@mat3ra/esse 2023.12.25-2

package/schema/definitions/units.json

@@ -0,0 +1,103 @@
+{
+    "$id": "definitions/units",
+    "length": {
+        "enum": [
+            "km",
+            "m",
+            "pm",
+            "nm",
+            "angstrom",
+            "a.u.",
+            "bohr",
+            "fractional",
+            "crystal",
+            "cartesian",
+            "alat"
+        ]
+    },
+    "energy": {
+        "enum": [
+            "kJ/mol",
+            "eV",
+            "J/mol",
+            "hartree",
+            "cm-1",
+            "rydberg",
+            "eV/atom"
+        ]
+    },
+    "surface_energy": {
+        "enum": [
+            "eV/A^2"
+        ]
+    },
+    "force": {
+        "enum": [
+            "eV/bohr",
+            "eV/angstrom",
+            "rydberg/a.u.",
+            "newton",
+            "kg*m/s^2",
+            "eV/a.u."
+        ]
+    },
+    "volume": {
+        "enum": [
+            "cm^3",
+            "angstrom^3"
+        ]
+    },
+    "numberDensity": {
+        "enum": [
+            "1/angstrom^3"
+        ]
+    },
+    "density": {
+        "enum": [
+            "g/cm^3"
+        ]
+    },
+    "frequency": {
+        "enum": [
+            "cm-1",
+            "THz",
+            "meV"
+        ]
+    },
+    "pressure": {
+        "enum": [
+            "kbar",
+            "pa"
+        ]
+    },
+    "phononDOS": {
+        "enum": [
+            "states/cm-1",
+            "states/THz",
+            "states/meV"
+        ]
+    },
+    "electronicDOS": {
+        "enum": [
+            "states/unitcell"
+        ]
+    },
+    "magnetic": {
+        "enum": [
+            "uB"
+        ]
+    },
+    "chargeDensity": {
+        "enum": [
+            "e/A"
+        ]
+    },
+    "spectralIntensity": {
+        "enum": [
+            "(debye/angstrom)^2",
+            "km/mol",
+            "m/mol",
+            "a.u."
+        ]
+    }
+}

package/schema/element.json

@@ -0,0 +1,28 @@
+{
+    "$id": "element",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "element schema",
+    "properties": {
+        "symbol": {
+            "description": "Element symbol.",
+            "type": "string"
+        },
+        "properties": {
+            "type": "array",
+            "description": "list of elemental properties",
+            "items": {
+                "anyOf": [
+                    {
+                        "$ref": "properties_directory/elemental/atomic_radius.json"
+                    },
+                    {
+                        "$ref": "properties_directory/elemental/electronegativity.json"
+                    },
+                    {
+                        "$ref": "properties_directory/elemental/ionization_potential.json"
+                    }
+                ]
+            }
+        }
+    }
+}

package/schema/in_memory_entity/base.json

@@ -0,0 +1,30 @@
+{
+    "$id": "in-memory-entity/base",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Base in-memory entity schema",
+    "allOf": [
+        {
+            "description": "entity schema version",
+            "$ref": "../system/schema_version.json"
+        }
+    ],
+    "properties": {
+        "_id": {
+            "description": "entity identity",
+            "type": "string"
+        },
+        "slug": {
+            "description": "entity slug",
+            "type": "string"
+        },
+        "systemName": {
+            "type": "string"
+        },
+        "consistencyChecks": {
+            "type": "array",
+            "items": {
+                "$ref": "../system/consistency_check.json"
+            }
+        }
+    }
+}

package/schema/in_memory_entity/defaultable.json

@@ -0,0 +1,13 @@
+{
+    "$id": "in-memory-entity/defaultable",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Defaultable in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/defaultable.json"
+        }
+    ]
+}

package/schema/in_memory_entity/named.json

@@ -0,0 +1,13 @@
+{
+    "$id": "in-memory-entity/named",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Named in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/name.json"
+        }
+    ]
+}

package/schema/in_memory_entity/named_defaultable.json

@@ -0,0 +1,16 @@
+{
+    "$id": "in-memory-entity/named-defaultable",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Named defaultable in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/name.json"
+        },
+        {
+            "$ref": "../system/defaultable.json"
+        }
+    ]
+}

