Define material data files from NIST

[vribgar]

We are trying to define material files from the NIST database, since we want to do simulations with materials and composites that you don't have in the library database.

According to this code:

McCode/mcxtrace-comps/samples/Abs_objects.comp

Line 163 in 84b3c26

else{fprintf(stderr,"Warning: %s: %s not found in header of %s, set to 1.\n",

the material files appear to be read using the Table_Read() function, which probably expects a table format where each column has a header that can be identified. The files should contain headers that correspond to the material properties, such as "Z", "A[r]", "rho", etc.

The problem is, when downloading the data directly from NIST, the header is not saved that way (I attach two files so you can compare: Ca.txt is the one from your database and Ca_v.txt was created by us), so it does not read it correctly. Do we have to manually modify the header? Or do you have a way to generate automatically the material files?

Ca.txt
Ca_v.txt

Thank you very much for your attention.

Regards,
Veronica.

[willend]

Hi @vribgar,

As I remember the Unix shell script get_xray_db_data in mcxtrace-comps/data (and present in your ${MCXTRACE}/data folder) is meant for this purpose.

The tool silently assumes that bash is in /usr/bin and that that the dependencies wget and w3m are installed so you will get the best mileage on a Linux, e.g. Ubuntu, here exemplified with atom 18 Ar:

bash $MCXTRACE/data/get_xray_db_data 18
/tmp/get_xray.BZt
URL transformed to HTTPS due to an HSTS policy
--2024-05-09 20:48:46--  https://physics.nist.gov/cgi-bin/ffast/ffast.pl?Z=18&Formula=&gtype=4&range=S&lower=0&upper=500&density=&frames=noframes
Resolving physics.nist.gov (physics.nist.gov)... 129.6.13.19, 2610:20:6005:13::19
Connecting to physics.nist.gov (physics.nist.gov)|129.6.13.19|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: ‘/tmp/get_xray.BZt’

/tmp/get_xray.BZt                                       [ <=>                                                                                                                ]  20.18K  --.-KB/s    in 0.1s    

2024-05-09 20:48:47 (199 KB/s) - ‘/tmp/get_xray.BZt’ saved [20664]

writing output to Ar.txt

The resulting file has a header:
Ar.txt

[willend]

Admittedly a rewrite using e.g. Python would be better, platform independent and more user friendly....

[farhi]

And I would add that you may use the Fluorescence sample and the related Test_Absorption and Test_Fluorescence example to handle any compound via XRayLib. See my comment in #1620