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Subworkflows: Structured Representation

The JSON structured representation of subworkflows, together with an example, is contained below.

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{
    "title": "subworkflow schema", 
    "schemaId": "workflow-subworkflow", 
    "required": [
        "_id", 
        "name", 
        "units", 
        "model", 
        "application", 
        "properties"
    ], 
    "$schema": "http://json-schema.org/draft-04/schema#", 
    "type": "object", 
    "properties": {
        "compute": {
            "schemaId": "job-compute", 
            "required": [
                "queue", 
                "nodes", 
                "ppn", 
                "timeLimit"
            ], 
            "properties": {
                "errors": {
                    "items": {
                        "required": [
                            "domain", 
                            "reason", 
                            "message"
                        ], 
                        "type": "object", 
                        "properties": {
                            "domain": {
                                "enum": [
                                    "rupy", 
                                    "alfred", 
                                    "celim", 
                                    "webapp"
                                ], 
                                "type": "string", 
                                "description": "Domain of the error appearance (internal)."
                            }, 
                            "message": {
                                "type": "string", 
                                "description": "Human-readable error message. e.g. 'File Not Found: /home/demo/data/project1/job-123/job-config.json'"
                            }, 
                            "reason": {
                                "type": "string", 
                                "description": "Should be a short, unique, machine-readable error code string. e.g. FileNotFound"
                            }
                        }
                    }, 
                    "type": "array", 
                    "description": "Computation error. Optional. Appears only if something happens on jobs execution."
                }, 
                "maxCPU": {
                    "type": "integer", 
                    "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."
                }, 
                "cluster": {
                    "required": [
                        "fqdn", 
                        "jid"
                    ], 
                    "type": "object", 
                    "description": "Cluster where the job is executed. Optional on create. Required on job submission.", 
                    "properties": {
                        "jid": {
                            "type": "string", 
                            "description": "Job's identity in RMS. e.g. 1234.master-1-staging.exabyte.io"
                        }, 
                        "fqdn": {
                            "type": "string", 
                            "description": "FQDN of the cluster. e.g. master-1-staging.exabyte.io"
                        }
                    }
                }, 
                "excludeFilesPattern": {
                    "type": "string", 
                    "description": "A Python compatible regex to exclude files from upload. e.g. ^.*.txt& excludes all files with .txt suffix"
                }, 
                "ppn": {
                    "type": "integer", 
                    "description": "number of CPUs used for the job inside the RMS."
                }, 
                "queue": {
                    "enum": [
                        "D", 
                        "OR", 
                        "SR", 
                        "OF", 
                        "SF"
                    ], 
                    "type": "string", 
                    "description": "Name of the submission queue inside the Resource Management System (RMS). D: debug, OR: on-demand reuglar, SR: saving reuglar, OF: on-demand fast, SF: saving fast"
                }, 
                "timeLimit": {
                    "type": "string", 
                    "description": "Wallclock time limit for computing a job. Clock format: 'hh:mm:ss'"
                }, 
                "notify": {
                    "type": "string", 
                    "description": "Email notification for the job: n - never, a - job aborted, b - job begins, e - job ends. Last three could be combined."
                }, 
                "nodes": {
                    "type": "integer", 
                    "description": "number of nodes used for the job inside the RMS."
                }, 
                "email": {
                    "type": "string", 
                    "description": "Email address to notify about job execution."
