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

First ensure you have both Horace and Euphonic installed:

• Horace docs
• Euphonic docs

Now download the required files from Github:

git clone https://github.com/pace-neutrons/horace-euphonic-interface.git

Then add the horace-euphonic-interface folder to the MATLAB search path.

>> addpath('/path/to/horace-euphonic-interface')

The Python executable that you installed Euphonic with also 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 using:

>> pyversion('/path/to/python')

Note

Running on Linux

If running on Linux, the following must also be set from MATLAB to avoid clashes between Python/MATLAB mathematics libraries:

>> py.sys.setdlopenflags(int32(10));

This must be done before Python has been loaded in MATLAB (use pyversion to see if Python is already loaded). The only way to unload Python once it has been loaded is to restart MATLAB

Now that the MATLAB path and pyversion have been set up, test the installation in MATLAB using:

>> euphonic_on

If there are no warnings everything should be installed correctly.

The above commands can be added to a startup.m file so they are executed automatically at the start of every MATLAB session

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'
py.sys.setdlopenflags(int32(10))
euphonic_on

That’s it!

Usage

In Horace, the disp2sqw_eval simulation function is used to simulate experimental data with Euphonic - this requires a function handle, to use Euphonic this is euphonic_sf. For information on euphonic_sf parameters, type:

>> help euphonic_sf

Many of the parameters are passed straight to Euphonic, so see the Euphonic docs for more details.

An example script simulating a simple cut is below:

% Read in experimental cut
cut = read_horace('quartz.d2d');

% Set required parameters
fwhh = 4.0;
temperature = 5;
scale = 1.0;
par = [temperature, scale];
scattering_lengths = struct('Si', 4.1491, 'O', 5.803);

% Set extra parameters
opts = {'model_args', {'quartz.castep_bin'}, ...
        'phonon_kwargs', {'asr', 'reciprocal', 'reduce_qpts', true, ...
                          'use_c', true, 'n_threads', int32(2), ...
                          'eta_scale', 0.75}, ...
        'dw_grid', [6,6,6], ...
        'conversion_mat', [1,0,0; 0,1,0; 0,0,-1],
        'negative_e', true, ...
        'chunk', 5000, ...
        'lim', 1e-7};

% Finally simulate
cut_sim = disp2sqw_eval( ...
    cut, @euphonic_sf, {par, scattering_lengths, opts}, fwhh, 'all');

% Plot
plot(cut_sim);

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!)