2. Verdi shell and AiiDA objects¶
In this section we will use an interactive IPython environment with all the basic AiiDA classes already loaded. We propose two realizations of such a tool. The first consists of a special IPython shell where all the AiiDA classes, methods and functions are accessible. Type in the terminal
For all the everyday AiiDA-based operations, i.e. creating, querying, and using AiiDA objects, the
verdi shell is probably the best tool.
In this case, we suggest that you use two terminals, one for the
verdi shell and one to execute bash commands.
The second option is based on Jupyter notebooks and is probably most suitable to the purposes of our tutorial.
Go to the browser where you have opened
jupyter and click
Python 3 (top right corner).
This will open an IPython-based Jupyter notebook, made of cells in which you can type portions of python code.
The code will not be executed until you press
Shift+Enter from within a cell.
Type in the first cell
and execute it.
This will set exactly the same environment as the
The notebook will be automatically saved upon any modification and when you think you are done, you can export your notebook in many formats by going to
We suggest you to have a look at the drop-down menus
Cell where you will find the main commands to manage the cells of your notebook.
verdi shell and Jupyter notebook are completely equivalent.
Use either according to your personal preference.
You will still sometimes need to type command-line instructions in
bash in the first terminal you opened.
To differentiate these from the commands to be typed in the
verdi shell, the latter will be marked in this document by a green background, like:
some verdi shell command
while command-line instructions in
bash to be typed into a terminal will be written with a blue background:
some bash command
Alternatively, to avoid changing terminal, you can execute
bash commands within the
verdi shell or the notebook by adding an exclamation mark before the command itself:
!some bash command
The background colors of the code sections may be displayed differently by different browsers. For the color scheme mentioned here, we recommend using Google Chrome.
2.1. Loading a node¶
Most AiiDA objects are represented by nodes, identified in the database by its
PK (an integer).
You can access a node using the following command in the shell:
node = load_node(PK)
Load a node using one of the calculation
PK s visible in the graph you displayed in the previous section of the tutorial.
Then get the energy of the calculation with the command
You can also type
and then press
TAB to see all the available output results of the calculation.
2.2. Loading specific kinds of nodes¶
From the graph you generated in section Your first AiiDA graph, find the
UUID of the pseudopotential files (
Load one of them and show what elements it corresponds to by typing:
upf = load_node("<UUID>") upf.element
All methods of
UpfData are accessible by typing
upf. and then pressing
A set of k-points in the Brillouin zone is represented by an instance of the
Choose one from the graph of produced in section Your first AiiDA graph, load it as
kpoints and inspect its content:
Then get the full (explicit) list of k-points belonging to this mesh using
If this throws an
AttributeError, it means that the kpoints instance does not represent a regular mesh but rather a list of k-points defined by their crystal coordinates (typically used when plotting a band structure).
In this case, get the list of k-points coordinates using
Conversely, if the KpointsData node does actually represent a mesh, this method is the one, that when called, will throw an
If you prefer Cartesian (rather than crystal) coordinates, type
For later use in this tutorial, let us try now to create a kpoints instance, to describe a regular (2 x 2 x 2) mesh of k-points, centered at the Gamma point (i.e. without offset). This can be done with the following commands:
KpointsData = DataFactory('array.kpoints') kpoints = KpointsData() kpoints_mesh = 2 kpoints.set_kpoints_mesh([kpoints_mesh] * 3) kpoints.store()
This function loads the appropriate class defined in a string (here
KpointsData is not a class instance, but the kpoints class itself!
While it is also possible to import
KpointsData directly, it is recommended to use the
DataFactory function instead, as this is more future-proof:
even if the import path of the class changes in the future, its entry point string (
array.kpoints) will remain stable.
Dictionaries with various parameters are represented in AiiDA by
Get the PK and load the input parameters of a calculation in the graph produced in section Your first AiiDA graph.
Then display its content by typing
params = load_node('<IDENTIFIER>') YOUR_DICT = params.get_dict() YOUR_DICT
Modify the python dictionary
YOUR_DICT so that the wave-function cutoff is now set to 20 Ry.
Note that you cannot modify an object already stored in the database.
To write the modified dictionary to the database, create a new object of class
Dict = DataFactory('dict') new_params = Dict(dict=YOUR_DICT)
YOUR_DICT is the modified python dictionary.
new_params is not yet stored in the database.
In fact, typing
new_params in the verdi shell will print a string notifying you of its ‘unstored’ status.
Let’s finish by storing the
new_params dictionary node in the datbase:
Find a structure in the graph you generated in section Your first AiiDA graph and load it. Display its chemical formula, atomic positions and species using
structure is the structure you loaded.