                }, 
                "arguments": {
                    "type": "object", 
                    "description": "Optional arguments specific to using application - VASP, Quantum Espresso, etc. Specified elsewhere"
                }
            }, 
            "description": "compute parameters", 
            "title": "compute arguments schema"
        }, 
        "name": {
            "type": "string", 
            "description": "Human-readable name of the subworkflow. e.g. Total-energy"
        }, 
        "isDraft": {
            "default": false, 
            "type": "boolean", 
            "description": "Defines whether to store the results/properties extracted in this unit to properties collection"
        }, 
        "application": {
            "description": "information about the simulation engine/application.", 
            "title": "application schema (base)", 
            "schemaId": "software-application", 
            "required": [
                "name"
            ], 
            "type": "object", 
            "properties": {
                "build": {
                    "type": "string", 
                    "description": "Application build. e.g. VTST"
                }, 
                "shortName": {
                    "type": "string", 
                    "description": "The short name of the application. e.g. qe"
                }, 
                "version": {
                    "type": "string", 
                    "description": "Application version. e.g. 5.3.5"
                }, 
                "name": {
                    "type": "string", 
                    "description": "The name of the application. e.g. espresso"
                }, 
                "summary": {
                    "type": "string", 
                    "description": "Application's short description."
                }
            }
        }, 
        "units": {
            "items": {
                "schemaId": "workflow-unit", 
                "required": [
                    "type", 
                    "flowchartId"
                ], 
                "type": "object", 
                "properties": {
                    "status": {
                        "enum": [
                            "idle", 
                            "active", 
                            "warning", 
                            "error", 
                            "finished"
                        ], 
                        "type": "string", 
                        "description": "Status of the unit."
                    }, 
                    "head": {
                        "type": "boolean", 
                        "description": "Whether this unit is the first one to be executed."
                    }, 
                    "flowchartId": {
                        "type": "string", 
                        "description": "Identity of the unit in the workflow. Used to trace the execution flow of the workflow."
                    }, 
                    "name": {
                        "type": "string", 
                        "description": "name of the unit. e.g. pw_scf"
                    }, 
                    "next": {
                        "type": "string", 
                        "description": "Next unit's flowchartId. If empty, the current unit is the last."
                    }, 
                    "type": {
                        "type": "string", 
                        "description": "type of the unit"
                    }
                }, 
                "title": "workflow unit schema"
            }, 
            "type": "array", 
            "description": "Contains the Units of the subworkflow"
        }, 
        "model": {
            "oneOf": [
                {
                    "schemaId": "models-directory-dft", 
                    "allOf": [
                        {
                            "schemaId": "model", 
                            "required": [
                                "type", 
                                "subtype", 
                                "method"
                            ], 
                            "properties": {
                                "subtype": {
                                    "type": "string", 
                                    "description": "general subtype of the model, eg. `lda`"
                                }, 
                                "type": {
                                    "type": "string", 
                                    "description": "general type of the model, eg. `dft`"
                                }, 
                                "method": {
                                    "schemaId": "method", 
                                    "required": [
                                        "type", 
                                        "subtype"
                                    ], 
                                    "properties": {
                                        "subtype": {
                                            "type": "string", 
                                            "description": "general subtype of this method, eg. `ultra-soft`"
                                        }, 
                                        "type": {
                                            "type": "string", 
                                            "description": "general type of this method, eg. `pseudopotential`"
                                        }, 
                                        "precision": {
                                            "type": "object", 
                                            "description": "Object showing the actual possible precision based on theory and implementation"
                                        }, 
                                        "data": {
                                            "type": "object", 
                                            "description": "additional data specific to method, eg. array of pseudopotentials"
                                        }
                                    }, 
                                    "title": "method schema (base)"
                                }
                            }, 
                            "title": "model schema (base)"
                        }
                    ], 
                    "properties": {
                        "subtype": {
                            "enum": [
                                "gga", 
                                "lda", 
                                "mgga", 
                                "ldau"
                            ]
                        }, 
                        "refiners": {
                            "items": {
                                "type": "object", 
                                "properties": {
                                    "slug": {
                                        "enum": [
                                            "hse", 
                                            "g0w0"
                                        ]
                                    }
                                }
                            }, 
                            "type": "array"
                        }, 
                        "modifiers": {
                            "items": {
                                "type": "object", 
                                "properties": {
                                    "slug": {
                                        "enum": [
