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save fit parameter and agr; more doc

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dominik
2022-03-24 17:35:10 +01:00
parent ef81030213
commit 73e4a2b4d9
19 changed files with 209 additions and 284 deletions
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4
doc/Makefile
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@@ -5,8 +5,8 @@
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= /autohome/dominik/miniconda3/bin/sphinx-build
SOURCEDIR = /autohome/dominik/nmreval/docs/source
BUILDDIR = /autohome/dominik/nmreval/docs/build
SOURCEDIR = /autohome/dominik/nmreval/doc/source
BUILDDIR = /autohome/dominik/nmreval/doc/_build
# Put it first so that "make" without argument is like "make help".
help:

70
doc/examples/nmr/plot_RelaxationEvaluation.py
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@@ -1,12 +1,19 @@
"""
=======================
Spin-lattice relaxation
=======================
==========
T1 minimum
==========
Example for
``RelaxationEvaluation`` is used to get width parameter from a T1 minimum.
As a subclass of ``Relaxation`` it can also be used to calculate Relaxation times.
The basic steps are:
* Determine a T1 minimum with `nmreval.nmr.RelaxationEvaluation.calculate_t1_min`
* Calculate width parameter of a spectral density/coupling constants/... with
``RelaxationEvaluation.get_increase``
* Calculate correlation times from these values with ``RelaxationEvaluation.correlation_from_t1``
"""
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.pyplot as plt
from nmreval.distributions import ColeDavidson
from nmreval.nmr import Relaxation, RelaxationEvaluation
@@ -20,7 +27,7 @@ temperature = 1000/inv_temp
# spectral density parameter
ea = 0.45
tau = 1e-21 * np.exp(ea / kB / temperature)
gamma_cd = 0.1
gamma_cd = 0.4
# interaction parameter
omega = 2*np.pi*46e6
@@ -28,40 +35,57 @@ delta = 120e3
eta = 0
r = Relaxation()
r.set_distribution(ColeDavidson) # the only parameter that has to be set beforehand
r.set_distribution(ColeDavidson) # the only parameter that set beforehand
t1_values = r.t1(omega, tau, gamma_cd, mode='bpp',
prefactor=Quadrupolar.relax(delta, eta))
# add noise
rng = np.random.default_rng(123456789)
rng = np.random.default_rng()
noisy = (rng.random(t1_values.size)-0.5) * 0.5 * t1_values + t1_values
# set parameter and data
ax_t1 = plt.figure().add_subplot()
ax_t1.semilogy(inv_temp, t1_values, label='Calculated T1')
ax_t1.semilogy(inv_temp, noisy, 'o', label='Noise')
ax_t1.legend()
plt.show()
# Actual evaluation starts here
# setting necessary parameter
r_eval = RelaxationEvaluation()
r_eval.set_distribution(ColeDavidson)
r_eval.set_coupling(Quadrupolar, (delta, eta))
r_eval.data(temperature, noisy)
r_eval.set_data(temperature, noisy)
r_eval.omega = omega
# Find a T1 minumum
t1_min_data, _ = r_eval.calculate_t1_min() # second argument is None
t1_min_inter, line = r_eval.calculate_t1_min(interpolate=1, trange=(160, 195), use_log=True)
fig, ax = plt.subplots()
ax.semilogy(1000/t1_min_data[0], t1_min_data[1], 'rx', label='Data minimum')
ax.semilogy(1000/t1_min_inter[0], t1_min_inter[1], 'r+', label='Parabola')
ax.semilogy(1000/line[0], line[1])
ax_min = plt.figure().add_subplot()
ax_min.semilogy(inv_temp, noisy, 'o', label='Data')
ax_min.semilogy(1000/line[0], line[1], '--')
ax_min.semilogy(1000/t1_min_data[0], t1_min_data[1], 'C2X',label='Data minimum')
ax_min.semilogy(1000/t1_min_inter[0], t1_min_inter[1], 'C3P',label='Parabola')
ax_min.set_xlim(4.5, 7)
ax_min.set_ylim(1e-3, 1e-1)
ax_min.legend()
# Vary the first (and for Cole-Davidson, only) parameter of the spectral density
found_gamma, found_height = r_eval.get_increase(t1_min_inter[1], idx=0, mode='distribution')
print(found_gamma)
plt.axhline(found_height)
print(f'Minimum at {found_height} for {found_gamma}; input is {gamma_cd}')
plt.show()
#%%
# Now we found temperature and height of the minimum we can calculate the correlation time
##################################################################################
# Calculation of correlation times uses previously parameter for spectral density
# and prefactor
plt.semilogy(1000/temperature, tau)
tau_from_t1, opts = r_eval.correlation_from_t1()
print(opts)
plt.semilogy(1000/tau_from_t1[:, 0], tau_from_t1[:, 1], 'o')
tau_from_t1, opts = r_eval.correlation_from_t1(mode='mean')
print(f'Used options: {opts}')
ax_tau = plt.figure().add_subplot()
ax_tau.semilogy(inv_temp, tau*gamma_cd, label='Original input')
ax_tau.semilogy(1000/tau_from_t1[:, 0], tau_from_t1[:, 1], 'o', label='Calculated')
ax_tau.legend()
plt.show()

