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Merged master into beta-NMR

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This commit is contained in:
Zaher Salman
2018-12-18 10:01:28 +01:00
parent 8207aea183 91e2eca915
commit d1cf374354
49 changed files with 1603 additions and 266 deletions
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159
doc/examples/test-histo-HAL9500.msr
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@@ -1,107 +1,107 @@
153
MnSi, FLC68.2, 50 K
###############################################################
FITPARAMETER
# Nr. Name Value Step Pos_Error Boundaries
1 Rate_1 1.6687 0.0083 none
2 Field_1 73089.883 0.089 none
3 Rate_2 1.968 0.031 none
1 Rate_1 1.6687 0.0086 none
2 Field_1 73089.883 0.090 none
3 Rate_2 1.968 0.032 none
4 Field_2 72289.02 0.24 none
5 Asym_1 0.2949 0.0027 none
6 Frc_1 0.7316 0.0052 none
5 Asym_1 0.2949 0.0030 none
6 Frc_1 0.7316 0.0059 none
7 Phase_1 55.61 0.52 none
8 N0_1 940.35 0.44 none
9 Bkg_1 1.523 0.052 none
8 N0_1 940.35 0.54 none
9 Bkg_1 1.523 0.064 none
10 Asym_2 0.2960 0.0026 none
11 Frc_2 0.7475 0.0051 none
10 Asym_2 0.2960 0.0030 none
11 Frc_2 0.7475 0.0059 none
12 Phase_2 30.77 0.50 none
13 N0_2 961.49 0.45 none
14 Bkg_2 1.928 0.053 none
13 N0_2 961.49 0.55 none
14 Bkg_2 1.928 0.065 none
15 Asym_3 0.3002 0.0026 none
16 Frc_3 0.7462 0.0050 none
15 Asym_3 0.3002 0.0029 none
16 Frc_3 0.7462 0.0056 none
17 Phase_3 18.03 0.48 none
18 N0_3 1024.28 0.46 none
19 Bkg_3 1.919 0.055 none
18 N0_3 1024.28 0.57 none
19 Bkg_3 1.919 0.067 none
20 Asym_4 0.3088 0.0026 none
21 Frc_4 0.7333 0.0048 none
20 Asym_4 0.3088 0.0029 none
21 Frc_4 0.7333 0.0054 none
22 Phase_4 336.94 0.47 none
23 N0_4 1029.36 0.46 none
24 Bkg_4 1.863 0.055 none
23 N0_4 1029.36 0.57 none
24 Bkg_4 1.863 0.067 none
25 Asym_5 0.3094 0.0026 none
26 Frc_5 0.7416 0.0049 none
25 Asym_5 0.3094 0.0029 none
26 Frc_5 0.7416 0.0055 none
27 Phase_5 280.32 0.48 none
28 N0_5 1002.69 0.46 none
29 Bkg_5 1.979 0.054 none
28 N0_5 1002.69 0.56 none
29 Bkg_5 1.979 0.067 none
30 Asym_6 0.3153 0.0028 none
31 Frc_6 0.7403 0.0051 none
32 Phase_6 211.07 0.50 none
33 N0_6 853.43 0.42 none
34 Bkg_6 1.656 0.050 none
30 Asym_6 0.3153 0.0032 none
31 Frc_6 0.7403 0.0058 none
32 Phase_6 211.07 0.51 none
33 N0_6 853.43 0.52 none
34 Bkg_6 1.656 0.061 none
35 Asym_7 0.3118 0.0028 none
36 Frc_7 0.7378 0.0052 none
35 Asym_7 0.3118 0.0032 none
36 Frc_7 0.7378 0.0059 none
37 Phase_7 161.74 0.51 none
38 N0_7 858.76 0.42 none
39 Bkg_7 1.594 0.050 none
38 N0_7 858.76 0.52 none
39 Bkg_7 1.594 0.061 none
40 Asym_8 0.2985 0.0028 none
41 Frc_8 0.7373 0.0053 none
42 Phase_8 133.70 0.53 none
43 N0_8 871.20 0.42 none
44 Bkg_8 1.746 0.051 none
40 Asym_8 0.2985 0.0031 none
41 Frc_8 0.7373 0.0061 none
42 Phase_8 133.69 0.53 none
43 N0_8 871.20 0.52 none
44 Bkg_8 1.746 0.062 none
45 Asym_9 0.2874 0.0024 none
46 Frc_9 0.7341 0.0048 none
45 Asym_9 0.2874 0.0027 none
46 Frc_9 0.7340 0.0054 none
47 Phase_9 158.63 0.47 none
48 N0_9 1184.29 0.50 none
49 Bkg_9 2.542 0.060 none
48 N0_9 1184.29 0.61 none
49 Bkg_9 2.542 0.073 none
50 Asym_10 0.2846 0.0026 none
51 Frc_10 0.7453 0.0053 none
52 Phase_10 128.05 0.49 none
53 N0_10 1193.66 0.50 none
54 Bkg_10 2.394 0.060 none
50 Asym_10 0.2846 0.0027 none
51 Frc_10 0.7453 0.0055 none
52 Phase_10 128.05 0.47 none
53 N0_10 1193.66 0.61 none
54 Bkg_10 2.394 0.073 none
55 Asym_11 0.2876 0.0024 none
56 Frc_11 0.7463 0.0049 none
57 Phase_11 102.57 0.46 none
58 N0_11 1280.00 0.52 none
59 Bkg_11 2.730 0.061 none
55 Asym_11 0.2877 0.0026 none
56 Frc_11 0.7463 0.0053 none
57 Phase_11 102.43 0.45 none
58 N0_11 1280.00 0.63 none
59 Bkg_11 2.730 0.075 none
60 Asym_12 0.2919 0.0022 none
61 Frc_12 0.7405 0.0045 none
62 Phase_12 42.97 0.44 none
63 N0_12 1383.96 0.54 none
64 Bkg_12 2.807 0.064 none
60 Asym_12 0.2919 0.0025 none
61 Frc_12 0.7405 0.0050 none
62 Phase_12 42.97 0.43 none
63 N0_12 1383.96 0.66 none
64 Bkg_12 2.807 0.078 none
65 Asym_13 0.2903 0.0021 none
