Skip to content

Commit

Permalink
update: merge latest dev
Browse files Browse the repository at this point in the history
  • Loading branch information
unsigned6 committed Sep 13, 2023
2 parents 37fdab3 + 172188e commit 303543c
Show file tree
Hide file tree
Showing 551 changed files with 3,717 additions and 3,876 deletions.
1 change: 0 additions & 1 deletion .gitattributes

This file was deleted.

11 changes: 3 additions & 8 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -94,17 +94,13 @@ Primitives are solely defined by the default primitives and can not be re-constr

This directory contains the examples formed according to the schemas and implements the same directory structure as the schema directory.

Note: A list of DFT unit functionals (`dft_unit_functionals.json`) is generated during the Python test from the corresponding prototype file (`dft_unit_functionals_proto.json`).

### src

This directory contains Python and Javascript interfaces implementing the functionality to access and validate schemas and examples.

### A word on functionals
The list of DFT unit functionals (`dft_unit_functionals.json`) is currently tracked via [git LFS](https://git-lfs.github.com).
If one wishes to add a new unit functional to that list, please
- edit the [prototype file](schema/models_directory/pb/qm/dft/dft_unit_functionals_proto.json) and
- generate a new list of unit functional by running python tests, for example (via `generate_dft_unit_functionals()` from the [esse.functionals](src/py/esse/functionals.py) python module).
### Generative vs Non-generative keys
Generative keys are the fields which allow for user input prior to calculation of the final property values. A flag is included in the schema comments on the fields in [property schemas](schema/properties_directory): `isGenerative:true` marks which fields to use as subschemas in the generation of a user input schema.
- On properties allowing user inputs, additional fields may be tagged, as in [the `file_content` property](schema/properties_directory/non-scalar/file_content.json)

## Tests

Expand Down Expand Up @@ -132,4 +128,3 @@ This repository is an [open-source](LICENSE.md) work-in-progress and we welcome
2: [CateCom: A Practical Data-Centric Approach to Categorization of Computational Models](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.2c00112)

3: [GitHub Standard Fork & Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962)

4 changes: 1 addition & 3 deletions example/method.json
Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
{
"data": {
"dataset": {
"...": "include(methods_directory/pseudopotential/dataset.json)"
}
"pseudo": []
},
"subtype": "us",
"type": "pseudopotential"
Expand Down
47 changes: 47 additions & 0 deletions example/method/categorized_method.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
{
"name": "PW-NCPP (Davidson Diagonalization, Gaussian Smearing)",
"path": "/qm/wf/pw:/qm/wf/psp/nc?functional=pbe:/qm/wf/smearing/gaussian:/linalg/diag/davidson",
"units": [
{
"name": "Plane-wave",
"path": "/qm/wf/pw",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "pw"
}
},
{
"name": "Norm-conserving PSP",
"path": "/qm/wf/psp/nc?functional=pbe",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "psp",
"subtype": "nc"
},
"parameters": {
"functional": "pbe"
}
},
{
"name": "Gaussian Smearing method",
"path": "/qm/wf/smearing/gaussian",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "smearing",
"subtype": "gaussian"
}
},
{
"name": "Davidson Diagonalization",
"path": "/linalg/diag/davidson",
"categories": {
"tier1": "linalg",
"tier2": "diag",
"type": "davidson"
}
}
]
}
7 changes: 0 additions & 7 deletions example/methods_directory/local-orbital.json

This file was deleted.

10 changes: 10 additions & 0 deletions example/methods_directory/mathematical/cg.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
{
"name": "Conjugate gradient method",
"path": "/opt/diff/ordern/cg",
"categories": {
"tier1": "opt",
"tier2": "diff",
"tier3": "ordern",
"type": "cg"
}
}
Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,17 @@
]
},
"precision": {
"perProperty": {
"...": "include(regression/precision.json)"
}
"perProperty": [
{
"score": 0.8,
"trainingError": 0.002
}
]
},
"categories": {
"type": "linear",
"subtype": "least_squares"
},
"subtype": "least_squares",
"type": "linear"
"name": "Linear least squares regression",
"path": "/linear/leastsq"
}
13 changes: 13 additions & 0 deletions example/methods_directory/physical/ao/dunning.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
{
"name": "cc-pVTZ basis set",
"path": "/qm/wf/ao/dunning?basisSlug=cc-pvtz",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "ao",
"subtype": "dunning"
},
"parameters": {
"basisSlug": "cc-pvtz"
}
}
31 changes: 31 additions & 0 deletions example/methods_directory/physical/psp.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
{
"name": "PAW Pseudopotential method (VASP)",
"path": "/qm/wf/psp/paw",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "psp",
"subtype": "paw"
},
"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"
],
"element": "Si",
"source": "vasp",
"version": "5.2",
"path": "/export/share/pseudo/si/gga/pbe/vasp/5.2/paw/default/POTCAR",
"type": "paw",
"exchangeCorrelation": "/pb/qm/dft/ksdft/gga?functional=pbe",
"filename": "POTCAR",
"schemaVersion": "0.2.0",
"inSet": [],
"tags": []
}
]
}
}
9 changes: 9 additions & 0 deletions example/methods_directory/physical/pw.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
{
"name": "Plane wave basis",
"path": "/qm/wf/pw",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "pw"
}
}
10 changes: 10 additions & 0 deletions example/methods_directory/physical/smearing.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
{
"name": "Methfessel-Paxton smearing",
"path": "/qm/wf/smearing/methfessel-paxton",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "smearing",
"subtype": "methfessel-paxton"
}
}
10 changes: 10 additions & 0 deletions example/methods_directory/physical/tetrahedron.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
{
"name": "Optimized Tetrahedron method (Kawamura)",
"path": "/qm/wf/tetrahedron/optimized",
"categories": {
"tier1": "qm",
"tier2": "wf",
"type": "tetrahedron",
"subtype": "optimized"
}
}
12 changes: 0 additions & 12 deletions example/methods_directory/pseudopotential.json

This file was deleted.

23 changes: 0 additions & 23 deletions example/methods_directory/pseudopotential/dataset.json

This file was deleted.

25 changes: 0 additions & 25 deletions example/methods_directory/pseudopotential/file.json

This file was deleted.

This file was deleted.

This file was deleted.

7 changes: 0 additions & 7 deletions example/methods_directory/pseudopotential/file/radii.json

This file was deleted.

16 changes: 0 additions & 16 deletions example/methods_directory/pseudopotential/precision.json

This file was deleted.

4 changes: 0 additions & 4 deletions example/methods_directory/regression/data_per_feature.json

This file was deleted.

13 changes: 0 additions & 13 deletions example/methods_directory/regression/dataset.json

This file was deleted.

This file was deleted.

14 changes: 0 additions & 14 deletions example/methods_directory/regression/linear/data_per_property.json

This file was deleted.

4 changes: 0 additions & 4 deletions example/methods_directory/regression/precision.json

This file was deleted.

This file was deleted.

Loading

0 comments on commit 303543c

Please sign in to comment.