@mat3ra/esse 2023.12.25-2

package/schema/properties_directory/structural/symmetry.json

@@ -0,0 +1,35 @@
+{
+    "$id": "properties-directory/structural/symmetry",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "symmetry schema",
+    "properties": {
+        "pointGroupSymbol": {
+            "description": "point group symbol in Schoenflies notation",
+            "type": "string"
+        },
+        "spaceGroupSymbol": {
+            "description": "space group symbol in Hermann–Mauguin notation",
+            "type": "string"
+        },
+        "tolerance": {
+            "description": "tolerance used for symmetry calculation",
+            "allOf": [
+                {
+                    "$ref": "../../core/primitive/scalar.json"
+                }
+            ],
+            "properties": {
+                "units": {
+                    "enum": [
+                        "angstrom"
+                    ]
+                }
+            }
+        },
+        "name": {
+            "enum": [
+                "symmetry"
+            ]
+        }
+    }
+}

package/schema/properties_directory/structural/volume.json

@@ -0,0 +1,22 @@
+{
+    "$id": "properties-directory/structural/volume",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "volume schema",
+    "allOf": [
+        {
+            "$ref": "../../core/primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "enum": [
+                "volume"
+            ]
+        },
+        "units": {
+            "enum": [
+                "angstrom^3"
+            ]
+        }
+    }
+}

package/schema/properties_directory/workflow/convergence/electronic.json

@@ -0,0 +1,31 @@
+{
+    "$id": "properties-directory/workflow/convergence/electronic",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "electronic self consistency convergence schema",
+    "properties": {
+        "name": {
+            "enum": [
+                "convergence_electronic"
+            ]
+        },
+        "units": {
+            "enum": [
+                "eV",
+                "rydberg",
+                "hartree"
+            ]
+        },
+        "data": {
+            "type": "array",
+            "items": {
+                "type": "array",
+                "items": {
+                    "type": "number"
+                }
+            }
+        }
+    },
+    "required": [
+        "data"
+    ]
+}

package/schema/properties_directory/workflow/convergence/ionic.json

@@ -0,0 +1,60 @@
+{
+    "$id": "properties-directory/workflow/convergence/ionic",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "ionic convergence schema",
+    "properties": {
+        "name": {
+            "enum": [
+                "convergence_ionic"
+            ]
+        },
+        "tolerance": {
+            "description": "for ionic convergence tolerance shows force tolerance"
+        },
+        "units": {
+            "description": "units for force tolerance",
+            "enum": [
+                "eV"
+            ]
+        },
+        "data": {
+            "description": "energetic and structural information",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "energy": {
+                        "description": "converged electronic energy for this structure (last in `electronic`)",
+                        "type": "number"
+                    },
+                    "structure": {
+                        "description": "TODO: structural information at each step to be here",
+                        "type": "object"
+                    },
+                    "electronic": {
+                        "description": "data about electronic at this ionic step",
+                        "type": "object",
+                        "properties": {
+                            "units": {
+                                "description": "units for force tolerance",
+                                "enum": [
+                                    "eV",
+                                    "rydberg",
+                                    "hartree"
+                                ]
+                            },
+                            "data": {
+                                "type": "array",
+                                "items": {
+                                    "type": "number"
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    },
+    "required": [
+        "data"
+    ]
+}

package/schema/properties_directory/workflow/convergence/kpoint.json

@@ -0,0 +1,46 @@
+{
+    "$id": "properties-directory/workflow/convergence/kpoint",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "convergence schema for converging a property wrt kpoints",
+    "properties": {
+        "tolerance": {
+            "description": "tolerance for the property under investigation"
+        },
+        "units": {
+            "description": "units for the property under investigation",
+            "type": "string"
+        },
+        "property": {
+            "description": "name of the property under investigation",
+            "type": "string"
+        },
+        "data": {
+            "description": "kpoint grid and property information",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "value": {
+                        "description": "value of the property at this step"
+                    },
+                    "grid": {
+                        "description": "information about the kpoint grid",
+                        "type": "object"
+                    },
+                    "spacing": {
+                        "description": "optional kpoint spacing information",
+                        "type": "number"
+                    }
+                },
+                "required": [
+                    "value",
+                    "grid"
+                ]
+            }
+        }
+    },
+    "required": [
+        "tolerance",
+        "units",
+        "data"
+    ]
+}

package/schema/property/base.json

@@ -0,0 +1,57 @@
+{
+    "$id": "property/base",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Schema of base material's preliminary property",
+    "allOf": [
+        {
+            "description": "entity schema",
+            "$ref": "../in_memory_entity/base.json"
+        }
+    ],
+    "properties": {
+        "slug": {
+            "description": "property slug, e.g. total_energy",
+            "type": "string"
+        },
+        "group": {
+            "description": "property group, e.g. qe:dft:gga:pbe",
+            "type": "string"
+        },
+        "data": {
+            "description": "container of the information, specific to each property",
+            "type": "object"
+        },
+        "source": {
+            "$ref": "source.json"
+        },
+        "exabyteId": {
+            "description": "Id of the corresponding item in the entity bank that this property is obtained for",
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        },
+        "precision": {
+            "type": "object"
+        },
+        "count": {
+            "description": "total number of properties among which this property is the best.",
+            "type": "number"
+        },
+        "systemTags": {
+            "description": "property system tags, marks property system characteristics, values refined or best (could be both)",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "enum": [
+                    "isRefined",
+                    "isBest"
+                ]
+            }
+        }
+    },
+    "required": [
+        "data",
+        "source"
+    ]
+}

