diff --git a/sphinxman/master/.buildinfo b/sphinxman/master/.buildinfo index cd43ed90955..178496a1600 100644 --- a/sphinxman/master/.buildinfo +++ b/sphinxman/master/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 90f04b54ad3f9de09f0a54d6e76fac06 +config: 7ad4046aa4f98ff7fd98ecc8996b9fa3 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/sphinxman/master/_downloads/15093ea218ca0a61a6f46db92e78ed97/gdma-2.3.pdf b/sphinxman/master/_downloads/15093ea218ca0a61a6f46db92e78ed97/gdma-2.3.pdf new file mode 100644 index 00000000000..2e5121132b3 Binary files /dev/null and b/sphinxman/master/_downloads/15093ea218ca0a61a6f46db92e78ed97/gdma-2.3.pdf differ diff --git a/sphinxman/master/_downloads/bb210d30fde032b2d23ae4dcb2ad36e2/gdma-2.2.06.pdf b/sphinxman/master/_downloads/bb210d30fde032b2d23ae4dcb2ad36e2/gdma-2.2.06.pdf deleted file mode 100644 index 0fc6cca340d..00000000000 Binary files a/sphinxman/master/_downloads/bb210d30fde032b2d23ae4dcb2ad36e2/gdma-2.2.06.pdf and /dev/null differ diff --git a/sphinxman/master/_images/inheritance-88de7a842b7851ce59b6337a714418048cda197e.png b/sphinxman/master/_images/inheritance-e850a6ad900d8c0535876adee97e7fc9807893b8.png similarity index 100% rename from sphinxman/master/_images/inheritance-88de7a842b7851ce59b6337a714418048cda197e.png rename to sphinxman/master/_images/inheritance-e850a6ad900d8c0535876adee97e7fc9807893b8.png diff --git a/sphinxman/master/_images/inheritance-88de7a842b7851ce59b6337a714418048cda197e.png.map b/sphinxman/master/_images/inheritance-e850a6ad900d8c0535876adee97e7fc9807893b8.png.map similarity index 96% rename from sphinxman/master/_images/inheritance-88de7a842b7851ce59b6337a714418048cda197e.png.map rename to sphinxman/master/_images/inheritance-e850a6ad900d8c0535876adee97e7fc9807893b8.png.map index 2b78dc26791..fe40fad4e5f 100644 --- a/sphinxman/master/_images/inheritance-88de7a842b7851ce59b6337a714418048cda197e.png.map +++ b/sphinxman/master/_images/inheritance-e850a6ad900d8c0535876adee97e7fc9807893b8.png.map @@ -1,5 +1,5 @@ - + diff --git a/sphinxman/master/_modules/index.html b/sphinxman/master/_modules/index.html index 2bdc0f61949..35bd7ea1786 100644 --- a/sphinxman/master/_modules/index.html +++ b/sphinxman/master/_modules/index.html @@ -46,7 +46,7 @@ - + @@ -92,7 +92,7 @@

Navigation

  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  • so_dkh() (psi4.core.MintsHelper method) -
  • -
  • so_ecp() (psi4.core.MintsHelper method)
  • so_kinetic() (psi4.core.IntegralFactory method) @@ -10017,7 +10013,7 @@

    Navigation

  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  • -
  • bsse_type (str or list) –

    'cp' || ['nocp', 'vmfc'] || \(\Rightarrow\) None \(\Leftarrow\) || etc.

    +
  • bsse_type (str or list) –

    'cp' || ['nocp', 'vmfc'] || \(\Rightarrow\) None \(\Leftarrow\) || etc.

    Type of BSSE correction to compute: CP for counterpoise correction, NoCP for plain supramolecular interaction energy, or VMFC for Valiron-Mayer Function Counterpoise correction. If a list is provided, the first string in the list determines which interaction or total energies/gradients/Hessians are returned by this function. By default, many-body treatments are inactive.

  • -
  • max_nbody (int) –

    3 || etc.

    +
  • max_nbody (int) –

    3 || etc.

    Maximum n-body to compute, cannot exceed the number of fragments in the molecule.

  • return_total_data (boolean) –

    'on' || \(\Rightarrow\) 'off' \(\Leftarrow\)

    @@ -163,12 +163,12 @@

    Navigation

    may carry out more computations than return_total_data = False. For gradients and Hessians, return_total_data = False is rarely useful.