66 Frc_13 0.7494 0.0044 none
65 Asym_13 0.2903 0.0025 none
66 Frc_13 0.7494 0.0050 none
67 Phase_13 350.74 0.43 none
68 N0_13 1393.01 0.55 none
69 Bkg_13 2.738 0.064 none
68 N0_13 1393.01 0.66 none
69 Bkg_13 2.738 0.078 none
70 Asym_14 0.2968 0.0022 none
71 Frc_14 0.7327 0.0045 none
70 Asym_14 0.2968 0.0025 none
71 Frc_14 0.7327 0.0049 none
72 Phase_14 288.56 0.43 none
73 N0_14 1374.46 0.54 none
74 Bkg_14 2.768 0.064 none
73 N0_14 1374.46 0.66 none
74 Bkg_14 2.768 0.078 none
75 Asym_15 0.2799 0.0021 none
76 Frc_15 0.7427 0.0044 none
77 Phase_15 282.56 0.47 none
78 N0_15 1365.97 0.54 none
79 Bkg_15 2.809 0.063 none
75 Asym_15 0.2799 0.0025 none
76 Frc_15 0.7427 0.0052 none
77 Phase_15 282.56 0.45 none
78 N0_15 1365.97 0.65 none
79 Bkg_15 2.809 0.078 none
80 Asym_16 0.2771 0.0023 none
81 Frc_16 0.7344 0.0048 none
82 Phase_16 212.46 0.47 none
83 N0_16 1256.93 0.52 none
84 Bkg_16 2.458 0.062 none
80 Asym_16 0.2771 0.0026 none
81 Frc_16 0.7344 0.0055 none
82 Phase_16 212.46 0.48 none
83 N0_16 1256.94 0.63 none
84 Bkg_16 2.458 0.074 none
###############################################################
THEORY
@@ -265,17 +265,18 @@ SAVE
###############################################################
PLOT 0 (single histo plot)
lifetimecorrection
runs 1 11
runs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
range 0 9.07 -0.5 0.5
###############################################################
FOURIER
units Tesla # units either 'Gauss', 'MHz', or 'Mc/s'
units Tesla # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
fourier_power 12
apodization STRONG # NONE, WEAK, MEDIUM, STRONG
plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
plot REAL # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
phase par(7, 5, 16)
range 7.1 7.5
###############################################################
STATISTIC --- 2014-12-03 15:42:56
STATISTIC --- 2018-10-15 15:55:36
maxLH = 1286508.7, NDF = 1246064, maxLH/NDF = 1.032458

20
doc/examples/test-histo-MusrRoot.msr
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@@ -2,7 +2,7 @@ LSCO x=0.02 (224-227), T=12.00 (K), E=5.57 keV, WEW B=~49(G)/8.62(A), Tr=15.02 (
###############################################################
FITPARAMETER
# No Name Value Step Pos_Error Boundaries
1 AsymT 0.05052 -0.00071 0.00072 0 0.33
1 AsymT 0.05053 -0.00071 0.00072 0 0.33
2 Field 48.298 -0.094 0.095
3 RateT 0.129 -0.010 0.010 0 none
4 AsymL 0 0 none 0 0.33
@@ -10,15 +10,15 @@ FITPARAMETER
6 AlphaLR 0.9784 -0.0013 0.0013
7 PhaseL 6.6 -1.6 1.6 -40 40
8 BkgL 6.920 -0.048 0.048
9 RelPhaseR 178.7 -1.9 1.9 150 210
10 NormR 419.47 -0.40 0.40
9 RelPhaseR 178.8 -1.9 1.9 150 210
10 NormR 419.46 -0.40 0.40
11 BkgR 8.393 -0.050 0.050
12 AlphaTB 1.1025 -0.0015 0.0015
13 RelPhaseT 269.0 -1.9 1.9 240 300
13 RelPhaseT 269.1 -1.9 1.9 240 300
14 BkgT 7.466 -0.049 0.049
15 NormB 393.08 -0.39 0.38
15 NormB 393.08 -0.39 0.39
16 RelPhaseB 90.7 -2.0 2.0 60 120
17 BkgB 7.091 -0.047 0.048
17 BkgB 7.092 -0.048 0.048
18 One 1 0 none
19 Zero 0 0 none
@@ -84,17 +84,17 @@ FOURIER
units Gauss # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
fourier_power 10
apodization STRONG # NONE, WEAK, MEDIUM, STRONG
plot REAL # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
plot REAL # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
dc-corrected true
phase par7
phase parR7, par9, par13, par16
###############################################################
PLOT 0 (single histo plot)
lifetimecorrection
runs 1 3
runs 1 2 3 4
range 0 9 -0.15 0.15
view_packing 500
###############################################################
STATISTIC --- 2015-01-05 13:58:40
STATISTIC --- 2018-11-13 07:58:56
maxLH = 3971.7, NDF = 4001, maxLH/NDF = 0.992668

4
doc/html/_sources/index.txt
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@@ -3,8 +3,8 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to musrfit documentation!
=================================
Welcome to the musrfit documentation!
