chore: pw.x schema improvements

Exabyte-io · Sep 11, 2023 · e5ce061 · e5ce061
1 parent 0fbbb1e
commit e5ce061
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Showing 8 changed files with 48 additions and 30 deletions.
diff --git a/example/3pse/file/applications/espresso/7.2/pw.x.json b/example/3pse/file/applications/espresso/7.2/pw.x.json
@@ -26,13 +26,13 @@
         ],
         "Hubbard_occ": [
             [
-                1.1,
-                0.00,
+                1,
+                1,
                 0.00
             ],
             [
-                0.02,
-                0.02,
+                1,
+                2,
                 0.02
             ]
         ]
@@ -49,12 +49,12 @@
     "ATOMIC_SPECIES": {
         "values": [
             {
-                "x": "Cs",
+                "X": "Cs",
                 "Mass_X": 132.90543,
                 "PseudoPot_X": "Cs.upf"
             },
             {
-                "x": "Cl",
+                "X": "Cl",
                 "Mass_X": 35.4527,
                 "PseudoPot_X": "Cl.upf"
             }

diff --git a/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_positions.json b/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_positions.json
@@ -25,7 +25,7 @@
                 "properties": {
                     "X": {
                         "type": "string",
-                        "description": "label of the atom as specified in ATOMIC_SPECIE"
+                        "description": "label of the atom as specified in ATOMIC_SPECIES"
                     },
                     "x": {
                         "type": "number",
@@ -40,24 +40,18 @@
                         "description": "atomic positions"
                     },
                     "if_pos(1)": {
-                        "type": "number",
+                        "$ref": "../../../../../../core/primitive/integer_one_or_zero.json",
                         "default": 1,
-                        "minimum": 0,
-                        "maximum": 1,
                         "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1.  Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run."
                     },
                     "if_pos(2)": {
-                        "type": "number",
+                        "$ref": "../../../../../../core/primitive/integer_one_or_zero.json",
                         "default": 1,
-                        "minimum": 0,
-                        "maximum": 1,
                         "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1.  Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run."
                     },
                     "if_pos(3)": {
-                        "type": "number",
+                        "$ref": "../../../../../../core/primitive/integer_one_or_zero.json",
                         "default": 1,
-                        "minimum": 0,
-                        "maximum": 1,
                         "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1.  Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run."
                     }
                 },

diff --git a/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_species.json b/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_species.json
@@ -11,7 +11,7 @@
                 "type": "object",
                 "additionalProperties": false,
                 "properties": {
-                    "x": {
+                    "X": {
                         "type": "string",
                         "description": "label of the atom. Acceptable syntax: chemical symbol X (1 or 2 characters, case-insensitive) or chemical symbol plus a number or a letter, as in \"Xn\" (e.g. Fe1) or \"X_*\" or \"X-*\" (e.g. C1, C_h; max total length cannot exceed 3 characters)"
                     },

diff --git a/schema/3pse/file/applications/espresso/7.2/pw.x/control.json b/schema/3pse/file/applications/espresso/7.2/pw.x/control.json
@@ -159,7 +159,8 @@
         },
         "gate": {
             "type": "boolean",
-            "default": false
+            "default": false,
+            "description": "In the case of charged cells (tot_charge .ne. 0) setting gate = .TRUE. represents the counter charge (i.e. -tot_charge) not by a homogeneous background charge but with a charged plate, which is placed at zgate (see below). Details of the gate potential can be found in T. Brumme, M. Calandra, F. Mauri; PRB 89, 245406 (2014). Note, that in systems which are not symmetric with respect to the plate, one needs to enable the dipole correction! (dipfield=.true.). Currently, symmetry can be used with gate=.true. but carefully check that no symmetry is included which maps z to -z even if in principle one could still use them for symmetric systems (i.e. no dipole correction). For nosym=.false. verbosity is set to 'high'. Note: this option was called \"monopole\" in v6.0 and 6.1 of pw.x"
         },
         "twochem": {
             "type": "boolean",
@@ -173,7 +174,8 @@
         },
         "trism": {
             "type": "boolean",
-            "default": false
+            "default": false,
+            "description": "If .TRUE. perform a 3D-RISM-SCF calculation [for details see H.Sato et al., JCP 112, 9463 (2000), doi:10.1063/1.481564]. The solvent's distributions are calculated by 3D-RISM, though solute is treated as SCF. The charge density and the atomic positions are optimized, simultaneously with the solvents. To perform the calculation, you must set a namelist RISM and a card SOLVENTS. If assume_isolated = 'esm' and esm_bc = 'bc1', Laue-RISM is calculated instead of 3D-RISM and coupled with ESM method (i.e. ESM-RISM). [for details see S.Nishihara and M.Otani, PRB 96, 115429 (2017)]. The default of mixing_beta is 0.2 for both 3D-RISM and Laue-RISM. For structural relaxation with BFGS, ignore_wolfe is always .TRUE. ."
         }
     }
 }
diff --git a/schema/3pse/file/applications/espresso/7.2/pw.x/system.json b/schema/3pse/file/applications/espresso/7.2/pw.x/system.json
@@ -78,7 +78,9 @@
             "type": "array",
             "items": {
                 "type": "number",
-                "default": 0
+                "default": 0,
+                "minimum": -1,
+                "maximum": 1
             }
         },
         "ecutwfc": {
@@ -304,11 +306,20 @@
             "type": "array",
             "items": {
                 "type": "array",
-                "items": {
-                    "type": "number"
-                },
-                "maxItems": 3,
-                "minItems": 3
+                "items": [
+                    {
+                        "type": "integer",
+                        "minimum": 1
+                    },
+                    {
+                        "type": "integer",
+                        "minimum": 1,
+                        "maximum": 3
+                    },
+                    {
+                        "type": "number"
+                    }
+                ]
             }
         },
         "Hubbard_alpha": {

diff --git a/schema/core/primitive/integer_one_or_zero.json b/schema/core/primitive/integer_one_or_zero.json
@@ -0,0 +1,8 @@
+{
+    "$id": "core/primitive/integer-one-or-zero",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "integer one or zero",
+    "type": "number",
+    "minimum": 0,
+    "maximum": 1
+}
diff --git a/src/js/esse/index.js b/src/js/esse/index.js
@@ -25,7 +25,13 @@ export class ESSE {
      */
     validate = (example, schema) => {
         const ajv = new Ajv({ allErrors: true });
-        return ajv.validate(schema, example);
+        const isValid = ajv.validate(schema, example);
+
+        if (!isValid) {
+            console.error(ajv.errors);
+        }
+
+        return isValid;
     };
 
     buildGlobalSchema() {

diff --git a/src/js/scripts/createEnumsFromYaml.mjs b/src/js/scripts/createEnumsFromYaml.mjs
@@ -39,8 +39,5 @@ walkDir(SCHEMA_DIR, (filePath) => {
     const obj = yaml.load(fileContents);
     const enumObj = lodash.mapValues(obj, (value) => ({ enum: value }));
 
-    fs.writeFileSync(
-        `${path.join(dirname, outFilename)}`,
-        `${JSON.stringify(enumObj, null, 4)}\n`,
-    );
+    fs.writeFileSync(`${path.join(dirname, outFilename)}`, `${JSON.stringify(enumObj, null, 4)}\n`);
 });