If you are familiar with ASE and PYMATGEN, you can convert this structure to those formats by typing
Let’s try now to define a new structure to study, specifically a silicon crystal.
verdi shell, define a cubic unit cell as a 3 x 3 matrix, with lattice parameter alat= 5.4 Å:
alat = 5.4 the_cell = [[alat/2, alat/2, 0.], [alat/2, 0., alat/2], [0., alat/2, alat/2]]
Default units for crystal structure cell and coordinates in AiiDA are Å (Ångström).
Structures in AiiDA are instances of the class
StructureData: load it in the verdi shell
StructureData = DataFactory('structure')
Now, initialize the class instance (i.e. the actual structure we want to study) by the command
structure = StructureData(cell=the_cell)
which sets the cubic cell defined before. From now on, you can access the cell with the command
Finally, append each of the 2 atoms of the cell command. You can do it using commands like
structure.append_atom(position=(0., 0., 0.), symbols="Si") structure.append_atom(position=(alat/4., alat/4., alat/4.), symbols="Si")
for the first ‘Si’ atom. You can access and inspect the structure sites with the command
If you make a mistake, start over from
structure = StructureData(cell=the_cell), or equivalently use
structure.clear_kinds() to remove all kinds (atomic species) and sites.
Alternatively, AiiDA structures can also be converted directly from ASE structures 1 using
from ase.spacegroup import crystal ase_structure = crystal('Si', [(0, 0, 0)], spacegroup=227, cellpar=[alat, alat, alat, 90, 90, 90], primitive_cell=True) structure = StructureData(ase=ase_structure)
Now you can store the new structure object in the database with the command:
Finally, we can also import the silicon structure from an external (online) repository such as the Crystallography Open Database (COD):
from aiida.tools.dbimporters.plugins.cod import CodDbImporter importer = CodDbImporter() for entry in importer.query(formula='Si', spacegroup='F d -3 m'): structure = entry.get_aiida_structure() print("Formula", structure.get_formula()) print("Unit cell volume: ", structure.get_cell_volume())
In that case two duplicate structures are found for ‘Si’. A more in-depth tutorial can be found in this appendix.
2.3. Accessing inputs and outputs¶
Load again the calculation node used in Section Loading a node:
calc = load_node(PK)
TAB: you will see all the link names between the calculation and its input nodes.
You can use a specific linkname to access the corresponding input node, e.g.:
Similarly, if you type:
TAB, you will list all output link names of the calculation.
One of them leads to the structure that was the input of
calc we loaded previously:
Note that links have a single name, that was assigned by the calculation that used the corresponding input or produced the corresponding output, as illustrated in section Your first AiiDA graph.
For a more programmatic approach, you can get a represenation of the inputs and outputs of a node, say
calc, through the following methods:
calc_incoming = calc.get_incoming() calc_outgoing = calc.get_outgoing()
These methods will return an instance of the
You can iterate over the neighboring nodes by calling the
for entry in calc.get_outgoing(): print(entry.link_label, entry.link_type, entry.node)
each entry returned by
.all() is a
LinkTriple, a named tuple, from which you can get the link label and type and the neighboring node itself.
If you print one, you will see something like:
LinkTriple(node=<Dict: uuid: fac99f59-c69e-4ccd-9655-c7da1d469145 (pk: 1050)>, link_type=<LinkType.CREATE: 'create'>, link_label=u'output_parameters')
There are many other convenience methods on the
For example if you are only interested in the link labels you can use:
which will return a list of all the labels of the outgoing links.
.all_nodes() will give you a list of all the nodes to which links are going out from the
If you are looking for the node with a specific label, you can use:
get_incoming methods also support filtering on various properties, such as the link label.
For example, if you only want to get the outgoing links whose label starts with
output, you can do the following:
2.4. Pseudopotential families¶
Pseudopotentials in AiiDA are grouped in ‘families’ that contain one single pseudo per element. We will see how to work with UPF pseudopotentials (the format used by Quantum ESPRESSO and some other codes). Download and untar the SSSP pseudopotentials via the commands (due to slow network from Japan to Europe, we temporarily put the aiida data on Kyoto university web server):
wget http://phonondb.mtl.kyoto-u.ac.jp/aiida_tutorial/SSSP_efficiency_pseudos.tar.gz tar -zxvf SSSP_efficiency_pseudos.tar.gz
But the original data is found here:
Then you can upload the whole set of pseudopotentials to AiiDA by using the following
verdi data upf uploadfamily SSSP_efficiency_pseudos 'SSSP' 'SSSP pseudopotential library'
In the command above,
SSSP_efficiency_pseudos is the folder containing the pseudopotentials,
'SSSP' is the name given to the family, and the last argument is its description.
Finally, you can list all the pseudo families present in the database with
verdi data upf listfamilies
A more in-depth tutorial about working with
UpfData nodes and pseudopotential families can be found in this appendix.
We purposefully do not provide advanced commands for crystal structure manipulation in AiiDA, because python packages that accomplish such tasks already exist (such as ASE or pymatgen).