replace schema with autogen from qcelemental

README.md

@@ -13,3 +13,29 @@ matrices in a consistent format that can be easily parsed.
 
 Please see the [website](http://molssi-qc-schema.readthedocs.io/en/latest/index.html#) for the current specification. 
 
+## Modifying the Schema
+
+JSON Schema can specify only data layout, descriptions, and basic
+defaults and type information for the models that compose QCSchema. To
+supplement data layout validation, physics validation, defaulting,
+serialization, and helper functions, a reference implementation in
+Python for the latest development version of QCSchema is available
+at the [QCElemental](https://github.com/MolSSI/QCElemental/)
+project. QCElemental uses
+[Pydantic](https://github.com/samuelcolvin/pydantic) to encode the
+models into Python classes which undergo considerable testing. Since
+the classes can auto-generate JSON Schema, it makes sense to use them
+as the definition of QCSchema, rather than hand-writing schema here
+and synching versions.
+
+The gist of the above is that schema in this repository are read-only. To
+propose a change, open an issue here at QCSchema or open a pull
+request at QCElemental. Any discussion of changes to QCSchema will
+take place here or will be cross-linked to here in accordance with [The
+Guidance](https://github.com/MolSSI/QCSchema/issues/68#issuecomment-578256825).
+
+* [`qcschema/dev/QCSchema.schema`](qcschema/dev/QCSchema.schema) — single-file, human-readable development schema exported from QCElemental.
+* [`qcschema/data/vdev/`](qcschema/data/vdev) — multi-file, compressed development schema exported from QCElemental. contents redundant to above.
+* [`qcschema/data/v2/`](qcschema/data/v2) — multi-file, compressed version 2 schema hand-written here. contents were `qcschema/dev/` until September 2020.
+* [`qcschema/data/v1/`](qcschema/data/v1) — multi-file, compressed version 1 schema hand-written here.
+

docs/source/faq.rst

@@ -10,7 +10,9 @@ found at the `JSON-Schema website <http://json-schema.org/implementations.html>`
 Does the schema accept arbitrary extra fields if my software piece needs internal extensions?
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Yes, we are currently discussing which fields are reserved and where the best
-place for arbitrary fields would be.
+place for arbitrary fields would be. Most high-level schema do *not* accept
+additional arbitrary fields, but they do have an ``extras`` dictionary-like field
+that can be used for schema development and scratch space.
 
 Are there libraries for writing the schema in [programming-language]?
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

