Standard and Custom Computational Workflows in NOMAD

The following examples contain the basic knowledge on understanding and learning to use NOMAD workflows, and its relation with DFT and beyond-DFT (GW, BSE, DMFT, etc.) methodologies. You will use a fictitious example of a simulation workflow with the following files and folder structure:

.
├── pressure1
│   ├── temperature1
│   │   ├── dmft_p1_t1.hdf5
│   │   └── ...extra auxiliary files
│   ├── temperature2
│   │   ├── dmft_p1_t2.hdf5
│   │   └── ...extra auxiliary files
│   ├── dft_p1.xml
│   ├── tb_p1.wout
│   └── ...extra auxiliary files
└── pressure2
    ├── temperature1
    │   ├── dmft_p2_t1.hdf5
    │   └── ...extra auxiliary files
    ├── temperature2
    │   ├── dmft_p2_t2.hdf5
    │   └── ...extra auxiliary files
    ├── dft_p2.xml
    ├── tb_p2.wout
    └── ...extra auxiliary files

which can be downloaded here:

Download example_files.zip

Each of the mainfiles represent an electronic-structure calculation (either DFT{:target="blank"}, TB, or DMFT) which in turn is then parsed into a singular _entry in NOMAD. When dragged into the NOMAD Upload page{:target="blank"}, these files should generate 8 entries in total. This folder structure presents a typical workflow calculation which can be represented as a provenance graph:

graph LR;
    A2((Inputs)) --> B2[DFT];
    A1((Inputs)) --> B1[DFT];
    subgraph pressure P<sub>2</sub>
    B2[DFT] --> C2[TB];
    C2[TB] --> D21[DMFT at T<sub>1</sub>];
    C2[TB] --> D22[DMFT at T<sub>2</sub>];
    end
    D21[DMFT at T<sub>1</sub>] --> E21([Output calculation P<sub>2</sub>, T<sub>1</sub>])
    D22[DMFT at T<sub>2</sub>] --> E22([Output calculation P<sub>2</sub>, T<sub>2</sub>])
    subgraph pressure P<sub>1</sub>
    B1[DFT] --> C1[TB];
    C1[TB] --> D11[DMFT at T<sub>1</sub>];
    C1[TB] --> D12[DMFT at T<sub>2</sub>];
    end
    D11[DMFT at T<sub>1</sub>] --> E11([Output calculation P<sub>1</sub>, T<sub>1</sub>])
    D12[DMFT at T<sub>2</sub>] --> E12([Output calculation P<sub>1</sub>, T<sub>2</sub>])

Here, "Input" refers to the all _input information given to perform the calculation (e.g., atom positions, model parameters, experimental initial conditions, etc.). "DFT", "TB" and "DMFT" refer to individual tasks of the workflow, which each correspond to a SinglePoint entry in NOMAD. "Output calculation" refers to the output data of each of the final DMFT tasks.

The goal of this part is to set up the following workflows:

1. A SinglePoint workflow for one of the calculations (e.g., the DFT one) in the pressure1 subfolder.
2. An overarching workflow entry for each pressure P_i=1,2, grouping all SinglePoint "DFT", "TB", "DMFT at T₁", and "DMFT at T₂" tasks.
3. A top level workflow entry, grouping together all pressure calculations.

The files for all these cases can be downloaded here:

Download worfklowyaml_files.zip

You can try writing these files yourself first, and then compare them with the tested files.

Starting example: SinglePoint workflow

NOMAD is able to recognize certain workflows in an automatic way, such as the SinglePoint case mentioned above. However, to showcase how to the use workflows in NOMAD, you will learn how to "manually" construct the SinglePoint workflow, represented by the following provenance graph:

graph LR;
    A((Inputs)) --> B[DFT];
    B[DFT] --> C([Output calculation]);

To define a workflow manually in NOMAD, you must add a YAML file to the upload folder that contains the relevant input, output, and task information. This file should be named <filename>.archive.yaml. In this case, you should include the file single_point.archive.yaml with the following content:

workflow2:
  name: SinglePoint
  inputs:
    - name: Input structure
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
  outputs:
    - name: Output calculation
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'
  tasks:
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/dft_p1.xml#/workflow2'
      name: DFT at Pressure P1
      inputs:
        - name: Input structure
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
      outputs:
        - name: Output calculation
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'

Note several things about the content of this file:

1. name keys are optional.
2. The root path of the upload can be referenced with ../upload/archive/mainfile/. Starting from there, the original directory tree structure of the upload is maintained.
3. inputs reference the section containing inputs of the whole workflow. In this case this is the section run[0].system[-1] parsed from the mainfile in the path pressure1/dft_p1.xml.
4. outputs reference the section containing outputs of the whole workflow. In this case this is the section run[0].calculation[-1] parsed from the mainfile in the path pressure1/dft_p1.xml.
5. tasks reference the section containing tasks of each step in the workflow. These must also contain inputs and outputs properly referencing the corresponding sections; this will then link inputs/outputs/tasks in the NOMAD Archive. In this case this is a TaskReference to the section workflow2 parsed from the mainfile in the path pressure1/dft_p1.xml.
6. section reference to the uploaded mainfile specific section. The left side of the # symbol contains the path to the mainfile, while the right contains the path to the section.

