How to use Phonopy automatic module

  • Start from scratch.

  • Start with a blank template.

Phonopy from scratch using a structure file

  • Initiate Phonopy module: Phonopy module can be initiated from CASCADE toolbar by clicking XXX icon.


Fig. 40 Invoke Phonopy module, and choose mode.

  • Load the structure: browse the structure file from disk. In the current version of CINEMAS supported structure file formats are \(\texttt{POSCAR/*.vasp/*.cif/*.in/*.xsf}\).

  • Choose method/property for Phonopy run:


Fig. 41 Invoke Phonopy module, and choose mode.

  • Settings for input-files:


    Fig. 42 Snapshot of window showing CINEMAS-default settings to prepare rest of the input files.

    • In Fig. 42, the first field is a list of established connections.

    • In ‘default’ mode workflow is submitted automatically to a connection marked as default in connection workspace.

    • In default mode, all the setting fields will be disabled and show parameters in ‘read-only’ mode.

    • Setting mode has to be changed to user mode to make customized settings.

    • In the user mode of settings, remote server can be selected from a list of established connections as show in the figure below.

    • As well as all the setting fields can be set to desired parameters.

    • Additionally Save and Load buttons are enabled, and can be used to save user-settings as a template or to load a saved one.


    Fig. 43 CINEMAS: selecting k-path for band-structure calculation.

  • Automatic creation of workflows: - Workflows are created for the choice selected for method/property. - For DFPT method, a module with a single workflow is created.


    Fig. 44 Automatic workflows creation for DFPT method.

    • For Finite-Difference method, a module with several(depending uplong supercell size) workflows is created.


    Fig. 45 Automatic workflows creation for a \(2\times2\times2\) supercell of \(\mathrm{NaCl}\) using finite-difference method.

  • Automatic submission and download:.

    • Once workflows created, CINEMAS submits the same to a remote connection marked as default in Connections workspace.

    • A different connection other than defult can be selected, as discussed in the previous step settings.

  • Phonopy post-processing:

    • Invoke Phonopy-post-processing workspace by clicking the incon XXX.

    • Select type of the calculation i.e. Band, DOS, or Band & DOS.

    • Click Run button, to run an instance of Phonopy program.

    • A success or an error message will be displayed above the Run button.

    • Just of the information both of the messages are shown together, in Fig. 46. In a real case, either of them will be displayed.

    • Run button exectues an instance of ‘phonoppy’ command.

    • View button shows a Matplotlib-graph (equivalent of adding an argument -p in command-line usage of Phonopy) using the output of Phonopy execution. However, this is a ‘view-only’ graph. See Fig. 47.

    • Load in CINEMAS button reformats the output(from YAML format by default or from HDF5 by choice) of the phonopy-execution and loads a formatted table and a graph into CINEMAS-plot. See Fig. 48.

    • The loaded graph in CINEAMS-plot, is further available for user-desired customizations, and to prepare and export a publication-quality figure.

    • View logs button opens the output logs of Phonopy program in a native application installed for text files.


Fig. 46 CINEMAS-Phonopy module post-processing window.


Fig. 47 Matplotlib graph for phonon dispersion invoked from CINEMAS-GUI, similar to Phonopy command-line.


Fig. 48 CINEMAS-Phonopy GUI: A one-click extraction of tabular-data and graph from Phonopy output.

  • Generation of coordinates and labels of high-symmetry points:

    Especially for phonon bandstructure, there are three modes to provide coordinates of high-symmetry points in the Brillouin zone, Manual, Pymatgen-auto, and Phonopy-auto. In the Manual mode, the user has to provide coordinates and labels of each high-symmetry point to be considered in the Phonopy calculation. In Cinemas-auto mode coordinates and lables of high-symmetry points are generated by Pymatgen package and shown in the Phonopy-postprocess workspace, while for Phonopy-auto mode this is done by Seekpath program, which is the original behavior of command-line Phonopy.