=====================================
.. toctree::
:maxdepth: 2

338
doc/html/_sources/user-libs.txt
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@@ -407,3 +407,341 @@ Nonlocal superconductivity related Meissner screening functions (AS libs)
-------------------------------------------------------------------------
To be written yet ...
.. index:: BNMR-libs
.. _BNMR-libs:
Functions to analyze |bgr|-NMR data (BNMR libs)
-------------------------------------------------------------------------
This is a collection of ``C++`` classes using the ``musrfit`` :ref:`user-functions <user-functions>`
interface in order to facilitate the usage in conjunction with ``musrfit``. It consists of two libraries:
* ``libBNMR`` contains functions to fit spin lattice relaxation (SLR) data.
* ``libLineProfile`` contains functions to fit resonance lineshapes.
.. note::
Currently it is recommended to read in the data in ASCII format as a non-|mgr|\SR fit :ref:`(fit type 8) <non-musr-fit>`.
.. index:: libBNMR
libBNMR
++++++++++
In |bgr|-NMR the SLR is usually measured by implanting a pulse of :math:`^8`\ Li with a length :math:`t_0` into the sample.
The asymmetry is measured both during the pulse and afterwards. For a a general spin relaxation function :math:`f(t)` the time evolution of the asymmetry is then given by [`Z. Salman, et al., PRL 96, 147601 (2006) <http://dx.doi.org/10.1103/PhysRevLett.96.147601>`_]:
.. index:: SLR
.. _SLR:
.. math::
P(t) = \left\{\begin{matrix}
\frac{\int_0^t e^{-(t-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^t e^{-t'/\tau_{\mathrm{Li}}}dt' } & t\leq t_0\\[6pt]
\frac{\int_0^{t_0}e^{-(t_0-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^{t_0}e^{-t'/\tau_{\mathrm{Li}}}dt'} & t> t_0,
\end{matrix}\right.
where :math:`\tau_{\mathrm{Li}}=1.21`\ s is the :math:`^8`\ Li lifetime.
Functions
^^^^^^^^^^^^
The ``libLineProfile`` library currently contains the following functions:
.. index:: ExpRlx
**Exponential relaxation**
::
userFcn libBNMR ExpRlx 1 2
The parameters are:
#. pulse length :math:`t_0` (ms)
#. relaxation rate :math:`\sigma` (ms\ :math:`^{-1}`\ )
This function implements :math:`f(t)=e^{-\sigma t}`.
.. index:: SExpRlx
**Stretched exponential relaxation**
::
userFcn libBNMR SExpRlx 1 2 3
The parameters are:
#. pulse length :math:`t_0` (ms)
#. relaxation rate :math:`\sigma` (ms\ :math:`^{-1}`\ )
#. stretching exponent :math:`\beta`
This function implements :math:`f(t)=e^{-(\sigma t)^{\beta}}`.
.. index:: libLineProfile
libLineProfile
+++++++++++++++++
In addition to some simple line shapes ``libLineProfile`` contains functions to fit chemical shift anisotropies in the powder average.
Their functional form can be found in `M. Mehring, Principles of High Resolution NMR in Solids (Springer 1983) <http://dx.doi.org/10.1007/978-3-642-68756-3_2>`_.
For an axially symmetric interaction it is given by:
.. index:: Iax
.. _Iax:
.. math::
I_{\mathrm ax}(f)=\left\{\begin{matrix} \frac{1}{2\sqrt{(f_\parallel-f_\perp)(f-f_\perp)}}& f\in(f_\perp,f_\parallel)\cup(f_\parallel,f_\perp)\\[6pt] 0 & \text{otherwise}\end{matrix} \right.
where :math:`f_\parallel` and :math:`f_\perp` are the frequencies that would be observed if the field is oriented paralell or perpendicular to the symmetry axis, respectively.
| In case of a completely anisotropic interaction, the powder average can be described by the frequencies along the three principle axis :math:`f_1,f_2,f_3`.
| Assume without loss of generality that :math:`f_1<f_2<f_3`, then
.. index:: Ianiso
.. _Ianiso:
.. math::
I(f)&=\left\{\begin{matrix}
\frac{K(m)}{\pi\sqrt{(f-f_1)(f_3-f_2)}},& f_3\geq f>f_2 \\[9pt]
\frac{K(m)}{\pi\sqrt{(f_3-f)(f_2-f_1)}},& f_2>f\geq f_1\\[9pt]
0 & \text{otherwise}
\end{matrix} \right. \\
\\
m&=\left\{\begin{matrix}
\frac{(f_2-f_1)(f_3-f)}{(f_3-f_2)(f-f_1)},& f_3\geq f>f_2 \\[6pt]
\frac{(f-f_1)(f_3-f_2)}{(f_3-f)(f_2-f_1)},& f_2>f\geq f_1\\[6pt]
\end{matrix} \right. \\
\\
K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},
:math:`K(m)` is the complete elliptic integral of the first kind.
