Initial commit of PastaELN

PASTA_ELN/Procedures/Auriga SEM imaging procedure.md

+# Zeiss Auriga SEM imaging procedure
+- If the workstation is in the Standby mode, switch on the workstation by pressing on the green button
+- Start the SmartSEM user interface
+- In the "EM Server Log On" dialogue, enter the user name and the password
+- Check the status of the drivers in the EM Server window. All the drivers should be initialized by the end of the starting procedure
+- Attach the specimen to the stub. Use adhesive metal, carbon tape or glue the sample with crystal bond or SEM glue. Wear gloves at all times when handling the sample
+- Insert the stub into the sample holder
+- Fix the stub to the sample holder by tightening the srew 
+- In the SmartSEM, check that EHT acceleration voltage is off before loading the sample into the chamber
+- Go to the SEM Control Panel, open the Vacuum tab
+- Click on the Vent button to ventilate the specimen chamber
+- After ensuring that the chamber was properly vented, slowly open the chamber door
+- Load the specimen into the chamber, by mounting the sample holder on the specimen stage
+- Close the chamber door, check the seal
+- In the Vacuum tab of the SEM control panel, click on the Pump button
+- Check the vacuum status and wait until the required vacuum level is reached. The microscope can be operated, when the system vaccum reached |pressure|1e-5| mbar, and the gun vacuum reached |pressure|1e-9..1e-10| mbar
+- Switch to the ChamberScope view in the SmartSEM
+- While in the ChamberScope, move the specimen closer to the objective lens
+- The distance between the objective lens and specimen surface should be less than |distance|10| mm
+- In the Vacuum tab of the SEM control panel, check that "EHT Vac ready=Yes" is indicated
+- Click on the Gun button in the status bar, and select Gun On to run up the gun
+- In the Vacuum tab of the SEM control panel, check that "Vac Status ready=Yes" is indicated
+- Go to the Gun tab and change the EHT target acceleration voltage to the desired value. For instance, one can use |voltage|5| kV
+- Click on the EHT button in the status bar, and select EHT On to run up the EHT and make the electron beam ready
+- Go to the Detectors tab and Select SE2 as the detector
+- Go to the Scanning tab and select a fast scan speed, for instance |scanning speed setting|1|
+- Reduce the magnification to find the area of interest. For example, use |magnification|500| x
+- Adjust Brightness and Contrast in the Detectors tab
+- Focus on the detail on the specimen surface by changing the working distance. Focus can be changed in a Coarse or Fine mode
+- Increase the magnification in a step-wise manner and focus in between. For example, use |magnification|500000| x
+- Optimize the image, by selecting a small scan frame the Reduced Raster option, then focusing on a specific feature on the surface. 
+- Align the aperture by using the Focus Wobble and then aligning the aperture until no lateral shift is observed during wobbling. Turn off the Focus Wobble
+- Correct astigmatism by selecting the Stigmation option and then using the sliders to obtain the sharpest possible image
+- Deactivate the Reduced Raster
+- To produce an image, move over a region of interest and select the |scan speed|9..11| in the Scanning tab
+- Click on the Freeze button and wait until the image is produced
+- Select File/Save Image and save the file in the user directory.
+- To finish the work session, click on the All button in the status bar and select EHT Off
+- Go to the SEM Control Panel, open the Vacuum tab
+- Click on the Vent button to ventilate the specimen chamber
+- After ensuring that the chamber was properly vented, slowly open the chamber door
+- Remove the sample holder from the specimen stage
+- Close the chamber door, check the seal
+- In the Vacuum tab of the SEM control panel, click on the Pump button
+- Close SmartSEM
+- Remove the sample from the sample holder
+
+<!--- |filename|| -->
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PASTA_ELN/Procedures/Doli_Tensile_Test.md

