JupyLabBook @ SIRIUS

Experimental setup

$\LARGE \textbf{SIRIUS Beamline}:\textbf{Experiment 1234}$

$\Large \color{red}{\bf Example\ }$

Beamline alignment

Here we show functions used during beamline alignment.

LaTeX formula can be used in the text:
$$\frac{786-558}{2 \times 2069} \times 0.0355 = 1.9mrad$$

Subsection

SIRIUS_2020_03_11_0744: dscan basez -.2 .2 50 .1

Fit with erf function.

SIRIUS_2020_03_11_0752: continuous_ascan delta -.15 .15 100 1

Fit with Gaussian function.

Calibration thetaz

GIXD

SIRIUS_2020_03_12_0756: continuous_ascan delta -24 -19 100 5

Extraction of the Yoneda-Vineyard peak.

SIRIUS_2020_03_12_0756: continuous_ascan delta -24 -19 100 5

Classic GIXD with: $$q_{xy} = \frac{4\pi}{\lambda}\sin{\left(\frac{2\theta}{2}\right)}$$

Generates:

Isotherm

SIRIUS_Isotherm_2019_02_17_01544: isotherm 1.97 46 35000 1

1D plot

SIRIUS_2020_03_12_0760: run cont_regh.ipy

Add a 1D plot by clicking on Add plot to report. Generates SIRIUS_2020_03_12_0760.dat

GIXS

GIXS: $q_z$ vs $q_{xy}$.
Image and profiles with the approximation $q_{xy} = \frac{4\pi}{\lambda}\sin{\left(\frac{2\theta}{2}\right)}$.
Generates:

SIRIUS_2021_11_26_6088: tscan 5 5

WAXS on Ag Behenate for calibration. Use the GIXS command with thetai forced to 0.

SIRIUS_2021_11_26_6103: tscan 10 10

GIWAXS on a P3HT film.

SIRIUS_2021_10_16_2739: run scan_0_18.ipy

GISAXS image. Delta and gamma have to be forced to zero (the detector is not on the diffractometer).

Plot 2D detector

Plot the sum of the images from a 2D detector. Can also extract and save all the individual images if save='all'.

SIRIUS_2021_11_26_6088: tscan 5 5

Here with the Pilatus.
Generates:

SIRIUS_2021_11_11_3728: tscan 2 9

Works also with the detector UFXC.

XRF

SIRIUS_2017_12_11_08042: run xsw7.ipy

Plot XRF from the 4-elements detector, in channels and without peak identification.
Generates:

SIRIUS_Fluo_2020_07_03_0042: tscan 500 30

Plot XRF from the 1-element detector, in eVs and with peak identification.
Generates:

XRR

Calibration XRR (liquid)

To start the calibration click on Calib. XRR (liquid).

Scan XRR (liquid)

Select the first scan of the XRR series and click on Plot XRR (liquid). Here we show only a few points for the example.

SIRIUS_2021_04_14_4298: No command found

Scan XRR (solid)

Select all the scans of the XRR series and click on Plot XRR (solid). Here we show only a few points for the example.

SIRIUS_2022_02_23_4081: run scan_XRR.ipy

Insert script

Script inserted (with automatic scan numbering) using Insert script.

script_with_loop.ipy

%shopen
%amove delta -40
%run reset_motors.ipy
%continuous_ascan delta -35 -25 250 5 #123
%tscan 10 10 #124

for i in range(4):
    %amove delta -20
    %continuous_ascan delta -10 -3 175 5 #125 #127 #129 #131
    %run reset_motors.ipy
    %run cont_regh_abs.ipy #126 #128 #130 #132

for i in range(3):
    %amove delta -20
    %dscan delta -10 -3 175 5 #133 #135 #137
    %run reset_motors.ipy

    #%run cont_regh_abs.ipy
    %run cont_regh_abs.ipy #134 #136 #138

for i in range(2):
    %amove delta -20
    %tscan 10 100 #139 #140
    %slist scan add camxdirect

%continuous_ascan delta -35 -25 250 5 #141
# %tscan 10 10
%shclose

Insert positions

Positions extracted from the logs, using Insert positions.

wm alphax gamma

alphax gamma
2.0679 4.1401

wm diffracto

deltacodeur euchi euth euphi kappa_h kappa_k
1.00196 -89.57961 90.42039 -0.00580 -0.08252
Degrees deg deg deg
kappa_l qxy qxy0 qz basexPoint basexTrait
-0.18486 2.0556 23.82 -0.92 -15.7275 -15.7274
nm-1 nm-1 nm-1
basezPlan basezPoint basezTrait basepitch baseroll basex
71.1257 71.1257 71.1257 -0.0000 0.000 -15.727
mrad mrad mm
baseyaw basez alphax alphay delta delta0
-0.000 71.126 0.2998 0.2000 -2.9110 -34.2322
mrad mm
deltaa etaa gamma kappav mu kphi
0.0000 0.0000 1.2997 1.3080 -179.9997 0.0000
thetaa thetah komega xs ky ys
0.0000 0.0185 0.0000 0.0000 -0.1000 0.0000
kz zs kx
0.0000 -41.9999 -0.1000

Insert commands

Commands extracted from the logs, using Insert commands.

Fri, 26 Nov 2021 14:13:34 ct 1 pilatus
Fri, 26 Nov 2021 14:13:56 tscan 10 10 #6109
Fri, 26 Nov 2021 14:17:29 shclose
Fri, 26 Nov 2021 14:26:40 run config_alignment.ipy
Fri, 26 Nov 2021 10:34:48 ct 1 pilatus

Convert logs

Human-readable logs generated in the folder /working/readable_logs/ by clicking on Convert logs.

Insert an image

Using the command Insert image.

Save/load state

Save the current state of the notebook (the variable expt) by clicking on Save state.

Load the previous state of the notebook by clicking on Load state (for example after creating a new notebook).

Insert text

Use the button Insert text to insert text into the report.

Export to pdf

PDF generated by clicking on Export to pdf.