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Abins dialog.
Table of Contents
| 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’, ‘VASP’] |
| VibrationalOrPhononFile | Input | string | Mandatory | File with the data from a vibrational or phonon calculation. Allowed values: [‘phonon’, ‘out’, ‘outmol’, ‘log’, ‘xml’] |
| 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. Allowed values: [‘1’, ‘2’] |
| OutputWorkspace | Output | Workspace | Mandatory | Name to give the output workspace. |
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), DMOL3 (.outmol) or VASP (.xml) 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 you are developing or hacking on Abins, see the Abins: Implementation details notes which outline some of the key conventions, practices and pitfalls.
If Abins is used as part of your data analysis routines, please cite the relevant reference [1].
Note
To run these usage examples please first download the usage data, and add these to your path. In Mantid 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
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