seto77/recipro

The software ReciPro makes various crystallographic calculations, visualizes a crystal structure, simulates a diffraction pattern and high-resolution TEM image, indexes diffraction spots, plots stereographic projection, and so on.

ReciPro is free software that provides a variety of crystallographic calculations and simulations, and has been downloaded >10,000 times since its release on github (Mar 2020). See also Wiki to learn how to use!

recipro_demo.mp4

• ReciPro makes various crystallographic calculations, visualizes a crystal structure, simulates a diffraction pattern and high-resolution TEM image, indexes diffraction spots, plots stereographic projection, and so on.
• ReciPro is developed by Seto Y. (Osaka Meteropolitan University, Japan) and Ohtsuka M. (Nagoya University, Japan). The functions and algorithms are also presented in the paper. If you use this software to write an academic paper, we would appreciate it if you would cite the following information.
  • Seto, Y. & Ohtsuka, M. (2022). J. Appl. Cryst. 55, 397-410, doi: 10.1107/S1600576722000139.

---

Install

• Access https://github.com/seto77/ReciPro/releases/latest, download ReciProSetup.msi, and execute it.
• ReciPro runs on Windows OS with .Net Desktop Runtime 8.0 (not .Net Runtime 8.0), which can be installed from here.

Manual

• Japanese version : https://raw.githubusercontent.com/seto77/ReciPro/master/ReciPro/doc/ReciProManual(ja).pdf
• English version : https://raw.githubusercontent.com/seto77/ReciPro/master/ReciPro/doc/ReciProManual(en).pdf

---

Main features

• Makes crystallographic calculations.

  • 530 (Hall symbol) space groups are available.
    • General conditions (or extinction rules), Wyckoff positions, multiplicities of all space groups.
    • Geometrical calculation of periodicity and/or angle between planes and/or axes.
    • Generation of equivalent atomic positions.

• Provides crystal database.

  • Over 20,000 crystal structures are available after installation.
    • The database is provided by American Mineralogist Crystal Database (AMCSD, Downs & Hall-Wallace, 2003, American Mineralogist 88, 247-250)

• Includes atomic properties.

  • Characteristic X-ray wavelength/energy.
  • Atomic scattering factor for X-ray, electron and neutron.

• Simulates diffraction patterns.

  • X-ray, electron, and neutron sources are available for incident beams.
  • Kinematic simulations for the all sources.
  • Dynamical simulations for electron diffraction based on the Bloch wave method.
    • Parallel electron diffraction (SAED)
    • Precession electron diffraction (PED)
    • Convergent beam electron diffraction (CBED)

• Draws crystal structure using OpenGL4

  • Atom, bonds, polyhedra, unit cell and lattice planes.

• Plots stereonet (Wulf-net).

  • Axes and planes of any indices.
  • Large and small circles.

• Identifies diffraction spots in the observed image.

  • Major file formats (dm3, dm4, tiff, …) are supported.
  • Automatically detects diffraction spots, and identifies (or indexes) the spots for the selected crystal(s).

• Manages crystal data base.

  • ~80 crystal data are initially bundled.
  • Import/export CIF, AMC format files.
  • Possible to use COD and AMCSD database through CSManager (https://github.com/seto77/CSManager/releases/latest).

---

Screenshots

　　　

---

recipro's Issues

Some advises in CBED simulation

V4.810

• The "Gamma" slide range is too small, and it only has very little effect on image
• Overlapped disk will cover each other, rather than add-together in real world. This will be messior with weak disk

Anyway, thank you for providing this great tool for EM research

Underestimated infomation limit for moderm TEM in HRTEM simulation

Hi Seto,
When I set the TEM properties in HRTEM simulation, the resulted resolution is much lower than the real TEM.
As you can see in the picture, Cc=1.6 mm and dE=0.8 eV only give ~0.1nm infomation limit. In modern aberration-corrected TEM, we can easily get ~0.06-0.07nm. Meanwhile, the Sidorov's ctfExplorer gives resonable esitimate.
In his website http://www.maxsidorov.com/ctfexplorer/, he said he changed the temporal envelope in latest version
And I finally found a different formula here http://ctfsimulation.bio.purdue.edu/java/, in which the coefficient changed from 1/2 to 1/16*ln(2)

Sequence contains no elements

Error will be reported when opening the diffusion simulator
Unhandled exception has occurred in your application .ou click Continue , the application will ignore this errorand attempt to continue . If you click Quit , the applicationwill close immediately .
Sequence contains no elements .