Functions
^^^^^^^^^^^^
The ``libLineProfile`` library currently contains the following functions:
.. index:: LineGauss
**Gaussian**
::
userFcn libLineProfile LineGauss 1 2
The parameters are:
#. center of the line :math:`f_0`
#. FWHM of the line :math:`\sigma`
| The height of the peak is 1.
| The functional form is given by
.. math::
A(f)=e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}}
.. index:: LineLorentzian
**Lorentzian**
::
userFcn libLineProfile LineLorentzian 1 2
The parameters are:
#. center of the line :math:`f_0`
#. FWHM of the line :math:`w`
| The height of the peak is 1.
| The functional form is given by
.. math::
A(f)= \frac{w^2}{4(f-f_0)^2+w^2}
.. index:: LineLaplace
**Laplacian**
::
userFcn libLineProfile LineLaplace 1 2
The parameters are:
#. center of the line :math:`f_0`
#. FWHM of the line :math:`w`
| The height of the peak is 1.
| The functional form is given by
.. math::
A(f)=e^{-2\ln 2 \left|\frac{f-f_0}{w}\right|}
.. index:: LineSkewLorentzian
**Skewed Lorentzian**
::
userFcn libLineProfile LineSkewLorentzian 1 2 3
The parameters are:
#. center of the line :math:`f_0`
#. width of the line :math:`w`
#. skewness parameter :math:`a`
| The height of the peak is 1.
| The functional form is given by
.. math::
A(f)= \frac{w w_a}{4(f-f_0)^2+w_a^2}, \quad w_a=\frac{2w}{1+e^{a(f-f_0)}}
.. index:: LineSkewLorentzian2
**Skewed Lorentzian 2**
::
userFcn libLineProfile LineSkewLorentzian2 1 2 3
The parameters are:
#. center of the line :math:`f_0`
#. width left of the center :math:`w_1`
#. width right of the center :math:`w_2`
| The height of the peak is 1.
| The functional form is given by
.. math::
A(f)= \left\{\begin{matrix}\frac{{w_1}^2}{4{(f-f_0)}^2+{w_1}^2},&f\leq f_0\\[9pt] \frac{{w_2}^2}{4{(f-f_0)}^2+{w_2}^2},&f>f_0\end{matrix}\right.
.. index:: PowderLineAxialLor
**Powder average of an axially symmetric interaction convoluted with a Lorentzian**
::
userFcn libLineProfile PowderLineAxialLor 1 2 3
The parameters are:
#. frequency for the field oriented paralell to the symmetry axis :math:`f_\parallel`
#. frequency for the field oriented perpendicular to the symmetry axis :math:`f_\parallel`
#. FWHM of the Lorentzian :math:`w`
| The height of the peak is :math:`\sim`\ 1.
| The functional form is given by
.. math::
A(f)= I_{\mathrm ax}(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)
with :math:`I_{\mathrm ax}(f)` defined :ref:`above <Iax>`.
.. index:: PowderLineAxialGss
**Powder average of an axially symmetric interaction convoluted with a Gaussian**
::
userFcn libLineProfile PowderLineAxialGss 1 2 3
The parameters are:
#. frequency for the field oriented paralell to the symmetry axis :math:`f_\parallel`
#. frequency for the field oriented perpendicular to the symmetry axis :math:`f_\parallel`
#. FWHM of the Gaussian :math:`\sigma`
| The height of the peak is :math:`\sim`\ 1.
| The functional form is given by
.. math::
A(f)= I_{\mathrm ax}(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)
with :math:`I_{\mathrm ax}(f)` defined :ref:`above <Iax>`.
.. index:: PowderLineAsymLor
**Powder average of an anisotropic interaction convoluted with a Lorentzian**
::
userFcn libLineProfile PowderLineAsymLor 1 2 3 4
The parameters are:
#. :math:`f_1`
#. :math:`f_1`
#. :math:`f_3` frequencies along the principal axes
#. FWHM of the Lorentzian :math:`w`
| The height of the peak is :math:`\sim`\ 1.
| The functional form is given by
.. math::
A(f)= I(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)
with :math:`I(f)` defined :ref:`above <Ianiso>`. Note that :math:`f_1<f_2<f_3` is not required by the code.
.. index:: PowderLineAsymGss
**Powder average of an anisotropic interaction convoluted with a Gaussian**
::
userFcn libLineProfile PowderLineAsymGss 1 2 3 4
The parameters are:
#. :math:`f_1`
#. :math:`f_1`
#. :math:`f_3` frequencies along the principal axes
#. FWHM of the Gaussian :math:`\sigma`
| The height of the peak is :math:`\sim`\ 1.
| The functional form is given by
.. math::
A(f)= I(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)
with :math:`I(f)` defined :ref:`above <Ianiso>`. Note that :math:`f_1<f_2<f_3` is not required by the code.

67
doc/html/_sources/user-manual.txt
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@@ -1497,8 +1497,68 @@ The block starts with the *FOURIER* keyword and may contain the following entrie
.. _msr-fourier-block-phase:
**phase**
The initial phase of the input data is given here in degrees. Optionally the phase parameter from the :ref:`FITPARAMETER block <msr-fitparameter-block>` can be given,
*e.g.* par3, which would take the value of parameter number 3.
If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either **one**, which means that this phase will be applied to *all* Fourier spectra,
or the number of phases have to correspond to the number of runs in the plot block.
Currently there are three options:
#. The phases for each run/detector are given explicitly, *i.e.*
.. code-block:: bash
phase val0 sep val1 sep ... sep valN
where ``val0``, ``val1``, etc. are explicitly given phases (*i.e.* doubles), and ``sep`` is one of the following allowed separators: ``space``, ``,``, ``;``, or ``tab``.