  • -
  • levels (dict) –

    {1: 'ccsd(t)', 2: 'mp2', 'supersystem': 'scf'} || {1: 2, 2: 'ccsd(t)', 3: 'mp2'} || etc

    +
  • levels (dict) –

    {1: 'ccsd(t)', 2: 'mp2', 'supersystem': 'scf'} || {1: 2, 2: 'ccsd(t)', 3: 'mp2'} || etc

    Dictionary of different levels of theory for different levels of expansion Note that method_string is not used in this case. supersystem computes all higher order n-body effects up to the number of fragments.

  • -
  • embedding_charges (dict) –

    {1: [-0.834, 0.417, 0.417], ..}

    +
  • embedding_charges (dict) –

    {1: [-0.834, 0.417, 0.417], ..}

    Dictionary of atom-centered point charges. keys: 1-based index of fragment, values: list of charges for each fragment. Add atom-centered point charges for fragments whose basis sets are not included in the computation.

  • @@ -213,7 +213,7 @@

    Navigation

    API

    -class psi4.driver.driver_nbody.BsseEnum(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
    +class psi4.driver.driver_nbody.BsseEnum(value)[source]

    Available basis-set superposition error (BSSE) treatments.

    @@ -715,12 +715,12 @@

    API

    -field basis: str = '(auto)'
    +field basis: str = '(auto)'
    -field bsse_type: List[BsseEnum] = [BsseEnum.cp]
    +field bsse_type: List[BsseEnum] = [BsseEnum.cp]

    Requested BSSE treatments. First in list determines which interaction or total energy/gradient/Hessian returned.

    Validated by:
    @@ -739,7 +739,7 @@

    API

    -field embedding_charges: Dict[int, List[float]] = {}
    +field embedding_charges: Dict[int, List[float]] = {}

    Atom-centered point charges to be used on molecule fragments whose basis sets are not included in the computation. Keys: 1-based index of fragment. Values: list of atom charges for that fragment.

    Validated by:
    @@ -752,13 +752,13 @@

    API

    -field keywords: Dict[str, Any] = {}
    +field keywords: Dict[str, Any] = {}

    The computation keywords/options.

    -field max_nbody: int = -1
    +field max_nbody: int = -1

    Maximum number of bodies to include in the many-body treatment. Possible: max_nbody <= nfragments. Default: max_nbody = nfragments.

    Validated by:
    @@ -771,12 +771,12 @@

    API

    -field method: str = '(auto)'
    +field method: str = '(auto)'
    -field molecule: Any [Required]
    +field molecule: Any [Required]

    The target molecule, if not the last molecule defined.

    Validated by:
    @@ -789,13 +789,13 @@

    API

    -field nbodies_per_mc_level: List[List[Union[int, Literal['supersystem']]]] = []
    +field nbodies_per_mc_level: List[List[Union[int, Literal['supersystem']]]] = []

    Distribution of active n-body levels among model chemistry levels. All bodies in range [1, self.max_nbody] must be present exactly once. Number of items in outer list is how many different modelchems. Each inner list specifies what n-bodies to be run at the corresponding modelchem (e.g., [[1, 2]] has max_nbody=2 and 1-body and 2-body contributions computed at the same level of theory; [[1], [2]] has max_nbody=2 and 1-body and 2-body contributions computed at different levels of theory. An entry ‘supersystem’ means all higher order n-body effects up to the number of fragments. The n-body levels are effectively sorted in the outer list, and any ‘supersystem’ element is at the end.

    -field nfragments: int = -1
    +field nfragments: int = -1

    Number of distinct fragments comprising full molecular supersystem.

    Validated by:
    @@ -808,13 +808,13 @@

    API

    -field quiet: bool = False
    +field quiet: bool = False

    Whether to print/log formatted n-body energy analysis. Presently used by multi to suppress output. Candidate for removal from class once in-class/out-of-class functions sorted.

    -field return_total_data: Optional[bool] = None
    +field return_total_data: Optional[bool] = None

    When True, returns the total data (energy/gradient/Hessian) of the system, otherwise returns interaction data. Default is False for energies, True for gradients and Hessians. Note that the calculation of total counterpoise corrected energies implies the calculation of the energies of monomers in the monomer basis, hence specifying return_total_data = True may carry out more computations than return_total_data = False.