3D rendering disable mode

Dear Seto,

Thank you for creating Recipro. I recently had a strange issue. I clicked on r"Refine thickness and direction" on spotID V2, this lead to the program crash. And after restrating the program it now says in the main window header (3D rendering disable mode). Now my access to Rotation Geometry and Structure Viewer are disabled.

May you please let me know how I may revoke this issue.

Thank you for your time!
Sandeep

Scattering factors for electron diffraction

Hi,

I cannot find which scattering factors are being used to simulate electron diffraction patterns? Can you please let me know. And is there any possibility to change them?

Thanks

Error in equivalent positions in exported CIF file

In space group 225 (Fm-3m) and 227 (Fd-3m), translation symmetry equivalent positions can be expressed in this pattern:
(x, y, z)
(x, y+1/2, z+1/2)
(x+1/2, y, z+1/2)
(x+1/2, y+1/2, z)

In the CIF of crystals with space group 225 or 227 exported with ReciPro ver4.779, the translation symmetry equivalent positions are expressed as:
(x, y, z)
(x, y+1/2, z+1/2)
(x+1/2, y, z+1/2)
(x, y+1/2, z+1/2)
the 4th position is mistaken as the same as the 2nd.

Not for sure but other cubic-F space groups might also suffer from the same error.

Failed to load Database, sorry

Version 4.785, on Crystal Database load button, error message ==> " Failed to load database, sorry"

please rectify

unable to cast object of type 'system.single' to type 'system.double'

Hello, thanks for providing such a nice software for TEM analysis. When I use the app, I had a trouble in reading one image of 'diffraction patterns' using 'Spot ID 2'. I am sure the format of the image is '.dm3', but dont know how to solve the problem. Could you please give me some help?

Kind regards

Yuanguo

Suggestions for Diffraction Simulator: Pixel Size Calibration and Option for simple Bragg-Position Markers

Hello!

Thanks for sharing and maintaining this great software! I use it mainly for electron diffraction and want to suggest to add the following features if you find time at some point:

1. Scaling the simulated diffraction pattern with a given pixel size (e.g., nm-1) to more easily match it with the exp. patterns.
   At the moment, one must set the image size in pixels, the camera length, and a mm/px value. I think it would be great to add a "pixel size" option as well (very similar to #25 ). Then, a user can directly provide the image size (e.g., 512 x 512) and the pixel size in nm-1 from their exp. patterns.
   To match my DPs with ReciPro, I use an Excel file to help me calibrate the width of the ReciPro patterns to match my experimental patterns (https://github.com/lukmuk/em-stuff/blob/main/Excel%20Sheets/ReciPro_DiffractionScaler.xlsx) by fixing the camera length to an arbitrary value (e.g. 100 mm) and calculating the mm/px value to match my exp. patterns. The proposed change would make it more easy to match the patterns directly in ReciPro.

2. Add an option to only show the "geometrical positions" of the Bragg spots (i.e., without any intensity consideration = same spot radius and brightness).
   Now the simulated spots always "fade" toward higher scattering angles when the Ewalds sphere/spot intensity is considered. Sometimes it may be useful to simply display the expected positions of the Bragg spots as points (i.e., a 2D grid of points). Maybe add something like "Simple geometry of spots" to the "Intensity calculation" section? That would be great!

Thanks again for providing this awesome toolbox and for consideration of these suggestions. :-)

Rotation Geometry and Structure Viewer does not work!!!!!