package/schema/in_memory_entity/named_defaultable_has_metadata.json

@@ -0,0 +1,19 @@
+{
+    "$id": "in-memory-entity/named-defaultable-has-metadata",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Named defaultable has metadata in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/name.json"
+        },
+        {
+            "$ref": "../system/defaultable.json"
+        },
+        {
+            "$ref": "../system/metadata.json"
+        }
+    ]
+}

package/schema/in_memory_entity/named_defaultable_runtime_items.json

@@ -0,0 +1,19 @@
+{
+    "$id": "in-memory-entity/named-defaultable-runtime-items",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Named defaultable runtime items in-memory entity schema",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/name.json"
+        },
+        {
+            "$ref": "../system/defaultable.json"
+        },
+        {
+            "$ref": "../workflow/unit/runtime/runtime_items.json"
+        }
+    ]
+}

package/schema/job/base.json

@@ -0,0 +1,80 @@
+{
+    "$id": "job/base",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "base job schema",
+    "allOf": [
+        {
+            "description": "in-memory entity",
+            "$ref": "../in_memory_entity/named_defaultable_has_metadata.json"
+        }
+    ],
+    "properties": {
+        "rmsId": {
+            "description": "Identity used to track jobs originated from command-line",
+            "type": "string"
+        },
+        "status": {
+            "description": "job status",
+            "enum": [
+                "pre-submission",
+                "queued",
+                "submitted",
+                "active",
+                "finished",
+                "terminate-queued",
+                "terminated",
+                "error",
+                "deleted",
+                "timeout"
+            ]
+        },
+        "startTime": {
+            "description": "Approximate start time of the job. e.g. within 10 min",
+            "type": "string"
+        },
+        "workDir": {
+            "description": "The path to the working directory of this job, when the job originates from command-line",
+            "type": "string"
+        },
+        "compute": {
+            "description": "Job's compute parameters",
+            "$ref": "./compute.json"
+        },
+        "_project": {
+            "description": "Subset of the full information about the project that this job belongs to.",
+            "$ref": "../system/entity_reference.json"
+        },
+        "_material": {
+            "description": "Subset of the full information about the materials used inside this job.",
+            "$ref": "../system/entity_reference.json"
+        },
+        "parent": {
+            "description": "Subset of the full information about the parent job for the job. Only a job from the same project can be assigned as a parent one.",
+            "$ref": "../system/entity_reference.json"
+        },
+        "runtimeContext": {
+            "description": "Context variables that the job will have access to at runtime",
+            "type": "object"
+        },
+        "scopeTrack": {
+            "description": "history of the workflow scope on each update",
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "repetition": {
+                        "type": "number"
+                    },
+                    "scope": {
+                        "$ref": "../workflow/scope.json"
+                    }
+                }
+            }
+        }
+    },
+    "required": [
+        "status",
+        "compute",
+        "_project"
+    ]
+}

