FCSXML file

[nim-hrkn]

The preparation stage of AiiDA CalcJob does not allow direct use of file paths, which makes it difficult to create AiiDA scripts using ALM.
Python code is

            reg = LinearRegression(fit_intercept=False).fit(X, y)
            alm.set_fc(reg.coef_)
            alm.save_fc(filename=fname_fcs, format="alamode")

and fname_fcs is used in anphon input as

 FCSXML = {fname_fcs}

But, AiiDA can't specify fname_fcs as far as I understand. AiiDA script must be something like

 with folder.open(self.options.input_filename, 'w', encoding='utf8') as handle:
            make_alm_in(alm_param, handle=handle)

Is it possible to use the file hander instead of fname_fcs?

Probably
fc2 = alm.get_fc(1, mode='all')
can obtain all the harmonic force costants.

Though https://alm.readthedocs.io/en/develop/python-module.html?highlight=create_dataset intoduces

    with h5py.File('fc.hdf5', 'w') as w:
        w.create_dataset('fc2', data=fc2, compression='gzip')
        w.create_dataset('fc3', data=fc3, compression='gzip')

how can I make the FCSXML file from fc2?

[ttadano]

The force constant writer in the FCSXML format is implemented as a C++ function, and the python method alm.save_fc is a simple wrapper to that function. I think it is not easy to use the C++ function in a way as with open() as f.

I implemented another class 'Fcsxml' (still in the alpha stage), which can write force constants in the FCSXML format. Could you have a look at https://github.com/ttadano/ALM/blob/develop/python/alm/fcsxml.py?

While this class still does not have a method like write(self, fileobj=f), implementing it would be straightforward.

[nim-hrkn]

Thank you for you quick reply.
Probably the usage is like this using ase,Atoms class.

lavec = atoms.cell
xcoord = atoms.get_scaled_potisions
numbers = atoms.numbers
fcsxml = Fcsxml(lavec, xcoord, numbers)
...
fc2 = alm.get_fc(1, mode='all')
fcsxml,set_force_constants(fc2, fc_indices)
fcsxml.write(filename)

fc_indices is explained as

        fc_indices: array_like, dtype='int', shape=(num_fc, fc_order + 1)
            Array of flattened indices 3 * index_atom + index_xyz of the
            force constants.

But I can't understand it. Could I ask you how to specify fc_indeces ?

[ttadano]

The get_fc method of alm returns the force constant values and element indices, and they can be passed to fcsxml.set_force_constants as

fc2_values, fc2_elems = alm.get_fc(1)
fcsxml.set_force_constants(fc2_values, fc2_elems)