Merge pull request #312 from Exabyte-io/feat/SOF-7323

SOF-7323: add norm-conserving full-relativistic pseudo type

dist/js/schema/methods_category/physical/qm/wf/enum_options.json

@@ -34,6 +34,7 @@
         "enum": [
             "us",
             "nc",
+            "nc-fr",
             "paw",
             "coulomb"
         ]

dist/js/schema/methods_category/physical/qm/wf/psp.json

@@ -42,6 +42,7 @@
             "enum": [
                 "us",
                 "nc",
+                "nc-fr",
                 "paw",
                 "coulomb"
             ],

dist/js/schema/methods_directory/physical/psp.json

@@ -51,6 +51,7 @@
                     "enum": [
                         "us",
                         "nc",
+                        "nc-fr",
                         "paw",
                         "coulomb"
                     ],
@@ -218,6 +219,7 @@
                                 "enum": [
                                     "us",
                                     "nc",
+                                    "nc-fr",
                                     "paw",
                                     "coulomb"
                                 ]

dist/js/schema/methods_directory/physical/psp/file.json

@@ -34,6 +34,7 @@
                     "enum": [
                         "us",
                         "nc",
+                        "nc-fr",
                         "paw",
                         "coulomb"
                     ]

dist/js/schema/methods_directory/physical/psp/file_data_item.json

@@ -24,6 +24,7 @@
             "enum": [
                 "us",
                 "nc",
+                "nc-fr",
                 "paw",
                 "coulomb"
             ]

dist/js/scripts/compileTs.js

@@ -1,9 +1,7 @@
 "use strict";
-var __importDefault =
-    (this && this.__importDefault) ||
-    function (mod) {
-        return mod && mod.__esModule ? mod : { default: mod };
-    };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const fs_1 = __importDefault(require("fs"));
 const json_schema_to_typescript_1 = require("json-schema-to-typescript");
@@ -49,11 +47,7 @@ const filesystem_1 = require("../utils/filesystem");
 function cleanSchema(schema) {
     let firstRun = true;
     return (0, schemaUtils_1.mapObjectDeep)(schema, (object) => {
-        if (
-            typeof object === "object" &&
-            (object === null || object === void 0 ? void 0 : object.title) &&
-            !firstRun
-        ) {
+        if (typeof object === "object" && (object === null || object === void 0 ? void 0 : object.title) && !firstRun) {
             firstRun = false;
             // eslint-disable-next-line @typescript-eslint/no-unused-vars
             const { title, $schema, ...restObject } = object;
@@ -65,24 +59,21 @@ function cleanSchema(schema) {
 async function compileTS(schemaPath, savePath) {
     try {
         await fs_1.default.promises.unlink(savePath);
-    } catch (err) {
+    }
+    catch (err) {
         console.log("File with types not exists");
     }
     await (0, filesystem_1.walkDir)(schemaPath, async (filePath) => {
         const data = await fs_1.default.promises.readFile(filePath, "utf8");
         const schema = cleanSchema(JSON.parse(data));
         console.log(`Compiling Typescript: ${filePath}`);
         // @ts-ignore
-        const compiledSchema = await (0, json_schema_to_typescript_1.compile)(
-            schema,
-            schema.title || "",
-            {
-                unreachableDefinitions: true,
-                additionalProperties: false,
-                enableConstEnums: false,
-                bannerComment: `/** Schema ${filePath} */`,
-            },
-        );
+        const compiledSchema = await (0, json_schema_to_typescript_1.compile)(schema, schema.title || "", {
+            unreachableDefinitions: true,
+            additionalProperties: false,
+            enableConstEnums: false,
+            bannerComment: `/** Schema ${filePath} */`,
+        });
         await fs_1.default.promises.appendFile(savePath, `${compiledSchema} \n`, { flag: "a+" });
     });
 }

dist/js/types.d.ts

@@ -10839,7 +10839,7 @@ export interface PseudopotentialCategorySchema {
          * machine-readable identifier
          */
         slug: string;
-    } | string) & ("us" | "nc" | "paw" | "coulomb");
+    } | string) & ("us" | "nc" | "nc-fr" | "paw" | "coulomb");
     /**
      * contains either object with slugified entry or slug only as a string
      */
@@ -12270,7 +12270,7 @@ export interface PseudopotentialFile {
          * MD5 hash of the pseudopotential file
          */
         hash?: string;
-        type: "us" | "nc" | "paw" | "coulomb";
+        type: "us" | "nc" | "nc-fr" | "paw" | "coulomb";
         /**
          * explains where this came from
          */
@@ -12341,7 +12341,7 @@ export interface FileDataItem {
      * MD5 hash of the pseudopotential file
      */
     hash?: string;
-    type: "us" | "nc" | "paw" | "coulomb";
+    type: "us" | "nc" | "nc-fr" | "paw" | "coulomb";
     /**
      * explains where this came from
      */
@@ -12428,7 +12428,7 @@ export interface UnitMethodPseudopotential {
              * machine-readable identifier
              */
             slug: string;
-        } | string) & ("us" | "nc" | "paw" | "coulomb");
+        } | string) & ("us" | "nc" | "nc-fr" | "paw" | "coulomb");
         /**
          * contains either object with slugified entry or slug only as a string
          */
@@ -12480,7 +12480,7 @@ export interface UnitMethodPseudopotential {
              * MD5 hash of the pseudopotential file
              */
             hash?: string;
-            type: "us" | "nc" | "paw" | "coulomb";
+            type: "us" | "nc" | "nc-fr" | "paw" | "coulomb";
             /**
              * explains where this came from
              */