For example
.. code-block:: bash
phase -3.2, 175.9
#. The phases for each run/detector are given as phase parameter from the :ref:`FITPARAMETER block <msr-fitparameter-block>`, *e.g.* par3, which would
take the value of parameter number 3. More explicitly
.. code-block:: bash
phase parX0 sep parX1 sep ... sep parXN
where the same rules applies as for explicit phase values. An example could look like this
.. code-block:: bash
phase par7, par12, par17, par22, par27, par32, par37, par42, par47, par52, par57, par62, par67, par72, par77, par82
One might prefer to express the phases in respect to a reference counter, *e.g.* the forward counter is the reference counter phase (fcp) whereas
the backward counter phase (bcp) is expressed as bcp = fcp + relative_bcp. If the fitting is done along these lines, the phases in the Fourier
block can be expressed the following way
.. code-block:: bash
phase parRX0 sep parX1 sep ... sep parXN
which means that ``X0`` is the reference phase, and all the other phases are relative phases in respect to ``X0``, *i.e.* the absolut phase of
``Xj`` would be the summ of the values of ``parX0`` and ``parXj`` etc. The reference phase in the list is marked by ``parR`` rather than ``par``.
Obviously only *one* reference phase can be defined!
#. Often the phases in the parameter block follow a clear list structure. This allows to write the Fourier phase parameters in a more compact form
.. code-block:: none
phase par(X0, offset, #param)
with ``X0`` the first phase parameter index, ``offset`` being the offset to the next phase parameter, and ``#param`` being the number of phase parameters to be used.
This means that the previous example can be compacted to
.. code-block:: none
phase par(7, 5, 16)
As in the phase parameter list examples before, also here a reference phase with relative phases might be wished. Differently to the phase parameter
list example, the first parameter number will be the reference phase. The compact notation here is
.. code-block:: none
phase parR(X0, offest, #param)
.. index:: fourier-block-range_for_phase_correction
.. _msr-fourier-block-range_for_phase_correction:
@@ -1522,8 +1582,7 @@ Altogether, a possible FOURIER block might look like that:
fourier_power 12
apodization NONE
plot real_and_imag
phase 22.6 # par3
range_for_phase_correction all
phase par5, par8
range 0.0 17.03
.. index:: msr-plot-block

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doc/html/acknowledgement.html
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@@ -113,7 +113,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
</div>
<div class="footer">
&copy; Copyright 2018, Andreas Suter.
Last updated on Jul 03, 2018.
Last updated on Oct 15, 2018.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>

2
doc/html/any2many.html
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@@ -107,7 +107,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
</div>
<div class="footer">
&copy; Copyright 2018, Andreas Suter.
Last updated on Jul 03, 2018.
Last updated on Oct 15, 2018.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>

2
doc/html/bugtracking.html
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@@ -98,7 +98,7 @@ or send an e-mail to A. Suter at PSI.</p>
</div>
<div class="footer">
&copy; Copyright 2018, Andreas Suter.
Last updated on Jul 03, 2018.
Last updated on Oct 15, 2018.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
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| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#H"><strong>H</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
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<dt><a href="user-manual.html#index-28">background-single-histo</a>
</dt>
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<dt><a href="user-libs.html#index-1">BMW-libs</a>
</dt>
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<dt><a href="user-libs.html#index-13">BMWlibs-XML</a>
</dt>
<dt><a href="user-libs.html#index-14">BNMR-libs</a>
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<dt><a href="setup-standard.html#index-2">boost-c++</a>
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<h2 id="E">E</h2>
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<dt><a href="user-libs.html#index-17">ExpRlx</a>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<dt><a href="user-libs.html#index-15">libBNMR</a>
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<dt><a href="user-libs.html#index-2">libFitPofB</a>
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<dt><a href="user-libs.html#index-19">libLineProfile</a>
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<dt><a href="setup-standard.html#index-6">libxml2</a>
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<dt><a href="user-manual.html#index-23">lifetime</a>
</dt>
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<dt><a href="user-manual.html#index-23">lifetime</a>
<dt><a href="user-libs.html#index-22">LineGauss</a>
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<dt><a href="user-libs.html#index-24">LineLaplace</a>
</dt>
<dt><a href="user-libs.html#index-23">LineLorentzian</a>
</dt>
<dt><a href="user-libs.html#index-25">LineSkewLorentzian</a>
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<dt><a href="user-libs.html#index-26">LineSkewLorentzian2</a>
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<dt><a href="user-manual.html#index-38">packing</a>
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<dt><a href="user-libs.html#index-29">PowderLineAsymLor</a>
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</dt>
<dt><a href="user-libs.html#index-16">SLR</a>
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<dt><a href="setup-standard.html#index-1">supported-operating-systems</a>
</dt>
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Welcome to musrfit documentation! &mdash; musrfit 1.4.0 documentation</title>
