@mat3ra/esse 2024.1.25-7 → 2024.1.26-1

package/manifest/models.yaml

@@ -0,0 +1,290 @@
+# --------------------------- #
+#      Physics Based          #
+# --------------------------- #
+- name: physics-based
+  slug: pb
+  children:
+    # --------------------------- #
+    #     Quantum Mechanical      #
+    # --------------------------- #
+    - name: quantum-mechanical
+      slug: qm
+      field: type
+      children:
+        # DFT
+        - name: density functional theory
+          slug: dft
+          field: subtype
+          children:
+            ## LDA
+            - name: local density approximation
+              slug: lda
+              schema:
+                type: object
+                properties:
+                  functional:
+                    type: object
+                    enum:
+                      - name: perdew-zunger
+                        slug: pz
+                        reference:
+                          doi: https://doi.org/10.1103/PhysRevB.23.5048
+                      - name: perdew-wang
+                        slug: pw
+                        reference:
+                          doi: https://doi.org/10.1103/PhysRevB.45.13244
+                      - name: vosko-wilk-nusair
+                        slug: vwn
+                        reference:
+                          doi: https://doi.org/10.1139/p80-159
+#                  modifiers:
+#                    type: array
+#                    items:
+#                      type: object
+#                      enum:
+#                        - name: hubbard-corrected
+#                          schema:
+#                            type: object
+#                            properties:
+#                              hubbardU:
+#                                type: number
+#                        - name: spin-resolved
+#                          schema:
+#                            type: object
+#                            properties:
+#                              non-collinear:
+#                                type: boolean
+                required:
+                  - functional
+            ## GGA
+            - name: generalized gradient approximation
+              slug: gga
+              schema:
+                type: object
+                properties:
+                  functional:
+                    type: object
+                    enum:
+                      - name: perdew-burke-ernzerhof
+                        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:
+#                      type: object
+#                      enum:
+#                        - name: hubbard-corrected
+#                          schema:
+#                          type: object
+#                          properties:
+#                            hubbardU:
+#                              type: number
+#                        - name: spin-resolved
+#                          schema:
+#                          type: object
+#                          properties:
+#                            non-collinear:
+#                              type: boolean
+                required:
+                  - functional
+            ## HSE
+            - name: hybrid functionals
+              slug: hyb
+              schema:
+                type: object
+                properties:
+                  functional:
+                    type: object
+                    enum:
+                      - name: heyd-scuseria-ernzerhof-03
+                        slug: hse03
+                        reference:
+                          doi: http://dx.doi.org/10.1063/1.1564060
+                      - name: heyd-scuseria-ernzerhof-06
+                        slug: hse06
+                        reference:
+                          doi: http://dx.doi.org/10.1063/1.2404663
+                      - name: perdew-burke-ernzerhof-0
+                        slug: hse03
+                        reference:
+                          doi: http://dx.doi.org/10.1063/1.472933
+                      - name: becke-3-lee-yang-parr
+                        slug: b3lyp
+                        reference:
+                          doi: http://dx.doi.org/10.1063/1.464913
+#                  modifiers:
+#                    type: array
+#                    items:
+#                      type: object
+#                      enum:
+#                        - name: spin-resolved
+#                          schema:
+#                          type: object
+#                          properties:
+#                            non-collinear:
+#                              type: boolean
+                required:
+                  - functional
+            ## GW
+            - name: gw approximation
+              omit: true
+              slug: gw
+              schema:
+                type: object
+                properties:
+                  category:
+                    type: object
+                    enum:
+                      - name: one-shot g0w0
+                        slug: g0w0
+                        reference:
+                          doi: https://doi.org/10.1103/PhysRevB.34.5390
+                      - name: self-consistent gw
+                        slug: scgw
+                        reference:
+                          doi: https://doi.org/10.1103/PhysRevLett.99.246403
+                  parent:
+                    oneOf:
+                      - $ref: "#/1/children/1/children/1/children/1"  # LDA
+                      - $ref: "#/1/children/1/children/1/children/2"  # GGA
+                  modifiers:
+                    type: array
+                    items:
+                      type: object
+                      enum:
+                        - name: spin-resolved
+                          schema:
+                          type: object
+                          properties:
+                            non-collinear:
+                              type: boolean
+                required:
+                  - category
+                  - parent
+
+        # QMC
+        - name: quantum monte carlo
+          omit: true
+          slug: qmc
+          children:
+            ## DMC
+            - name: diffusion monte carlo
+              slug: dmc
+              schema:
+                type: object
+                properties:
+                  category:
+                    type: object
+                    enum:
+                      # only one functional has to be selected
+                      - name: casino
+                        slug: csn
+                        reference:
+                          url: https://vallico.net/casinoqmc/what-is-casino/
+                  modifiers:
+                    type: array
+                    items:
+                      type: object
+                      enum:
+                required:
+                  - category
+    # --------------------------- #
+    #      Molecular modeling     #
+    # --------------------------- #
+    - name: molecular modeling
+      omit: true
+      slug: md
+      children:
+        # CL
+        - name: classical molecular dynamics
+          slug: clmd
+          children:
+            ## LJ
+            - name: lennard-jones
+              slug: lj
+              schema:
+                type: object
+                properties:
+                  # ???: this may need to go into method
+                  category:
+                    type: object
+                    enum:
+                      - name: <name of source used for potential coefficients>
+                        slug: <slug>
+                        reference:
+                          doi: <url>
+                  modifiers:
+                    type: array
+                    items:
+                      type: object
+                      enum:
+                required:
+                  - category
+        # AB
+        - name: ab-initio molecular dynamics
+          slug: aimd
+          children:
+            ## BO
+            - name: born-oppenheimer
+              slug: bo
+              schema:
+                type: object
+                properties:
+                  # ???: this may need to go into method
+                  parents:
+                    type: array
+                    items:
+                      enum:
+                        - name: <name of source used for ab-initio calculation>
+                          slug: <slug>
+                          reference:
+                            doi: <url>
+                        - name: <name of source used for md calculation>
+                          slug: <slug>
+                          reference:
+                            doi: <url>
+                      minItems: 2
+                required:
+                  - parents
+
+            ## CP
+            - name: car-parinello
+              slug: cp
+              schema:
+                type: object
+
+# --------------------------- #
+#      Statistical            #
+# --------------------------- #
+- name: statistical
+  slug: st
+  children:
+    # --------------------------- #
+    #      Deterministic          #
+    # --------------------------- #
+    - name: deterministic
+      slug: det
+      field: type
+      children:
+        # ML
+        - name: machine learning
+          slug: ml
+          field: subtype
+          children:
+            ## ML Classification
+            - name: classification
+              omit: true
+              slug: cl
+              schema:
+                type: object
+            ## ML Regression
+            - name: regression
+              slug: re
+              children:
+              schema:
+                type: object