@seto77 Thanks for your Recipro. It is very useful. It worked properly one month ago, but recently it comes to a trouble, when it is opened, it prompts"error during initializing GLcontrol", "the type initializer for crystallography.OpenGL. GLControlAlpha threw an exception". When I click on the structure viewer on the user interface, it comes up (3D rendering disable mode), but at this time, I do not check disable OpenGL. looking forward to your help.

drag and drop of some cif files from materials project cannot be read

Dear Seto,

I often encounter the issue of Recipro program not responding or reading some cif files when I drag and drop them in the cif read area of the main window.

I typically use cif files from materials project (for example: I see that Recipro can read and open SnS2 trigonal cif but cannot read SnS2 hexagonal cif file, both downloaded from materials project).

I wonder if you may have a solution around this issue.

A kind comment, may be providing the possibility of loading cif files in more conventional way (like open/load cif file), in future versions of the software, might be useful to all.

Thank you for your time!
Sandeep

Planes on axes

Dear Seto,

There are always some planes on the axes. Rotation control, Rotation geometry and Structure Viewer, where there is axe, there are planes.
Could you please help me to hide these planes. It is not easy to observe the axes with these planes.
Thank you.

Blank page in the diffraction simulator

I wonder why I am only seeing the blank page (black) in the diffraction simulator. I selected the material from the crystal list, but it showed nothing.

v4.864: 起動時に必ず応答なしになってしまう

瀬戸様

いつもソフトウェアを使わせていただき、たいへんお世話になっております。
ReciProの最新版 v4.864 で、"Reading registries again"のステップで止まってしまい、「応答なし」になってしまいます。
何度かアンインストールして入れ直したり、またv4.862, v4.861を試したりしましたが、同様でした。
手元の環境は、Windows 10, 64 bit, core i7-6700 CPUで、他のソフトウェア（IPAnalyzer, PDIndexer）は動いております。

なにか考えられる原因はありますでしょうか？
お手数ですが、ご教示いただければ幸いです。

東京大学理学系研究科
小林大輝

Issue adding new structures from the database

Thank you, I really like this program.

I have an issue when adding new structures from the crystal database.

For example, when I add Mn3Si with a lattice constant of 5.722 Å, the cell volume is given as 1873456270480000 Å^3. It seems that it is not correctly interpreting the decimal separator since 5722^3 = 1873456270480000.

I suspect the issue is due to using a danish language operating system where the "," (comma) is used as a decimal separator.

I would suggest always using the "." (dot) separator. I think most scientists prefer the dot separator, despite the convention of their respective countries.

I am also not able to open Structure Viewer for newly added structures, however, I think this is directly related to the above issue.

System:
Windows 11
.Net 6.0
ReciPro ver4.826(2021/11/18)

Indexing TEM diffraction pattern with Spot ID V2: Crystal info loading problem

Hi Seto,
Thank you so much for making available such comprehensive software I appreciate that. I am using your program to index collected TEM diffraction spots and I have no problem to loading images and identifying the spots with Spot ID V2. My question is when indexing the diffraction spots with Spot ID v2, it does upload the crystal data from the main window and not label the spots with their hkl index. Before identifying the spots, I select the reference crystal in the crystal list window (which is became blue). However, somehow the two windows (main window and spot ID v2) do not communicate or transfer the crystal info. Would you let me know what am I missing?
Thanks again for this software, I appreciate the effort
Selda

Program Version for Mac

Thank you for the program. I like it very much.
Since I'm normally working on a Mac M1 I'd like to ask if it would be possible for you to provide a Mac version of the program.

Error in opening the software

Hi,

I have been trying to open the software, but it always gives me a warning that ' you must install or update .NET to run this application.' I have downloaded both NET6.0 and 7.0 desktop Runtime but the software still not working.

Do you have any ideas what 's going wrong?

with regards
Di

Real type image from HRTEM simulation

Thank you for the program. The functions are extremely amazing to me! I mainly use the HRTEM simultion function, the live simulation is really powerful.
Now I am using the simulated peak intensity as a refer for quantitative analysis of experiment imge. It seems that the simulated HRTEM from ReciPro is normalized to 2^16, similar to integer data image maybe?. It is harder to compare intensity with each other. So is it possible to get a real data type image like QSTEM or mactempax, whose intensity from vacuum is normalized to 1? In that case, the peak intensity could be compared directly with experimental images Thank you very much.