+# Tensile testing with Doli
+
+- Setup controll box at instrument
+  - General information
+  - buttons F1..F3 correspond to three symbols above
+  - PC-mode: use for control by PC
+  - turn knob to get there and then press ESC to get move the control from the handheld to the PC
+- Start Software and hope that LAN connection works
+  - otherwise retry
+- Button Bike "Travel order"
+  - distance-controlled, relative: 100mm with 100mm/min
+  - direction clear
+- Measure the sample:
+  - |width||
+  - |thickness||
+- Mount sample: top first and then move into bottom
+- Button Setup experiment: Hammer button
+  - "Test procedure, speeds", "End of test" most important
+  - Switch from F0->F1 confusing
+  - choose F0 as max force
+  - Example speeds:
+    - metals=0.5mm/min
+    - polymers=5mm/min
+  - Adopt path: "Store data to"
+- all 3 tare-buttons should  be pressed
+- Button Traffic-Light: start experiments
+- Button Diagram (one line)
+  - open & close: rescale graph
+- After test: Travel order
+  - go back relative to 0
+- After all is done
+  - Close all wedges softly
+  - drive back to touch almost: s=35mm
+- Plot: click on series to plot all
+  - double click on test
+  - export by right click in graph and then copy-to-txt
+  - Results in C:\Versuchsergebnisse
+
+Author: Steffen Brinckmann, IMD-1, FZJ
+<!--- version:1.0 |filename|| -->
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PASTA_ELN/Procedures/FischerScope_Microindentation.md

+# Microindentation with Fischerscope H100C
+
+- Open the airlock chamber lid of the glovebox
+- Put the sample into the airlock chamber of the glovebox and close the lid
+- Evacuate the airlock until |pressure|-1| bar  is reached. Control the pressure inside the chamber with the vacuum gauge
+- Fill the chamber with Ar gas by pressing the "Fluten" button
+- Wait until the vacuum gauge shows the |pressure|0| bar
+- Repeat the refilling 3 times to achieve a sufficiently low residual oxygen content
+- Open the airlock chamber from the inside the glovebox and retrieve the sample
+- Place the sample on the indenter stage under the microscope objective. The sample is free standing, no glue is used for fixing the sample on the stage
+- Control the atmospheric conditions inside the glovebox using Siemens SIMATIC HMI monitor
+- The suitable conditions inside the glovebox for conducting the microindentation experiment are: |O content|0.3| ppm, |H2O content|0.1|, |dP range|+1.7-+2.3| mbar, |Temperature|18-19| C
+- Turn on the PC
+- Start the WIN-HCU software
+- The Vickers tip is pre-installed in the indenter and its shape is calibrated beforehand
+- Select the appropriate microscope magnification setting. The default setting is |magnification|40| x
+- In the microscope imaging mode, focus on the surface and find the area of interest
+- Define the measurement parameters for the indentation experiment: normal force, time until maximum load, hold time at maximum load and time for decreasing the load
+- Depending on the sample hardness and the investigated properties, an appropriate range of normal force might be between |normal force|0.4-1000| mN.
+- A typical loading duration until maximum load is reached is |time to maximum load|20| s
+- A typical duration for hold period under maximum load is |maximum load hold time|5| s. To investigate the materials creep properties, the period might be extended to |maximum load hold time|10| s
+- Select the number of the indents per each normal force
+- In the defined area of interest, select the positions for the indents while ensuring the appropriate spacing between them
+- Start the experiment
+- The indenter continuously measures indentation depth during the entire loading cycle
+- Observe the recorded load-displacement curve
+- After the experiment, compute the material properties using the WIN-HCU Software
+- If needed, switch to the microscope imaging mode, find the new area of interest and conduct further measurements
+- After all the measurements were completed, save the data files with indentation curves to the local storage
+- From the inside the glovebox, remove the sample from the indenter stage and place it in the airlock chamber
+- Close the lid of the airlock chamber from the inside of the glovebox
+- Open the lid of the airlock chamber from the outside
+- Remove the sample from the airlock chamber
+
+Author: Hanna Tsybenko, IMD-1, FZJ
+<!--- version:1.0 |filename|| -->
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PASTA_ELN/Procedures/Metallography.md