package/manifest/properties.yaml

@@ -0,0 +1,277 @@
+convergence_ionic:
+  defaults:
+    units: eV
+  schemaId: properties-directory/workflow/convergence/ionic
+  isMonitor: true
+
+convergence_electronic:
+  defaults:
+    units: eV
+  schemaId: properties-directory/workflow/convergence/electronic
+  isMonitor: true
+
+# SCALAR
+pressure:
+  defaults:
+    units: kbar
+  schemaId: properties-directory/scalar/pressure
+  isResult: true
+
+total_energy:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/total-energy
+  isResult: true
+
+surface_energy:
+  defaults:
+    units: eV/A^2
+  schemaId: properties-directory/scalar/surface-energy
+  isResult: true
+
+fermi_energy:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/fermi-energy
+  isResult: true
+
+total_force:
+  defaults:
+    units: eV/angstrom
+  schemaId: properties-directory/scalar/total-force
+  isResult: true
+
+zero_point_energy:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/zero-point-energy
+  isResult: true
+
+reaction_energy_barrier:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/reaction-energy-barrier
+  isResult: true
+
+electron_affinity:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/electron-affinity
+  isResult: true
+
+ionization_potential:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/ionization-potential
+  isResult: true
+
+valence_band_offset:
+  defaults:
+    units: eV
+  schemaId: properties-directory/scalar/valence-band-offset
+
+# NON-SCALAR
+phonon_dos:
+  defaults:
+    xAxis:
+      label: frequency
+      units: cm-1
+    yAxis:
+      label: Phonon DOS
+      units: states/cm-1
+  schemaId: properties-directory/non-scalar/phonon-dos
+  isResult: true
+
+phonon_dispersions:
+  defaults:
+    xAxis:
+      label: qpoints
+      units: crystal
+    yAxis:
+      label: frequency
+      units: cm-1
+  schemaId: properties-directory/non-scalar/phonon-dispersions
+  isResult: true
+
+total_energy_contributions:
+  defaults:
+    units: eV
+  schemaId: properties-directory/non-scalar/total-energy-contributions
+  isResult: true
+
+band_gaps:
+  types:
+    - direct
+    - indirect
+  defaults:
+    units: eV
+  schemaId: properties-directory/non-scalar/band-gaps
+  isResult: true
+
+stress_tensor:
+  defaults:
+    units: kbar
+  schemaId: properties-directory/non-scalar/stress-tensor
+  isResult: true
+
+band_structure:
+  defaults:
+    xAxis:
+      label: kpoints
+      units: crystal
+    yAxis:
+      label: energy
+      units: eV
+
+  schemaId: properties-directory/non-scalar/band-structure
+  isResult: true
+
+density_of_states:
+  defaults:
+    xAxis:
+      label: energy
+      units: eV
+    yAxis:
+      label: density of states
+      units: states/unitcell
+  schemaId: properties-directory/non-scalar/density-of-states
+  isResult: true
+
+reaction_energy_profile:
+  defaults:
+    xAxis:
+      label: reaction coordinate
+    yAxis:
+      label: energy
+      units: eV
+  schemaId: properties-directory/non-scalar/reaction-energy-profile
+  isResult: true
+
+potential_profile:
+  defaults:
+    xAxis:
+      label: z coordinate
+    yAxis:
+      label: energy
+      units: eV
+  schemaId: properties-directory/non-scalar/potential-profile
+  isResult: true
+
+charge_density_profile:
+  defaults:
+    xAxis:
+      label: z coordinate
+    yAxis:
+      label: charge density
+      units: e/A
+  schemaId: properties-directory/non-scalar/charge-density-profile
+  isResult: true
+
+vibrational_spectrum:
+  defaults:
+    xAxis:
+      label: wavenumber
+      units: cm-1
+    yAxis:
+      label: Absorption coefficient
+      units: km/mol
+  schemaId: properties-directory/non-scalar/vibrational-spectrum
+  isResult: true
+
+file_content:
+  schemaId: properties-directory/non-scalar/file-content
+  isResult: true
+
+average_potential_profile:
+  defaults:
+    xAxis:
+      label: z coordinate
+      units: angstrom
+    yAxis:
+      label: energy
+      units: eV
+  schemaId: properties-directory/non-scalar/average-potential-profile
+  isResult: true
+
+dielectric_tensor:
+  schemaId: properties-directory/non-scalar/dielectric-tensor
+  isResult: true
+
+# STRUCTURAL
+basis:
+  defaults:
+    units: angstrom
+  schemaId: properties-directory/structural/basis
+
+lattice:
+  defaults:
+    units: angstrom
+  schemaId: properties-directory/structural/lattice
+
+atomic_forces:
+  defaults:
+    units: eV/angstrom
+  schemaId: properties-directory/structural/atomic-forces
+  isResult: true
+
+atomic_constraints:
+  schemaId: properties-directory/structural/basis/atomic-constraints
+
+p-norm:
+  schemaId: properties-directory/structural/p-norm
+
+volume:
+  defaults:
+    units: angstrom^3
+  schemaId: properties-directory/structural/volume
+
+symmetry:
+  defaults:
+    units: angstrom
+  schemaId: properties-directory/structural/symmetry
+
+elemental_ratio:
+  schemaId: properties-directory/structural/elemental-ratio
+
+density:
+  defaults:
+    units: g/cm^3
+  schemaId: properties-directory/structural/density
+
+magnetic_moments:
+  defaults:
+    units: uB
+  schemaId: properties-directory/structural/magnetic-moments
+  isResult: true
+
+bonds:
+  defaults:
+    units: angstrom
+  schemaId: properties-directory/structural/basis/bonds
+
+inchi:
+  schemaId: properties-directory/structural/inchi
+
+inchi_key:
+  schemaId: properties-directory/structural/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
+
+hubbard_v_nn:
+  defaults:
+    units: eV
+  schemaId: properties-directory/non-scalar/hubbard-v-nn
+  isResult: true

