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Merge branch 'dev' into feat/SOF-6892
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@pranabdas
pranabdas committed Nov 23, 2023
2 parents 1f4124e + d223c5e commit 801f39f
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Showing 9 changed files with 156 additions and 120 deletions.
47 changes: 7 additions & 40 deletions example/methods_directory/physical/psp.json
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@@ -1,49 +1,16 @@
{
"name": "PAW Pseudopotential method (VASP)",
"name": "PAW Pseudopotential method",
"path": "/qm/wf/psp/paw",
"slug": "pseudopotential",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "psp",
"subtype": "paw"
},
"data": {
"pseudo": [
{
"hash": "4e058592231fc4e091ac0c92d87797b0",
"apps": ["vasp"],
"element": "Si",
"source": "vasp",
"version": "5.2",
"path": "/export/share/pseudo/si/gga/pbe/vasp/5.2/paw/default/POTCAR",
"type": "paw",
"exchangeCorrelation": {
"approximation": "gga",
"functional": "pbe",
"path": "/pb/qm/dft/ksdft/gga?functional=pbe"
},
"filename": "POTCAR",
"schemaVersion": "0.2.0",
"name": "pseudopotential",
"valenceConfiguration": [
{
"orbitalName": "3S",
"orbitalIndex": 1,
"principalNumber": 3,
"angularMomentum": 0,
"occupation": 2
},
{
"orbitalName": "3P",
"orbitalIndex": 2,
"principalNumber": 3,
"angularMomentum": 1,
"occupation": 2
}
],
"inSet": [],
"tags": []
}
]
}
"data": [
{
"...": "include(psp/file.json)"
}
]
}
49 changes: 49 additions & 0 deletions example/methods_directory/physical/psp/file.json
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@@ -0,0 +1,49 @@
{
"slug": "pseudopotential",
"source": {
"info": {},
"type": "exabyte"
},
"data": {
"element": "Ru",
"hash": "3349af97451e04faae570056fb6a110b",
"filename": "ru_pbe_dojo-oncv_0.4.upf",
"path": "/export/share/pseudo/ru/gga/pbe/dojo-oncv/0.4/nc/ru_pbe_dojo-oncv_0.4.upf",
"valenceConfiguration": [
{
"orbitalName": "4S",
"orbitalIndex": 1,
"principalNumber": 4,
"angularMomentum": 0,
"occupation": 2.0
},
{
"orbitalName": "4P",
"orbitalIndex": 2,
"principalNumber": 4,
"angularMomentum": 1,
"occupation": 6.0
},
{
"orbitalName": "4D",
"orbitalIndex": 3,
"principalNumber": 4,
"angularMomentum": 2,
"occupation": 7.0
},
{
"orbitalName": "5S",
"orbitalIndex": 4,
"principalNumber": 5,
"angularMomentum": 0,
"occupation": 1.0
}
],
"apps": ["espresso"],
"exchangeCorrelation": { "functional": "pbe", "approximation": "gga" },
"name": "pseudopotential",
"source": "dojo-oncv",
"type": "nc",
"version": "0.4"
}
}
4 changes: 4 additions & 0 deletions manifest/models.yaml
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Expand Up @@ -69,6 +69,10 @@
slug: pbe
reference:
doi: https://doi.org/10.1103/PhysRevLett.77.3865
- name: perdew-burke-ernzerhof-solid
slug: pbesol
reference:
doi: https://doi.org/10.1103/PhysRevLett.100.136406
# modifiers:
# type: array
# items:
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9 changes: 1 addition & 8 deletions schema/method/unit_method.json
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Expand Up @@ -22,13 +22,6 @@
"precision": {
"description": "Object showing the actual possible precision based on theory and implementation",
"type": "object"
},
"data": {
"description": "Additional numerically relevant data specific to method, eg. array of pseudopotentials",
"type": "object"
}
},
"required": [
"categories"
]
}
}
13 changes: 4 additions & 9 deletions schema/methods_directory/physical/psp.json
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Expand Up @@ -13,15 +13,10 @@
"$ref": "../../methods_category/physical/qm/wf/psp.json"
},
"data": {
"type": "object",
"properties": {
"pseudo": {
"description": "pseudopotential files",
"type": "array",
"items": {
"$ref": "./psp/file.json"
}
}
"type": "array",
"items": {
"description": "Specific data based on pseudopotential file.",
"$ref": "./psp/file.json"
}
}
},
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73 changes: 11 additions & 62 deletions schema/methods_directory/physical/psp/file.json
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@@ -1,77 +1,26 @@
{
"$id": "methods-directory/physical/psp/file",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "pseudopotential file",
