Render all notebooks

Calculations/rendered/Connector-Plate.md

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+```python
+from pint import UnitRegistry
+unit = UnitRegistry()
+unit.formatter.default_format = "~"
+
+preload_m4 = 3000 * unit.N
+n_screws = 4 # 2 on each side
+friction_coeff = 0.21 # Al on Al
+safety_factor = 1.5
+
+max_load = preload_m4 * friction_coeff * n_screws / safety_factor / unit.standard_gravity
+max_load.to(unit.kg)
+```
+
+
+
+
+171.312323780292 kg
+
+
+
+
+```python
+
+```

Calculations/rendered/Eddy-current-brake-simulation.md

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+```python
+import magpylib as magpy
+from scipy.spatial.transform import Rotation as R
+import pyvista as pv
+import numpy as np
+
+# Creation of our magnets including place and orientation in the space (all dimensions guessed, need to put in correct ones)
+# magnetic polarization of 1.5 T pointing in x-direction 
+# Dimensions assumed are 0.5, 1.5 and 3 cm (x,y,z) 
+
+
+# Question: Is there a more elegant way to do this? Should I make a for-loop for creating our magnet array?
+
+magnet1 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet1.position = (0, 0, 0)
+magnet1.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet2 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet2.position = (0.04, 0, 0)
+magnet2.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet3 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet3.position = (0, 0.04, 0)
+magnet3.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet4 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet4.position = (0.04, 0.04, 0)
+magnet4.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet5 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet5.position = (0, 0.08, 0)
+magnet5.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet6 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet6.position = (0.04, 0.08, 0)
+magnet6.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet7 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet7.position = (0, 0.12, 0)
+magnet7.orientation = R.from_euler("y", 90, degrees=True)
+
+magnet8 = magpy.magnet.Cuboid(polarization=(1.5, 0, 0), dimension=(0.005, 0.015, 0.03)) 
+magnet8.position = (0.04, 0.12, 0)
+magnet8.orientation = R.from_euler("y", 90, degrees=True)
+
+
+# Grouping the magnets to collection
+coll = magpy.Collection(magnet1, magnet2, magnet3, magnet4, magnet5, magnet6, magnet7, magnet8)
+
+# Plotting the magnet array
+magpy.show(coll, backend="plotly")
+```
+
+
+
+
+```python
+# Just for visualization: Showing the magnetic field vectors in 3D
+
+spacing = np.array([0.003, 0.003, 0.003]) # defines the grid where the magnetic field is calculated
+
+# The following is for getting the right dimensions and position of the grid
+magnets = [magnet1, magnet2, magnet3, magnet4, magnet5, magnet6, magnet7, magnet8]
+all_mins = []
+all_maxs = []
+
+for m in magnets:
+    pos = np.array(m.position)
+    dim = np.array(m.dimension) / 2
+    all_mins.append(pos - dim)
+    all_maxs.append(pos + dim)
+
+global_min = np.min(all_mins, axis=0) - 0.02  # add 2cm as buffer
+global_max = np.max(all_maxs, axis=0) + 0.02
+
+dimensions = ((global_max - global_min) / spacing).astype(int)
+
+grid = pv.ImageData(
+    spacing=tuple(spacing),
+    dimensions=tuple(dimensions),
+    origin=(-0.02, -0.02, -0.02),
+)
+
+# Calculation of the B-field  in mT
+grid["B"] = coll.getB(grid.points) * 1000  
+pl = pv.Plotter()
+pl.add_mesh(grid.outline(), color="blue", line_width=1)
+pl.add_points(grid.points, render_points_as_spheres=True, point_size=2, color='black')
+
+# Add magnetic field vectors as arrows (glyphs)
+pl.add_mesh(
+    grid.glyph(orient="B", scale=True, factor=0.00001),  # use "B" vectors, scaling according to field strength, factor to make arrows smaller for visibility
+    color="blue",
+    label="Magnetic field vectors"
+)
+
+magpy.show(coll, canvas=pl, units_length="m", backend="pyvista")
+
+
+
+pl.show()
+
+
+```
+
+
+    Widget(value='<iframe src="http://localhost:40551/index.html?ui=P_0x7d5c280f7fa0_15&reconnect=auto" class="pyv…
+
+
+
+```python
+# Introducing the aluminium plate
+
+z_position=0.01 # z_position = distance to the magnets (put in real number here!)
+plate_center = [0, 0, z_position]  
+plate_size = [0.15, 0.40, 0.005]  # [b,l, h]
+
+plate = pv.Box(bounds=(
+    plate_center[0] - plate_size[0]/2, plate_center[0] + plate_size[0]/2,
+    plate_center[1] - plate_size[1]/2, plate_center[1] + plate_size[1]/2,
+    plate_center[2] - plate_size[2]/2, plate_center[2] + plate_size[2]/2
+))
+pl.add_mesh(plate, color="silver", opacity=0.5, label="Aluminum plate")
+
+pl.show()
+```
+
+    A view with name (P_0x7d5c280f7fa0_15) is already registered
+     => returning previous one
+
+
+
+    Widget(value='<iframe src="http://localhost:40551/index.html?ui=P_0x7d5c280f7fa0_15&reconnect=auto" class="pyv…
+
+
+
+```python
+
+```

