magnetmatter 0.1.0

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

#### INTRODUCTION ####
Material Science Research Data Visualization of Neutron (DMC) and X-Ray Powder Diffraction.
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.

#### HOW TO INSTALL ####
This installation assumes that you have a plain python (version > 3.0) 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.

pip install magnetmatter

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

"numpy", "pandas", "matplotlib"

are automaticly 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-OS path
path = r"C:/give/a/valid/path/to/folder/with/datasubfolders/" # Linux-based-OS path
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 - this is 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 just like to keep a copy of an uncorrupted .pcr at hand.

./
│ CoKa_BB_ISx.irf
│ CoKa_PB_ISxmm.irf
│ FS_17nm_R1D1.png
│ FS_8nm_R1D1.png
│
├───FS_17nm_R1D1
│ │ 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
│
└───FS_8nm_R1D1
│ 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:

"EdPCR">>"output">>unclick"Classical Output Format for a Single Pattern in PCR".

#### LaTeX FORMAT OF PHASENAMES ####
take an example of a phase. 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 0.000000 0.380097 0.000000 0.000000 0
0.000 0.000 0.000 0.000 131.000 0.000 0.000
! 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 can be found at

https://github.com/pgarbus/magnetmatter