The format of the exported CIF file.

[sitoald456]

The CIF file exported by the software cannot be properly recognized by Python. Could the format be adjusted to follow the standard used by the Materials Project website for better compatibility? Additionally, the STEM simulation output defaults to bright-field mode and currently does not support macro functions for customization. Would it be possible to enable macro functionality to allow more flexible simulation settings?

[seto77]

Thank you for your comment.

I think the CIF files output by ReciPro are in accordance with the IUCR recommendations (https://www.iucr.org/resources/cif/dictionaries), but it is possible that some of the tags used by ReciPro are inappropriate or out of date.
Do you know which tags cannot be read in your environment? Or, could you tell me what your Python app is specifically?

In the STEM simulation, the inner and outer diameters of the annular detector can be changed using the macro. Please see the following page.
https://github.com/seto77/ReciPro/wiki/20.2.-Examples

[sitoald456]

Thank you very much for your kind reply. I’ve revised my code, and it turns out that the CIF format is working correctly. I apologize for my earlier hasty question.

As for the STEM simulation, I’m currently working on batch-generating dark-field STEM images. I was wondering if you could kindly recommend suitable values for the inner and outer angles of the annular detector?

[seto77]

if you could kindly recommend suitable values for the inner and outer angles of the annular detector?

I may have misunderstood the intent of your question, but I will answer to the best of my ability.

The following diagram shows the optical system of a STEM in an extremely simplified form.
As you can see, the angle range of transmitted electrons captured by the annular detector depends on both the camera length (which is adjusted by the lens current of the projection lens) and the physical size of the annular detector.
The values for the inner and outer diameters of the annular detector are not independent.

It is a good idea to look at the specifications of your STEM (or contact the manufacturer) to determine the appropriate values.

[sitoald456]

Thank you for your response. I would like to know if there is a macro function available that can extract the chemical formula from a crystal structure and use it as the name of the CIF file when exporting.

[seto77]

a macro function available that can extract the chemical formula from a crystal structure

I haven't implemented that function yet, but it's a good idea. I'll do it in the next version. Please wait a little while.

[seto77]

The following built-in macro functions have been added in ver 4.901.

ReciPro.Crystal.Name
ReciPro.Crystal.ChemicalFormula
ReciPro.Crystal.Density

[sitoald456]

I sincerely appreciate it!

[sitoald456]

I want to convert the default axes of the CIF file and output it with its chemical formula and default axes as the file name, and automate the process. However, I don't know what the problem is, and I am unable to output the files

path = ReciPro.File.GetDirectoryPath()

for num in range(10):
ReciPro.CrystalList.SelectedIndex = num
ReciPro.Crystal.ChemicalFormula = Name
ReciPro.Dir.ProjectAlongAxis(0,0,1)
ReciPro.File.ExportCIF(path + str(Name) +' 001')
ReciPro.Dir.ProjectAlongAxis(1,0,0)
ReciPro.File.ExportCIF(path + str(Name) +' 100')
ReciPro.Dir.ProjectAlongAxis(0,1,0)
ReciPro.File.ExportCIF(path + str(Name) +' 101')

[seto77]

If you rewrite it as follows, the macro itself should work.

path = ReciPro.File.GetDirectoryPath()
for num in range(10):
	ReciPro.CrystalList.SelectedIndex = num
	Name = ReciPro.Crystal.ChemicalFormula
	ReciPro.Dir.ProjectAlongAxis(0,0,1)
	ReciPro.File.ExportAsCIF(path + Name +' 001')
	ReciPro.Dir.ProjectAlongAxis(1,0,0)
	ReciPro.File.ExportAsCIF(path + Name +' 100')
	ReciPro.Dir.ProjectAlongAxis(0,1,0)
	ReciPro.File.ExportAsCIF(path + Name +' 101')

However, unfortunately, the CIF file you are looking for will not be output.
The function "ProjectAlongAxis(u,v,w)" only changes the orientation of the crystal being drawn, not the structure of the crystal.

If you want to change the standard axis settings to something else, you have to take symmetry (space group) into account. It is not enough to simply swap the x, y, and z positions of the atoms or swap the cell constants a, b, and c.

[sitoald456]

Is there another method to redefine the default cell axes?

[seto77]

Again, when changing the axis settings, we need to take the space group into account.

If you can tell me the specific space group, I can give you a specific answer.