magnetmatter 0.2.1

Visualization of FullProf-refined neutron and X-ray powder diffraction data

Materials science research visualization of FullProf-refined neutron (DMC::SINQ::PSI) and X-ray powder diffraction data. FullProf .prf, .out and .pcr files are read and informations on:

• refined parameters,

• phases,

• apparent crystalline sizes,

• phase fractions

are hardcoded next to the graph of “Yobs”, “Ycal” and “Yobs-Ycal”.

see section HOW SHOULD FILES BE ORGANIZED to understand how your files should be organized. The example folders shown are possible to download.

TOC:

• INSTALLATION

• HOW TO USE

• HOW SHOULD FILES BE ORGANIZED

• NEW FORMAT OF PCR FILE

• LaTeX FORMAT OF PHASENAMES

• REPOSITORY

• TODO

INSTALLATION

This installation assumes that you have access to python3 (version > 3.6). If on Ubuntu/MacTos, python 2.7 will be preinstalled. Then use “python3” and “pip3” for all purposes. Otherwise “python” and “pip” will be enough. Check version of python installation by typing “python –version” into command prompt or terminal.

Before installing, try

$ pip search magnetmatter

and you should see

• “magnetmatter (?.?.?) - Visualization of FullProf-refined neutron and X-ray powder diffraction data”

now go ahead with the installation

$ pip install magnetmatter

now be patient while “magnetmatter” is installed. Installation may be longer because dependencies such as:

• “numpy”, “pandas”, “matplotlib”

are installed if missing.

HOW TO USE

Initiate python in a terminal or use your favorite editor. Then type

>>> import magnetmatter as mogens

Type now

>>> path = r"C:\give\a\valid\path\to\folder\with\datasubfolders\"  # Windows
>>> path = r"C:/give/a/valid/path/to/folder/with/datasubfolders/"  # Linux
>>> mogens.plot_prf(path)

The default printed size is 8 cm (two plots fit into a docx document). other options include

>>> mogens.plot_prf(path, printsize = "two_in_docx") # 8  cm wide - default!
>>> mogens.plot_prf(path, printsize = "one_in_docx") # 15 cm wide
>>> mogens.plot_prf(path, printsize = "two_in_ppt")  # 17 cm wide
>>> mogens.plot_prf(path, printsize = "one_in_ppt")  # 32 cm wide

The files are saved as .png in the “path” folder.

HOW SHOULD FILES BE ORGANIZED

The script goes into each subfolder and looks for an .out, a .pcr and a .prf file. If no such files are found (or if indeed multiple files are found), the script will skip the respective folder. Note the “backup” folder is not mandatory. I like to keep a copy of an uncorrupted .pcr at hand.

The below examples can be downloaded from here.

|./
|   CoKa_BB_ISx.irf
|   CoKa_PB_ISxmm.irf
|   17nm.png
|   8nm.png
|
|---17nm
|   |   size_bigger_10nm.dat
|   |   size_bigger_10nm.ras
|   |   size_bigger_10nm_Theta_2-Theta.asc
|   |   size_bigger_10nm_Theta_2-Theta.raw
|   |   _gFe2O3_Fe3O4_.out
|   |   _gFe2O3_Fe3O4_.pcr
|   |   _gFe2O3_Fe3O4_.prf
|   |   _gFe2O3_Fe3O4_.sum
|   |   _gFe2O3_Fe3O4_1.fst
|   |   _gFe2O3_Fe3O4_1.mic
|   |   _gFe2O3_Fe3O4_2.fst
|   |   _gFe2O3_Fe3O4_2.mic
|   |
|   `---backup
|           _gFe2O3_Fe3O4_.pcr
|
`---8nm
    |   size_smaller_10nm.dat
    |   size_smaller_10nm.ras
    |   size_smaller_10nm_Theta_2-Theta.asc
    |   size_smaller_10nm_Theta_2-Theta.raw
    |   _gFe2O3_Fe3O4_.out
    |   _gFe2O3_Fe3O4_.pcr
    |   _gFe2O3_Fe3O4_.prf
    |   _gFe2O3_Fe3O4_.sum
    |   _gFe2O3_Fe3O4_1.fst
    |   _gFe2O3_Fe3O4_1.mic
    |   _gFe2O3_Fe3O4_2.fst
    |   _gFe2O3_Fe3O4_2.mic
    |
    `---backup
            _gFe2O3_Fe3O4_.pcr

NEW FORMAT OF PCR FILE

The new FullProf .pcr format is expected. Make sure that you have this format by using the FullProf toolbar:

• click “EdPCR”

• click “output”

• unclick “Classical Output Format for a Single Pattern in PCR”.

LaTeX FORMAT OF PHASENAMES

Below is a phase-example from a .pcr file. Note that the phasename is given by “$gamma$-Fe$_2$O$_3$”. The dollarsigns indicate that LaTeX format should be used for the from dollarsigns-inclosed characters.

!-------------------------------------------------------------------------------
!  Data for PHASE number:   1  ==> Current R_Bragg for Pattern#  1:     3.75
!-------------------------------------------------------------------------------
$\gamma$-Fe$_2$O$_3$
!
!Nat Dis Ang Jbt Isy Str Furth        ATZ     Nvk More
  8   0   0   0   0   0   0       1703.3091   0   0
!Contributions (0/1) of this phase to the  1 patterns
1
!Irf Npr Jtyp  Nsp_Ref Ph_Shift for Pattern#  1
  0   7    0      0      0
! Pr1    Pr2    Pr3   Brind.   Rmua   Rmub   Rmuc     for Pattern#  1
 0.000  0.000  1.000  1.000  0.000  0.000  0.000
!
!
P 43 21 2                <--Space group symbol
!Atom   Typ       X        Y        Z     Biso       Occ     In Fin N_t Spc /Codes
Fe1    Fe      0.74400  0.99600  0.12000  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
Fe2    Fe      0.62000  0.62000  0.00000  0.10000   0.50000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
Fe3    Fe      0.36400  0.86700 -0.01600  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
Fe4    Fe      0.14000  0.14000  0.00000  0.10000   0.16650   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
O1     O       0.61500  0.86900 -0.01400  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
O2     O       0.11900  0.37700 -0.00500  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
O3     O       0.13700  0.86100  0.00700  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
O4     O       0.38300  0.63100 -0.00300  0.10000   1.00000   0   0   0    0
      0.00       0.00     0.00     0.00     0.00
!-------> Profile Parameters for Pattern #  1
!  Scale        Shape1      Bov      Str1      Str2      Str3   Strain-Model
  0.90441E-03   0.00000   2.25111   0.00000   0.00000   0.00000       0
  111.00000     0.000   151.000     0.000     0.000     0.000
!       U         V          W           X          Y        GauSiz   LorSiz Size-Model
  0.000000   0.000000   0.000000   0.00000     0.380097    0.00000   0.0000     0
  0.000000   0.000000   0.000000   0.00000   131.000       0.00000   0.0000
!     a          b         c        alpha      beta       gamma      #Cell Info
  8.362284   8.362284   8.319425  90.000000  90.000000  90.000000
  11.00000   11.00000   61.00000    0.00000    0.00000    0.00000
!  Pref1    Pref2      Asy1     Asy2     Asy3     Asy4      S_L      D_L
  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.02957  0.02957
  0.00     0.00     0.00     0.00     0.00     0.00     0.00     0.00

REPOSITORY

The source code and examples can be found at GitHub.

TODO

• make plot of .dat/.xye file if plot_prf fails to finish.

• indicate Bragg Reflections at bottom of graph with color code.

  • add corresponding color to the compound names in the info text by LaTeX.