Visualization of neutron and X-ray powder diffraction FullProf-refined data
Project description
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,
appearent 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
This installation assumes that you have a plain python (version > 3.6) installed that can be accessed through the command prompt. If on Ubuntu/MacTos, python 2.7 will be preinstalled. Then use “python3” and “pip3” for all purposes.
Before installing, try
pip search magnetmatter
and you should see
“magnetmatter (?.?.?) - Visualization of neutron and X-ray powder diffraction FullProf-refined 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
type python/python3 in command prompt. 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.
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