                                            "soc", 
                                            "magn"
                                        ]
                                    }
                                }
                            }, 
                            "type": "array"
                        }, 
                        "type": {
                            "enum": [
                                "dft"
                            ]
                        }, 
                        "functional": {
                            "oneOf": [
                                {
                                    "type": "object", 
                                    "properties": {
                                        "slug": {
                                            "enum": [
                                                "pz", 
                                                "pw", 
                                                "vwn"
                                            ], 
                                            "type": "string"
                                        }
                                    }
                                }, 
                                {
                                    "type": "object", 
                                    "properties": {
                                        "slug": {
                                            "enum": [
                                                "pbe", 
                                                "pw91", 
                                                "rpbe"
                                            ], 
                                            "type": "string"
                                        }
                                    }
                                }, 
                                {
                                    "type": "object", 
                                    "properties": {
                                        "slug": {
                                            "enum": [
                                                "ldau", 
                                                "bp", 
                                                "lyp", 
                                                "b3lyp", 
                                                "pbesol", 
                                                "hse", 
                                                "am05", 
                                                "rtpss", 
                                                "tpss", 
                                                "m06l", 
                                                "mbj", 
                                                "vdwd3", 
                                                "fci"
                                            ], 
                                            "type": "string"
                                        }
                                    }
                                }
                            ]
                        }
                    }, 
                    "description": "density function theory schema (deprecated - to be replaced with manifest)", 
                    "title": "density function theory schema"
                }, 
                {
                    "schemaId": "models-directory-ml", 
                    "allOf": [
                        {
                            "schemaId": "model", 
                            "required": [
                                "type", 
                                "subtype", 
                                "method"
                            ], 
                            "properties": {
                                "subtype": {
                                    "type": "string", 
                                    "description": "general subtype of the model, eg. `lda`"
                                }, 
                                "type": {
                                    "type": "string", 
                                    "description": "general type of the model, eg. `dft`"
                                }, 
                                "method": {
                                    "schemaId": "method", 
                                    "required": [
                                        "type", 
                                        "subtype"
                                    ], 
                                    "properties": {
                                        "subtype": {
                                            "type": "string", 
                                            "description": "general subtype of this method, eg. `ultra-soft`"
                                        }, 
                                        "type": {
                                            "type": "string", 
                                            "description": "general type of this method, eg. `pseudopotential`"
                                        }, 
                                        "precision": {
                                            "type": "object", 
                                            "description": "Object showing the actual possible precision based on theory and implementation"
                                        }, 
                                        "data": {
                                            "type": "object", 
                                            "description": "additional data specific to method, eg. array of pseudopotentials"
                                        }
                                    }, 
                                    "title": "method schema (base)"
                                }
                            }, 
                            "title": "model schema (base)"
                        }
                    ], 
                    "properties": {
                        "subtype": {
                            "enum": [
                                "re"
                            ]
                        }, 
                        "type": {
                            "enum": [
                                "ml"
                            ]
                        }, 
                        "method": {
                            "oneOf": [
                                {
                                    "required": [
                                        "precision", 
                                        "data"
                                    ], 
                                    "schemaId": "methods-directory-regression", 
                                    "allOf": [
                                        {
                                            "schemaId": "method", 
                                            "required": [
                                                "type", 
                                                "subtype"
                                            ], 
                                            "properties": {
                                                "subtype": {
                                                    "type": "string", 
                                                    "description": "general subtype of this method, eg. `ultra-soft`"
                                                }, 
                                                "type": {
                                                    "type": "string", 