<title>Welcome to the musrfit documentation! &mdash; musrfit 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" />
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<h1>Welcome to musrfit documentation!<a class="headerlink" href="#welcome-to-musrfit-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="welcome-to-the-musrfit-documentation">
<h1>Welcome to the musrfit documentation!<a class="headerlink" href="#welcome-to-the-musrfit-documentation" title="Permalink to this headline"></a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <tt class="docutils literal"><span class="pre">musrfit</span></tt>?</a></li>
@@ -68,6 +68,7 @@
<li class="toctree-l1"><a class="reference internal" href="user-libs.html">Documentation of user libs (user functions)</a><ul>
<li class="toctree-l2"><a class="reference internal" href="user-libs.html#meissner-profiles-vortex-lattice-related-functions-bmw-libs">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-libs.html#nonlocal-superconductivity-related-meissner-screening-functions-as-libs">Nonlocal superconductivity related Meissner screening functions (AS libs)</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-libs.html#functions-to-analyze-bgr-nmr-data-bnmr-libs">Functions to analyze β-NMR data (BNMR libs)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a><ul>
@@ -141,7 +142,7 @@
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<h3><a href="#">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Welcome to musrfit documentation!</a></li>
<li><a class="reference internal" href="#">Welcome to the musrfit documentation!</a></li>
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<h2>Nonlocal superconductivity related Meissner screening functions (AS libs)<a class="headerlink" href="#nonlocal-superconductivity-related-meissner-screening-functions-as-libs" title="Permalink to this headline"></a></h2>
<p>To be written yet ...</p>
</div>
<div class="section" id="functions-to-analyze-bgr-nmr-data-bnmr-libs">
<span id="bnmr-libs"></span><span id="index-14"></span><h2>Functions to analyze β-NMR data (BNMR libs)<a class="headerlink" href="#functions-to-analyze-bgr-nmr-data-bnmr-libs" title="Permalink to this headline"></a></h2>
<p>This is a collection of <tt class="docutils literal"><span class="pre">C++</span></tt> classes using the <tt class="docutils literal"><span class="pre">musrfit</span></tt> <a class="reference internal" href="user-manual.html#id20"><em>user-functions</em></a>
interface in order to facilitate the usage in conjunction with <tt class="docutils literal"><span class="pre">musrfit</span></tt>. It consists of two libraries:</p>
<ul class="simple">
<li><tt class="docutils literal"><span class="pre">libBNMR</span></tt> contains functions to fit spin lattice relaxation (SLR) data.</li>
<li><tt class="docutils literal"><span class="pre">libLineProfile</span></tt> contains functions to fit resonance lineshapes.</li>
</ul>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently it is recommended to read in the data in ASCII format as a non-μSR fit <a class="reference internal" href="user-manual.html#non-musr-fit"><em>(fit type 8)</em></a>.</p>
</div>
<div class="section" id="libbnmr">
<span id="index-15"></span><h3>libBNMR<a class="headerlink" href="#libbnmr" title="Permalink to this headline"></a></h3>
<p>In β-NMR the SLR is usually measured by implanting a pulse of <span class="math">\(^8\)</span>Li with a length <span class="math">\(t_0\)</span> into the sample.
The asymmetry is measured both during the pulse and afterwards. For a a general spin relaxation function <span class="math">\(f(t)\)</span> the time evolution of the asymmetry is then given by [<a class="reference external" href="http://dx.doi.org/10.1103/PhysRevLett.96.147601">Z. Salman, et al., PRL 96, 147601 (2006)</a>]:</p>
<div class="math" id="slr">
<span id="index-16"></span>\[\begin{split}P(t) = \left\{\begin{matrix}
\frac{\int_0^t e^{-(t-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^t e^{-t'/\tau_{\mathrm{Li}}}dt' } &amp; t\leq t_0\\[6pt]
\frac{\int_0^{t_0}e^{-(t_0-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^{t_0}e^{-t'/\tau_{\mathrm{Li}}}dt'} &amp; t&gt; t_0,
\end{matrix}\right.\end{split}\]</div>
<p>where <span class="math">\(\tau_{\mathrm{Li}}=1.21\)</span>s is the <span class="math">\(^8\)</span>Li lifetime.</p>
<div class="section" id="functions">
<h4>Functions<a class="headerlink" href="#functions" title="Permalink to this headline"></a></h4>
<p>The <tt class="docutils literal"><span class="pre">libLineProfile</span></tt> library currently contains the following functions:</p>
<p id="index-17"><strong>Exponential relaxation</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libBNMR ExpRlx 1 2
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>pulse length <span class="math">\(t_0\)</span> (ms)</li>
<li>relaxation rate <span class="math">\(\sigma\)</span> (ms<span class="math">\(^{-1}\)</span>)</li>
</ol>
<p>This function implements <span class="math">\(f(t)=e^{-\sigma t}\)</span>.</p>
<p id="index-18"><strong>Stretched exponential relaxation</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libBNMR SExpRlx 1 2 3
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>pulse length <span class="math">\(t_0\)</span> (ms)</li>
<li>relaxation rate <span class="math">\(\sigma\)</span> (ms<span class="math">\(^{-1}\)</span>)</li>
<li>stretching exponent <span class="math">\(\beta\)</span></li>
</ol>
<p>This function implements <span class="math">\(f(t)=e^{-(\sigma t)^{\beta}}\)</span>.</p>
</div>
</div>
<div class="section" id="liblineprofile">
<span id="index-19"></span><h3>libLineProfile<a class="headerlink" href="#liblineprofile" title="Permalink to this headline"></a></h3>
<p>In addition to some simple line shapes <tt class="docutils literal"><span class="pre">libLineProfile</span></tt> contains functions to fit chemical shift anisotropies in the powder average.