package/schema/property/meta.json

@@ -0,0 +1,10 @@
+{
+    "$id": "property/meta",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Schema of material's meta properties",
+    "allOf": [
+        {
+            "$ref": "raw.json"
+        }
+    ]
+}

package/schema/property/raw.json

@@ -0,0 +1,57 @@
+{
+    "$id": "property/raw",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Schema of material's preliminary property",
+    "allOf": [
+        {
+            "description": "entity schema",
+            "$ref": "../in_memory_entity/base.json"
+        }
+    ],
+    "properties": {
+        "slug": {
+            "description": "property slug, e.g. total_energy",
+            "type": "string"
+        },
+        "group": {
+            "description": "property group, e.g. qe:dft:gga:pbe",
+            "type": "string"
+        },
+        "data": {
+            "description": "container of the information, specific to each property",
+            "type": "object"
+        },
+        "source": {
+            "$ref": "source.json"
+        },
+        "exabyteId": {
+            "description": "Id of the corresponding item in the entity bank that this property is obtained for",
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        },
+        "precision": {
+            "type": "object"
+        },
+        "count": {
+            "description": "total number of properties among which this property is the best.",
+            "type": "number"
+        },
+        "systemTags": {
+            "description": "property system tags, marks property system characteristics, values refined or best (could be both)",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "enum": [
+                    "isRefined",
+                    "isBest"
+                ]
+            }
+        }
+    },
+    "required": [
+        "data",
+        "source"
+    ]
+}

package/schema/property/source.json

@@ -0,0 +1,26 @@
+{
+    "$id": "property/source",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "The source of a property. This could be an article, a simulation on Exabyte, an external simulation, etc.",
+    "type": "object",
+    "properties": {
+        "type": {
+            "description": "Type of the material property's source.",
+            "type": "string"
+        },
+        "url": {
+            "description": "Internet address of the reference.",
+            "type": "string"
+        },
+        "info": {
+            "oneOf": [
+                {
+                    "$ref": "../core/reference/exabyte.json"
+                },
+                {
+                    "$ref": "../core/reference/experiment.json"
+                }
+            ]
+        }
+    }
+}

package/schema/software/application.json

@@ -0,0 +1,40 @@
+{
+    "$id": "software/application",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "application schema (base)",
+    "type": "object",
+    "properties": {
+        "name": {
+            "description": "The name of the application. e.g. espresso",
+            "type": "string"
+        },
+        "shortName": {
+            "description": "The short name of the application. e.g. qe",
+            "type": "string"
+        },
+        "summary": {
+            "description": "Application's short description.",
+            "type": "string"
+        },
+        "version": {
+            "description": "Application version. e.g. 5.3.5",
+            "type": "string"
+        },
+        "build": {
+            "description": "Application build. e.g. VTST",
+            "type": "string"
+        },
+        "hasAdvancedComputeOptions": {
+            "description": "Whether advanced compute options are present",
+            "type": "boolean"
+        },
+        "isLicensed": {
+            "description": "Whether licensing is present",
+            "type": "boolean"
+        }
+    },
+    "additionalProperties": true,
+    "required": [
+        "name"
+    ]
+}

package/schema/software/executable.json

@@ -0,0 +1,32 @@
+{
+    "$id": "software/executable",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "executable schema",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "../workflow/unit/runtime/runtime_items.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "description": "The name of the executable. e.g. pw.x",
+            "type": "string"
+        },
+        "applicationId": {
+            "description": "_ids of the application this executable belongs to",
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        },
+        "hasAdvancedComputeOptions": {
+            "description": "Whether advanced compute options are present",
+            "type": "boolean"
+        }
+    },
+    "required": [
+        "name",
+        "applicationId"
+    ]
+}

package/schema/software/flavor.json

@@ -0,0 +1,40 @@
+{
+    "$id": "software/flavor",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "flavor schema",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "../workflow/unit/runtime/runtime_items.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "description": "The name of the executable flavor. e.g. `pw_scf`",
+            "type": "string"
+        },
+        "executableId": {
+            "description": "_id of the executable this flavor belongs to",
+            "type": "string"
+        },
+        "executableName": {
+            "description": "name of the executable this flavor belongs to",
+            "type": "string"
+        },
+        "applicationName": {
+            "description": "name of the application this flavor belongs to",
+            "type": "string"
+        },
+        "input": {
+            "title": "execution unit input schema",
+            "type": "array",
+            "items": {
+                "$ref": "../workflow/unit/input/_inputItemId.json"
+            }
+        }
+    },
+    "required": [
+        "name",
+        "executableId"
+    ]
+}