"title": "Pseudopotential file",
"properties": {
"element": {
"type": "string",
"description": "chemical element"
},
"hash": {
"type": "string",
"description": "MD5 hash of the pseudopotential file"
"slug": {
"enum": ["pseudopotential"]
},
"type": {
"type": "string",
"description": "type of pseudization",
"$ref": "../../../methods_category/physical/qm/wf/enum_options.json#/pseudoSubtypes"
"data": {
"description": "Specific data based on pseudopotential file.",
"$ref": "file_data_item.json"
},
"source": {
"type": "string",
"description": "explains where this came from"
},
"version": {
"type": "string",
"description": "explains the version of where this came from"
},
"exchangeCorrelation": {
"type": "object",
"description": "TODO: remove in the future",
"properties": {
"approximation": {
"description": "DFT approximation",
"type": "string"
"info": {
"type": "object"
},
"functional": {
"description": "Exchange correlation functional",
"type": {
"type": "string"
},
"path": {
"description": "DFT model path, e.g. '/pb/qm/dft/ksdft/gga?functional=pbe'",
"$ref": "../../../core/reusable/category_path.json"
}
}
},
"valenceConfiguration": {
"type": "array",
"description": "contains pseudo orbital information, including orbital names and occupations",
"items": {
"$ref": "../../../core/reusable/atomic_orbital.json"
}
},
"path": {
"type": "string",
"description": "location of the pseudopotential file on filesystem"
},
"apps": {
"type": "array",
"description": "simulation engines that can use this pseudopotential"
},
"filename": {
"type": "string",
"description": "filename of pseudopotential file on filesystem"
},
"name": {
"type": "string",
"description": "name of the data category",
"enum": ["pseudopotential"]
}
},
"required": [
"element",
"type",
"exchangeCorrelation",
"source",
"path",
"apps"
]
}
}
77 changes: 77 additions & 0 deletions schema/methods_directory/physical/psp/file_data_item.json
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{
"$id": "methods-directory/physical/psp/file-data-item",
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "File data item",
"properties": {
"element": {
"type": "string",
"description": "chemical element"
},
"hash": {
"type": "string",
"description": "MD5 hash of the pseudopotential file"
},
"type": {
"type": "string",
"description": "type of pseudization",
"$ref": "../../../methods_category/physical/qm/wf/enum_options.json#/pseudoSubtypes"
},
"source": {
"type": "string",
"description": "explains where this came from"
},
"version": {
"type": "string",
"description": "explains the version of where this came from"
},
"exchangeCorrelation": {
"type": "object",
"properties": {
"approximation": {
"description": "DFT approximation",
"type": "string"
},
"functional": {
"description": "Exchange correlation functional",
"type": "string"
},
"path": {
"description": "DFT model path, e.g. '/pb/qm/dft/ksdft/gga?functional=pbe'",
"$ref": "../../../core/reusable/category_path.json"
}
}
},
"valenceConfiguration": {
"type": "array",
"description": "contains pseudo orbital information, including orbital names and occupations",
"items": {
"$ref": "../../../core/reusable/atomic_orbital.json"
}
},
"path": {
"type": "string",
"description": "location of the pseudopotential file on filesystem"
},
"apps": {
"type": "array",
"description": "simulation engines that can use this pseudopotential"
},
"filename": {
"type": "string",
"description": "filename of pseudopotential file on filesystem"
},
"name": {
"type": "string",
"description": "name of the data category",
"enum": ["pseudopotential"]
}
},
"required": [
"element",
"type",
"exchangeCorrelation",
"source",
"path",
"apps"
]
}
3 changes: 2 additions & 1 deletion schema/model/mixins/dft/enum_options.json
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Expand Up @@ -7,7 +7,8 @@
},
"gga": {
"enum": [
"pbe"
"pbe",
"pbesol"
]
},
"mgga": {
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1 change: 1 addition & 0 deletions schema/model/mixins/dft/enum_options.yml
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Expand Up @@ -3,6 +3,7 @@ lda:
- pz
gga:
- pbe
- pbesol
mgga:
- scan
hybrid:
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