Their functional form can be found in <a class="reference external" href="http://dx.doi.org/10.1007/978-3-642-68756-3_2">M. Mehring, Principles of High Resolution NMR in Solids (Springer 1983)</a>.</p>
<p>For an axially symmetric interaction it is given by:</p>
<div class="math" id="iax">
<span id="index-20"></span>\[\begin{split}I_{\mathrm ax}(f)=\left\{\begin{matrix} \frac{1}{2\sqrt{(f_\parallel-f_\perp)(f-f_\perp)}}&amp; f\in(f_\perp,f_\parallel)\cup(f_\parallel,f_\perp)\\[6pt] 0 &amp; \text{otherwise}\end{matrix} \right.\end{split}\]</div>
<p>where <span class="math">\(f_\parallel\)</span> and <span class="math">\(f_\perp\)</span> are the frequencies that would be observed if the field is oriented paralell or perpendicular to the symmetry axis, respectively.</p>
<div class="line-block">
<div class="line">In case of a completely anisotropic interaction, the powder average can be described by the frequencies along the three principle axis <span class="math">\(f_1,f_2,f_3\)</span>.</div>
<div class="line">Assume without loss of generality that <span class="math">\(f_1&lt;f_2&lt;f_3\)</span>, then</div>
</div>
<div class="math" id="ianiso">
<span id="index-21"></span>\[\begin{split}I(f)&amp;=\left\{\begin{matrix}
\frac{K(m)}{\pi\sqrt{(f-f_1)(f_3-f_2)}},&amp; f_3\geq f&gt;f_2 \\[9pt]
\frac{K(m)}{\pi\sqrt{(f_3-f)(f_2-f_1)}},&amp; f_2&gt;f\geq f_1\\[9pt]
0 &amp; \text{otherwise}
\end{matrix} \right. \\
\\
m&amp;=\left\{\begin{matrix}
\frac{(f_2-f_1)(f_3-f)}{(f_3-f_2)(f-f_1)},&amp; f_3\geq f&gt;f_2 \\[6pt]
\frac{(f-f_1)(f_3-f_2)}{(f_3-f)(f_2-f_1)},&amp; f_2&gt;f\geq f_1\\[6pt]
\end{matrix} \right. \\
\\
K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\end{split}\]</div>
<p><span class="math">\(K(m)\)</span> is the complete elliptic integral of the first kind.</p>
<div class="section" id="id1">
<h4>Functions<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h4>
<p>The <tt class="docutils literal"><span class="pre">libLineProfile</span></tt> library currently contains the following functions:</p>
<p id="index-22"><strong>Gaussian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineGauss 1 2
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>center of the line <span class="math">\(f_0\)</span></li>
<li>FWHM of the line <span class="math">\(\sigma\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is 1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)=e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}}\]</div>
<p id="index-23"><strong>Lorentzian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineLorentzian 1 2
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>center of the line <span class="math">\(f_0\)</span></li>
<li>FWHM of the line <span class="math">\(w\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is 1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= \frac{w^2}{4(f-f_0)^2+w^2}\]</div>
<p id="index-24"><strong>Laplacian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineLaplace 1 2
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>center of the line <span class="math">\(f_0\)</span></li>
<li>FWHM of the line <span class="math">\(w\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is 1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)=e^{-2\ln 2 \left|\frac{f-f_0}{w}\right|}\]</div>
<p id="index-25"><strong>Skewed Lorentzian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineSkewLorentzian 1 2 3
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>center of the line <span class="math">\(f_0\)</span></li>
<li>width of the line <span class="math">\(w\)</span></li>
<li>skewness parameter <span class="math">\(a\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is 1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= \frac{w w_a}{4(f-f_0)^2+w_a^2}, \quad w_a=\frac{2w}{1+e^{a(f-f_0)}}\]</div>
<p id="index-26"><strong>Skewed Lorentzian 2</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineSkewLorentzian2 1 2 3
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>center of the line <span class="math">\(f_0\)</span></li>
<li>width left of the center <span class="math">\(w_1\)</span></li>
<li>width right of the center <span class="math">\(w_2\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is 1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[\begin{split}A(f)= \left\{\begin{matrix}\frac{{w_1}^2}{4{(f-f_0)}^2+{w_1}^2},&amp;f\leq f_0\\[9pt] \frac{{w_2}^2}{4{(f-f_0)}^2+{w_2}^2},&amp;f&gt;f_0\end{matrix}\right.\end{split}\]</div>
<p id="index-27"><strong>Powder average of an axially symmetric interaction convoluted with a Lorentzian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAxialLor 1 2 3
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>frequency for the field oriented paralell to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
<li>FWHM of the Lorentzian <span class="math">\(w\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= I_{\mathrm ax}(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)\]</div>
<p>with <span class="math">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><em>above</em></a>.</p>
<p id="index-28"><strong>Powder average of an axially symmetric interaction convoluted with a Gaussian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAxialGss 1 2 3
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li>frequency for the field oriented paralell to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
<li>FWHM of the Gaussian <span class="math">\(\sigma\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= I_{\mathrm ax}(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)\]</div>
<p>with <span class="math">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><em>above</em></a>.</p>
<p id="index-29"><strong>Powder average of an anisotropic interaction convoluted with a Lorentzian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAsymLor 1 2 3 4
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li><span class="math">\(f_1\)</span></li>
<li><span class="math">\(f_1\)</span></li>
<li><span class="math">\(f_3\)</span> frequencies along the principal axes</li>
<li>FWHM of the Lorentzian <span class="math">\(w\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= I(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)\]</div>
<p>with <span class="math">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><em>above</em></a>. Note that <span class="math">\(f_1&lt;f_2&lt;f_3\)</span> is not required by the code.</p>
<p id="index-30"><strong>Powder average of an anisotropic interaction convoluted with a Gaussian</strong></p>
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAsymGss 1 2 3 4
</pre></div>
</div>
<p>The parameters are:</p>
<ol class="arabic simple">
<li><span class="math">\(f_1\)</span></li>
<li><span class="math">\(f_1\)</span></li>
<li><span class="math">\(f_3\)</span> frequencies along the principal axes</li>
<li>FWHM of the Gaussian <span class="math">\(\sigma\)</span></li>
</ol>
<div class="line-block">
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
<div class="line">The functional form is given by</div>
</div>
<div class="math">
\[A(f)= I(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)\]</div>
<p>with <span class="math">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><em>above</em></a>. Note that <span class="math">\(f_1&lt;f_2&lt;f_3\)</span> is not required by the code.</p>
</div>
</div>
</div>
</div>
@@ -386,6 +613,11 @@ The expected name of the <tt class="docutils literal"><span class="pre">RGE</spa
</ul>
</li>
<li><a class="reference internal" href="#nonlocal-superconductivity-related-meissner-screening-functions-as-libs">Nonlocal superconductivity related Meissner screening functions (AS libs)</a></li>
<li><a class="reference internal" href="#functions-to-analyze-bgr-nmr-data-bnmr-libs">Functions to analyze β-NMR data (BNMR libs)</a><ul>
<li><a class="reference internal" href="#libbnmr">libBNMR</a></li>
<li><a class="reference internal" href="#liblineprofile">libLineProfile</a></li>
</ul>
</li>
</ul>
</li>
</ul>
@@ -435,7 +667,7 @@ The expected name of the <tt class="docutils literal"><span class="pre">RGE</spa
</div>
<div class="footer">
&copy; Copyright 2018, Andreas Suter.
