The multibinit software¶

The MULTIBINIT software implements a second-principles approach for lattice dynamics simulations based on atomic potentials fitted on first-principles calculations [Wojdel2013]. The second-principles effective potential accounts for harmonic (short-range and long-range dipole-dipole interactions) and anharmonic contributions, as well as the explicit treatment of homogeneous strain and its coupling with the lattice. On the one hand, parameters associated to second energy derivatives (harmonic interatomic force constants -IFC-, elastic constants, strain-phonon coupling, etc.) are determined exactly and provided by the Density Functional Perturbation Theory (DFPT). On the other hand, the anharmonic lattice contribution is restricted to a limited number of terms (short-range interaction and low order) and treated in a more effective way: it is fitted [Escorihuela-Sayalero2017] to reproduce stresses and forces on a training set which should include representative configurations properly sampling the phase space.

0 Installation¶

The MULTIBINIT software is included in the ABINIT package, thus to install this code, you can follow the instructions of the installation guide of the package.

However, in order to be able to use all the MULTIBINIT features, you might need to recompile ABINIT if you have not activated some flags in the configure (config.ac) file:

• MULTIBINIT generates the output of the molecular dynamics in the NetCDF format: the NetCDF library is linked by using the flag:

with_trio_flavor="netcdf"

• MULTIBINIT uses Libxml2 to parse the XML files (not mandatory, but more efficient for heavy XML files): this library is linked by using the flags:

enable_xml=yes
CFLAGS_EXTRA="-I/usr/include/libxml2"


1 How to run the code¶

1.1 Introducing the “files” file¶

Once you have prepared the input file (see below for the parameters description) and the required files for the generation of the model, you must create a “.files” file which lists (one for each line) the filenames the job will require: the main input file, the main output file, the file for the model (model.DDB or model.XML), the XML file for the anharmonic part of the model and the NetCDF file for the training set. The files file (called for example multibinit.files) looks like:

  multibinit.in
multibinit.out
model.DDB or model.XML
model_anharmonic.XML
training_set_HIST.nc


In this example:

• The main input file is called “multibinit.in”.
• The main output will be written as “multibinit.out”.
• model.DDB or model.XML is the Database from ABINIT or XML.
• model_anharmonic.XML (optional) is the XML with the coefficients from fitted polynomial.
• training_set_HIST.nc is the history file in NetCDF format containing the training set.

The model.DDB (or model.XML) file contains the system definition and the list of the total energy derivatives with respect to three kind of perturbations: phonons, electric field and strain. The optional XML file contains the list of coefficients obtained by fitting a polynomila to the energy. The last file is mandatory to obtain the “model_anharmonic.XML” file.

1.2 Running the code¶

The main executable file is called “multibinit”. Supposing that the executable is located in your working directory, you can run it interactively (in Unix) with the command:

multibinit < multibinit.files > log


or, in the background, with the command:

multibinit < multibinit.files > log &


Here, the standard output and standard error are piped to the file called “log”.

The user has the full freedom to change the filenames. Moreover, modifications of the above commands could be needed, depending on the UNIX flavour that is used on the platform supposed to execute the code.

The syntax of the input file is completely similar to the one of the main ABINIT: this file is parsed, keywords are identified, comments are also identified. However, the multidataset mode is not available.

2 Input variables¶

Multibinit is able to perform many different tasks. For example, it is possible to generate a second principles model by extracting the harmonic part from a DFPT calculation and fitting the related anharmonic part with a polynomial expression. Such a model can contain phonons instabilities and can be bound with an automatic procedure. In addition, for a given model, it is also possible to perform a molecular dynamics using MULTIBINIT. Each feature can be selected by a set of input variables for which the corresponding ‘flag’ variables activate the different tasks, e.g. prt_model, fit_coeff, bound_model and dynamics. The full list of the input variables are presented in the multibinit variable set.

3 How to generate a model¶

Before learning how to generate a model, we encourage you to read the papers [Wojdel2013] and [Escorihuela-Sayalero2017].

3.1 How to compute the harmonic contribution using ABINIT¶

MULTIBINIT requires a DDB file from ABINIT to build the harmonic part of the potential. To produce this file, you are first supposed to learn how to perform DFPT calculations with ABINIT. For this purpose, it is useful to follow the different tutorials: start with the second lesson about response functions (rf2 lesson) to compute the phonon dispersion and build the related DDB file, then follow the lesson on elasticity (elastic lesson) to compute elastic contribution and build the related DDB. At the end, use the DDB merge tool to generate the “model.DDB” file seen before.

To learn the procedure to compute the harmonic part of the potential, have a look at the topic_LatticeModel, where input variables and selected input files are mentioned. Later, a tutorial will be available.

3.2 How to compute the anharmonic contribution using a training set¶

To compute the anharmonic part of the model, MULTIBINIT requires a training set containing several DFT calculations. Such training set will contain an ensemble of atomic configurations sampling the potential energy surface. This file will be used to fit a polynomial following the method developed by [Escorihuela-Sayalero2017]. To generate the training set, the user requires to get some experience in molecular dynamics simulation within ABINIT. Alternatively, the user can generate the training set configurations by means of phonon population procedure at fixed temperature (DDB file mandatory) activated by imposing ionmov=27.

3.3 How to bound a model¶

MULTIBINIT includes an automatic binding process. Have a look at the topic_BoundingProcess, where input variables and selected input files are mentioned. Later, a tutorial will be available.

3.4 How to run a dynamics¶

MULTIBINIT uses routines of ABINIT which perform atomic relaxation, molecular dynamics, and Monte Carlo simulations. Have a look at the topic_DynamicsMultibinit, where input variables and selected input files are mentioned. Later, a tutorial will be available.