                                                    "description": "general type of this method, eg. `pseudopotential`"
                                                }, 
                                                "precision": {
                                                    "type": "object", 
                                                    "description": "Object showing the actual possible precision based on theory and implementation"
                                                }, 
                                                "data": {
                                                    "type": "object", 
                                                    "description": "additional data specific to method, eg. array of pseudopotentials"
                                                }
                                            }, 
                                            "title": "method schema (base)"
                                        }
                                    ], 
                                    "properties": {
                                        "subtype": {
                                            "enum": [
                                                "least_squares", 
                                                "ridge"
                                            ]
                                        }, 
                                        "type": {
                                            "enum": [
                                                "linear"
                                            ]
                                        }, 
                                        "precision": {
                                            "perProperty": {
                                                "items": {
                                                    "type": "object", 
                                                    "properties": {
                                                        "name": {
                                                            "type": "string", 
                                                            "description": "property name in 'flattened' format"
                                                        }
                                                    }, 
                                                    "allOf": [
                                                        {
                                                            "schemaId": "methods-directory-regression-precision", 
                                                            "oneOf": [
                                                                {
                                                                    "schemaId": "methods-directory-regression-linear-precision-per-property", 
                                                                    "required": [
                                                                        "trainingError"
                                                                    ], 
                                                                    "properties": {
                                                                        "score": {
                                                                            "type": "number", 
                                                                            "description": "prediction score of the estimator. Eg: r2_score"
                                                                        }, 
                                                                        "trainingError": {
                                                                            "type": "number", 
                                                                            "description": "training error of the estimator"
                                                                        }
                                                                    }, 
                                                                    "title": "precision schema for regression"
                                                                }
                                                            ], 
                                                            "title": "regression precision"
                                                        }
                                                    ]
                                                }
                                            }
                                        }, 
                                        "data": {
                                            "perProperty": {
                                                "items": {
                                                    "type": "object", 
                                                    "properties": {
                                                        "name": {
                                                            "type": "string", 
                                                            "description": "property name in 'flattened' format"
                                                        }
                                                    }, 
                                                    "allOf": [
                                                        {
                                                            "schemaId": "methods-directory-regression-data", 
                                                            "oneOf": [
                                                                {
                                                                    "schemaId": "methods-directory-regression-linear-data-per-property", 
                                                                    "required": [
                                                                        "intercept", 
                                                                        "perFeature"
                                                                    ], 
                                                                    "properties": {
                                                                        "perFeature": {
                                                                            "items": {
                                                                                "required": [
                                                                                    "name", 
                                                                                    "coefficient"
                                                                                ], 
                                                                                "type": "object", 
                                                                                "properties": {
                                                                                    "coefficient": {
                                                                                        "type": "number", 
                                                                                        "description": "coefficient in linear regression"
                                                                                    }, 
                                                                                    "importance": {
                                                                                        "type": "number", 
