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SOF-6892: include new hubbard parameters property #277

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merged 12 commits into from
Dec 8, 2023
Merged

SOF-6892: include new hubbard parameters property #277

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7f1c15e
SOF-6892: include new hubbard parameters property
pranabdas Nov 1, 2023
0871d75
SOF-6892: include siteNumber, category and headers
pranabdas Nov 6, 2023
1f4124e
SOF-6892: reusable atomic_per_orbital and _per_orbital_pair, unify hu…
pranabdas Nov 21, 2023
801f39f
Merge branch 'dev' into feat/SOF-6892
pranabdas Nov 23, 2023
ce6b2d9
SOF-6892: separate schemas for Hubbard U and V
pranabdas Nov 23, 2023
176ec74
include node v18 to run tests + bump actions/checkout to v4
pranabdas Nov 23, 2023
6bab86c
SOF-6892: specify required properties in hubbard_u and hubbard_v
pranabdas Dec 7, 2023
84c77d6
SOF-6892: rename siteName -> atomicSpecies
pranabdas Dec 7, 2023
c08e946
SOF-6892: store numeric and string atomic data in separate files
pranabdas Dec 7, 2023
e0cefa4
SOF-6892: refactoring atomic data per orbital and orbital pair
pranabdas Dec 8, 2023
1f8d90f
SOF-6892: array items in separate lines, drop node v12 from gh action…
pranabdas Dec 8, 2023
d837293
Merge branch 'dev' into feat/SOF-6892
pranabdas Dec 8, 2023
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24 changes: 12 additions & 12 deletions .github/workflows/cicd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,12 @@ jobs:

steps:
- name: Checkout this repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
lfs: true

- name: Checkout actions repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: Exabyte-io/actions
token: ${{ secrets.BOT_GITHUB_TOKEN }}
Expand All @@ -39,12 +39,12 @@ jobs:

steps:
- name: Checkout this repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
lfs: true

- name: Checkout actions repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
repository: Exabyte-io/actions
token: ${{ secrets.BOT_GITHUB_TOKEN }}
Expand All @@ -60,16 +60,16 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
node-version: [12.x, 14.x, 16.x]
node-version: [12.x, 14.x, 16.x, 18.x]
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steps:
- name: Checkout this repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
lfs: true

- name: Checkout actions repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
repository: Exabyte-io/actions
token: ${{ secrets.BOT_GITHUB_TOKEN }}
Expand All @@ -79,7 +79,7 @@ jobs:
uses: ./actions/js/validate
with:
node-version: '14.x'

- name: Run JS tests
uses: ./actions/js/test
with:
Expand All @@ -92,12 +92,12 @@ jobs:

steps:
- name: Checkout this repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
lfs: true

- name: Checkout actions repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
repository: Exabyte-io/actions
token: ${{ secrets.BOT_GITHUB_TOKEN }}
Expand All @@ -118,12 +118,12 @@ jobs:

steps:
- name: Checkout this repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
lfs: true

- name: Checkout actions repository
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
repository: Exabyte-io/actions
token: ${{ secrets.BOT_GITHUB_TOKEN }}
Expand Down
18 changes: 18 additions & 0 deletions example/properties_directory/non-scalar/hubbard_u.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
{
"name": "hubbard_u",
"units": "eV",
"values": [
{
"id": 1,
"siteName": "Co",
"orbitalName": "3d",
"value": 6.7553
},
{
"id": 2,
"siteName": "O",
"orbitalName": "3p",
"value": 2.2438
}
]
}
26 changes: 26 additions & 0 deletions example/properties_directory/non-scalar/hubbard_v.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
{
"name": "hubbard_v",
"units": "eV",
"values": [
{
"id": 1,
"siteName": "Co",
"orbitalName": "3d",
"id2": 1,
"siteName2": "Co",
"orbitalName2": "3d",
"distance": 0,
"value": 6.7553
},
{
"id": 1,
"siteName": "Co",
"orbitalName": "3d",
"id2": 2,
"siteName2": "O",
"orbitalName2": "3p",
"distance": 3.5423,
"value": 2.2438
}
]
}
14 changes: 13 additions & 1 deletion manifest/properties.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
convergence_ionic:
defaults:
units: eV
schemaId: properties-directory/workflow/convergence/ionic
schemaId: properties-directory/workflow/convergence/ionic
isMonitor: true

