lib22pt

Libraries for AB-22PT data analysis

Basic usage

To analyse a rate measurement in file r1006_06.dat, you need to import the rate module:

>>> from lib22pt.rate import *

load the file using class Rate:

>>> R = MultiRate("r1006_06.dat")

Assuming that you want to fit a decay curve, use the fit_decay method to do the fit:

>>> param, pval, fitresult = R.fit_decay()

The method returns the fit parameters stored in param, the fit p-value (goodness of fit) in pval, and the lmfit MinimizerResult object in fitresult. The fit has two parameters - initial number N0 and decay rate r. The fitted parameter values and estimated errors can be printed as

>>> param.pretty_print()
Name     Value      Min      Max   Stderr     Vary     Expr Brute_Step
N0     142.2     -inf      inf    2.326     True     None     None
r      4.522     -inf      inf   0.2545     True     None     None

and the values can be extracted as

>>> print("r = (%.4g +/- %.2g) s^-1" % (param["r"].value, param["r"].stderr))
r = (21.05 +/- 0.45) s^-1

The fitted rate must be divided by the reactant number density to obtain the reaction rate coefficient. It can be obtained from the measured pressure in the chamber Paml22PT, the trap temperature temp and the gas-specific calibration factor f_22PT using the function concentration from the rate module. Assuming a reaction with H2 and the following experimental parameters:

T22 = 314.          # K
Paml_H2 = 1.4e-8    # Pa
Paml_H2_SIS = 0.    # Pa
f_H2_SIS = 38       # calibration from 2015-03-24

the number density is

>>> from lib22pt.util import concentration
>>> n_H2 = concentration(T22, Paml_H2, Paml_H2_SIS, f_H2_SIS)
>>> print("%.3g cm^-3" % n_H2)
1.26e+10 cm^-3

and the rate coefficient is:

>>> k, k_err = param["r"].value/n_H2, param["r"].stderr/n_H2
>>> print("k = (%.4g +/- %.2g) cm^3 s^-1" % (k, k_err))
k = (1.676e-09 +/- 3.6e-11) cm^3 s^-1

Installation

The recommended way to make "self-contained" data analysis folders is to copy the lib22pt folder into working directory.

Regular installation:

python3 setup.py install

To install for development:

python3 setup.py develop

To uninstall:

pip3 uninstall lib22pt

Run tests:

python3 setup.py test