                                                                                        "description": "pvalue: https://en.wikipedia.org/wiki/P-value"
                                                                                    }, 
                                                                                    "name": {
                                                                                        "type": "string", 
                                                                                        "description": "feature name in 'flattened' format"
                                                                                    }
                                                                                }
                                                                            }, 
                                                                            "type": "array", 
                                                                            "description": "per-feature (property used for training the ML method/model) paramters"
                                                                        }, 
                                                                        "intercept": {
                                                                            "type": "number", 
                                                                            "description": "intercept (shift) from the linear or non-linear fit of data points"
                                                                        }
                                                                    }, 
                                                                    "title": "linear regression parameters schema"
                                                                }
                                                            ], 
                                                            "title": "regression data"
                                                        }
                                                    ]
                                                }
                                            }, 
                                            "dataSet": {
                                                "schemaId": "methods-directory-regression-dataset", 
                                                "required": [
                                                    "exabyteIds"
                                                ], 
                                                "type": "object", 
                                                "description": "dataset for ml", 
                                                "properties": {
                                                    "exabyteIds": {
                                                        "items": {
                                                            "type": "string"
                                                        }, 
                                                        "type": "array", 
                                                        "description": "array of exabyteIds for materials in dataset"
                                                    }, 
                                                    "extra": {
                                                        "description": "holder for any extra information, eg. coming from user-uploaded CSV file"
                                                    }
                                                }
                                            }
                                        }
                                    }, 
                                    "title": "linear methods schema"
                                }
                            ]
                        }
                    }, 
                    "description": "machine learning model type/subtype schema", 
                    "title": "machine learning model schema"
                }, 
                {
                    "schemaId": "models-directory-unknown", 
                    "allOf": [
                        {
                            "schemaId": "model", 
                            "required": [
                                "type", 
                                "subtype", 
                                "method"
                            ], 
                            "properties": {
                                "subtype": {
                                    "type": "string", 
                                    "description": "general subtype of the model, eg. `lda`"
                                }, 
                                "type": {
                                    "type": "string", 
                                    "description": "general type of the model, eg. `dft`"
                                }, 
                                "method": {
                                    "schemaId": "method", 
                                    "required": [
                                        "type", 
                                        "subtype"
                                    ], 
                                    "properties": {
                                        "subtype": {
                                            "type": "string", 
                                            "description": "general subtype of this method, eg. `ultra-soft`"
                                        }, 
                                        "type": {
                                            "type": "string", 
                                            "description": "general type of this method, eg. `pseudopotential`"
                                        }, 
                                        "precision": {
                                            "type": "object", 
                                            "description": "Object showing the actual possible precision based on theory and implementation"
                                        }, 
                                        "data": {
                                            "type": "object", 
                                            "description": "additional data specific to method, eg. array of pseudopotentials"
                                        }
                                    }, 
                                    "title": "method schema (base)"
                                }
                            }, 
                            "title": "model schema (base)"
                        }
                    ], 
                    "properties": {
                        "subtype": {
                            "enum": [
                                "unknown"
                            ]
                        }, 
                        "type": {
                            "enum": [
                                "unknown"
                            ]
                        }, 
                        "method": {
                            "schemaId": "methods-directory-unknown", 
                            "allOf": [
                                {
                                    "schemaId": "method", 
                                    "required": [
                                        "type", 
                                        "subtype"
                                    ], 
                                    "properties": {
                                        "subtype": {
                                            "type": "string", 