HRTEM simulation: bcc Fe(alpha) [110] axis

no atom columns are distinguished.

virus reported by windows defender

Returned csv header from Marco's `ReciPro.DifSim.SpotInfo()` always lists "Ug" etc. regardless of the "Vg [eV]" option (while the values are indeed Vg)

As the title suggests, when the "Unit of poteintial" is set to "Vg [eV]", the ReciPro.DifSim.SpotInfo() function in Marco still has "Ug" etc in the returned csv header, although the values will actually be Vg values.

On the other hand, when using the "Copy to clipboard" button from GUI, the returned text has the correct "Vg" in header, accordingly.

BTW, a typo in "Unit of poteintial".

On version 4.884.

Cheers

query about STEM simulator Detector angles

Dear Seto,

I have a query related to STEM simulator. Is there any rule on minimum inner detector radius with respect to the convergence angle? I ask this because I am noticing that if choose inner detector radius much higher than twice of convergence angle the simulated image result is giving me just a blank dark image. For example, if my convergence angle is 21 mrad and inner and outer detector collection angles (annular detector range radius) are 79 mrad and 200 mrad the simulated result is just blank image. If I remeber correctly I didnt face this issue few months ago when I used the STEM simulator. Looking forward to hear from you. Thank you...Sandeep

Error in using AMD CPU's integrated GPU

I'm using Recipro on a laptop PC with integrated CPU graphics (Ryzen pro 7 4750U).
3D graphics is disabled" in the compass window and the "Structure Viewer" and "Goniometer" icons are grayed out and not available.
Under similar usage conditions, I was able to use 3D graphics functions successfully with Intel's integrated graphics (i5-8250U, i5-8500...). .

I have tried the following
-Downgrade the version from latest to v.4.776 in steps.
-Update the display driver from device manager.

Request: Diffraction simulator - display of reciprocal distance

In the diffraction simulator, would it be possible to add the display of the reciprocal distances of the diffraction spots?

The distance is also "kind of" available with the live readout of the position of the cursor and after double clicking an individual spot.
Also, could the length of the vector would also be a nice information to be displayed in that window.

And of course I want to use the chance to thank you for this amazing piece of software!

SpotID v1 (zone axis)

Thank you Dr. Sato for producing ReciPro which is very useful software for me.
The zone axis was outupted as [00-1] (please find an attaced file).
This means that the c-axis direction is under the screan (left-handed system). Is it correct?

program cannot be executed

Downloaded the .Net 5.9 x64, unfortunately, the program did not respond after click.

Acknowledgment or citation in article

I am very grateful to ReciPro software. It help me a lot to analysis plenty of diffraction data from TEM.

I am writing the article and ready to explain your contribution in my work. So, I prepare to cite your article (https://doi.org/10.1107/S1600576722000139) in the article.

Other than that, is there anything else I need to state?

HRTEM/STEM Simulator: config sidebar not fully visible

The sidebar in the HRTEM/STEM Simulator contains important configurational inputs. However, in the latest version, the sidebar is only partially visible. I tried to drag its edge, but it does not expand the sidebar either.

Simulated HRTEM image has a flip compared to structure viewer

For example, here is the potential of DyScO3 and the structure viewer window.

Spot ID v2 - image calibration

Hello,

In the 'Optics' menu, there are two inputs for calibration, which are 'Camera Length' and 'Pixel Size'.
I'm not sure how to set those values.

Usually, camera length of DP images are not well known and correct. So I use the pixel size to calibrate the DP images.
But the dimension in DP should be reciprocal. However, in the 'Pixel Size', the value is mm unit. So I'm confused.

Please guide how to set the values to properly calibrate DP images.
Thanks.

Back Laue does not work ?

I think old version of recipro can show the back-laue mode. But current ver. can not do so.