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SOF-6873: include valence configuration in pseudopotential schema #262

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merged 9 commits into from
Sep 16, 2023
Merged

SOF-6873: include valence configuration in pseudopotential schema #262

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fd586bc
SOF-6873: include valence configuration in pseudopotential schema
pranabdas Sep 2, 2023
ef767ae
adjust schema fields to match with current web-app implementation
pranabdas Sep 5, 2023
3ae1503
update example json for validation tests
pranabdas Sep 5, 2023
e82f1f0
generate schema id using setSchemaIds.mjs, removes file extension
pranabdas Sep 7, 2023
286a1cc
adapt exchange correlation to the current web-app schema
pranabdas Sep 7, 2023
4f57789
enforce interger validation instead of number where applicable
pranabdas Sep 7, 2023
a74617e
add exchange correlation path in the example data
pranabdas Sep 8, 2023
8950642
specify data category as enum instead of arbitrary string
pranabdas Sep 16, 2023
4aea0c3
Merge branch 'dev' into feat/SOF-6873
pranabdas Sep 16, 2023
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24 changes: 19 additions & 5 deletions example/methods_directory/physical/psp.json
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,8 @@
"data": {
"pseudo": [
{
"_id": "56f26f3c9abea1134ba0c50e",
"textHeading": "VRHFIN =Si: s2p2\n LEXCH = PE\n EATOM = 103.0669 eV, 7.5752 Ry\n\n TITEL = PAW_PBE Si 05Jan2001\n LULTRA = F use ultrasoft PP ?\n IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no\n RPACOR = 1.500 partial core radius\n POMASS = 28.085; ZVAL = 4.000 mass and valenz\n RCORE = 1.900 outmost cutoff radius\n RWIGS = 2.480; RWIGS = 1.312 wigner-seitz radius (au A)\n ENMAX = 245.345; ENMIN = 184.009 eV\n ICORE = 2 local potential\n LCOR = T correct aug charges\n LPAW = T paw PP\n EAUG = 322.069\n DEXC = 0.000\n RMAX = 1.950 core radius for proj-oper\n RAUG = 1.300 factor for augmentation sphere\n RDEP = 1.993 radius for radial grids\n RDEPT = 1.837 core radius for aug-charge\n \n Atomic configuration\n 6 entries\n n l j E occ.\n 1 0 0.50 -1785.8828 2.0000\n 2 0 0.50 -139.4969 2.0000\n 2 1 1.50 -95.5546 6.0000\n 3 0 0.50 -10.8127 2.0000\n 3 1 0.50 -4.0811 2.0000\n 3 2 1.50 -4.0817 0.0000\n Description\n l E TYP RCUT TYP RCUT\n 0 -10.8127223 23 1.900\n 0 -7.6451159 23 1.900\n 1 -4.0811372 23 1.900\n 1 2.4879257 23 1.900\n 2 -4.0817478 7 1.900\n Error from kinetic energy argument (eV)\n NDATA = 100\n STEP = 20.000 1.050\n 10.1 9.04 8.56 7.65 7.23 6.44 5.73 5.40\n 4.79 4.25 4.00 3.54 3.13 2.77 2.45 2.16\n 1.91 1.69 1.50 1.24 1.10 0.975 0.812 0.718\n 0.636 0.529 0.440 0.388 0.322 0.266 0.219 0.180\n 0.148 0.121 0.986E-01 0.804E-01 0.614E-01 0.504E-01 0.392E-01 0.328E-01\n 0.265E-01 0.220E-01 0.189E-01 0.166E-01 0.149E-01 0.135E-01 0.123E-01 0.109E-01\n 0.977E-02 0.840E-02 0.707E-02 0.605E-02 0.488E-02 0.387E-02 0.290E-02 0.229E-02\n 0.185E-02 0.152E-02 0.134E-02 0.125E-02 0.121E-02 0.117E-02 0.112E-02 0.102E-02\n 0.915E-03 0.776E-03 0.640E-03 0.524E-03 0.425E-03 0.369E-03 0.331E-03 0.310E-03\n 0.294E-03 0.273E-03 0.242E-03 0.210E-03 0.175E-03 0.146E-03 0.124E-03 0.113E-03\n 0.105E-03 0.973E-04 0.879E-04 0.755E-04 0.633E-04 0.539E-04 0.478E-04 0.438E-04\n 0.404E-04 0.362E-04 0.308E-04 0.264E-04 0.229E-04 0.209E-04 0.192E-04 0.170E-04\n 0.145E-04 0.126E-04 0.112E-04 0.103E-04",
"apps": [
"vasp"
],
"hash": "4e058592231fc4e091ac0c92d87797b0",
"apps": ["vasp"],
"element": "Si",
"source": "vasp",
"version": "5.2",
Expand All @@ -23,6 +20,23 @@
"exchangeCorrelation": "/pb/qm/dft/ksdft/gga?functional=pbe",
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"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": []
}
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31 changes: 31 additions & 0 deletions schema/core/reusable/atomic_orbital.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
{
"$id": "core/reusable/atomic_orbital.json",
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"$schema": "http://json-schema.org/draft-04/schema#",
"title": "atomic orbital schema",
"type": "object",
"properties": {
"orbitalName": {
"type": "string",
"pattern": "^[1-7][sSpPdDfF]$"
},
"orbitalIndex": {
"type": "number",
"minimum": 1
},
"principalNumber": {
"type": "number",
"minimum": 1,
"maximum": 7
},
"angularMomentum": {
"type": "number",
"minimum": 0,
"maximum": 3
},
"occupation": {
"type": "number",
"minimum": 0,
"maximum": 14
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}
}
}
15 changes: 13 additions & 2 deletions schema/methods_directory/physical/psp/file.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
"type": "string",
"description": "chemical element"
},
"textHeading": {
"hash": {
"type": "string",
"description": "text of pseudopotential file header"
"description": "MD5 hash of the pseudopotential file"
},
"type": {
"type": "string",
Expand All @@ -28,6 +28,13 @@
"$ref": "../../../core/reusable/category_path.json",
"description": "DFT model path, e.g. '/pb/qm/dft/ksdft/gga?functional=pbe'"
},
"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"
Expand All @@ -39,6 +46,10 @@
"filename": {
"type": "string",
"description": "filename of pseudopotential file on filesystem"
},
"name": {
"type": "string",
"description": "name of the data category: pseudopotential"
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As it is fixed, we can also use

"name": {
    "type": "string",
    "description": "name of the data category",
    "enum": ["pseudopotential"]
}

}
},
"required": [
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