qcschema/data/vdev/AtomicResultProperties.schema

@@ -0,0 +1 @@
+{"title": "AtomicResultProperties", "description": "Named properties of quantum chemistry computations following the MolSSI QCSchema.\n\n    Notes\n    -----\n    All arrays are stored flat but must be reshapable into the dimensions in attribute ``shape``, with abbreviations as follows:\n        nao: number of atomic orbitals = calcinfo_nbasis\n        nmo: number of molecular orbitals\n\n\nParameters\n----------\ncalcinfo_nbasis : int, Optional\n    The number of basis functions for the computation.\ncalcinfo_nmo : int, Optional\n    The number of molecular orbitals for the computation.\ncalcinfo_nalpha : int, Optional\n    The number of alpha electrons in the computation.\ncalcinfo_nbeta : int, Optional\n    The number of beta electrons in the computation.\ncalcinfo_natom : int, Optional\n    The number of atoms in the computation.\nnuclear_repulsion_energy : float, Optional\n    The nuclear repulsion energy.\nreturn_energy : float, Optional\n    The energy of the requested method, identical to ``return_result`` for ``driver=energy`` computations.\nscf_one_electron_energy : float, Optional\n    The one-electron (core Hamiltonian) energy contribution to the total SCF energy.\nscf_two_electron_energy : float, Optional\n    The two-electron energy contribution to the total SCF energy.\nscf_vv10_energy : float, Optional\n    The VV10 functional energy contribution to the total SCF energy.\nscf_xc_energy : float, Optional\n    The functional (XC) energy contribution to the total SCF energy.\nscf_dispersion_correction_energy : float, Optional\n    The dispersion correction appended to an underlying functional when a DFT-D method is requested.\nscf_dipole_moment : Array, Optional\n    The SCF X, Y, and Z dipole components\nscf_quadrupole_moment : Array, Optional\n    The quadrupole components (redundant; 6 unique).\nscf_total_energy : float, Optional\n    The total electronic energy of the SCF stage of the calculation.\nscf_iterations : int, Optional\n    The number of SCF iterations taken before convergence.\nmp2_same_spin_correlation_energy : float, Optional\n    The portion of MP2 doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.\nmp2_opposite_spin_correlation_energy : float, Optional\n    The portion of MP2 doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.\nmp2_singles_energy : float, Optional\n    The singles portion of the MP2 correlation energy. Zero except in ROHF.\nmp2_doubles_energy : float, Optional\n    The doubles portion of the MP2 correlation energy including same-spin and opposite-spin correlations.\nmp2_total_correlation_energy : float, Optional\n    The MP2 correlation energy.\nmp2_correlation_energy : float, Optional\n    The MP2 correlation energy.\nmp2_total_energy : float, Optional\n    The total MP2 energy (MP2 correlation energy + HF energy).\nmp2_dipole_moment : Array, Optional\n    The MP2 X, Y, and Z dipole components.\nccsd_same_spin_correlation_energy : float, Optional\n    The portion of CCSD doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.\nccsd_opposite_spin_correlation_energy : float, Optional\n    The portion of CCSD doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.\nccsd_singles_energy : float, Optional\n    The singles portion of the CCSD correlation energy. Zero except in ROHF.\nccsd_doubles_energy : float, Optional\n    The doubles portion of the CCSD correlation energy including same-spin and opposite-spin correlations.\nccsd_correlation_energy : float, Optional\n    The CCSD correlation energy.\nccsd_total_energy : float, Optional\n    The total CCSD energy (CCSD correlation energy + HF energy).\nccsd_dipole_moment : Array, Optional\n    The CCSD X, Y, and Z dipole components.\nccsd_iterations : int, Optional\n    The number of CCSD iterations taken before convergence.\nccsd_prt_pr_correlation_energy : float, Optional\n    The CCSD(T) correlation energy.\nccsd_prt_pr_total_energy : float, Optional\n    The total CCSD(T) energy (CCSD(T) correlation energy + HF energy).\nccsd_prt_pr_dipole_moment : Array, Optional\n    The CCSD(T) X, Y, and Z dipole components.\nccsdt_correlation_energy : float, Optional\n    The CCSDT correlation energy.\nccsdt_total_energy : float, Optional\n    The total CCSDT energy (CCSDT correlation energy + HF energy).\nccsdt_dipole_moment : Array, Optional\n    The CCSDT X, Y, and Z dipole components.\nccsdt_iterations : int, Optional\n    The number of CCSDT iterations taken before convergence.\nccsdtq_correlation_energy : float, Optional\n    The CCSDTQ correlation energy.\nccsdtq_total_energy : float, Optional\n    The total CCSDTQ energy (CCSDTQ correlation energy + HF energy).\nccsdtq_dipole_moment : Array, Optional\n    The CCSDTQ X, Y, and Z dipole components.\nccsdtq_iterations : int, Optional\n    The number of CCSDTQ iterations taken before convergence.", "type": "object", "properties": {"calcinfo_nbasis": {"title": "Calcinfo Nbasis", "description": "The number of basis functions for the computation.", "type": "integer"}, "calcinfo_nmo": {"title": "Calcinfo Nmo", "description": "The number of molecular orbitals for the computation.", "type": "integer"}, "calcinfo_nalpha": {"title": "Calcinfo Nalpha", "description": "The number of alpha electrons in the computation.", "type": "integer"}, "calcinfo_nbeta": {"title": "Calcinfo Nbeta", "description": "The number of beta electrons in the computation.", "type": "integer"}, "calcinfo_natom": {"title": "Calcinfo Natom", "description": "The number of atoms in the computation.", "type": "integer"}, "nuclear_repulsion_energy": {"title": "Nuclear Repulsion Energy", "description": "The nuclear repulsion energy.", "type": "number"}, "return_energy": {"title": "Return Energy", "description": "The energy of the requested method, identical to ``return_result`` for ``driver=energy`` computations.", "type": "number"}, "scf_one_electron_energy": {"title": "Scf One Electron Energy", "description": "The one-electron (core Hamiltonian) energy contribution to the total SCF energy.", "units": "E_h", "type": "number"}, "scf_two_electron_energy": {"title": "Scf Two Electron Energy", "description": "The