4. Working with data and querying your results¶
In this section of the tutorial we will focus on how to organise and explore the data in an AiiDA database. As in First taste of AiiDA, we will be using the previously created database entries for this tutorial. To follow the tutorial then, you can use the profile in to which you have previously imported this data, or you may wish to create a fresh profile and import the archive into that:
$ verdi quicksetup --profile data $ verdi profile setdefault data $ verdi import https://object.cscs.ch/v1/AUTH_b1d80408b3d340db9f03d373bbde5c1e/marvel-vms/tutorials/aiida_tutorial_2020_07_perovskites_v0.9.aiida
4.1. How to group nodes¶
AiiDA’s database is great for automatically storing all your data, but sometimes it can be tricky to navigate this flat data store. To create some order in this mass of data, you can group sets of nodes together, just as you would with files in folders on your filesystem. Each group instance can hold any amount of nodes and any node can be contained in any number of groups. A typical use case is to store all nodes that share a common property in a single group.
4.1.1. Listing existing groups¶
Lets explore the groups already present in the imported archive:
$ verdi group list -a -A PK Label Type string User ---- --------------- ------------- --------------- 1 tutorial_pbesol core aiida@localhost 2 tutorial_lda core aiida@localhost 3 tutorial_pbe core aiida@localhost 4 GBRV_pbe core.upf aiida@localhost 5 GBRV_pbesol core.upf aiida@localhost 6 GBRV_lda core.upf aiida@localhost 7 20200705-071658 core.import aiida@localhost
The default table shows us four pieces of information:
The Primary Key of the group
The label by which the group has been named
- Type string
This tells us what “sub-class” of group this is. Type strings can be used to class certain types of data, for example here we have general groups (
core), groups containing pseudopotentials (
core.upf), and an auto-generated group containing the nodes we imported from the archive (
core.import). For advanced use, you can create your own group subclass plugins, with specialised methods.
The email of the user that created this group.
-A flags we used above ensure that groups for all type strings and users are shown respectively.
We can then inspect the content of a group by its label (if it is unique) or the PK:
$ verdi group show tutorial_pbesol ----------------- ---------------- Group label tutorial_pbesol Group type_string core Group description <no description> ----------------- ---------------- # Nodes: PK Type Created ---- ----------- ----------------- 380 CalcJobNode 2078D:17h:46m ago 1273 CalcJobNode 2078D:18h:03m ago ...
Conversely, if you want to see all the groups a node belongs to, you can run:
$ verdi group list -a -A --node 380 PK Label Type string User ---- --------------- ------------- --------------- 1 tutorial_pbesol core aiida@localhost 7 20200705-071658 core.import aiida@localhost
4.1.2. Creating and manipulating groups¶
Lets make a new group:
$ verdi group create a_group Success: Group created with PK = 8 and name 'a_group'
If we want to change the name of the group at any time:
$ verdi group relabel a_group my_group Success: Label changed to my_group
Now we can add one or more nodes to it:
$ verdi group add-nodes -G my_group 380 1273 Do you really want to add 2 nodes to Group<my_group>? [y/N]: y
We can also copy the nodes from an existing group to another group:
$ verdi group copy tutorial_pbesol my_group Warning: Destination group<my_group> already exists and is not empty. Do you wish to continue anyway? [y/N]: y Success: Nodes copied from group<tutorial_pbesol> to group<my_group> $ verdi group show my_group ----------------- ---------------- Group label my_group Group type_string core Group description <no description> ----------------- ---------------- # Nodes: PK Type Created ---- ----------- ----------------- 74 CalcJobNode 2078D:17h:51m ago 76 CalcJobNode 2078D:17h:57m ago ...
To remove nodes from the group run:
$ verdi group remove-nodes -G my_group 74 Do you really want to remove 1 nodes from Group<my_group>? [y/N]: y
and finally to remove the group entirely:
$ verdi group delete --clear my_group Are you sure to delete Group<my_group>? [y/N]: y Success: Group<my_group> deleted.
Any deletion operation related to groups won’t affect the nodes themselves. For example if you delete a group, the nodes that belonged to the group will remain in the database. The same happens if you remove nodes from the group – they will remain in the database but won’t belong to the group any more.
4.2. Organising groups in hierarchies¶
Earlier we mentioned that groups are like files in folders on your filesystem.
As with folders and sub-folders then, as the amount of groups we have grows, we may also wish to structure our groups in a hierarchy.
Groups in AiiDA are inherently “flat”, in that groups may only contain nodes and not other groups.
However it is possible to construct virtual group hierarchies based on delimited group labels, using the
Like folder paths grouppath requires delimitation by
/ (forward slash) characters.
Lets copy and rename the three tutorial groups:
$ verdi group copy tutorial_lda tutorial/lda/basic $ verdi group copy tutorial_pbe tutorial/gga/pbe $ verdi group copy tutorial_pbesol tutorial/gga/pbesol
We can now list the groups in a new way:
$ verdi group path ls -l Path Sub-Groups --------------- ------------ tutorial 3 tutorial_lda 0 tutorial_pbe 0 tutorial_pbesol 0
In the terminal, paths that contain nodes are listed in bold
You can see that the actual groups that we create do not show, only the initial part of the “path”, and how many sub-groups that path contains. We can then step into a path:
$ verdi group path ls -l tutorial Path Sub-Groups ------------ ------------ tutorial/gga 2 tutorial/lda 1
This feature is also particularly useful in the verdi shell:
In : from aiida.tools.groups import GroupPath In : for subpath in GroupPath("tutorial/gga").walk(return_virtual=False): ...: print(subpath.get_group()) ...: "tutorial/gga/pbesol" [type core], of user aiida@localhost "tutorial/gga/pbe" [type core], of user aiida@localhost
Please see the corresponding section in the documentation for more details on groups and how to use them.
4.3. Querying for data¶
For this part of the tutorial, we shall move to interacting with AiiDA using a Jupyter notebook, which you will be able to run in your browser.
For instructions on starting the Jupyter server, please refer to the setup section.
Once the server is running,
download this tutorial notebook on to your Virtual Machine, using the instructions in this section, and open it in Jupyter.
The notebook will show you how the
QueryBuilder can be used to query your
database for specific data. It will demonstrate certain concepts and then ask
you to use those to perform certain queries on your own database. Some of these
question cells will have partial solutions that you will have to complete.
Once you have finished the notebook, you can download a
notebook with the solutions
but try not to use them at first!
Go to any of the sections below for a rendered version of the notebook: