Adding the trajectories endpoint to OPTIMADE #377
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
JPBergsma
force-pushed
the
JPBergsma_add_Trajectories
branch
3 times, most recently
from
08f1bf7
to
b907b2c
Compare
JPBergsma
commented
Jul 21, 2021
JPBergsma
force-pushed
the
JPBergsma_add_Trajectories
branch
from
b907b2c
to
716ad2e
Compare
JPBergsma
added
PR/major-edits
type/proposal
JPBergsma
commented
Jul 22, 2021
JPBergsma
commented
Jul 22, 2021
ml-evs
reviewed
Jul 22, 2021
There was a problem hiding this comment.
Thanks for the hard work on this @JPBergsma!
My comments below are mostly around maintaining our compliance with the JSON:API format.
JPBergsma
force-pushed
the
JPBergsma_add_Trajectories
branch
from
716ad2e
to
7c1b646
Compare
Placed all sentences on seperate lines.
JPBergsma
force-pushed
the
JPBergsma_add_Trajectories
branch
from
7c1b646
to
a291b59
Compare
JPBergsma
commented
Jul 22, 2021
ml-evs
reviewed
Jul 22, 2021
…eferences for frames.
JPBergsma
commented
Jul 26, 2021
…lso possible to do this via the next field in the links field of the JSON response.
|
Can we add an endpoint for bulk downloads? |
…gsma/OPTIMADE into JPBergsma_add_Trajectories
Co-authored-by: Rickard Armiento <gitcommits@armiento.net>
…t_frame and frame_step parameters for servers.
…gsma/OPTIMADE into JPBergsma_add_Trajectories # Conflicts: # optimade.rst
vaitkus
reviewed
Jun 16, 2023
vaitkus
reviewed
Jun 16, 2023
Co-authored-by: Antanas Vaitkus <antanas.vaitkus90@gmail.com>
… can contain multiple values.
vaitkus
reviewed
Jan 17, 2024
Comment on lines
+3136
to
+3263
| }, | ||
| { | ||
| "name":"H2", | ||
| "chemical_symbols":["H"], | ||
| "concentration":[1.0] | ||
| } | ||
| ]], | ||
| "reference_frames": [1], | ||
| "nframes": [360], | ||
| "_exmpl_temperature": null, | ||
| "_exmpl_ekin": null | ||
| }, | ||
| "meta":{ | ||
| "property_metadata":{ | ||
| "cartesian_site_positions":{ | ||
| "range":{ | ||
| "indexable_dim": ["frames"], | ||
| "data_range": [{ | ||
| "start": 1, | ||
| "step": 1, | ||
| "stop": 360, | ||
| },{ | ||
| "start": 1, | ||
| "step": 1, | ||
| "stop": 3, | ||
| },{ | ||
| "start": 1, | ||
| "step": 1, | ||
| "stop": 3, | ||
| }], | ||
| "layout":"dense", | ||
| "nvalues": 3240 | ||
| }, | ||
| }, | ||
| "_exmpl_temperature":{ | ||
| "range": { | ||
| "nvalues": 144, | ||
| "indexable_dim": ["frames"], | ||
| "data_range": [ | ||
| { | ||
| "start": 1, | ||
| "stop": 360, | ||
| "step": null | ||
| } | ||
| ], | ||
| "layout": "sparse" | ||
| } | ||
| }, | ||
| "_exmpl_ekin":{ | ||
| "range": { | ||
| "nvalues": 180, | ||
| "indexable_dim": ["frames"], | ||
| "data_range": [ | ||
| { | ||
| "start": 1, | ||
| "stop": 360, | ||
| "step": 2 | ||
| } | ||
| ], | ||
| "layout":"dense", | ||
| } | ||
| } | ||
| }, | ||
| "partial_data_links": { | ||
| "cartesian_site_positions": [ | ||
| { | ||
| "format": "jsonlines", | ||
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/jsonlines" | ||
| },{ | ||
| "format": "_exmpl_xyz", | ||
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/xyz" | ||
| }, | ||
| ], | ||
| "_exmpl_temperature": [ | ||
| { | ||
| "format": "jsonlines", | ||
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/temperature/jsonlines" | ||
| }, | ||
| ], | ||
| "_exmpl_ekin": [ | ||
| { | ||
| "format": "jsonlines", | ||
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/ekin/jsonlines" | ||
| }, | ||
| ] | ||
| } | ||
| }, | ||
| "relationships": { | ||
| "references": { | ||
| "data": [ | ||
| { | ||
| "type": "references", | ||
| "id": "dummy/2019" | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| //... | ||
| } |
There was a problem hiding this comment.
Suggested change
| { | |
| "data":{ | |
| "id": "traj00000001", | |
| "type": "trajectories", | |
| "attributes": { | |
| "last_modified":"2021-07-16T18:02:03Z", | |
| "elements": [["H","O"]], | |
| "nelements": [2], | |
| "elements_ratios": [[0.666667,0.333333]], | |
| "chemical_formula_descriptive": ["H2O"], | |
| "chemical_formula_reduced": ["H2O"], | |
| "chemical_formula_anonymous": ["A2B"], | |
| "dimension_types":[[0,0,0]], | |
| "nperiodic_dimensions": [0], | |
| "lattice_vectors" : [[[4.0,0.0,0.0],[0.0,4.0,0.0],[0.0,0.0,4.0]]], | |
| "cartesian_site_positions" : null, | |
| "nsites":[3], | |
| "species_at_sites":[["O1","H1","H2"]], | |
| "species":[[ | |
| { | |
| "name":"O1", | |
| "chemical_symbols":["O"], | |
| "concentration":[1.0] | |
| }, | |
| { | |
| "name":"H1", | |
| "chemical_symbols":["H"], | |
| "concentration":[1.0] | |
| }, | |
| { | |
| "name":"H2", | |
| "chemical_symbols":["H"], | |
| "concentration":[1.0] | |
| } | |
| ]], | |
| "reference_frames": [1], | |
| "nframes": [360], | |
| "_exmpl_temperature": null, | |
| "_exmpl_ekin": null | |
| }, | |
| "meta":{ | |
| "property_metadata":{ | |
| "cartesian_site_positions":{ | |
| "range":{ | |
| "indexable_dim": ["frames"], | |
| "data_range": [{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 360, | |
| },{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 3, | |
| },{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 3, | |
| }], | |
| "layout":"dense", | |
| "nvalues": 3240 | |
| }, | |
| }, | |
| "_exmpl_temperature":{ | |
| "range": { | |
| "nvalues": 144, | |
| "indexable_dim": ["frames"], | |
| "data_range": [ | |
| { | |
| "start": 1, | |
| "stop": 360, | |
| "step": null | |
| } | |
| ], | |
| "layout": "sparse" | |
| } | |
| }, | |
| "_exmpl_ekin":{ | |
| "range": { | |
| "nvalues": 180, | |
| "indexable_dim": ["frames"], | |
| "data_range": [ | |
| { | |
| "start": 1, | |
| "stop": 360, | |
| "step": 2 | |
| } | |
| ], | |
| "layout":"dense", | |
| } | |
| } | |
| }, | |
| "partial_data_links": { | |
| "cartesian_site_positions": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/jsonlines" | |
| },{ | |
| "format": "_exmpl_xyz", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/xyz" | |
| }, | |
| ], | |
| "_exmpl_temperature": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/temperature/jsonlines" | |
| }, | |
| ], | |
| "_exmpl_ekin": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/ekin/jsonlines" | |
| }, | |
| ] | |
| } | |
| }, | |
| "relationships": { | |
| "references": { | |
| "data": [ | |
| { | |
| "type": "references", | |
| "id": "dummy/2019" | |
| } | |
| ] | |
| } | |
| } | |
| } | |
| //... | |
| } | |
| { | |
| "data":{ | |
| "id": "traj00000001", | |
| "type": "trajectories", | |
| "attributes": { | |
| "last_modified":"2021-07-16T18:02:03Z", | |
| "elements": [["H","O"]], | |
| "nelements": [2], | |
| "elements_ratios": [[0.666667,0.333333]], | |
| "chemical_formula_descriptive": ["H2O"], | |
| "chemical_formula_reduced": ["H2O"], | |
| "chemical_formula_anonymous": ["A2B"], | |
| "dimension_types":[[0,0,0]], | |
| "nperiodic_dimensions": [0], | |
