiment") and the recommended py4DSTEM input are the EMD attributes.
Luis RD
@lerandc

@ahinroy by changed the top group, do you mean you created a copy of the original top group with "4DSTEM_experiment" key? I couldn't find a way to change the name of an existing group with h5py; relinking stuff like this is generally prety hairy with HDF5 in my experience

in any case, though, the EMD attributes are attached to the top group as emd_group_type = 2, major version = 0, minor version = 5. with h5py, I see them with the command f['4DSTEM_simulation'].attrs.keys()--can you verify that this is the same case for you? py4DSTEM is currently on v0.9, so there are a host of little changes to be made to the file format anyway, and after poking around and testing a couple of other things, there doesn't seem to be a legacy reader for v0.5 in py4DSTEM at the moment, so even if things were aligned we'll run into issues

this can, in the time between now and the next release of prismatic, be much more quickly adressed on the py4DSTEM side, so I'll see what I can manage there in terms of a quick patch
ahinroy
@ahinroy
@lerandc right, I created a copy and tried to use that as py4dstem input, and that didn't work. With hdfview, I could not see the attributes in the prismatic output. I also agree that this will be better resolved on the py4dstem side. And thanks a ton for arranging the quick patch :)
Eric Prestat
@ericpre
@lerandc, would it more simple to keep 4DSTEM_simulation and avoid introducing breaking changes?
https://emdatasets.com/format says "This group may have any name: files saved by py4DSTEM name this group “4DSTEM_experiment” while files produced by Prismatic name it “4DSTEM_simulation.”"
assuming that this page is a reference for what is the emd file format, 4DSTEM_simulation would be fine as top group name
Luis RD
@lerandc
@ahinroy interesting, is this happening with the current GUI version or have you compiled your own?
@ericpre yes, it would be simpler to keep it-- and we would want to keep it so that the semantic separation is clear when analyzing data anyway. the top group situation has been sorted out already by Ben Savitzky, we now just need to check if the v0.6 legacy reader would work for prismatic (which is at v0.5 in terms of py4DSTEM versioning), and if not, write in a new legacy reader simlar to the one already implemented
ahinroy
@ahinroy
@lerandc I am not using the GUI. I have installed the Prismatic using conda and running the simulations in a parallel CPU architecture.
Paul Voyles
@paul-voyles
I've tried using Prismatic for the first time. On my Windows 10 laptop, GUI v1.2.1 and v1.2 non-GPU do not complete "full calculations". A dialog pops up that looks like it might be the computational progress dialog, but it disappears too quickly for me to read, and the code generates no output. v1.1 generate output with the same inputs. Is this is known problem with the later versions? Or should I try to describe it in more detail?
Luis RD
@lerandc
Hi @paul-voyles, this usually happens because Prismatic doesn't have write access to the output directory (often because the default output folder on windows is the program files install directory)-- either running in admin mode or setting the output path to something you're sure that Prismatic has privileges to write to should hopefully fix this
Luis RD
@lerandc
if not, and the error is something else, you could capture the standard output by invoking the GUI from a terminal (I use Git bash, but command prompt and powershell might work if you have the windows subsystem for linux)
MrDator
@MrDator
Hi, I am new user to prismatic. I think I successfully install the pyprismatic on our supercomputer server. However, when I tested it using pr.demo(), there is an error: Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/users/PAS1009/osu8981/.local/lib/python3.6/site-packages/pyprismatic/init.py", line 51, in demo
meta.go()
File "/users/PAS1009/osu8981/.local/lib/python3.6/site-packages/pyprismatic/params.py", line 334, in go
pyprismatic.core.go(*l)
TypeError: function takes exactly 46 arguments (55 given)
Luis RD
@lerandc
hi @MrDator - did you build pyprismatic from scratch, or did you use the conda-forge package?
Paul Voyles
@paul-voyles
@lerandc Thanks for the advice. I tried uninstalling 1.1, reinstalling 1.2.1, then running as admin from Program Files \ prismatic. Now it crashes in with no error message during the "calculating S-matrix" under "Probe Analyzer" part of the tutorial. I'm going out backwards, so I won't try to use this for class. My group still uses the commandline version for research, so I appreciate the project, but the GUI version doesn't seem ready for primetime yet.
Luis RD
@lerandc
@paul-voyles unfortunately so :( it definitely can be unstable and in a completely non-transparent way-- hopefuly this upcoming iteration will be much more friendly to use!
MrDator
@MrDator
@lerandc I tried both methods for CPU version, conda, pip and from source file. It told me it has been successfully installed and can be imported in python. But it has this problem. I didn't test GPU one since there are always some error when I compile it.
Thomas Aarholt
@thomasaarholt
Just to say - I just installed prismatic for the first time since ~September, and there are so many nice new settings!
Luis RD
@lerandc
@MrDator I'm working on some minor pyprismatic updates soon, I'll try to look into it and see what I can find, but I don't tend to use it so I'm not 100% sure where the error is coming from!
Colin Ophus
@cophus
@thomasaarholt Just wait a liiiiittle bit longer and there will be all sorts of new pieces!!
Thomas Aarholt
@thomasaarholt
@cophus :D
Ning Wang
@NingWang1990
Dear All, I am running the conda version of pyprismatic in our cluster. I just received an error message 'killed' in a simulation for ~ 5000 atoms. I am wondering if pyprismatic has a debugging mode, which can return more error messages. Did anyone see similar issues before?
Colin Ophus
@cophus
@NingWang1990 Sorry I don't think it does
I've never seen that even for much larger simulations
Thomas Aarholt
@thomasaarholt
@NingWang1990 Can you post the output immediately before the error message?
Oh, just realised this is 1.5 months old
Colin Ophus
@cophus
Yeah this year I have lost contact with a lot of my contact channels - @thomasaarholt if you're interested you could join our Slack where most of the development talk happens
Thomas Aarholt
@thomasaarholt
Sure! Send me an invite at thomasaarholt@gmail.com
Espendb
@Espendb
Hi all - feel free to ignore this if you feel that it’s to far from the topic. I am in the midst of grant writing to upgrade our current setup in Aarhus. I aim at building our 4D stem capabilities and was wondering if people could share some experiences with the different cameras. I myself have experience with the Empad and the ceta cam in fast mode and was wondering if people would mind sharing their experience / thoughts about the various options out there with me (over e-mail or dm if you prefer) .
Shuoyuan Huang
@SyHuang19
Hi all, I've been running parallel beam diffraction simulation on amorphous structure using the Multislice algorithm and a single scan position. I keep getting this dark grid-like feature overlaid on my diffraction pattern. I don't know if it is a sampling issue or it's just real. My other speculation would be unit cell tiling in x and y directions which induce periodic boundary condition that would otherwise not exists in amorphous samples. Has anyone encountered this before?
image.png
Here is an example of the simulated pattern