179
doc/source/gallery/index.rst
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@@ -1,179 +0,0 @@
:orphan:
.. _sphx_glr_gallery:
.. examples-index:
.. _gallery:
========
Examples
========
This page contains example plots. Click on any image to see the full image and source code.
.. raw:: html
<div class="sphx-glr-clear"></div>
.. _sphx_glr_gallery_distribution:
.. _distribution_examples:
.. _distribution-examples-index:
Distribution of correlation times
=================================
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for KWW distributions">
.. only:: html
.. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_KWW_thumb.png
:alt: Kohlrausch-Williams-Watts
:ref:`sphx_glr_gallery_distribution_plot_KWW.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/distribution/plot_KWW
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for Cole-Cole distributions">
.. only:: html
.. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_ColeCole_thumb.png
:alt: Cole-Cole
:ref:`sphx_glr_gallery_distribution_plot_ColeCole.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/distribution/plot_ColeCole
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for Log-Gaussian distributions">
.. only:: html
.. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_LogGaussian_thumb.png
:alt: Log-Gaussian
:ref:`sphx_glr_gallery_distribution_plot_LogGaussian.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/distribution/plot_LogGaussian
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for Cole-Davidson distributions">
.. only:: html
.. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_ColeDavidson_thumb.png
:alt: Cole-Davidson
:ref:`sphx_glr_gallery_distribution_plot_ColeDavidson.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/distribution/plot_ColeDavidson
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for Havriliak-Negami distributions">
.. only:: html
.. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_HavriliakNegami_thumb.png
:alt: Havriliak-Negami
:ref:`sphx_glr_gallery_distribution_plot_HavriliakNegami.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/distribution/plot_HavriliakNegami
.. raw:: html
<div class="sphx-glr-clear"></div>
.. _sphx_glr_gallery_nmr:
.. _nmr_examples:
.. _nmr-examples-index:
NMR specifics
=============
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Example for">
.. only:: html
.. figure:: /gallery/nmr/images/thumb/sphx_glr_plot_RelaxationEvaluation_thumb.png
:alt: Spin-lattice relaxation
:ref:`sphx_glr_gallery_nmr_plot_RelaxationEvaluation.py`
.. raw:: html
</div>
.. toctree::
:hidden:
/gallery/nmr/plot_RelaxationEvaluation
.. raw:: html
<div class="sphx-glr-clear"></div>

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doc/source/gallery/searchindex.bak
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'/autohome/dominik/nmreval/doc/_build/html/index.html', (0, 6969)
'/autohome/dominik/nmreval/doc/_build/html/_static/documentation_options.js', (7168, 364)
'/autohome/dominik/nmreval/doc/_build/html/searchindex.js', (7680, 29280)

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doc/source/gallery/searchindex.dat
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doc/source/gallery/searchindex.dir
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'/autohome/dominik/nmreval/doc/_build/html/index.html', (0, 6969)
'/autohome/dominik/nmreval/doc/_build/html/_static/documentation_options.js', (7168, 364)
'/autohome/dominik/nmreval/doc/_build/html/searchindex.js', (7680, 29280)