                                            "description": "general subtype of this method, eg. `ultra-soft`"
                                        }, 
                                        "type": {
                                            "type": "string", 
                                            "description": "general type of this method, eg. `pseudopotential`"
                                        }, 
                                        "precision": {
                                            "type": "object", 
                                            "description": "Object showing the actual possible precision based on theory and implementation"
                                        }, 
                                        "data": {
                                            "type": "object", 
                                            "description": "additional data specific to method, eg. array of pseudopotentials"
                                        }
                                    }, 
                                    "title": "method schema (base)"
                                }
                            ], 
                            "properties": {
                                "subtype": {
                                    "enum": [
                                        "unknown"
                                    ]
                                }, 
                                "type": {
                                    "enum": [
                                        "unknown"
                                    ]
                                }
                            }, 
                            "title": "unknown methods schema"
                        }
                    }, 
                    "description": "schema for cases when model is unknown", 
                    "title": "unknown model schema"
                }
            ], 
            "description": "Model used inside the subworkflow"
        }, 
        "_id": {
            "type": "string", 
            "description": "subworkflow identity"
        }, 
        "properties": {
            "items": {
                "type": "string", 
                "description": "property names, eg. `band_gaps`, `band_structure`"
            }, 
            "type": "array", 
            "description": "Array of characteristic properties calculated by this subworkflow"
        }
    }
}
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{
    "name": "Band Structure", 
    "application": {
        "shortName": "qe", 
        "version": "5.1.1", 
        "name": "espresso", 
        "summary": "Quantum Espresso"
    }, 
    "units": [
        {
            "status": "idle", 
            "type": "execution", 
            "head": true, 
            "flowchartId": "pw-scf", 
            "name": "pw_scf"
        }
    ], 
    "model": {
        "modifiers": [
            {
                "slug": "soc"
            }
        ], 
        "functional": {
            "slug": "pbe"
        }, 
        "subtype": "gga", 
        "refiners": [
            {
                "slug": "hse"
            }
        ], 
        "type": "dft", 
        "method": {
            "subtype": "us", 
            "data": {
                "searchText": "", 
                "pseudo": [
                    {
                        "files": [
                            {
                                "valenceElectrons": 4, 
                                "name": "pseudopotential file", 
                                "electronicConfiguration": "s2p2", 
                                "generationDate": "05Jan2001", 
                                "textHeading": "PAW_PBE Si 05Jan2001\n   4.00000000000000\nparameters from PSCTR are:\n   VRHFIN =Si: s2p2\n   LEXCH  = PE\n   EATOM  =   103.0669 eV,    7.5752 Ry\n \n   TITEL  = PAW_PBE Si 05Jan2001\n   LULTRA =        F    use ultrasoft PP ?\n   IUNSCR =        1    unscreen: 0-lin 1-nonlin 2-no\n   RPACOR =    1.500    partial core radius\n   POMASS =   28.085; ZVAL   =    4.000    mass and valenz\n   RCORE  =    1.900    outmost cutoff radius\n   RWIGS  =    2.480; RWIGS  =    1.312    wigner-seitz radius (au A)\n   ENMAX  =  245.345; ENMIN  =  184.009 eV\n   ICORE  =        2    local potential\n   LCOR   =        T    correct aug charges\n   LPAW   =        T    paw PP\n   EAUG   =  322.069\n   DEXC   =    0.000\n   RMAX   =    1.950    core radius for proj-oper\n   RAUG   =    1.300    factor for augmentation sphere\n   RDEP   =    1.993    radius for radial grids\n   RDEPT  =    1.837    core radius for aug-charge\n \n   Atomic configuration\n    6 entries     n  l   j            E        occ.\n     1  0  0.50     -1785.8828   2.0000\n     2  0  0.50      -139.4969   2.0000\n     2  1  1.50       -95.5546   6.0000\n     3  0  0.50       -10.8127   2.0000\n     3  1  0.50        -4.0811   2.0000\n     3  2  1.50        -4.0817   0.0000\n   Description\n     l       E           TYP  RCUT    TYP  RCUT\n     0    -10.8127223     23  1.900\n     0     -7.6451159     23  1.900\n     1     -4.0811372     23  1.900\n     1      2.4879257     23  1.900\n     2     -4.0817478      7  1.900\n   Error from kinetic energy argument (eV)\n", 
                                "title": "Si paw pbe vasp 5.2", 
                                "apps": [
                                    "vasp"
                                ], 
                                "element": "Si", 
                                "source": "vasp", 
                                "radii": {
                                    "units": "angstrom", 
                                    "cutoff": 1.9, 
                                    "wignerSeitz": 1.312, 
                                    "name": "radii", 
                                    "partialCore": 1.5
                                }, 
                                "mass": 28.085, 
                                "energyCutoff": {
                                    "units": "eV", 
                                    "max": 245.345, 
                                    "name": "energy cutoff", 
                                    "min": 184.009
                                }, 
                                "path": "/export/share/pseudo/ag/gga/pbe/gbrv/1.4/us/ag_pbe_gbrv_1.4.upf", 
                                "type": "paw", 
                                "exchangeCorrelation": {
                                    "approximation": "gga", 
                                    "functional": "pbe"
                                }
                            }
                        ], 
                        "elements": [
                            "Si", 
                            "Ge", 
                            "As"
                        ], 
                        "name": "my set", 
                        "format": "upf", 
                        "apps": [
                            "espresso"
                        ], 
                        "source": "gbrv", 
                        "version": "1.5", 
                        "type": "us", 
                        "exchangeCorrelation": {
                            "approximation": "gga", 
                            "functional": "pbe"
                        }
                    }
                ]
            }, 
            "type": "pseudopotential"
        }
    }, 
    "_id": "LCthJ6E2QabYCZqf4", 
    "properties": [
        "band_structure"
    ]
}