package/schema/job/compute.json

@@ -0,0 +1,145 @@
+{
+    "$id": "job/compute",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "compute arguments schema",
+    "description": "Custom keywords prefixed with validate correspond to custom validation methods implemented downstream",
+    "properties": {
+        "queue": {
+            "description": "Name of the submission queues: https://docs.mat3ra.com/infrastructure/resource/queues/. Below enums are for Azure, then AWS circa 2022-08, hence the duplication.",
+            "type": "string",
+            "enum": [
+                "D",
+                "OR",
+                "OF",
+                "OFplus",
+                "SR",
+                "SF",
+                "SFplus",
+                "GPOF",
+                "GP2OF",
+                "GP4OF",
+                "GPSF",
+                "GP2SF",
+                "GP4SF",
+                "OR4",
+                "OR8",
+                "OR16",
+                "SR4",
+                "SR8",
+                "SR16",
+                "GOF",
+                "G4OF",
+                "G8OF",
+                "GSF",
+                "G4SF",
+                "G8SF"
+            ]
+        },
+        "nodes": {
+            "description": "number of nodes used for the job inside the RMS.",
+            "type": "integer",
+            "validateNodes": {}
+        },
+        "ppn": {
+            "description": "number of CPUs used for the job inside the RMS.",
+            "type": "integer",
+            "validatePpn": {}
+        },
+        "timeLimit": {
+            "description": "Wallclock time limit for computing a job. Clock format: 'hh:mm:ss'",
+            "type": "string",
+            "validateTimeLimit": {}
+        },
+        "timeLimitType": {
+            "description": "Convention to use when reasoning about time limits",
+            "type": "string",
+            "default": "per single attempt",
+            "enum": [
+                "per single attempt",
+                "compound"
+            ]
+        },
+        "isRestartable": {
+            "description": "Job is allowed to restart on termination.",
+            "type": "boolean",
+            "default": true
+        },
+        "notify": {
+            "description": "Email notification for the job: n - never, a - job aborted, b - job begins, e - job ends. Last three could be combined.",
+            "type": "string"
+        },
+        "email": {
+            "description": "Email address to notify about job execution.",
+            "type": "string"
+        },
+        "maxCPU": {
+            "description": "Maximum CPU count per node. This parameter is used to let backend job submission infrastructure know that this job is to be charged for the maximum CPU per node instead of the actual ppn. For premium/fast queues where resources are provisioned on-demand and exclusively per user.",
+            "type": "integer"
+        },
+        "arguments": {
+            "description": "Optional arguments specific to using application - VASP, Quantum Espresso, etc. Specified elsewhere",
+            "type": "object",
+            "default": {},
+            "oneOf": [
+                {
+                    "$ref": "../software_directory/modeling/espresso/arguments.json"
+                }
+            ]
+        },
+        "cluster": {
+            "description": "Cluster where the job is executed. Optional on create. Required on job submission.",
+            "type": "object",
+            "properties": {
+                "fqdn": {
+                    "description": "FQDN of the cluster. e.g. master-1-staging.exabyte.io",
+                    "type": "string"
+                },
+                "jid": {
+                    "description": "Job's identity in RMS. e.g. 1234.master-1-staging.exabyte.io",
+                    "type": "string"
+                }
+            }
+        },
+        "errors": {
+            "description": "Computation error. Optional. Appears only if something happens on jobs execution.",
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "domain": {
+                        "description": "Domain of the error appearance (internal).",
+                        "type": "string",
+                        "enum": [
+                            "rupy",
+                            "alfred",
+                            "celim",
+                            "webapp"
+                        ]
+                    },
+                    "reason": {
+                        "description": "Should be a short, unique, machine-readable error code string. e.g. FileNotFound",
+                        "type": "string"
+                    },
+                    "message": {
+                        "description": "Human-readable error message. e.g. 'File Not Found: /home/demo/data/project1/job-123/job-config.json'",
+                        "type": "string"
+                    },
+                    "traceback": {
+                        "description": "Full machine-readable error traceback. e.g. FileNotFound",
+                        "type": "string"
+                    }
+                }
+            }
+        },
+        "excludeFilesPattern": {
+            "description": "A Python compatible regex to exclude files from upload. e.g. ^.*.txt& excludes all files with .txt suffix",
+            "type": "string"
+        }
+    },
+    "required": [
+        "queue",
+        "nodes",
+        "ppn",
+        "timeLimit"
+    ]
+}

package/schema/job.json

@@ -0,0 +1,19 @@
+{
+    "$id": "job",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "job schema",
+    "allOf": [
+        {
+            "$ref": "job/base.json"
+        }
+    ],
+    "properties": {
+        "workflow": {
+            "description": "Arch-workflow for the job",
+            "$ref": "workflow.json"
+        }
+    },
+    "required": [
+        "workflow"
+    ]
+}

package/schema/material/conventional.json

@@ -0,0 +1,10 @@
+{
+    "$id": "material/conventional",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "material conventional schema",
+    "properties": {
+        "conventional": {
+            "type": "object"
+        }
+    }
+}