+# Metallography
+
+## Grinding
+- rounding all corners
+- semi auto grinding: 500 -> 800 -> 1000 -> 2400 (30s) -> 4000 (30s) paper
+  - significant pressure, two directions, last paper 3-4 directions
+    - starting at #1000: rpm = 100
+  - cleaning after each step (sample: with much water >> ethanol >> compressed, plate: with wiper)
+  - Check the scratch which was made at the previous grinding.
+
+## Auto polishing
+- mount sample on sample holder for auto polisher
+- cleaning all clothes & polishing sample holder with water / dry it
+- 3 um diamond suspension (1 spray every 1 min)
+  - 30N (force reduction) / 10min 2 step (total time: 20 min) / 150 rpm
+
+- 1 um diamond suspension (1 spray every 1 min)
+  - 1st step: 15N (force reduction) / 10min / 150 rpm
+  - 2nd step: 20N (force reduction) / 5min / 150 rpm
+  - blue lubricant : stage 8
+
+- cleaning after each step
+  - sample: rinsing with ethanol, ultra sonic cleaning, rinsing with ethanol again and drying with compressed air.
+  - holder: cleaning with water
+
+- check the surface in OM. If the surface is not good enough, one more step polishing is required.
+
+## Final polishing
+- cleaning clothes with water & dry it
+- one solution [OPS (100ml) + soap (~5ml)] (much OPS at the beginning and then 1 spray every 1 min)
+- 35N (force reduction) / 15 min / 150 rpm
+- Right after picking up the sample after finishing polishing, clean the sample one by one: swabbing with cotton
+which is soaked in much ethanol+soap, rinsing with ethanol, ultra sonic cleaning, rinsing with ethanol again and
+drying with compressed air. Cleaning plate & holder with much water.
+
+**With manual polishing, normally you can get good sample surface with shorter polishing time.**
+
+Author: Steffen Brinckmann, IMD-1, FZJ
+<!--- version:1.0 -->
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PASTA_ELN/Procedures/Nanoindentation KLA+ G200X procedure.md

+# Nanoindentation KLA+ G200X procedure
+- Open the G200X hood
+- Check that that the Tip Change Pins are not in the Actuator (measurement tip is inserted beforehand)
+- Check that the motion System is initialized. Go to Initialize Axes and click Load Sample Tray. If does not initialize, restart the computer
+- During motion towards loading, extension should be |extension|0| mm
+- Afterwards the extension should be always |extension|7| mm
+- After the sample tray move is complete, open the G200X cabinet and remove the Sample Tray
+- Start the InView RunTest software
+- Select the user Profile
+- To select the tip, go to System, then click Tip and Settings. Click on Save & Close. 
+- Mount the specimen in one of the locations on the Sample Tray
+- Adjust the height of the spectmen surface to make it close to the reference sample height using the wheels
+- Open the cabinet and load the Sample Tray into the Nanoindenter
+- Click on the location of the specimen in the Motion Control Pane
+- Use the Microscope to focus on the surface of the specimen. The microscope has |focus height|15.74| mm
+- After focusing on the surface, fix the sample position with the thumbscrews
+- Close the G200X hood
+- Move the specimen relative to the Microscope by dragging the cursor across the video screen, or by clicking on a desired location on the video screen
+- Perform the Microscope to Indenter calibration. Select the Settings Icon in the Video Pane and select Calibrate Video Source
+- The Video Calibration Assistant Window will open. The red Crosshair will be the Target Location for the
+indentations. 
+- Click Next Step. The Motion System will translate the specimen under the microscope and automatically perform five indentations at the desired location. 
+- Once the indentations are complete, the Sample tray will be moved back under the microscope.
+- Using the Video Screen motion control, move the red Crosshair to the central indentation and finish
+- Search for the area of the specimen where the indents should be placed
+- Go to the Sample Definition Pane and Settings to set the System in MultiSample Mode
+- Select the existing Project Name or create a new one
+- Click on the Add button to add a Sample. Enter the Sample Name
+- Select the Method: Advanced Dynamic E and H to a Load/Depth. Click Continue
+- Click on the Add Array button. 
+- When the dialog window appears, select a 3 x 3 Array with |spacing|50,50| µm spacing and a |rotation|0| deg
+- The array of indents will be placed with the first indent at the current location of the Crosshair on the Video Screen
+- Check the summary of all tests to be performed
+- Click on the green Run button to start the test
+- Wait untill all tests are completed
+- Review the results. Open the InView ReviewData Program
+- Click on the New Data Available notification at the top of the ReviewData Program
+- Select the tests and observe the Modulus vs Depth and Load vs Depth graphs
+- Go to Sample File. Then, select Save As or Save if you have already saved the results. Note that Samples
+are saved automatically from InView Run Test. 
+- Click on the Sample File menu and select Export. Select either a CSV or an Excel file to export
+- After completing all the planned tests, open the G200X hood and use the Motion Control Pane to Load Tray. After the sample tray move is complete, open the G200X cabinet and remove the Sample Tray. 
+- Unscrew the sample from the tray and remove it.
+- Load the emptied Sample Tray into the Nanoindenter
+- Close the the G200X hood
+
+
+<!--- |filename|| -->
\ No newline at end of file

