Merge pull request #50 from MDverse/update-docs

Update docs

Author: pierrepo

README.md

@@ -46,13 +46,13 @@ This file is automatically ignored by git and won't be pushed on GitHub.
 Scrape Zenodo for MD-related datasets and files:
 
 ```bash
-uv run scrape-zenodo --query params/query.yml --output-path data
+uv run scrape-zenodo --query-file params/query.yml --output-dir data
 ```
 
 Scrape Zenodo with a small query, for development or demo purpose:
 
 ```bash
-uv run scrape-zenodo --query params/query_dev.yml --output-path tmp
+uv run scrape-zenodo --query-file params/query_dev.yml --output-dir tmp
 ```
 
 The scraping takes some time (about 5 hours). A mechanism has been set up to avoid overloading the Zenodo API. Be patient.
@@ -68,13 +68,13 @@ Have a look to the notes regarding [Figshare](docs/figshare.md) and how its API
 Scrape FigShare for MD-related datasets and files:
 
 ```bash
-uv run scrape-figshare --query params/query.yml --output-path data
+uv run scrape-figshare --query-file params/query.yml --output-dir data
 ```
 
 Scrape FigShare with a small query, for development or demo purpose:
 
 ```bash
-uv run scrape-figshare --query params/query_dev.yml --output-path tmp
+uv run scrape-figshare --query-file params/query_dev.yml --output-dir tmp
 ```
 
 The scraping takes some time (about 5 hours). Be patient.
@@ -112,6 +112,8 @@ Eventually, the scraper will produce three files: `osf_datasets.tsv`, `osf_datas
 
 ## Scrape NOMAD
 
+Have a look to the notes regarding [NOMAD](docs/nomad.md) and its API.
+
 Scrape NOMAD:
 
 ```bash

docs/nomad.md

@@ -0,0 +1,43 @@
+# NOMAD
+
+> NOMAD is a free, and open-source data management platform for materials science, whose goal is to make scientific research data FAIR (findable, accessible, interoperable and reusable).
+
+- web site: https://nomad-lab.eu/nomad-lab/
+- documentation: https://nomad-lab.eu/prod/v1/docs/api.html
+- API: https://nomad-lab.eu/prod/v1/api/v1/
+
+No account / token is needed to access NOMAD API.
+
+## Finding molecular dynamics datasets and files
+
+### Datasets
+
+In NOMAD, datasets (a simulation and its related files) are called "entry" and datasets are sets of multiple entries.
+
+Entries related to molecular dynamics corresponds to "workflow name = MolecularDynamics": https://nomad-lab.eu/prod/v1/gui/search/entries?results.method.workflow_name=MolecularDynamics
+
+API entrypoint to search for entries:
+
+- Path: `/entries/rawdir/query`
+- [documentatation](https://nomad-lab.eu/prod/v1/api/v1/extensions/docs#/entries%2Fraw/post_entries_rawdir_query_entries_rawdir_query_post)
+
+### Files
+
+API endpoint to get files for a given entry:
+- Path: `/entries/{entry_id}/rawdir`
+- [documentation](https://nomad-lab.eu/prod/v1/api/v1/extensions/docs#/entries%2Fraw/get_entry_rawdir_entries__entry_id__rawdir_get)
+
+## Examples
+
+### x7sBrcHMgkcZcurdULy_qlxnnf6K
+
+- entry id: x7sBrcHMgkcZcurdULy_qlxnnf6K
+- [entry on NOMAD GUI](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/x7sBrcHMgkcZcurdULy_qlxnnf6K)
+- [entry on NOMAD API](https://nomad-lab.eu/prod/v1/api/v1/entries/x7sBrcHMgkcZcurdULy_qlxnnf6K)
+
+Description (called "Comment") :
+
+> MD simulations of wastewater pollutants on amorphous TiO2 at pH 7.4 in TIP3P water with NaCl ions. One simulation is calculated without pollutants, but with additional salt. Originally, the trajectories contain a total of 100 ns simulation time with a 10 ps time step. To compact the size, uploaded trajectories have a lower frequency of 100 ps time steps. If original trajectories are of interest, please contact the author. The two different topol.top files are for different stages in the equilibrium and production run: topol_I.top for the first equilibrium steps and topol_II.top for later equilibrium and production. They have different position restraints applied.
+
+- [files on NOMAD GUI](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/x7sBrcHMgkcZcurdULy_qlxnnf6K/files/)
+- [files on NOMAD API](https://nomad-lab.eu/prod/v1/api/v1/entries/x7sBrcHMgkcZcurdULy_qlxnnf6K/rawdir)