This will produce an extra entry with the following Overview content:

Note that you are referencing sections which are lists. Thus, in each case you should be careful to reference the correct section for inputs and outputs (example: a GeometryOptimization workflow calculation will have the "Input structure" as run[0].system[0], while the "Output calculation" would also contain run[0].system[-1], and all intermediate steps must input/output the corresponding section system).

NOMAD workflow filename

The NOMAD workflow YAML file name, i.e., <filename> in the explanation above, can be any custom name defined by the user, but the file must keep the extension .archive.yaml at the end. This is done in order for NOMAD to recognize this file as a custom schema. Custom schemas are widely used in experimental parsing, and you can learn more about them in the FAIRmat tutorial 8.

You can extend the workflow meta-information by adding the metholodogical input parameters. These are stored in NOMAD in the section path run[0].method[-1]. The new single_point.archive.yaml will be:

workflow2:
  name: SinglePoint
  inputs:
    - name: Input structure
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
    - name: Input methodology parameters
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/method/-1'
  outputs:
    - name: Output calculation
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'
  tasks:
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/dft_p1.xml#/workflow2'
      name: DFT at Pressure P1
      inputs:
        - name: Input structure
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
        - name: Input methodology parameters
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/method/-1'
      outputs:
        - name: Output calculation
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'

which in turn produces a similar workflow than before, but with an extra input node:

Pressure workflows

Now that you know the basics of the workflow YAML schema, let's try to define an overarching workflow for each of the pressures. For this section, you will learn how to create the workflow YAML schema for the P₁ case; the extension for P₂ is then a matter of changing names and paths in the YAML files. For simplicity, you can skip referencing to methodologies.

Thus, the inputs can be defined as:

workflow2:
  name: DFT+TB+DMFT at P1
  inputs:
    - name: Input structure
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'

and there are two outputs, one for each of the DMFT calculations at distinct temperatures:

  outputs:
    - name: Output DMFT at P1, T1 calculation
      section: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/run/0/calculation/-1'
    - name: Output DMFT at P1, T2 calculation
      section: '../upload/archive/mainfile/pressure1/temperature2/dmft_p1_t2.hdf5#/run/0/calculation/-1'

Now, tasks are defined for each of the methodologies performed (each corresponding to an underlying SinglePoint workflow). To define a valid workflow, each task must contain an input that corresponds to one of the outputs of the previous task. Moreover, the first task should take as input the overall input of the workflow, and the final task should also have as an output the overall workflow output. Then:

  tasks:
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/dft_p1.xml#/workflow2'
      name: DFT at P1
      inputs:
        - name: Input structure
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
      outputs:
        - name: Output DFT at P1 calculation
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/tb_p1.wout#/workflow2'
      name: TB at P1
      inputs:
        - name: Input DFT at P1 calculation
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/calculation/-1'
      outputs:
        - name: Output TB at P1 calculation
          section: '../upload/archive/mainfile/pressure1/tb_p1.wout#/run/0/calculation/-1'
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/workflow2'
      name: DMFT at P1 and T1
      inputs:
        - name: Input TB at P1 calculation
          section: '../upload/archive/mainfile/pressure1/tb_p1.wout#/run/0/calculation/-1'
      outputs:
        - name: Output DMFT at P1, T1 calculation
          section: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/run/0/calculation/-1'
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/workflow2'
      name: DMFT at P1 and T2
      inputs:
        - name: Input TB at P1 calculation
          section: '../upload/archive/mainfile/pressure1/tb_p1.wout#/run/0/calculation/-1'
      outputs:
        - name: Output DMFT at P1, T2 calculation
          section: '../upload/archive/mainfile/pressure1/temperature2/dmft_p1_t2.hdf5#/run/0/calculation/-1'

Note here:

• The inputs for each subsequent step are the outputs of the previous step.
• The final two outputs coincide with the workflow2 outputs.

This workflow (pressure1.archive.yaml) file will then produce an entry with the following Overview page:

Similarly, for P₂ you can upload a new pressure2.archive.yaml file with the same content, except when substituting 'pressure1' and 'p1' by their counterparts. This will produce a similar graph than the one showed before but for "P2".

