horace-euphonic-interface¶
This is a simple interface to allow simulation of inelastic neutron scattering data from phonons in Horace using Euphonic. This is done using Horace simulation functions.
General Installation¶
2. Set up Python in Matlab¶
The Python executable that you installed Euphonic with needs to be specified in MATLAB. You can find the executable location in Python with:
>>> import sys
>>> print(sys.executable)
You can then set this executable in MATLAB (2019b or later) using:
>> pyenv('Version', '/path/to/python')
Or in MATLAB 2019a or earlier:
>> pyversion('/path/to/python')
Note
The Python version used in Matlab can only be changed if it has not yet been loaded. If you have already installed Horace-Euphonic-Interface, Python might be automatically loaded on startup. To prevent this, disable Horace-Euphonic-Interface first in Add-Ons > Manage Add-Ons then click the \(\vdots\) symbol to the right of the add-on to bring up the settings, and untick the Enabled box, then restart Matlab. Python will no longer be loaded. Remember to re-enable Horace-Euphonic-Interface afterwards.
3. Download and Install¶
Latest version (recommended)
Horace-Euphonic-Interface is packaged as a Matlab toolbox (.mltbx
), which
allows easy installation from a single file as a Matlab Add-On. In Matlab,
go to the Home tab, and in the Environment section, click Add-Ons,
and then Get Add-Ons. Search for horace-euphonic-interface, select it
and then click Add > Add to MATLAB. That’s it!
See here for more information on Matlab Add-Ons.
Older versions
The .mltbx
file for each release is also available at
https://github.com/pace-neutrons/horace-euphonic-interface/releases.
Open the .mltbx
file in Matlab and it should automatically be installed.
4. Test installation¶
To test everything has been installed ok, try:
>> help(euphonic.ForceConstants)
IDAaaS Installation¶
Euphonic is already installed in a Python virtual environment at
/usr/local/virtualenvs/euphonicenv
and horace-euphonic-interface
is available at /usr/local/mprogs
. To make use of these, add the following to
your startup.m
:
addpath('/usr/local/mprogs/horace-euphonic-interface')
pyversion '/usr/local/virtualenvs/euphonicenv/bin/python3'
Usage¶
Quick Guide¶
To view the available functions and classes, try:
help euphonic
1. Read force constants
First, the force constants must be read. The usage is very similar to Euphonic,
for example to read a CASTEP .castep_bin
file:
fc = euphonic.ForceConstants.from_castep('quartz.castep_bin')
Or, to read from Phonopy files:
fc = euphonic.ForceConstants.from_castep('path', 'phonopy.yaml')
2. Set up model
Next, the model must be set up. Currently, the CoherentCrystal
model
is available. The force constants must be passed in, then any other optional
parameters. For example:
coh_model = euphonic.CoherentCrystal(...
fc, ...
'conversion_mat', [1 0 0; 0 1 0; 0 0 -1],
'debye_waller_grid', [6 6 6], ...
'temperature', 100, ...
'asr', 'reciprocal', ...
'use_c', true);
To see all the available optional parameters, try:
help(euphonic.CoherentCrystal)
Note
conversion_mat
Pay particular attention to this parameter, this is a 3x3 matrix to convert from the q-points in Horace to the q-points in the modelling code. This will be required if you’ve used a different unit cell convention/orientation in Horace and your modelling code, and will depend on the cells chosen. If set incorrectly, the results will not make sense (or worse, may happen to make sense at first in certain cuts due to symmetry, but give incorrect results in other cuts later on!)
3. Simulate cut
In Horace, the disp2sqw_eval
simulation function is used to simulate
experimental data with Euphonic. This requires a function handle, which is provided
by CoherentCrystal.horace_disp
:
scale_factor = 1e12;
effective_fwhm = 1;
cut_sim = disp2sqw_eval(cut, @coh_model.horace_disp, {scale_factor}, effective_fwhm);
Full Example¶
An example script simulating a simple cut is below:
% Read in experimental cut
cut = read_horace('quartz.d2d');
% Read force constants
fc = euphonic.ForceConstants.from_castep('quartz.castep_bin')
% Set up model
coh_model = euphonic.CoherentCrystal(...
fc, ...
'conversion_mat', [1 0 0; 0 1 0; 0 0 -1],
'debye_waller_grid', [6 6 6], ...
'temperature', 100, ...
'asr', 'reciprocal', ...
'use_c', true);
% Simulate
scale_factor = 1e12;
effective_fwhm = 1;
cut_sim = disp2sqw_eval(...
cut, @coh_model.horace_disp, {scale_factor}, effective_fwhm);
% Plot
plot(cut_sim);