PASTA_ELN/Procedures/OlympusOLS4000_Confocal_Microscope.md

+# Confocal Image Acquisition with the Olympus LEXT OLS4000 3D Measuring Laser Microscope
+
+- Turn on the PC
+- Turn on the LEXT OLS4000 microscope
+- Start the LEXT OLS4000 software
+- Select the "Imaging" mode
+- Select the objective lens with the smallest setting of |magnification|5| x
+- Press the button "Move to load position" in the "Map screen" window
+- The objective lens will be moved upwards to avoid contact with the stage or the sample. The stage will then move to the load position.
+- Place the sample on the center of the stage
+- In the "Map screen" window, press the button "Move to origin"
+- The sample will be moved underneath the microscope under the objective lens.
+- Move the focus knob counterclockwise to adjust the hight of the stage until the sample top surface is displayed in focus in the "Live" window
+- Lock the focus knob to avoid further movement
+- Set the lower height limit by clicking the "Advanced settings" button, selecting "Lower limit" under the "Microscope" menu and pressing the "Register" button to define the current Z position as the lower limit
+- Ensure that the "Imaging" mode and the "Laser Microscope" interface are selected for the measurement
+- Search for the area of interest on the sample surface by clicking on the arrow button and navigating the stage or by clicking on the particular feature on the "Live image" to move it to the center
+- Increase the magnification step-wise by clicking on the objective lens in the "Magnification" setting
+- Select the desired objective lens magnification from the |magnification|5| x, |magnification|10| x, |magnification|20| x, |magnification|50| x, |magnification|100| x
+- After changing the objective lens, adjust height to reach a coarse focus and adjust the brightness
+- Click on the "Laser" button. The mode will change from the "Color" imaging mode to "Laser confocal" mode
+- Only the in-focus sections will be visible in the "Laser confocal" mode
+- Click the "Focus" tab to access the focus controls
+- Click the arrow buttons to raise or lower the objective lens and adjust focus manually or click the "AF" button to autofocus
+- Set the origin height by clicking the "Advanced settings" button, selecting "Z reference position" under the "Microscope" menu and pressing the "Register" button to define the current Z position as the reference origin height
+- Click the "Brightness" tab to change the brightness settings
+- Use the "Brightness" slider or click the "Auto" button to automatically define the optimum exposure time
+- Adjust the brightness settings to be as high as possible, without reaching oversaturation of the image areas (marked as red areas in the image)
+- Select the "Acquisition" setting for the measurement from "Fast", "Fine", "Step" and "Snapshot"
+- In the "Acquisition" setting, check the "Color" box to overlay the color image on top of the laser confocal image, if needed
+- In the "Acquisition" setting, check the "DIC" box for using differential interference contrast, if needed
+- In the "Acquisition" setting, uncheck the "Manual" box to make the software automatically determine the top and bottom confocal acquisition limits or check it and enter the range setting manually
+- For the manual selection of the top and bottom confocal acquisition limits, focus on the highest and lowest features to be recorded, and click "Top" and "Bottom", respectively
+- Acquire the confocal image by pressing the "Acquisition" button
+- View the image in the desired mode: "Laser intensity", "Color", "Height intensity", "Contour".
+- Select the "3D display" to visualise the image three-dimensionally
+- Save the image on the local storage device.
+- To move to a different area, select a lens with smaller magnification if needed (especially for the  |magnification|100| x objective) and repeat the above instructions
+- To finish the session, return to the "Color" imaging mode, and select the objective lens with |magnification|5| x
+- Press the button "Move to load position" in the "Map screen" window
+- The objective lens will be moved upwards to avoid contact with the stage or the sample. The stage will then move to the load position.
+- Remove the sample from the center of the stage
+- Close the LEXT OLS4000 software
+- Turn off the LEXT OLS4000 microscope
+- Turn off the PC
+
+Author: Hanna Tsybenko, IMD-1, FZJ
+<!--- version:1.0 |filename|| -->
+

PASTA_ELN/Procedures/ZeissAuriga_SEM.md

+# Zeiss SEM
+- Vent
+- Open chamber
+- Mount sample and close chamber
+- Use it at |voltage|20| kV
+- Use a aperture of |aperture|3|
+
+<!--- |filename|| -->

PASTA_ELN/workflow_example.py

+# head of workflow: always the same
+from urllib.parse import urlparse
+from common_workflow_description.common_workflow_description import Storage, Sample, step
+try:
+    from pyiron_workflow import Workflow
+except ImportError:
+    from common_workflow_description.common_workflow_description import Workflow
+from analysis_steps import plot_curves, calc_YoungsModulus
+
+# start code
+wf = Workflow('Sandia Fracture Challenge 3', automate_execution=False)         # name
+proceduresLibrary = urlparse('https://raw.githubusercontent.com/SteffenBrinckmann/common-workflow-description_Procedures/main')
+storage=Storage(proceduresLibrary)                                             # folder of database
+
+# body of workflow: this changes
+sample = Sample('AM_NA_05')
+
+wf.step1 = step(storage, sample, 'metallography', {}, autorun=True)   #define step and link to storage for procedures
+wf.step2 = step(storage, sample, 'light microscopy', {}, autorun=True)
+wf.step3 = step(storage, sample, 'tensile test', {}, autorun=True)
+wf.step4 = step(storage, sample, 'light microscopy', {}, autorun=True)
+wf.step5a = step(storage, sample, 'sem', {'voltage':'30'}, autorun=True)
+wf.step5b = step(storage, sample, 'sem', {'voltage':'30'}, autorun=True)
+
+wf.step6 = plot_curves(wf.step3.outputs.y[1], 'Strain (Gauge0)', 'Engr. Stress')
+wf.step7 = calc_YoungsModulus(wf.step3.outputs.y[1], 'Strain (Gauge0)', 'Engr. Stress')
+
+wf.step1 >> wf.step2 >> wf.step3 >> wf.step4 >> wf.step5a >> wf.step5b >> wf.step6 >> wf.step7
+wf.starting_nodes = [wf.step1]
+
+# footer, always the same
+print('Output:\n  ','\n   '.join([f"{k}: {v}" for k, v in list(wf.outputs.to_value_dict().items())]))
+wf.draw().render(filename="io_demo_2", format="png", cleanup=True) #plot to file
+
+# {"type":"common-workflow-description", "version":1.0, "shasum":"d5d8342b266851e28919e69039918d2c2a9ca4f2"}
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Readme.md

+# Introduction
+This platform serves as a hub for exchanging ideas and code related to **scientific workflows**. The collaboration includes Kadi4Mat from NFDI4Ing, as well as pyiron and Pasta-ELN from MatWerk.
+
+- [Kadi4Mat](https://kadi.iam.kit.edu/): the generic and open source virtual research environment
+- [Pasta-ELN](https://pasta-eln.github.io/pasta-eln/): The favorite ELN for experimental scientists
+- [pyiron](https://pyiron.org/): The materials science IDE
\ No newline at end of file