convergence_electronic:
Expand Down Expand Up @@ -257,3 +257,15 @@ inchi_key:

material:
schemaId: material

hubbard_u:
defaults:
units: eV
schemaId: properties-directory/non-scalar/hubbard-u
isResult: true

hubbard_v:
defaults:
units: eV
schemaId: properties-directory/non-scalar/hubbard-v
isResult: true
21 changes: 6 additions & 15 deletions package-lock.json
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22 changes: 22 additions & 0 deletions schema/core/reusable/atomic_data_per_orbital.json
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@@ -0,0 +1,22 @@
{
"$id": "core/reusable/atomic-data-per-orbital",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Atomic data per orbital",
"description": "Atomic properties per orbital e.g., Hubbard U parameters.",
"type": "object",
"properties": {
"id": {
"type": "number",
"description": "Site number in the lattice"
},
"siteName": {
"type": "string",
"description": "Atomic species name. Example: Co, Ni1, O"
},
"orbitalName": {
"type": "string",
"pattern": "^[1-7][sSpPdDfF]$",
"description": "Atomic orbital or Hubbard manifold."
}
}
}
37 changes: 37 additions & 0 deletions schema/core/reusable/atomic_data_per_orbital_pair.json
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@@ -0,0 +1,37 @@
{
"$id": "core/reusable/atomic-data-per-orbital-pair",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Atomic data per orbital pair",
"description": "Atomic properties per orbital pair e.g., Hubbard V parameters.",
"type": "object",
"properties": {
"id": {
"type": "number",
"description": "Site number or index in the lattice"
},
"id2": {
"type": "number",
"description": "Site number or index in the lattice of second site"
},
"siteName": {
"type": "string",
"description": "Example: Co1"
},
"siteName2": {
"type": "string",
"description": "Example: O"
},
"orbitalName": {
"type": "string",
"pattern": "^[1-7][sSpPdDfF]$"
},
"orbitalName2": {
"type": "string",
"pattern": "^[1-7][sSpPdDfF]$"
},
"distance": {
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We need to indicate the required and optional parameters - all but distance should be required

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Leaving orbitalName(s) as non-required as hp.x supports only main orbitals in DFT+U+V calculations, so orbital names can be omitted.

"type": "number",
"description": "Distance between to sites in angstrom."
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}
}
}
32 changes: 32 additions & 0 deletions schema/properties_directory/non-scalar/hubbard_u.json
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@@ -0,0 +1,32 @@
{
"$id": "properties-directory/non-scalar/hubbard-u",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Hubbard U parameters",
"description": "Hubbard U value in eV",
"properties": {
"name": {
"enum": ["hubbard_u"]
},
"units": {
"enum": ["eV"]
},
"values": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"$ref": "../../core/reusable/atomic_data_per_orbital.json"
}
],
"properties": {
"value": {
"type": "number",
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We should probably create atomic_data_per_orbital_number and atomic_data_per_orbital_string if needed, and then use them here - otherwise, it looks weird to be adding value of type number here directly

"description": "Hubbard U values in eV"
}
}
}
}
},
"required": ["name"]
}
32 changes: 32 additions & 0 deletions schema/properties_directory/non-scalar/hubbard_v.json
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@@ -0,0 +1,32 @@
{
"$id": "properties-directory/non-scalar/hubbard-v",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Hubbard V parameters",
"description": "Hubbard V value in eV",
"properties": {
"name": {
"enum": ["hubbard_v"]
},
"units": {
"enum": ["eV"]
},
"values": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"$ref": "../../core/reusable/atomic_data_per_orbital_pair.json"
}
],
"properties": {
"value": {
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Same as above

"type": "number",
"description": "Hubbard V values in eV"
}
}
}
}
},
"required": ["name"]
}
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