two-electron energy contribution to the total SCF energy.", "units": "E_h", "type": "number"}, "scf_vv10_energy": {"title": "Scf Vv10 Energy", "description": "The VV10 functional energy contribution to the total SCF energy.", "units": "E_h", "type": "number"}, "scf_xc_energy": {"title": "Scf Xc Energy", "description": "The functional (XC) energy contribution to the total SCF energy.", "units": "E_h", "type": "number"}, "scf_dispersion_correction_energy": {"title": "Scf Dispersion Correction Energy", "description": "The dispersion correction appended to an underlying functional when a DFT-D method is requested.", "units": "E_h", "type": "number"}, "scf_dipole_moment": {"title": "Scf Dipole Moment", "description": "The SCF X, Y, and Z dipole components", "units": "e a0", "type": "array", "items": {"type": "number"}}, "scf_quadrupole_moment": {"title": "Scf Quadrupole Moment", "description": "The quadrupole components (redundant; 6 unique).", "shape": [3, 3], "units": "e a0^2", "type": "array", "items": {"type": "number"}}, "scf_total_energy": {"title": "Scf Total Energy", "description": "The total electronic energy of the SCF stage of the calculation.", "units": "E_h", "type": "number"}, "scf_iterations": {"title": "Scf Iterations", "description": "The number of SCF iterations taken before convergence.", "type": "integer"}, "mp2_same_spin_correlation_energy": {"title": "Mp2 Same Spin Correlation Energy", "description": "The portion of MP2 doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.", "units": "E_h", "type": "number"}, "mp2_opposite_spin_correlation_energy": {"title": "Mp2 Opposite Spin Correlation Energy", "description": "The portion of MP2 doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.", "units": "E_h", "type": "number"}, "mp2_singles_energy": {"title": "Mp2 Singles Energy", "description": "The singles portion of the MP2 correlation energy. Zero except in ROHF.", "units": "E_h", "type": "number"}, "mp2_doubles_energy": {"title": "Mp2 Doubles Energy", "description": "The doubles portion of the MP2 correlation energy including same-spin and opposite-spin correlations.", "units": "E_h", "type": "number"}, "mp2_total_correlation_energy": {"title": "Mp2 Total Correlation Energy", "description": "The MP2 correlation energy.", "type": "number"}, "mp2_correlation_energy": {"title": "Mp2 Correlation Energy", "description": "The MP2 correlation energy.", "units": "E_h", "type": "number"}, "mp2_total_energy": {"title": "Mp2 Total Energy", "description": "The total MP2 energy (MP2 correlation energy + HF energy).", "units": "E_h", "type": "number"}, "mp2_dipole_moment": {"title": "Mp2 Dipole Moment", "description": "The MP2 X, Y, and Z dipole components.", "shape": [3], "units": "e a0", "type": "array", "items": {"type": "number"}}, "ccsd_same_spin_correlation_energy": {"title": "Ccsd Same Spin Correlation Energy", "description": "The portion of CCSD doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.", "units": "E_h", "type": "number"}, "ccsd_opposite_spin_correlation_energy": {"title": "Ccsd Opposite Spin Correlation Energy", "description": "The portion of CCSD doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.", "units": "E_h", "type": "number"}, "ccsd_singles_energy": {"title": "Ccsd Singles Energy", "description": "The singles portion of the CCSD correlation energy. Zero except in ROHF.", "units": "E_h", "type": "number"}, "ccsd_doubles_energy": {"title": "Ccsd Doubles Energy", "description": "The doubles portion of the CCSD correlation energy including same-spin and opposite-spin correlations.", "units": "E_h", "type": "number"}, "ccsd_correlation_energy": {"title": "Ccsd Correlation Energy", "description": "The CCSD correlation energy.", "units": "E_h", "type": "number"}, "ccsd_total_energy": {"title": "Ccsd Total Energy", "description": "The total CCSD energy (CCSD correlation energy + HF energy).", "units": "E_h", "type": "number"}, "ccsd_dipole_moment": {"title": "Ccsd Dipole Moment", "description": "The CCSD X, Y, and Z dipole components.", "shape": [3], "units": "e a0", "type": "array", "items": {"type": "number"}}, "ccsd_iterations": {"title": "Ccsd Iterations", "description": "The number of CCSD iterations taken before convergence.", "type": "integer"}, "ccsd_prt_pr_correlation_energy": {"title": "Ccsd Prt Pr Correlation Energy", "description": "The CCSD(T) correlation energy.", "units": "E_h", "type": "number"}, "ccsd_prt_pr_total_energy": {"title": "Ccsd Prt Pr Total Energy", "description": "The total CCSD(T) energy (CCSD(T) correlation energy + HF energy).", "units": "E_h", "type": "number"}, "ccsd_prt_pr_dipole_moment": {"title": "Ccsd Prt Pr Dipole Moment", "description": "The CCSD(T) X, Y, and Z dipole components.", "shape": [3], "units": "e a0", "type": "array", "items": {"type": "number"}}, "ccsdt_correlation_energy": {"title": "Ccsdt Correlation Energy", "description": "The CCSDT correlation energy.", "units": "E_h", "type": "number"}, "ccsdt_total_energy": {"title": "Ccsdt Total Energy", "description": "The total CCSDT energy (CCSDT correlation energy + HF energy).", "units": "E_h", "type": "number"}, "ccsdt_dipole_moment": {"title": "Ccsdt Dipole Moment", "description": "The CCSDT X, Y, and Z dipole components.", "shape": [3], "units": "e a0", "type": "array", "items": {"type": "number"}}, "ccsdt_iterations": {"title": "Ccsdt Iterations", "description": "The number of CCSDT iterations taken before convergence.", "type": "integer"}, "ccsdtq_correlation_energy": {"title": "Ccsdtq Correlation Energy", "description": "The CCSDTQ correlation energy.", "units": "E_h", "type": "number"}, "ccsdtq_total_energy": {"title": "Ccsdtq Total Energy", "description": "The total CCSDTQ energy (CCSDTQ correlation energy + HF energy).", "units": "E_h", "type": "number"}, "ccsdtq_dipole_moment": {"title": "Ccsdtq Dipole Moment", "description": "The CCSDTQ X, Y, and Z dipole components.", "shape": [3], "units": "e a0", "type": "array", "items": {"type": "number"}}, "ccsdtq_iterations": {"title": "Ccsdtq Iterations", "description": "The number of CCSDTQ iterations taken before convergence.", "type": "integer"}}, "additionalProperties": false}