The top-level workflow

After adding the workflow YAML files, Your upload folder directory now looks like:

.
├── pressure1
│   │   ├── dmft_p1_t1.hdf5
│   │   └── ...extra auxiliary files
│   ├── temperature2
│   │   ├── dmft_p1_t2.hdf5
│   │   └── ...extra auxiliary files
│   ├── dft_p1.xml
│   ├── tb_p1.wout
│   └── ...extra auxiliary files
├── pressure1.archive.yaml
├── pressure2
│   ├── temperature1
│   │   ├── dmft_p2_t1.hdf5
│   │   └── ...extra auxiliary files
│   ├── temperature2
│   │   ├── dmft_p2_t2.hdf5
│   │   └── ...extra auxiliary files
│   ├── dft_p2.xml
│   ├── tb_p2.wout
│   └── ...extra auxiliary files
├── pressure2.archive.yaml
└── single_point.archive.yaml

In order to define the general workflow that groups all pressure calculations, YOU can reference directly the previous pressureX.archive.yaml files as tasks. Still, inputs and outputs must be referenced to their corresponding mainfile and section paths.

Create a new fullworkflow.archive.yaml file with the inputs:

workflow2:
  name: Full calculation at different pressures for SrVO3
  inputs:
    - name: Input structure at P1
      section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
    - name: Input structure at P2
      section: '../upload/archive/mainfile/pressure2/dft_p2.xml#/run/0/system/-1'

And outputs:

  outputs:
    - name: Output DMFT at P1, T1 calculation
      section: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/run/0/calculation/-1'
    - name: Output DMFT at P1, T2 calculation
      section: '../upload/archive/mainfile/pressure1/temperature2/dmft_p1_t2.hdf5#/run/0/calculation/-1'
    - name: Output DMFT at P2, T1 calculation
      section: '../upload/archive/mainfile/pressure2/temperature1/dmft_p2_t1.hdf5#/run/0/calculation/-1'
    - name: Output DMFT at P2, T2 calculation
      section: '../upload/archive/mainfile/pressure2/temperature2/dmft_p2_t2.hdf5#/run/0/calculation/-1'

Finally, tasks references the previous YAML schemas as follows:

  tasks:
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure1.archive.yaml#/workflow2'
      name: DFT+TB+DMFT at P1
      inputs:
        - name: Input structure at P1
          section: '../upload/archive/mainfile/pressure1/dft_p1.xml#/run/0/system/-1'
      outputs:
        - name: Output DMFT at P1, T1 calculation
          section: '../upload/archive/mainfile/pressure1/temperature1/dmft_p1_t1.hdf5#/run/0/calculation/-1'
        - name: Output DMFT at P1, T2 calculation
          section: '../upload/archive/mainfile/pressure1/temperature2/dmft_p1_t2.hdf5#/run/0/calculation/-1'
    - m_def: nomad.datamodel.metainfo.workflow.TaskReference
      task: '../upload/archive/mainfile/pressure2.archive.yaml#/workflow2'
      name: DFT+TB+DMFT at P2
      inputs:
        - name: Input structure at P2
          section: '../upload/archive/mainfile/pressure2/dft_p2.xml#/run/0/system/-1'
      outputs:
        - name: Output DMFT at P2, T1 calculation
          section: '../upload/archive/mainfile/pressure2/temperature1/dmft_p2_t1.hdf5#/run/0/calculation/-1'
        - name: Output DMFT at P2, T2 calculation
          section: '../upload/archive/mainfile/pressure2/temperature2/dmft_p2_t2.hdf5#/run/0/calculation/-1'

This will produce the following entry and its Overview page:

Automatic workflows

There are some cases where the NOMAD infrastructure is able to recognize certain workflows automatically when processing the uploaded files. The simplest example is any SinglePoint calculation, as explained above. Other examples include GeometryOptimization, Phonons, GW, and MolecularDynamics. Automated workflow detection may require your folder structure to fulfill certain conditions.

Here are some general guidelines for preparing your upload folder in order to make it easier for the automatic workflow recognition to work:

• Always organize your files in an top-down structure, i.e., the initial tasks should be upper in the directory tree, while the later tasks lower on it.
• Avoid having to go up and down between folders if some properties are derived between these files. These situations are very complicated to predict for the current NOMAD infrastructure.
• Avoid duplication of files in subfolders. If initially you do a calculation A from which a later calculation B is derived and you want to store B in a subfolder, there is no need to copy the A files inside the subfolder B.

The folder structure used throughout this part is a good example of a clean upload which is friendly and easy to work with when defining NOMAD workflows.