package/schema/material.json

@@ -0,0 +1,57 @@
+{
+    "$id": "material",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "material schema",
+    "allOf": [
+        {
+            "description": "in-memory entity",
+            "$ref": "in_memory_entity/named_defaultable_has_metadata.json"
+        }
+    ],
+    "properties": {
+        "formula": {
+            "description": "reduced chemical formula",
+            "type": "string"
+        },
+        "unitCellFormula": {
+            "description": "chemical formula based on the number of atoms of each element in the supercell",
+            "type": "string"
+        },
+        "basis": {
+            "description": "object containing an array of elements and coordinates in the supercell",
+            "$ref": "properties_directory/structural/basis.json"
+        },
+        "lattice": {
+            "description": "object defining the lattice cell size and shape",
+            "$ref": "properties_directory/structural/lattice.json"
+        },
+        "derivedProperties": {
+            "description": "object defining the lattice cell size and shape",
+            "$ref": "properties_directory/derived_properties.json"
+        },
+        "external": {
+            "description": "information about external sources of this material",
+            "$ref": "system/database_source.json"
+        },
+        "src": {
+            "description": "File information if material was exported from POSCAR, XYZ or UPF file.",
+            "$ref": "system/file_source.json"
+        },
+        "scaledHash": {
+            "description": "Hash string for a scaled structure with lattice vector a set to 1 (eg. for materials under pressure).",
+            "type": "string"
+        },
+        "icsdId": {
+            "description": "Corresponding ICSD id of the material",
+            "type": "integer"
+        },
+        "isNonPeriodic": {
+            "description": "Whether to work in the finite molecular picture (usually with atomic orbital basis)",
+            "type": "boolean"
+        }
+    },
+    "required": [
+        "basis",
+        "lattice"
+    ]
+}

package/schema/method/categorized_method.json

@@ -0,0 +1,24 @@
+{
+    "$id": "method/categorized-method",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "categorized method",
+    "allOf": [
+        {
+            "$ref": "../system/path_entity.json"
+        },
+        {
+            "$ref": "../system/tags.json"
+        }
+    ],
+    "properties": {
+        "units": {
+            "type": "array",
+            "items": {
+                "$ref": "./unit_method.json"
+            }
+        }
+    },
+    "required": [
+        "units"
+    ]
+}

package/schema/method/method_parameters.json

@@ -0,0 +1,20 @@
+{
+    "$id": "method/method-parameters",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "MethodParameters",
+    "allOf": [
+        {
+            "oneOf": [
+                {
+                    "$ref": "../methods_directory/physical/ao/dunning.json#/definitions/ao-basis-dunning"
+                },
+                {
+                    "$ref": "../methods_directory/physical/ao/pople.json#/definitions/ao-basis-pople"
+                },
+                {
+                    "$ref": "../methods_directory/physical/ao/other.json#/definitions/ao-basis-other"
+                }
+            ]
+        }
+    ]
+}

package/schema/method/unit_method.json

@@ -0,0 +1,27 @@
+{
+    "$id": "method/unit-method",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "categorized unit method",
+    "allOf": [
+        {
+            "$ref": "../system/path_entity.json"
+        },
+        {
+            "$ref": "../system/tags.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "description": "Method categories",
+            "$ref": "../core/reusable/categories.json"
+        },
+        "parameters": {
+            "description": "Instructive parameters defining the method",
+            "type": "object"
+        },
+        "precision": {
+            "description": "Object showing the actual possible precision based on theory and implementation",
+            "type": "object"
+        }
+    }
+}

package/schema/method.json

@@ -0,0 +1,27 @@
+{
+    "$id": "method",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "base method",
+    "properties": {
+        "type": {
+            "description": "general type of this method, eg. `pseudopotential`",
+            "type": "string"
+        },
+        "subtype": {
+            "description": "general subtype of this method, eg. `ultra-soft`",
+            "type": "string"
+        },
+        "precision": {
+            "description": "Object showing the actual possible precision based on theory and implementation",
+            "type": "object"
+        },
+        "data": {
+            "description": "additional data specific to method, eg. array of pseudopotentials",
+            "type": "object"
+        }
+    },
+    "required": [
+        "type",
+        "subtype"
+    ]
+}

package/schema/methods_category/mathematical/diff/enum_options.json

@@ -0,0 +1,8 @@
+{
+    "$id": "methods-category/mathematical/diff/enum-options",
+    "finiteDifference": {
+        "enum": [
+            "fd"
+        ]
+    }
+}