dist/js/types.js

@@ -9,7 +9,7 @@ var Type;
 (function (Type) {
     Type["fromIframeToHost"] = "from-iframe-to-host";
     Type["fromHostToIframe"] = "from-host-to-iframe";
-})((Type = exports.Type || (exports.Type = {})));
+})(Type = exports.Type || (exports.Type = {}));
 /**
  * The action to be performed upon receiving the message.
  */
@@ -18,4 +18,4 @@ var Action;
     Action["setData"] = "set-data";
     Action["getData"] = "get-data";
     Action["info"] = "info";
-})((Action = exports.Action || (exports.Action = {})));
+})(Action = exports.Action || (exports.Action = {}));

schema/methods_category/physical/qm/wf/enum_options.json

@@ -34,6 +34,7 @@
         "enum": [
             "us",
             "nc",
+            "nc-fr",
             "paw",
             "coulomb"
         ]

schema/methods_category/physical/qm/wf/enum_options.yml

@@ -20,6 +20,7 @@ pseudization:
 pseudoSubtypes:
   - us # ultra-soft
   - nc # norm-conserving
+  - nc-fr # norm-conserving full-relativistic
   - paw # projector augmented wave
   - coulomb # Coulomb potential
 #

src/py/mat3ra/esse/data/properties.py

@@ -1,3 +1,3 @@
 import json
-PROPERTIES_MANIFEST = json.loads(r'''{"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},"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"},"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},"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}}''')
-RESULTS = json.loads(r'''["pressure","total_energy","surface_energy","fermi_energy","total_force","zero_point_energy","reaction_energy_barrier","electron_affinity","ionization_potential","phonon_dos","phonon_dispersions","total_energy_contributions","band_gaps","stress_tensor","band_structure","density_of_states","reaction_energy_profile","potential_profile","charge_density_profile","vibrational_spectrum","file_content","average_potential_profile","dielectric_tensor","atomic_forces","magnetic_moments","hubbard_u","hubbard_v","hubbard_v_nn"]''')
+PROPERTIES_MANIFEST = json.loads(json.dumps({'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}, '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'}, '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}, '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}}))
+RESULTS = json.loads(json.dumps(['pressure', 'total_energy', 'surface_energy', 'fermi_energy', 'total_force', 'zero_point_energy', 'reaction_energy_barrier', 'electron_affinity', 'ionization_potential', 'phonon_dos', 'phonon_dispersions', 'total_energy_contributions', 'band_gaps', 'stress_tensor', 'band_structure', 'density_of_states', 'reaction_energy_profile', 'potential_profile', 'charge_density_profile', 'vibrational_spectrum', 'file_content', 'average_potential_profile', 'dielectric_tensor', 'atomic_forces', 'magnetic_moments', 'hubbard_u', 'hubbard_v', 'hubbard_v_nn']))

src/py/mat3ra/esse/models/methods_category/physical/qm/wf/psp.py

@@ -28,6 +28,7 @@ class SlugifiedEntryOrSlug(Enum):
 class SlugifiedEntryOrSlug213(Enum):
     us = "us"
     nc = "nc"
+    nc_fr = "nc-fr"
     paw = "paw"
     coulomb = "coulomb"
 

src/py/mat3ra/esse/models/methods_directory/physical/psp/__init__.py

@@ -28,6 +28,7 @@ class SlugifiedEntryOrSlug(Enum):
 class SlugifiedEntryOrSlug209(Enum):
     us = "us"
     nc = "nc"
+    nc_fr = "nc-fr"
     paw = "paw"
     coulomb = "coulomb"
 
@@ -70,6 +71,7 @@ class Slug(Enum):
 class Type(Enum):
     us = "us"
     nc = "nc"
+    nc_fr = "nc-fr"
     paw = "paw"
     coulomb = "coulomb"
 

src/py/mat3ra/esse/models/methods_directory/physical/psp/file.py

@@ -17,6 +17,7 @@ class Slug(Enum):
 class Type(Enum):
     us = "us"
     nc = "nc"
+    nc_fr = "nc-fr"
     paw = "paw"
     coulomb = "coulomb"
 

src/py/mat3ra/esse/models/methods_directory/physical/psp/file_data_item.py

@@ -13,6 +13,7 @@
 class Type(Enum):
     us = "us"
     nc = "nc"
+    nc_fr = "nc-fr"
     paw = "paw"
     coulomb = "coulomb"