Abins v1

../_images/Abins-v1_dlg.png

Abins dialog.

Credits

Author:
Krzysztof Dymkowski
Contributors:
Sanghamitra Mukhopadhyay, Elliot Oram, Leonardo Bernasconi, Leandro Liborio, Adam Jackson

Summary

Calculates inelastic neutron scattering.

Properties

Name Direction Type Default Description
AbInitioProgram Input string CASTEP An ab initio program which was used for vibrational or phonon calculation. Allowed values: [‘CASTEP’, ‘CRYSTAL’, ‘DMOL3’, ‘GAUSSIAN’]
VibrationalOrPhononFile Input string Mandatory File with the data from a vibrational or phonon calculation. Allowed values: [‘phonon’, ‘out’, ‘outmol’, ‘log’]
ExperimentalFile Input string   File with the experimental inelastic spectrum to compare. Allowed values: [‘raw’, ‘dat’]
TemperatureInKelvin Input number 10 Temperature in K for which dynamical structure factor S should be calculated.
BinWidthInWavenumber Input number 1 Width of bins used during rebining.
Scale Input number 1 Scale the intensity by the given factor. Default is no scaling.
SampleForm Input string Powder Form of the sample: Powder. Allowed values: [‘Powder’]
Instrument Input string TOSCA Name of an instrument for which analysis should be performed. Allowed values: [‘TOSCA’]
Atoms Input str list   List of atoms to use to calculate partial S.If left blank, workspaces with S for all types of atoms will be calculated. Element symbols will be interpreted as a sum of all atoms of that element in the cell. ‘atomN’ or ‘atom_N’ (where N is a positive integer) will be interpreted as individual atoms, indexing from 1 following the order of the input data.
SumContributions Input boolean False Sum the partial dynamical structure factors into a single workspace.
ScaleByCrossSection Input string Incoherent Scale the partial dynamical structure factors by the scattering cross section. Allowed values: [‘Total’, ‘Incoherent’, ‘Coherent’]
QuantumOrderEventsNumber Input string 1 Number of quantum order effects included in the calculation (1 -> FUNDAMENTALS, 2-> first overtone + FUNDAMENTALS + 2nd order combinations, 3-> FUNDAMENTALS + first overtone + second overtone + 2nd order combinations + 3rd order combinations etc...). Allowed values: [‘1’, ‘2’, ‘3’, ‘4’]
OutputWorkspace Output Workspace Mandatory Name to give the output workspace.

Description

Abins is a plugin for Mantid which allows scientists to compare experimental and theoretical inelastic neutron scattering spectra (INS).

Abins requires a file with the ab-initio phonon data to perform INS analysis. Currently output data from CASTEP (.phonon), CRYSTAL (.out), GAUSSIAN (.log) or DMOL3 (.outmol) DFT programs can be used to perform analysis. Optionally, a user can provide an experimental file with measured dynamical structure factor S in order to directly compare theoretical and experimental spectra. A user can produce one dimensional INS spectrum which can be compared against TOSCA and TOSCA-like instruments; Abins uses a semi-empirical powder averaging model to account for q- and energy-dependent phenomena in this system. The user-input temperature value is included in a Debye-Waller term, recreating the intensity fall-off with increasing wavelength.

After successfully-performed analysis a user obtains a Mantid Workspace Group which stores theoretical spectra (and, optionally, experimental data). Currently a user can produce theoretical spectra for given atoms (e.g. ‘atom_1’, the first atom listed in the input data) or types of atom (for example for benzene two element symbols: C, H) and for each quantum event (up to fourth order). Total theoretical spectra can also be generated, summing over all considered quantum events for that atom or element. The user can also produce a total spectrum for the whole considered system. The dynamical structure factor S is calculated for all atoms in the system and results are cached, so if no settings have been changed then subsequent runs of Abins can quickly create more Mantid Workspaces without re-calculating any spectra.

More information about the implemented working equations can be found here.

Abins is in constant development and suggestions for improvements are very welcome. For any such contributions please contact Dr. Sanghamitra Mukhopadhyay (sanghamitra.mukhopadhyay@stfc.ac.uk).

If Abins is used as part of your data analysis routines, please cite the relevant reference [1].

Usage

Note

To run these usage examples please first download the usage data, and add these to your path. In MantidPlot this is done using Manage User Directories.

Example - loading CASTEP phonon data:

benzene_wrk = Abins(AbInitioProgram="CASTEP", VibrationalOrPhononFile="benzene.phonon",
                    QuantumOrderEventsNumber="1")


for name in benzene_wrk.getNames():
    print(name)

Output:

benzene_wrk_C_total
benzene_wrk_C
benzene_wrk_H_total
benzene_wrk_H

Example - loading CRYSTAL phonon data:

wrk=Abins(AbInitioProgram="CRYSTAL", VibrationalOrPhononFile="b3lyp.out", QuantumOrderEventsNumber="1")

for name in wrk.getNames():
    print(name)

Output:

wrk_C_total
wrk_C
wrk_H_total
wrk_H
wrk_N_total
wrk_N
wrk_Na_total
wrk_Na
wrk_O_total
wrk_O

Example - calling AbINS with more arguments:

wrk_verbose=Abins(AbInitioProgram="CASTEP", VibrationalOrPhononFile="benzene.phonon",
                  ExperimentalFile="benzene_experimental.dat",
                  TemperatureInKelvin=10, BinWidthInWavenumber=1.0, SampleForm="Powder", Instrument="TOSCA",
                  Atoms="H, atom1, atom2", SumContributions=True, QuantumOrderEventsNumber="1", ScaleByCrossSection="Incoherent")

for name in wrk_verbose.getNames():
    print(name)

Output:

experimental_wrk
wrk_verbose_total
wrk_verbose_H_total
wrk_verbose_H
wrk_verbose_atom_1_total
wrk_verbose_atom_1
wrk_verbose_atom_2_total
wrk_verbose_atom_2

Categories: AlgorithmIndex | Simulation

Source

Python: Abins.py (last modified: 2019-10-30)

References

[1]
  1. Dymkowski, S. F. Parker, F. Fernandez-Alonso and S. Mukhopadhyay, “AbINS: The modern software for INS interpretation” , Physica B, doi:10.1016/j.physb.2018.02.034 (2018).