package/schema/software/template.json

@@ -0,0 +1,33 @@
+{
+    "$id": "software/template",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "template schema",
+    "type": "object",
+    "allOf": [
+        {
+            "$ref": "../workflow/unit/input/_inputItem.json"
+        }
+    ],
+    "properties": {
+        "applicationName": {
+            "type": "string"
+        },
+        "applicationVersion": {
+            "type": "string"
+        },
+        "executableName": {
+            "type": "string"
+        },
+        "contextProviders": {
+            "type": "array",
+            "items": {
+                "description": "render context provider names",
+                "$ref": "../workflow/unit/runtime/_runtime_item_name_object.json"
+            }
+        }
+    },
+    "required": [
+        "name",
+        "content"
+    ]
+}

package/schema/software_directory/ml/exabyteml.json

@@ -0,0 +1,23 @@
+{
+    "$id": "software-directory/ml/exabyteml",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "exabyte machine learning engine schema",
+    "type": "object",
+    "properties": {
+        "name": {
+            "enum": [
+                "exabyteml"
+            ]
+        },
+        "summary": {
+            "enum": [
+                "exabyte machine learning engine"
+            ]
+        },
+        "version": {
+            "enum": [
+                "0.2.0"
+            ]
+        }
+    }
+}

package/schema/software_directory/ml/unit/execution/evaluate/cross-validate.json

@@ -0,0 +1,25 @@
+{
+    "$id": "software-directory/ml/unit/execution/evaluate/cross-validate",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "cross-validation unit schema",
+    "allOf": [
+        {
+            "$ref": "../../../../../workflow/unit/execution.json"
+        }
+    ],
+    "properties": {
+        "input": {
+            "description": "TODO: consider keeping executable `evaluate` and flavor `cross-validate` as before",
+            "type": "object",
+            "properties": {
+                "nSplits": {
+                    "description": "number of groups to split the training dataset for cross-validation",
+                    "type": "number"
+                }
+            },
+            "required": [
+                "nSplits"
+            ]
+        }
+    }
+}

package/schema/software_directory/ml/unit/execution/initialize.json

@@ -0,0 +1,29 @@
+{
+    "$id": "software-directory/ml/unit/execution/initialize",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "initialize unit schema",
+    "allOf": [
+        {
+            "$ref": "../../../../workflow/unit/execution.json"
+        }
+    ],
+    "properties": {
+        "input": {
+            "description": "model init unit (NOTE: info about method, eg. regression/linear is taken from (sub)workflow)",
+            "type": "object",
+            "properties": {
+                "targets": {
+                    "description": "target properties to predict (NOTE: must be a subset of targets for which training was done)",
+                    "type": "array",
+                    "items": {
+                        "description": "material features (properties) in a 'flattened' format",
+                        "type": "string"
+                    }
+                }
+            },
+            "required": [
+                "targets"
+            ]
+        }
+    }
+}

package/schema/software_directory/ml/unit/execution/score.json

@@ -0,0 +1,13 @@
+{
+    "$id": "software-directory/ml/unit/execution/score",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "train score schema",
+    "allOf": [
+        {
+            "$ref": "../../../../workflow/unit/execution.json"
+        }
+    ],
+    "properties": {
+        "input": {}
+    }
+}

package/schema/software_directory/ml/unit/execution/train.json

@@ -0,0 +1,38 @@
+{
+    "$id": "software-directory/ml/unit/execution/train",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "train unit schema",
+    "allOf": [
+        {
+            "$ref": "../../../../workflow/unit/execution.json"
+        }
+    ],
+    "properties": {
+        "input": {
+            "description": "model train unit (NOTE: info about method, eg. regression/linear is taken from (sub)workflow)",
+            "type": "object",
+            "properties": {
+                "features": {
+                    "description": "material features used for model fitting",
+                    "type": "array",
+                    "items": {
+                        "description": "material features (properties) in a 'flattened' format",
+                        "type": "string"
+                    }
+                },
+                "targets": {
+                    "description": "target properties to train for",
+                    "type": "array",
+                    "items": {
+                        "description": "material features (properties) in a 'flattened' format",
+                        "type": "string"
+                    }
+                }
+            },
+            "required": [
+                "features",
+                "targets"
+            ]
+        }
+    }
+}

package/schema/software_directory/ml/unit/execution.json

@@ -0,0 +1,17 @@
+{
+    "$id": "software-directory/ml/unit/execution",
+    "oneOf": [
+        {
+            "$ref": "execution/evaluate/cross-validate.json"
+        },
+        {
+            "$ref": "execution/train.json"
+        },
+        {
+            "$ref": "execution/score.json"
+        },
+        {
+            "$ref": "execution/initialize.json"
+        }
+    ]
+}