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Simulation Package for cw-EPR spectra

Project description

Open-source simulation package for cw-EPR spectra. EPRsim has been developed in the group of Prof. Dr. Stefan Weber at the University of Freiburg, Freiburg im Breisgau, Germany, during the last couple of years. EPRsim was developed by Stephan Rein. The program uses several concepts described in [1]. EPRsim is open-source and available free of charge.

Find the full documentation at the link below: https://www.radicals.uni-freiburg.de/de/software

Installation

Install EPRsim via pip:

$ pip install eprsim

Run EPRsim

Call it as package when running Python.

>>> import EPRsim.EPRsim as sim

Define parameters and run the simulation by invoking the simulate() function of EPRsim.

>>> Param = sim.Parameters()
>>> B, spc, flag = sim.simulate(Param)

The simulate() functions is discribed in the following:

Parameters

Parameters : object
Object with all simulation parameters.

Returns

field : numpy.ndarray
Magnetic field vector
spc : numpy.ndarray
Intesity vector of the cw-EPR signal
flag : list
Flags with warning codes (description pleas find below)

Notes

Main function for the simulation of cw-EPR in different motional regimes (isotropic, fast-motion and solid state) All spectra are simulated as field sweep spectra.

Isotropic/fast-motion For the fast-motion regime/isotropic limit, the program solves the implicit Breit-Rabi formula [1] in a fixed-point iteration. Anisotropic line-broadening effects in the fast-motion regime are calculated via the Kivelson formula [2]. Currently, Euler angles between tensors are ignored by the algorithm! All tensors (only relevant for fast-motion) need to be in their principal axis system and colinear to each other.

Solid-state In the solid-state regime, the program uses a full matrix diagonalization algorithm. Therefore, only spin systems with a Hilbert space dimension of dim(H) < 512 can be calculated. The powder average is partially generated by interpolation of eigenvalues and transition probabilitites (similar to [1]). The interpolation level is automatically set by the program. The solid state algorithm treats arbitrary spin systems as long as the Hilbert space dimension is within the threshold. Spin-polarization can be defined (withing the electronic sublevels) as zero-field populations. The program constructs (sparse) density matrices out of the zero-field eigenvectors, to efficiently calculate the population transformation from zero field to high field. Per default, the program calculates with thermal equilibrium. Nuclear quadrupolar couplings (for I > 0.5) are currently not implemented.

The warning codes are:

0: Everything is alright

1: Solid-state is not possible due to too large matrix dimension.

2: Fast-motion/iso is not possible due to S > 1/2.

The Parameter syntax was kept similar to the one used in EasySpin [1], to make it Optional Parameters (with their defaults):

Parameter Default Meaning
mwFreq 9.6 microwave frequency in GHz
A None Hyperfine couplings in MHz
abund_threshold 0.0001 Threshold for isotope mixtures
D None Zero-field splitting in MHz
g 2.0023193 g-tensor
Harmonic 1 Harmonic of the spectrum
J None Exchange coupling
tcorr None Rotational correlation time in ns
logtcorr None Decadic logarithm of tcorr
lw [0.1, 0.1] Line-widths (Gaussian, Lorentzian)
ModAmp 0 Modulation amplitude
motion ‘solid’ Motional regime
mwPhase 0 Microwave phase offset
n 1 Number of equivalent nuclei
nKnots 12 Initial number of theta values
Nucs None Isotope specification
Points 1024 Number of points
Range [330, 360] Magentic field range in mT
S 0.5 Electron spin quantum number
SNR None Signal-to-noise ratio
verbosity True Print output information
weight 1 Weighting (for multiple species)
gFrame None Euler angles for the g tensor
AFrame None Euler angles for the A tensors
DFrame None Euler angles for the D tensor
Temperature 300 Experimental temperature
Population None Zero-field populations
LevelSelect 5e-5 Threshold for level selection

Examples

Simple example for the simulation of an isotropic nitroxide spectrum.

>>> import EPRsim.EPRsim as sim
>>> P = sim.Parameters()
>>> P.Range = [335 ,350]
>>> P.mwFreq = 9.6
>>> P.g = 2.002
>>> P.A = 45.5
>>> P.Nucs = 'N'
>>> P.lw = [0.2, 0.2]
>>> P.motion = 'fast'
>>> B0, spc, flag = sim.simulate(P)

Simple example for the simulation of an anisotropic nitroxide spectrum (only 14N) in the fast-motion regime.