Last updated on Jul 03, 2018.
Last updated on Oct 15, 2018.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>

57
doc/html/user-manual.html
View File

@@ -1552,8 +1552,56 @@ The argument may be one of the following:</p>
</dl>
<span id="index-47"></span><dl class="docutils" id="msr-fourier-block-phase">
<dt><strong>phase</strong></dt>
<dd>The initial phase of the input data is given here in degrees. Optionally the phase parameter from the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a> can be given,
<em>e.g.</em> par3, which would take the value of parameter number 3.</dd>
<dd><p class="first">If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either <strong>one</strong>, which means that this phase will be applied to <em>all</em> Fourier spectra,
or the number of phases have to correspond to the number of runs in the plot block.</p>
<p>Currently there are three options:</p>
<ol class="last arabic">
<li><p class="first">The phases for each run/detector are given explicitly, <em>i.e.</em></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>phase val0 sep val1 sep ... sep valN
</pre></div>
</div>
<p>where <tt class="docutils literal"><span class="pre">val0</span></tt>, <tt class="docutils literal"><span class="pre">val1</span></tt>, etc. are explicitly given phases (<em>i.e.</em> doubles), and <tt class="docutils literal"><span class="pre">sep</span></tt> is one of the following allowed separators: <tt class="docutils literal"><span class="pre">space</span></tt>, <tt class="docutils literal"><span class="pre">,</span></tt>, <tt class="docutils literal"><span class="pre">;</span></tt>, or <tt class="docutils literal"><span class="pre">tab</span></tt>.
For example</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>phase -3.2, <span class="m">175</span>.9
</pre></div>
</div>
</li>
<li><p class="first">The phases for each run/detector are given as phase parameter from the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a>, <em>e.g.</em> par3, which would
take the value of parameter number 3. More explicitly</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>phase parX0 sep parX1 sep ... sep parXN
</pre></div>
</div>
<p>where the same rules applies as for explicit phase values. An example could look like this</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>phase par7, par12, par17, par22, par27, par32, par37, par42, par47, par52, par57, par62, par67, par72, par77, par82
</pre></div>
</div>
<p>One might prefer to express the phases in respect to a reference counter, <em>e.g.</em> the forward counter is the reference counter phase (fcp) whereas
the backward counter phase (bcp) is expressed as bcp = fcp + relative_bcp. If the fitting is done along these lines, the phases in the Fourier
block can be expressed the following way</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>phase parRX0 sep parX1 sep ... sep parXN
</pre></div>
</div>
<p>which means that <tt class="docutils literal"><span class="pre">X0</span></tt> is the reference phase, and all the other phases are relative phases in respect to <tt class="docutils literal"><span class="pre">X0</span></tt>, <em>i.e.</em> the absolut phase of
<tt class="docutils literal"><span class="pre">Xj</span></tt> would be the summ of the values of <tt class="docutils literal"><span class="pre">parX0</span></tt> and <tt class="docutils literal"><span class="pre">parXj</span></tt> etc. The reference phase in the list is marked by <tt class="docutils literal"><span class="pre">parR</span></tt> rather than <tt class="docutils literal"><span class="pre">par</span></tt>.
Obviously only <em>one</em> reference phase can be defined!</p>
</li>
<li><p class="first">Often the phases in the parameter block follow a clear list structure. This allows to write the Fourier phase parameters in a more compact form</p>
<div class="highlight-none"><div class="highlight"><pre><span></span>phase par(X0, offset, #param)
</pre></div>
</div>
<p>with <tt class="docutils literal"><span class="pre">X0</span></tt> the first phase parameter index, <tt class="docutils literal"><span class="pre">offset</span></tt> being the offset to the next phase parameter, and <tt class="docutils literal"><span class="pre">#param</span></tt> being the number of phase parameters to be used.
This means that the previous example can be compacted to</p>
<div class="highlight-none"><div class="highlight"><pre><span></span>phase par(7, 5, 16)
</pre></div>
</div>
<p>As in the phase parameter list examples before, also here a reference phase with relative phases might be wished. Differently to the phase parameter
list example, the first parameter number will be the reference phase. The compact notation here is</p>
<div class="highlight-none"><div class="highlight"><pre><span></span>phase parR(X0, offest, #param)
</pre></div>
</div>
</li>
</ol>
</dd>
</dl>
<span id="index-48"></span><dl class="docutils" id="msr-fourier-block-range-for-phase-correction">
<dt><strong>range_for_phase_correction</strong></dt>
@@ -1570,8 +1618,7 @@ units Mc/s
fourier_power 12
apodization NONE
plot real_and_imag
phase 22.6 # par3
range_for_phase_correction all
phase par5, par8
range 0.0 17.03
</pre></div>
</div>
@@ -2162,7 +2209,7 @@ In case this cannot be ensured, the parallelization can be disabled by <em>&#821
</div>
<div class="footer">
&copy; Copyright 2018, Andreas Suter.
Last updated on Jul 03, 2018.
Last updated on Nov 13, 2018.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>