2. Using the verdi command line

This part of the tutorial will help you familiarize with the command line utility verdi, one of the most common ways to interact with AiiDA. verdi with its subcommands enables a variety of operations such as inspecting the status of ongoing or terminated calculations, showing the details of calculations, computers, codes, or data structures, access the input and the output of a calculation, etc. Similar to the bash shell, verdi command support Tab compltion. Try right now to type verdi in a terminal and tap Tab twice to have a list of subcommands. Whenever you need the explanation of a command type verdi help or add -h flag if you are using any of the verdi subcommands. Finally, fields enclosed in angular brackets, such as <pk>, are placeholders to be replaced by the actual value of that field (an integer, a string, etc…).

2.1. The list of calculations

Let us try our first verdi commands. Type in the terminal

verdi calculation list

(Note: the first time you run this command, it might take some seconds as it is the first time you are accessing the database in the virtual machine. Following calls will be faster). This will print the list of ongoing calculations, which should be empty. The first output line should look like

# Last daemon state_updater check: 0h:00m:18s ago (at 17:17:26 on 2016-05-31)

In order to print a list with all calculations that finished correctly in the AiiDA database, you can use the -a/--all-states and -A/--all-users flag as follows:

verdi calculation list –all-states –all-users

Another very typical option combination allows to get calculations in any state (flag -a) d in the past NUM days (-p <NUM>): e.g., for calculation in the past 1 day: verdi calculation list -p1 -a.

Each row of the output identifies a calculation and shows several information about it. For a more detailed list of properties, choose one row by noting down its pk number and type in the terminal

verdi calculation show <pk>

The output depends on the specific pk chosen and should inform you about the input nodes (e.g. initial structure, settings etc.), the output nodes (e.g. output parameters, etc.). An example of RASPA calculation (pk=3006) output is provided below

    -----------  ------------------------------------
    type         RaspaCalculation
    pk           3006
    uuid         b09ee4b0-8bfe-4083-9371-09b47bf98dce
    ctime        2018-05-07 01:31:29.906303+00:00
    mtime        2018-05-07 10:33:39.871720+00:00
    computer     [1] deneb-lsmo
    code         raspa
    -----------  ------------------------------------
    ##### INPUTS:
    Link label      PK  Type
    ------------  ----  -------------
    parameters    2757  ParameterData
    structure     2886  CifData
    ##### OUTPUTS:
    Link label           PK  Type
    -----------------  ----  -------------
    remote_folder      3314  RemoteData
    retrieved          1132  FolderData
    output_parameters  1131  ParameterData
    component_0        1130  ParameterData

2.2. A typical AiiDA graph

Note that pk number shown in the examples may be different for your database.

AiiDA stores in the database the inputs required by a calculation as well as the its outputs.

![Dependency graph of a Raspa calculation.]({{ site.baseurl}}/assets/2018_EPFL_molsim/raspa_sample_graph.png “Dependency graph of a Raspa calculation.”)

You can create a similar graph for any calculation node by using the utility verdi graph  <pk>. For example, before you obtained information (in text form) for pk=3006. To visualize similar information in graph(ical) form, run (replacing <pk> with your number):

verdi graph  <pk>

This command creates the file <pk>.dot that can be rendered by means of the utility dot. Convert it to PDF and have a look:

dot -Tpdf -o <pk>.pdf <pk>.dot
evince <pk>.pdf

Spend some time to familiarize with the graph structure. Identify the root node (highlighted in blue) and trace back the structure used as an input. This is an example of a Raspa calculation. We will now inspect the different elements of this graph.

2.3. Inspecting the nodes of a graph

2.3.1. ParameterData and Calculations

Now, let us have a closer look to the some of the nodes appearing in the graph. Choose the node of the type ParameterData with input link name parameters (ex. pk=2757) and type in the terminal:

verdi data parameter show <pk>

A ParameterData contains a dictionary (i.e., key–value pairs), stored in the database in a format ready to be queried (we will learn how to run queries later on in this tutorial). The command above will print the content dictionary, containing the parameters used to define the input file for the calculation. You can compare the dictionary with the content of the raw input file to Raspa (that was d by AiiDA) via the command

verdi calculation inputcat <pk>

where you substitute the pk of the calculation node (e.g. pk=3006). Check the consistency of the parameters written in the input file and those stored in the ParameterData node. Even if you don’t know the meaning of the input flags of a Raspa calculation, you should be able to see how the input dictionary has been converted into the input file.

The previous command just printed the content of the “default” input file simulation.input. To see a list of all the files used to run a calculation (input file, submission script, etc.) type instead

verdi calculation inputls <pk>

(Adding a --color flag allows you to easily distinguish files from folders by a different coloring).

Once you know the name of the file you want to visualize, you can call the verdi calculation inputcat command specifying the path. For instance, to see the submission script, you can do:

verdi calculation inputcat <pk> -p ~a~iidasubmit.sh

2.3.2. CifData

Now let us focus on CifData objects, such as node pk=2886 of the graph. A CifData object contains a crystal structure and can be inspected interactively using viewers like jmol or vesta. Type in the terminal

verdi data cif show –format jmol 2886

to show the selected structure.

2.3.3. Codes and computers

Let us focus now on the nodes of type code. A code represents (in the database) the actual executable used to run the calculation. Find the pk of such a node in the graph and type

verdi code show <pk>

The command prints information on the plugin used to interface the code to AiiDA, the remote machine on which the code is executed, the path of its executable, etc. To have a list of all available codes type

verdi code list -a -A

Among the entries of the output you should also find the code just shown.

Similarly, the list of computers on which AiiDA can submit calculations is accessible by means of the command

verdi computer list -a

(-a shows all computers, also the one imported in your database but that you did not configure, i.e., to which you don’t have access). Details about each computer can be obtained by the command

verdi computer show <COMPUTERNAME>

Now you have the tools to answer the question:

What is the scheduler installed on the computer where the calculations of the graph have run?

2.3.4. Calculation results

The results of a calculation can be accessed directly from the calculation node. Type in the terminal

verdi calculation res <pk>

which will print the output dictionary of the “scalar” results parsed by AiiDA at the end of the calculation. Note that this is actually a shortcut for

verdi data parameter show <pk2>

where pk2 refers to the ParameterData node attached as an output of the calculation node, with link name output_parameters.

By looking at the output of the command, what is the averate total energy of the calculation having pk=3006?

One can access the component-specific output parameters in the same way (using pk = 1130 that corresponds to the component 0, methane)

verdi data parameter show <pk2>

Similarly to what you did for the calculation inputs, you can access the output files via the commands

verdi calculation outputls <pk>


verdi calculation outputcat -p <filename> <pk>

Use the latter to verify that the average total energy that you have found in the last step has been extracted correctly from the output file (Hint: filter the lines containing the string “Total energy”, e.g. using grep Total energy: -A 8, to isolate the relevant lines).