>>> import EPRsim.EPRsim as sim
>>> Ra = [335 ,350]
>>> freq = 9.6
>>> g = [2.0083, 2.0061, 2.0022]
>>> A = [12, 13, 110]
>>> Nucs = '14N'
>>> lw = [0.2, 0.2]
>>> tcorr = 1e-10
>>> motion = 'fast'
>>> Param = sim.Parameters(Range=Ra, g=g, A=A, Nucs=Nucs, mwFreq=freq,
                           lw=lw, tcorr=corr, motion=motion)
>>> B0, spc, flag = sim.simulate(Param)

Simple example for the simulation of an anisotropic nitroxide spectrum (only 14N) in the solid-state regime.

>>> import EPRsim.EPRsim as sim
>>> import EPRsim.Tools as tool
>>> P = sim.Parameters()
>>> P.Range = [335 ,350]
>>> P.mwfreq = 9.6
>>> P.g = [2.0083, 2.0061, 2.0022]
>>> P.A = [[12, 13, 110], [20, 30, 30]]
>>> P.Nucs = '14N,H'
>>> P.lw = [0.5, 0.2]
>>> P.motion = 'solid'
>>> B0, spc, flag = sim.simulate(P)
>>> tool.plot(B0, spc)

Simple example for the simulation of an anisotropic nitroxide spectrum (only 14N) in the solid-state regime, coupled to an additional hydrogen nucleus.

>>> import EPRsim.EPRsim as sim
>>> import EPRsim.Tools as tool
>>> P = sim.Parameters()
>>> P.Range = [335 ,350]
>>> P.mwfreq = 9.6
>>> P.g = [2.0083, 2.0061, 2.0022]
>>> P.A = [[12, 13, 110], [20, 30, 30]]
>>> P.Nucs = '14N,H'
>>> P.lw = [0.5, 0.2]
>>> P.motion = 'solid'
>>> B0, spc, flag = sim.simulate(P)
>>> tool.plot(B0, spc)

Simple example for the simulation of two radical species.

>>> import EPRsim.EPRsim as sim
>>> import EPRsim.Tools as tool
>>> P = sim.Parameters()
>>> P.Range = [335 ,350]
>>> P.mwfreq = 9.6
>>> P.g = [2.0083, 2.0061, 2.0022]
>>> P.A = [12, 13, 110]
>>> P.Nucs = '14N'
>>> P.lw = [0.5, 0.2]
>>> P.motion = 'solid'
>>> P2 = sim.Parameters()
>>> P2.Range = [335 ,350]
>>> P2.mwfreq = 9.6
>>> P2.g = 2.0003
>>> P2.lw = [0.3, 0.0]
>>> P2.motion = 'solid'
>>> P2.weight = 0.1
>>> B0, spc, flag = sim.simulate([P, P2])
>>> tool.plot(B0, spc)

Simple example for the simulation of a spin-polarized triplet spectrum.

>>> import EPRsim.EPRsim as sim
>>> import EPRsim.Tools as tool
>>> P = sim.Parameters()
>>> P.S = 1
>>> P.Range = [130 ,450]
>>> P.mwfreq = 9.6
>>> P.g = 2
>>> P.lw = [4, 1]
>>> P.D = [-1400, 20]
>>> P.Population = [0.2, 0.3, 0.4]
>>> P.Harmonic = 0
>>> B0, spc, flag = sim.simulate(P)
>>> tool.plot(B0, spc)

Properties

EPRsim provides:

  • Simulation for cw-EPR spectra in the solid-state limit and fast-motion regime
  • Flexible simualtion options
  • Highly-optimized performance of the simulation algorithm
  • Various EPR-data processing function
  • Open-source

Feedback

We are eager to hear about your experiences with GloPel. You can email me at stephan.rein@physchem.uni-freiburg.de.

References

[1] : S. Stoll, A. Schweiger, J. Magn. Reson., 2006, 178, 42-55

[2] : N. M. Atherton, Principles of Electron Spin Resonance, 1993

Acknowledgement

A number of people have helped shaping EPRsim and the ideas behind. First and foremost, Prof. Dr. Stefan Weber and Dr. Sylwia Kacprzak (now Bruker Biospin) were for years the driving force behind EPRsim.

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