Calculations/rendered/Laserbeam.md

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+```python
+import imageio.v2 as imageio
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy import ndimage
+
+# sensor horizontal size
+sensor_width = 7.75
+
+# image file
+laser = imageio.imread("laser-img/2025-09-07-012621-2mm-aperture.jpg")
+```
+
+
+```python
+dimensions = np.array([sensor_width * laser.shape[0] / laser.shape[1], sensor_width])
+half_size = dimensions / 2
+
+# Mean of all color channels as an approximation of the monochrome image
+laser_monochrome = np.mean(laser, axis=2)
+# Normalized intensity map
+intensity_map = laser_monochrome / np.max(laser_monochrome)
+
+# Summed intensity in each axis
+intensity_x = np.sum(laser_monochrome, axis=0)
+intensity_y = np.sum(laser_monochrome, axis=1)
+
+# Center of mass of the laser beam
+center = (
+    (ndimage.center_of_mass(laser_monochrome) / np.array(laser_monochrome.shape) - 0.5)
+    * dimensions
+    * [-1, 1]
+)
+print(f"Center of the beam is at {center[0]:.3f}/{center[1]:.3f}")
+
+
+# Calculate FWHM in each axis
+def fwhm(curve, width):
+    assert curve.ndim == 1
+    half_max = (np.max(curve) + np.min(curve)) / 2
+    diff = curve - half_max
+    indices = np.where(diff > 0)[0]
+    return (indices[-1] - indices[0]) / curve.size * width
+
+
+fwhm_y = fwhm(intensity_y, dimensions[0])
+fwhm_x = fwhm(intensity_x, dimensions[1])
+print(f"FWHM in X/Y: {fwhm_x:.2f}/{fwhm_y:.2f}")
+
+eccentricity = np.sqrt(1 - (min(fwhm_y, fwhm_x) ** 2 / max(fwhm_y, fwhm_x) ** 2))
+print(f"Eccentricity (along cartesian axes): {eccentricity:.5f}")
+```
+
+    Center of the beam is at -0.088/0.238
+    FWHM in X/Y: 2.16/1.46
+    Eccentricity (along cartesian axes): 0.73687
+
+
+
+```python
+with plt.style.context("dark_background"):
+    fig, ax = plt.subplots(figsize=(14, 14))
+    im = ax.imshow(
+        intensity_map,
+        cmap="magma",
+        extent=(-half_size[1], half_size[1], -half_size[0], half_size[0]),
+        interpolation="none",
+        vmin=0,
+    )
+    ax.set_xlim(-np.max(half_size), np.max(half_size))
+    ax.set_ylim(-np.max(half_size), np.max(half_size))
+
+    xy_scale = max(np.max(intensity_x), np.max(intensity_y))
+    ax.plot(
+        np.linspace(-half_size[1], half_size[1], intensity_x.size),
+        intensity_x / xy_scale - np.max(half_size),
+        color="red",
+    )
+    ax.plot(
+        intensity_y / xy_scale - np.max(half_size),
+        np.linspace(half_size[0], -half_size[0], intensity_y.size),
+        color="red",
+    )
+
+    # reticle
+    ax.axvline(x=center[1], color="white", linestyle=":")
+    ax.axhline(y=center[0], color="white", linestyle=":")
+
+    ax.axvline(x=center[1] - fwhm_x / 2, color="gray", linestyle=":")
+    ax.axvline(x=center[1] + fwhm_x / 2, color="gray", linestyle=":")
+    ax.axhline(y=center[0] - fwhm_y / 2, color="gray", linestyle=":")
+    ax.axhline(y=center[0] + fwhm_y / 2, color="gray", linestyle=":")
+
+    cax = fig.add_axes(
+        [
+            ax.get_position().x1 + 0.01,
+            ax.get_position().y0,
+            0.02,
+            ax.get_position().height,
+        ]
+    )
+    fig.colorbar(im, cax=cax)
+
+    text = (
+        f"FWHM X/Y: {fwhm_x:.2f} mm/{fwhm_y:.2f} mm\n"
+        f"Eccentricity: {eccentricity:.5f}\n"
+        f"Offset X/Y: {center[1]:+.3f} mm/{center[0]:+.3f} mm"
+    )
+    fig.text(0.5, 0.05, text, ha="center")
+
+fig
+```
+
+
+
+
+    
+![png](Laserbeam_files/Laserbeam_2_0.png)
+    
+
+
+
+
+    
+![png](Laserbeam_files/Laserbeam_2_1.png)
+    
+
+
+
+```python
+
+```