package/npmignore

@@ -1,6 +1,5 @@
 src/py/
 tests/
 pyproject.toml
-/manifest/
 .github
 .husky

package/package.json

@@ -1,12 +1,13 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2024.1.25-7",
+    "version": "2024.1.26-1",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
         "prepublishOnly": "rm -rf lib; npm run transpile",
         "transpile": "mkdir -p lib; babel src/js --out-dir lib/js; node build_schemas.js",
         "transpile-and-build-assets": "mkdir -p lib; babel src/js --out-dir lib/js; BUILD_ASSETS=true BUILD_PATH='./lib/js' node build_schemas.js",
         "build:assets": "node build_schemas.js",
+        "build:js-and-python-modules": "BUILD_PYTHON_MODULES=true node build_schemas.js",
         "build:assets-with-docs": "BUILD_ASSETS=true node build_schemas.js",
         "test": "nyc --reporter=text mocha --bail --require @babel/register tests/js/",
         "lint": "eslint src/js && prettier --write src/js",

package/src/js/esse/index.js

@@ -1,17 +1,27 @@
 import Ajv from "ajv";
+import fs from "fs";
+import yaml from "js-yaml";
 
 import { buildSchemaDefinitions } from "./schemaUtils";
-import { EXAMPLES_DIR, SCHEMAS_DIR } from "./settings";
+import { EXAMPLES_DIR, PROPERTIES_MANIFEST_PATH, SCHEMAS_DIR } from "./settings";
 import { parseIncludeReferenceStatementsByDir } from "./utils";
 
 const SCHEMAS = parseIncludeReferenceStatementsByDir(SCHEMAS_DIR);
 const EXAMPLES = parseIncludeReferenceStatementsByDir(EXAMPLES_DIR, true);
+const PROPERTIES_MANIFEST = yaml.load(
+    fs.readFileSync(PROPERTIES_MANIFEST_PATH, { encoding: "utf-8" }),
+);
+const RESULTS = Object.entries(PROPERTIES_MANIFEST)
+    .map((k) => (k[1].isResult ? k[0] : null))
+    .filter((x) => x);
 
 export class ESSE {
-    constructor() {
-        this.schemas = SCHEMAS;
-        this.wrappedExamples = EXAMPLES;
-        this.examples = EXAMPLES.map((example) => example.data);
+    constructor(config = {}) {
+        this.schemas = config.schemas || SCHEMAS;
+        this.wrappedExamples = config.wrappedExamples || EXAMPLES;
+        this.examples = this.wrappedExamples.map((example) => example.data);
+        this.propertiesManifest = config.propertiesManifest || PROPERTIES_MANIFEST;
+        this.results = config.results || RESULTS;
     }
 
     getSchemaById(schemaId) {

package/src/js/esse/settings.js

@@ -2,3 +2,7 @@ import path from "path";
 
 export const SCHEMAS_DIR = path.resolve(__dirname, "../../../schema");
 export const EXAMPLES_DIR = path.resolve(__dirname, "../../../example");
+export const PROPERTIES_MANIFEST_PATH = path.resolve(
+    __dirname,
+    "../../../manifest/properties.yaml",
+);