| "lattice_vectors" : [[[4.0,0.0,0.0],[0.0,4.0,0.0],[0.0,0.0,4.0]]], | |
| "cartesian_site_positions" : null, | |
| "nsites":[3], | |
| "species_at_sites":[["O1","H1","H2"]], | |
| "species":[[ | |
| { | |
| "name":"O1", | |
| "chemical_symbols":["O"], | |
| "concentration":[1.0] | |
| }, | |
| { | |
| "name":"H1", | |
| "chemical_symbols":["H"], | |
| "concentration":[1.0] | |
| }, | |
| { | |
| "name":"H2", | |
| "chemical_symbols":["H"], | |
| "concentration":[1.0] | |
| } | |
| ]], | |
| "reference_frames": [1], | |
| "nframes": [360], | |
| "_exmpl_temperature": null, | |
| "_exmpl_ekin": null | |
| }, | |
| "meta":{ | |
| "property_metadata":{ | |
| "cartesian_site_positions":{ | |
| "range":{ | |
| "indexable_dim": ["frames"], | |
| "data_range": [{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 360 | |
| },{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 3 | |
| },{ | |
| "start": 1, | |
| "step": 1, | |
| "stop": 3 | |
| }], | |
| "layout":"dense", | |
| "nvalues": 3240 | |
| } | |
| }, | |
| "_exmpl_temperature":{ | |
| "range": { | |
| "nvalues": 144, | |
| "indexable_dim": ["frames"], | |
| "data_range": [ | |
| { | |
| "start": 1, | |
| "stop": 360, | |
| "step": null | |
| } | |
| ], | |
| "layout": "sparse" | |
| } | |
| }, | |
| "_exmpl_ekin":{ | |
| "range": { | |
| "nvalues": 180, | |
| "indexable_dim": ["frames"], | |
| "data_range": [ | |
| { | |
| "start": 1, | |
| "stop": 360, | |
| "step": 2 | |
| } | |
| ], | |
| "layout":"dense" | |
| } | |
| } | |
| }, | |
| "partial_data_links": { | |
| "cartesian_site_positions": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/jsonlines" | |
| },{ | |
| "format": "_exmpl_xyz", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/cartesian_site_positions/xyz" | |
| } | |
| ], | |
| "_exmpl_temperature": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/temperature/jsonlines" | |
| } | |
| ], | |
| "_exmpl_ekin": [ | |
| { | |
| "format": "jsonlines", | |
| "link": "https://example.org/optimade/v1.2/extensions/partial_data/trajectories/traj00000001/ekin/jsonlines" | |
| } | |
| ] | |
| } | |
| }, | |
| "relationships": { | |
| "references": { | |
| "data": [ | |
| { | |
| "type": "references", | |
| "id": "dummy/2019" | |
| } | |
| ] | |
| } | |
| } | |
| } | |
| //... | |
| } |
Co-authored-by: Antanas Vaitkus <antanas.vaitkus90@gmail.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
During the OPTIMADE meeting in June 2021, we discussed in room 2 how the OPTIMADE standard could be expanded to allow the sharing of trajectory data. Based on the discussions with amongst others @giovannipizzi, @gmrigna, Adam Hospital, Tristan Bereau, Amit Gupta, Corey Oses, Ellad Tadmor, Maithilee Motlag, and Daniel S Karls, I have written a first draft for adding a trajectory endpoint. This will hopefully be a good base for further discussion.
The PR adds a trajectories section (in this PR section 7.3), that defines how a client can query and retrieve data from trajectories and how the server can share this data. We have tried to do this in a general way so that many different kinds of trajectories can be shared.