Calculations/rendered/Preamp-Current.md

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+```python
+import matplotlib.pyplot as plt
+import numpy as np
+from pint import UnitRegistry
+unit = UnitRegistry()
+unit.formatter.default_format = "~"
+unit.setup_matplotlib()
+
+
+gain_first_stage = 10e6 * unit.V / unit.A
+gain_second_stage = 100e3 / 1e3
+
+tunnel_current_in = np.linspace(1e-12, 10e-9, 100) * unit.A
+volts_out = tunnel_current_in * gain_first_stage * gain_second_stage
+
+plt.xscale("log")
+plt.plot(tunnel_current_in, volts_out)
+xticks = [1e-12, 10e-12, 100e-12, 1e-9, 10e-9] * unit.A
+plt.xticks(xticks, [f'{t.to("nA"):.3f~}' for t in xticks], minor=False)
+plt.xlabel("Tunneling Current")
+
+plt.yscale("log")
+yticks = [0.001, 0.010, 0.1, 1.0, 5] * unit.V
+plt.yticks(yticks, [f'{t.to("V"):.3f~}' for t in yticks], minor=False)
+plt.ylabel("Preamp Voltage")
+plt.grid(True, "both")
+```
+
+
+    
+![png](Preamp-Current_files/Preamp-Current_0_0.png)
+    
+
+
+
+```python
+v = 0.359 * unit.V
+a = v / (gain_first_stage * gain_second_stage)
+a.to("pA")
+```
+
+
+
+
+359.0 pA
+
+
+
+
+```python
+
+```

