Merge pull request #62 from bennybp/master

Clean up basis set schema
MolSSI · Jun 5, 2019 · 9524643 · 9524643
2 parents a4329e6 + a00a967
commit 9524643
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Showing 6 changed files with 187 additions and 182 deletions.
diff --git a/qcschema/dev/__init__.py b/qcschema/dev/__init__.py
@@ -1 +1 @@
-from .dev_schema import input_dev_schema, output_dev_schema, molecule_dev_schema
+from .dev_schema import input_dev_schema, output_dev_schema, molecule_dev_schema, basis_dev_schema
diff --git a/qcschema/dev/basis.py b/qcschema/dev/basis.py
@@ -0,0 +1,43 @@
+"""
+The json-schema for the Basis Set definition
+"""
+
+basis = {
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "name": "qcschema_basis",
+    "version": "1.dev",
+    "description": "The MolSSI Quantum Chemistry Basis Set Schema",
+    "type": "object",
+    "required": [
+        "basis_data",
+        "basis_atom_map"
+    ],
+    "additionalProperties": False,
+    "properties": {
+        "schema_name": {
+            "type": "string",
+            "pattern": "^(qcschema_basis)$"
+        },
+        "schema_version": {
+            "type": "integer"
+        },
+        "description": {
+            "description": "Brief description of the basis set",
+            "type": "string"
+        },
+        "basis_data": {
+            "description": "Shared basis data for all atoms/centers in the molecule",
+            "type": "object",
+            "additionalProperties": {
+                "$ref": "#/definitions/center_basis"
+            }
+        },
+        "basis_atom_map": {
+            "description": "Mapping of all atoms/centers in the molecule to data in basis_data",
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        }
+    }
+}
diff --git a/qcschema/dev/definitions.py b/qcschema/dev/definitions.py
@@ -40,21 +40,17 @@
     "additionalProperties": True
 }
 
-definitions["basis_electron_shell"] = {
+definitions["electron_shell"] = {
     "description": "Information for a single electronic shell",
     "additionalProperties": False,
     "required": [
-        "shell_angular_momentum",
-        "shell_exponents",
-        "shell_coefficients"
+        "angular_momentum",
+        "harmonic_type",
+        "exponents",
+        "coefficients"
     ],
     "properties": {
-        "shell_region": {
-            "description": "The region this shell describes",
-            "type": "string",
-            "enum": [ "valence", "polarization", "core", "tight", "diffuse" ]
-        },
-        "shell_angular_momentum": {
+        "angular_momentum": {
             "description": "Angular momentum (as an array of integers)",
             "type": "array",
             "minItems": 1,
@@ -64,15 +60,20 @@
                 "minimum": 0
             }
         },
-        "shell_exponents": {
+        "harmonic_type": {
+            "description": "Whether this shell is spherical or cartesian",
+            "type": "string",
+            "enum": ["spherical", "cartesian"]
+        },
+        "exponents": {
             "description": "Exponents for this contracted shell",
             "type": "array",
             "minItems": 1,
             "items": {
                 "type": "string"
             }
         },
-        "shell_coefficients": {
+        "coefficients": {
             "description": "General contraction coefficients for this contracted shell",
             "type": "array",
             "minItems": 1,
@@ -86,23 +87,23 @@
     }
 }
 
-definitions["basis_ecp_potential"] = {
+definitions["ecp_potential"] = {
     "description": "ECP potential",
     "additionalProperties": False,
     "required": [
-        "potential_ecp_type",
-        "potential_angular_momentum",
-        "potential_r_exponents",
-        "potential_gaussian_exponents",
-        "potential_coefficients"
+        "ecp_type",
+        "angular_momentum",
+        "r_exponents",
+        "gaussian_exponents",
+        "coefficients"
     ],
     "properties": {
-        "potential_ecp_type": {
+        "ecp_type": {
             "description": "Type of the ECP Potential",
             "type": "string",
             "enum": [ "scalar", "spinorbit" ]
         },
-        "potential_angular_momentum": {
+        "angular_momentum": {
             "description": "Angular momentum (as an array of integers)",
             "type": "array",
             "minItems": 1,
@@ -112,24 +113,24 @@
                 "minimum": 0
             }
         },
-        "potential_r_exponents": {
+        "r_exponents": {
             "description": "Exponents of the r term",
             "type": "array",
             "minItems": 1,
             "items": {
                 "type": "integer"
             }
         },
-        "potential_gaussian_exponents": {
+        "gaussian_exponents": {
             "description": "Exponents of the gaussian term",
             "type": "array",
             "minItems": 1,
             "items": {
                 "type": "string"
             }
         },
-        "potential_coefficients": {
-            "description": "General contraction coefficients for this contracted shell",
+        "coefficients": {
+            "description": "General contraction coefficients for this potential",
             "type": "array",
             "minItems": 1,
             "items": {
@@ -142,77 +143,34 @@
     }
 }
 
-definitions["basis_single_data"] = {
+definitions["center_basis"] = {
     "description": "Data for a single atom/center in the basis set",
     "type": "object",
     "additionalProperties": False,
     "properties": {
-        "element_electron_shells": {
+        "electron_shells": {
             "description": "(Electronic) shells for this element",
             "type": "array",
             "minItems": 1,
             "uniqueItems": True,
             "items": {
-                "$ref": "#/definitions/basis_electron_shell"
+                "$ref": "#/definitions/electron_shell"
             }
         },
-        "element_ecp_electrons":
+        "ecp_electrons":
         {
             "description": "Number of electrons replaced by ECP",
             "type": "integer",
             "minimum": 1
         },
-        "element_ecp": {
+        "ecp_potentials": {
             "description": "Effective Core Potential for this element",
             "type": "array",
             "minItems": 1,
             "uniqueItems": True,
             "items": {
-                "$ref": "#/definitions/basis_ecp_potential"
+                "$ref": "#/definitions/ecp_potential"
             }
         }
     }
 }
-
-definitions["basis_spec"] = {
-    "description": "Specification for a basis applied to a molecule",
-    "type": "object",
-    "additionalProperties": False,
-    "properties":
-    {
-        "basis_set_description": {
-            "description": "Brief description of the basis set",
-            "type": "string"
-        },  
-        "basis_function_type": {
-            "description": "Type of function for this basis",
-            "type": "string",
-            "enum": [ "gto", "sto" ]
-        },
-        "basis_harmonic_type": {
-            "description": "Harmonic type (spherical, cartesian)",
-            "type": "string",
-            "enum": [ "spherical", "cartesian" ]
-        },
-        "basis_set_elements": {
-            "description": "Per-element basis data",
-            "type": "object",
-            "additionalProperties": False,
-            "patternProperties":   {   
-                "^\\d+$" : { 
-                    "$ref" : "#/definitions/basis_single_data"
-                }   
-            }   
-        },  
-        "basis_set_atoms": {
-            "description": "Basis set overrides for particular atoms or centers",
-            "type": "object",
-            "additionalProperties": False,
-            "patternProperties":   {   
-                "^\\d+$" : { 
-                    "$ref" : "#/definitions/basis_single_data"
-                }   
-            }   
-        }   
-    }
-}
diff --git a/qcschema/dev/dev_schema.py b/qcschema/dev/dev_schema.py
@@ -7,6 +7,7 @@
 from . import molecule
 from . import definitions
 from . import properties
+from . import basis
 
 # The base schema definition
 base_schema = {
@@ -35,21 +36,16 @@
                     "type": "string"
                 },
                 "basis": {
-                    "type": "string"
-                },
-                "basis_spec": {
-                    "$ref": "#/definitions/basis_spec"
+                  "anyOf": [
+                    basis.basis,
+                    {
+                        "description": "Name of the basis set to apply to the whole molecule",
+                        "type": "string"
+                    },
+                  ]
                 }
             },
-            "required": [ "method" ],
-            "oneOf": [
-                {
-                    "required": ["basis"]
-                },
-                {
-                    "required": ["basis_spec"]
-                }
-            ],
+            "required": [ "method", "basis" ],
             "description": "The quantum chemistry model to be run."
         },
         "keywords": {
@@ -110,6 +106,9 @@
 # Build out the molecule schema
 molecule_dev_schema = copy.deepcopy(molecule.molecule)
 
+# Build out the basis schema
+basis_dev_schema = copy.deepcopy(basis.basis)
+
 #import json
 #print(json.dumps(input_dev_schema, indent=2))
 #print(json.dumps(output_dev_schema, indent=2))