Spintrum/spintrum/examples/ZULF/formamide.py

81 lines
2.1 KiB
Python

#!/usr/bin/python3
import spintrum
import math
import matplotlib.pyplot as plt
import numpy as np
import time
gammas = [-431.6e4,4257.7e4,4257.7e4,4257.7e4]
multips = [2,2,2,2]
jCouplings = \
[
[0,-89.3,-89.3,-13.5],
[0,0,0,8],
[0,0,0,8],
[0,0,0,0],
]
BThermal = 1.8e0
T2 = 5
sampleRate = 2e3
T= 1/sampleRate
points = 80000
specRange = [[0,50],[100,200]]
gammah = 2*math.pi*4257.7e4
spinOp = spintrum.SpinOperations()
spinOp.add_operation(spintrum.SpinOperations.OPERATION__THERMAL_POPULATE,
{'Bx': 0, 'By': 0, 'Bz': BThermal, 'T': 293.778})
spinOp.add_operation(spintrum.SpinOperations.OPERATION__TIP_SPINS,
{'direction': 'y', 'BVsTArea': 4*math.pi/gammah})
spinOp.add_operation(spintrum.SpinOperations.OPERATION__SET_HAMILTONIAN,
{'Bx': 0, 'By': 0, 'Bz': 0})
spinOp.add_operation(spintrum.SpinOperations.OPERATION__INIT_TIME_INDEPENDENT_EVOLUTION,
{'samplingRate': sampleRate, 'measurementDirection': 'z'})
spinOp.add_operation(spintrum.SpinOperations.OPERATION__EVOLVE_TIME_INDEPENDENT,
{'points': points, 'threads': 4})
def filterSpectrum(spec, freqLim):
xAxis = np.array([])
yAxis = np.array([])
for i in range(len(freqLim)):
for j in range(len(spec["x"])):
if spec["x"][j] >= freqLim[i][0] and spec["x"][j] <= freqLim[i][1]:
xAxis = np.insert(xAxis,-0,spec["x"][j])
yAxis = np.insert(yAxis,-0,spec["y"][j])
return {"x": xAxis, "y": yAxis}
start_time = time.time()
signal = spintrum.simulate(gyromagneticRatios=gammas,
jCouplings=jCouplings,
spinMultiplicities=multips,
spinOperations=spinOp)
print("Simulation lastet: " + repr(time.time()-start_time) + "s")
signal = signal - np.mean(signal)
signal = [signal[i]*math.exp(-i/sampleRate/T2) for i in range(len(signal))]
plt.plot(signal)
plt.show()
FFT = spintrum.FFTSpectralDensity(signal, sampleRate)
fft = filterSpectrum(FFT,specRange)
plt.plot(fft['x'], fft['y'])
plt.show()