Calculations/rendered/Spring-Dimensioning.md

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+```python
+import math
+import numpy as np
+from pint import UnitRegistry
+unit = UnitRegistry()
+unit.formatter.default_format = "~"
+
+
+# Parameters
+spring_constant = 1.1 * 4 * unit.N / unit.mm
+spring_length_resting = 112 * unit.mm
+
+weight_total = 14 * unit.kg
+
+dampening = 1 * unit.N / (unit.m / unit.s)
+
+def spring_length_at(weight):
+    return (weight * unit.standard_gravity / spring_constant + spring_length_resting).to(unit.mm)
+
+def resonant_freq_at(weight):
+    return (1 / (2 * math.pi) * np.sqrt(spring_constant / weight)).to(unit.Hz)
+
+spring_length = spring_length_at(weight_total)
+f0 = resonant_freq_at(weight_total)
+
+print(f"Length: {spring_length:~.1f}")
+print(f"Freq:   {f0:~.3f}")
+```
+
+    Length: 143.2 mm
+    Freq:   2.822 Hz
+
+
+
+```python
+def lehr_dampening_factor(d, k, m):
+    return d / (2 * np.sqrt(m * k))
+
+lehr_dampening = lehr_dampening_factor(dampening, spring_constant, weight_total)
+lehr_dampening.ito_reduced_units()
+lehr_dampening
+```
+
+
+
+
+0.00201455741006345
+
+
+
+
+```python
+def amplitude_ratio(lehr, f0, f):
+    eta = f / f0
+    return 1 / np.sqrt((1 - eta**2)**2 + (2 * eta * lehr)**2)
+
+f_in = np.geomspace(0.5, 90, 100) * unit.Hz
+ratio = amplitude_ratio(lehr_dampening, f0, f_in)
+
+import matplotlib.pyplot as plt
+plt.plot(f_in, ratio)
+
+def transmissibility_plot_setup(plt):
+    plt.xscale('log')
+    xticks = [1, 3, 10, 50]
+    plt.xticks(xticks, [f"{t} Hz" for t in xticks], minor=False)
+    plt.xlabel("Excitation Frequency")
+    
+    plt.ylim(0.001, 10)
+    plt.yscale('log')
+    plt.ylabel("Transmissibility Ratio")
+    
+    plt.grid(True, "both")
+
+transmissibility_plot_setup(plt)
+```
+
+    /usr/lib/python3.13/site-packages/matplotlib/cbook.py:1355: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
+      return np.asarray(x, float)
+
+
+
+    
+![png](Spring-Dimensioning_files/Spring-Dimensioning_2_1.png)
+    
+
+
+
+```python
+def ratio_for_dkm(d, k, m, f_in):
+    f0 = (1 / (2 * math.pi) * np.sqrt(k / m)).to(unit.Hz)
+    lehr = lehr_dampening_factor(d, k, m)
+    return amplitude_ratio(lehr, f0, f_in)
+
+d = dampening
+k = [
+    spring_constant,
+    spring_constant / 4,
+]
+m = [
+    weight_total,
+    24 * unit.kg,
+]
+
+import matplotlib.pyplot as plt
+for k_ in k:
+    m_ = m[0]
+    plt.plot(f_in, ratio_for_dkm(d, k_, m_, f_in), label=f"{k_:~.1f}, {m_:~.1f}")
+for m_ in m[1:]:
+    k_ = k[0]
+    plt.plot(f_in, ratio_for_dkm(d, k_, m_, f_in), label=f"{k_:~.1f}, {m_:~.1f}")
+
+ref_thorlabs_f = [3, 4, 4.42, 5, 6,   7,   8,   9,    10,   40]
+ref_thorlabs_r = [2, 5, 15.0, 4, 1.5, 0.7, 0.5, 0.35, 0.28, 0.018]
+plt.plot(ref_thorlabs_f, ref_thorlabs_r, label="Thorlabs PTP702 (Passive)")
+
+ref_thorlabs_f = [1, 1.35, 2,   3,   5,   9,    20,   27,     30]
+ref_thorlabs_r = [2, 3,    0.9, 0.3, 0.1, 0.02, 0.009, 0.007, 0.0023]
+plt.plot(ref_thorlabs_f, ref_thorlabs_r, label="Thorlabs PTS601 (Active)")
+    
+plt.legend(loc="upper right")
+transmissibility_plot_setup(plt)
+```
+
+    /usr/lib/python3.13/site-packages/matplotlib/cbook.py:1355: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
+      return np.asarray(x, float)
+
+
+
+    
+![png](Spring-Dimensioning_files/Spring-Dimensioning_3_1.png)
+    
+
+
+
+```python
+
+```

