nqrduck/nqr-blochsimulator
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Added calculation of reference voltage.

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This commit is contained in:
jupfi 2023-08-23 16:18:22 +02:00
parent 87232bdaec
commit df7bf4f2ce
2 changed files with 51 additions and 14 deletions
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53
src/nqr_blochsimulator/classes/simulation.py
View file

@ -1,6 +1,6 @@
import numpy as np
import logging
from scipy import signal
from scipy.constants import h, Boltzmann
from .sample import Sample
from .pulse import PulseArray
@ -25,7 +25,8 @@ class Simulation:
power_amplifier_power : float,
pulse : PulseArray,
averages: int,
gain: float
gain: float,
temperature: float
) -> None:
"""
Constructs all the necessary attributes for the simulation object.
@ -56,6 +57,8 @@ class Simulation:
The number of averages that are used for the simulation.
gain:
The gain of the amplifier.
temperature:
The temperature of the sample in Kelvin.
"""
self.sample = sample
@ -70,9 +73,13 @@ class Simulation:
self.pulse = pulse
self.averages = averages
self.gain = gain
self.temperature = temperature
def simulate(self):
reference_voltage = self.calculate_reference_voltage()
logger.debug(reference_voltage * 1e6)
B1 = self.calc_B1() * 1e3 # I think this is multiplied by 1e3 because everything is in mT
# B1 = 17.3 # Something might be wrong with the calculation of the B1 field. This has to be checked.
self.sample.gamma = self.sample.gamma * 1e-6 # We need our gamma in MHz / T
self.sample.T1 = self.sample.T1 * 1e3 # We need our T1 in ms
self.sample.T2 = self.sample.T2 * 1e3 # We need our T2 in ms
@ -82,8 +89,6 @@ class Simulation:
real_pulsepower = self.pulse.get_real_pulsepower()
imag_pulsepower = self.pulse.get_imag_pulsepower()
M_sy1 = self.bloch_symmetric_strang_splitting(B1, xdis, real_pulsepower, imag_pulsepower)
logger.debug("Shape of Msy1: %s", M_sy1.shape)
# Z-Component
Mlong = np.squeeze(M_sy1[2,:,:]) # Indices start at 0 in Python
@ -94,8 +99,8 @@ class Simulation:
Mtrans = np.squeeze(M_sy1[0,:,:] + 1j*M_sy1[1,:,:]) # Indices start at 0 in Python
Mtrans_avg = np.mean(Mtrans, axis=0)
Mtrans_avg = np.delete(Mtrans_avg, -1) # Remove the last element
reference = 4.5502
sigtrans = Mtrans_avg * reference * self.averages * self.gain
sigtrans = Mtrans_avg * reference_voltage * 1e6 * self.averages * self.gain
return sigtrans
@ -108,6 +113,12 @@ class Simulation:
The B1 field of the solenoid coil.
xdis : np.array
The x distribution of the isochromats.
real_pulsepower : np.array
The real part of the pulse power.
imag_pulsepower : np.array
The imaginary part of the pulse power.
relax : float
If relax = 1, the relaxation is taken into account. If relax = 0, the relaxation is not taken into account.
"""
Nx = self.number_isochromats
Nu = real_pulsepower.shape[0]
@ -146,8 +157,6 @@ class Simulation:
D = np.diag([np.exp(-1 / self.sample.T2 * relax * dt), np.exp(-1 / self.sample.T2 * relax * dt), np.exp(-1 / self.sample.T1 * relax * dt)])
b = np.array([0, 0, self.initial_magnetization]) - np.array([0, 0, self.initial_magnetization * np.exp(-1 / self.sample.T1 * relax * dt)])
logger.debug(b)
for n in range(Nu): # time loop
Mrot = np.zeros((3, Nx))
@ -187,7 +196,6 @@ class Simulation:
"""
# Df is the Full Width at Half Maximum (FWHM) of Lorentzian in Hz
Df = 1 / np.pi / self.sample.T2_star
logger.debug("Df: %s", Df)
# Randomly generating frequency offset using Cauchy distribution
uu = np.random.rand(self.number_isochromats, 1) - 0.5
@ -195,10 +203,26 @@ class Simulation:
# xdis is a spatial function, but it is being repurposed here to convert through the gradient to a phase difference per time -> T2 dispersion of the isochromats
xdis = np.linspace(-1, 1, self.number_isochromats)
logger.debug(self.sample.gamma)
xdis = (foffr.T * 1e-6) / (self.sample.gamma / 2 / np.pi) / (self.gradient * 1e-3)
return xdis
def calculate_reference_voltage(self):
"""This calculates the reference voltage of the measurement setup for the sample at a certain temperature.
Returns
-------
reference_voltage : float
The reference voltage of the measurement setup for the sample at a certain temperature in Volts.
"""
u = 4 * np.pi * 1e-7 # permeability of free space
magnetization = self.sample.gamma * 2 * self.sample.atoms / (2 * self.sample.nuclear_spin +1) * h**2 * self.sample.resonant_frequency/ Boltzmann / self.temperature * self.sample.spin_factor
coil_crossection = np.pi * (self.diameter_coil / 2) ** 2
reference_voltage = self.number_turns * coil_crossection * u * self.sample.gamma * 2 * self.sample.atoms / (2 * self.sample.nuclear_spin +1) * h**2 * self.sample.resonant_frequency **2 / Boltzmann / self.temperature * self.sample.spin_factor
reference_voltage = reference_voltage * self.sample.powder_factor * self.sample.filling_factor
return reference_voltage
@property
def sample(self) -> Sample:
@ -307,3 +331,12 @@ class Simulation:
@gain.setter
def gain(self, gain):
self._gain = gain
@property
def temperature(self) -> float:
"""Temperature of the sample."""
return self._temperature
@temperature.setter
def temperature(self, temperature):
self._temperature = temperature

12
tests/simulation.py
View file

@ -16,9 +16,9 @@ class TestSimulation(unittest.TestCase):
gamma=4.342e7, #Hz/T
nuclear_spin=9/2,
spin_factor=2,
powder_factor=1,
powder_factor=0.75,
filling_factor=0.7,
T1=82.6e-5, #s
T1=83.5e-5, #s
T2=396e-6, #s
T2_star=50e-6, #s
)
@ -50,12 +50,16 @@ class TestSimulation(unittest.TestCase):
power_amplifier_power=500,
pulse = self.pulse,
averages = 1,
gain = 6000
gain = 6000,
temperature=77,
)
def test_simulation(self):
M = self.simulation.simulate()
# Plotting the results
plt.plot(self.time_array, abs(M))
plt.plot(self.time_array * 1e6, abs(M))
plt.xlabel("Time (µs)")
plt.ylabel("Magnetization (a.u.)")
plt.title("FID of BiPh3")
plt.show()