Calculations/rendered/Tunneling-Current-Distance.md

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+```python
+import matplotlib.pyplot as plt
+import numpy as np
+from pint import UnitRegistry
+
+# Set up unit system
+unit = UnitRegistry()
+unit.formatter.default_format = "~"
+unit.setup_matplotlib()
+
+# Physical constants
+e=-1.602176634e-19 * unit.C # electron charge
+m=9.109e-31 * unit.kg # electron mass
+hbar=6.62607015e-34/2/np.pi * unit.joule * unit.second # Planck constant
+phi=4 * unit.eV # Work function (see table)
+phi_joule=phi.to("joule")
+U=5 *unit.V
+
+# Table working functions different metals
+
+# Metal F(eV)
+# (Work Function)
+# Ag (silver) 4.26
+# Al (aluminum) 4.28
+# Au (gold) 5.1
+# Cs (cesium) 2.14
+# Cu (copper) 4.65
+# Li (lithium) 2.9
+# Pb (lead) 4.25
+# Sn (tin) 4.42
+# Chromium 4.6
+# Molybdenum 4.37
+# Stainless Steel 4.4
+# Gold 4.8
+# Tungsten 4.5
+# Copper 4.5
+# Nickel 4.6
+
+# Distance range
+Distance_tip_sample=np.linspace(10e-13,2e-10,100)* unit.m
+Tunneling_current=U*np.exp(-2*np.sqrt(2*m*phi_joule)/hbar*Distance_tip_sample) /unit.V #please note: This is not the tunneling current as this formular gives just the proportionality. Calculating the current constant is difficult as there are for us unknown parameters
+Distance_tip_sample_nm=Distance_tip_sample.to("nm")
+
+plt.plot(Distance_tip_sample_nm, Tunneling_current)
+plt.xlabel(f"Distance tip sample [{Distance_tip_sample_nm.units:~P}]")
+plt.ylabel(f"Tunneling-Proportionality [arb. Unit]")
+plt.xticks(ticks=np.linspace(0, 0.2, 5), labels=[f"{x:.2f}" for x in np.linspace(0, 0.2, 5)])
+#plt.yscale("log")
+
+```
+
+
+
+
+    ([<matplotlib.axis.XTick at 0x7e10b04929b0>,
+      <matplotlib.axis.XTick at 0x7e10b04b0310>,
+      <matplotlib.axis.XTick at 0x7e10b034ba60>,
+      <matplotlib.axis.XTick at 0x7e10b0328670>,
+      <matplotlib.axis.XTick at 0x7e10b0329360>],
+     [Text(0.0, 0, '0.00'),
+      Text(0.05, 0, '0.05'),
+      Text(0.1, 0, '0.10'),
+      Text(0.15000000000000002, 0, '0.15'),
+      Text(0.2, 0, '0.20')])
+
+
+
+
+    
+![png](Tunneling-Current-Distance_files/Tunneling-Current-Distance_0_1.png)
+    
+

Misc/Temp-Monitor/rendered/Temperature-Data.md

@@ -0,0 +1,53 @@
+```python
+from matplotlib import pyplot as plt
+import pandas as pd
+
+df = pd.read_csv('20250824-temperature-02.csv')
+df["Time"] = df["Time [ms]"] / 1000. / 60.
+
+fig, ax = plt.subplots(figsize=(24, 8))
+ax.set_ylim(25.4, df["Raw"].max() + 0.01)
+ax.plot(df["Time"], df["Raw"])
+ax.plot(df["Time"], df["Temperature"])
+ax.set_ylabel("Temperature / °C")
+ax.set_xlabel("Time / minutes")
+ax.legend(["Raw Temperature", "Temperature"])
+ax.grid()
+
+def event(time_minutes, label, yoff=0):
+    y = ax.get_ylim()[1] - yoff
+    ax.annotate(label, xy=(time_minutes, y))
+    ax.axvline(x=time_minutes, color="red")
+
+event(3330 / 60, "Start install aluminum")
+event(4440 / 60, "Start remove aluminum")
+event(5208 / 60, "New tip")
+event(5450 / 60, "Aluminum back on STM")
+event(5720 / 60, "First tunneling", 0.03)
+event(6860 / 60, "Stable tunneling started", 0.26)
+event(7100 / 60, "Stable tunneling stopped", 0.23)
+event(7200 / 60, "Heated up the STM externally")
+event(7669 / 60, "Stable tunneling start 80pA", 0.42)
+event(7780 / 60, "Changed to 210pA", 0.26)
+event(7990 / 60, "Drifted out of range", 0.38)
+event(8300 / 60, "Heated again")
+event(8327 / 60, "STM spontaneously starts tunneling", 0.52)
+event(8500 / 60, "Very noisy but long term tunneling", 0.2)
+event(8950 / 60, "End tunneling", 0.25)
+```
+
+
+    
+![png](Temperature-Data_files/Temperature-Data_0_0.png)
+    
+
+
+
+```python
+
+```
+
+
+```python
+
+```