    Validated by:
    @@ -827,7 +827,7 @@

    API

    -field task_list: Dict[str, Union[AtomicComputer, CompositeComputer, FiniteDifferenceComputer]] = {}
    +field task_list: Dict[str, Union[AtomicComputer, CompositeComputer, FiniteDifferenceComputer]] = {}
    @@ -838,14 +838,14 @@

    API

    Parameters:
      -
    • mb_computer (Union[AtomicComputer, CompositeComputer, FiniteDifferenceComputer]) – Class of task computers to instantiate and add to self.task_list. Usually AtomicComputer but may be other when wrappers are layered.

    • -
    • mc_level_idx (int) – Position in field self.nbodies_per_mc_level used to obtain nbodies, the list of n-body +

    • mb_computer (Union[AtomicComputer, CompositeComputer, FiniteDifferenceComputer]) – Class of task computers to instantiate and add to self.task_list. Usually AtomicComputer but may be other when wrappers are layered.

    • +
    • mc_level_idx (int) – Position in field self.nbodies_per_mc_level used to obtain nbodies, the list of n-body levels (e.g., [1] or [1, 2] or [“supersystem”]) to which the modelchem specified in kwargs applies. That is, nbodies = self.nbodies_per_mc_level[mc_level_idx]. Note the natural 1-indexing of nbodies _contents_, so [1] covers one-body contributions. The corresponding user label is the 1-indexed counterpart, mc_level_lbl = mc_level_idx + 1 Formerly nlevel as in nbody = self.nbody_list[nbody_level=nlevel].

    • -
    • kwargs (Dict[str, Any]) – Other arguments for initializing mb_computer. In particular, specifies model chemistry.

    • +
    • kwargs (Dict[str, Any]) – Other arguments for initializing mb_computer. In particular, specifies model chemistry.

    Returns:
    @@ -853,7 +853,7 @@

    API

    Return type:
    -

    int

    +

    int

    @@ -864,7 +864,7 @@

    API

    Run quantum chemistry.

    Parameters:
    -

    client (FractalClient | None) –

    +

    client (qcportal.FractalClient | None) –

    @@ -877,7 +877,7 @@

    API

    Parameters:
      -
    • return_wfn (bool) –

      Whether to additionally return the dummy Wavefunction +

    • return_wfn

      Whether to additionally return the dummy Wavefunction calculation result as the second element of a tuple. Contents are:

      • supersystem molecule

      • @@ -886,19 +886,19 @@

        API

        QCVariables

    • -
    • client (FractalClient | None) –

    • +
    • client (qcportal.FractalClient | None) –

    -
    Return type:
    -

    Union[float, Matrix, Tuple[Union[float, Matrix], Wavefunction]]

    -
    -
    Returns:
    -

      +
      Returns:
      +

      • ret – Energy, gradient, or Hessian according to self.driver.

      • wfn – Wavefunction described above when return_wfn specified.

      +
      Return type:
      +

      float | Matrix | Tuple[float | Matrix, Wavefunction]

      +
    @@ -907,11 +907,11 @@

    API

    get_results(client=None)[source]

    Return results as ManyBody-flavored QCSchema.

    -
    Return type:
    -

    AtomicResult

    +
    Parameters:
    +

    client (qcportal.FractalClient | None) –

    -
    Parameters:
    -

    client (FractalClient | None) –

    +
    Return type:
    +

    AtomicResult

    @@ -928,9 +928,9 @@

    API

    Parameters:
      -
    • results (Optional[Dict[str, Union[AtomicComputer, CompositeComputer, FiniteDifferenceComputer]]]) – A set of tasks to process instead of self.task_list. Used in multilevel processing to pass a subset of +

    • results – A set of tasks to process instead of self.task_list. Used in multilevel processing to pass a subset of self.task_list filtered to only one modelchem level.

    • -
    • client (Optional[FractalClient]) – QCFractal client if using QCArchive for distributed compute.

    • +
    • client – QCFractal client if using QCArchive for distributed compute.

    Returns:
    @@ -1649,7 +1649,7 @@

    Navigation

  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  • Notes

    @@ -366,7 +366,7 @@

    Navigation

  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  · 
  •  · 
  • -
  • 1.9a1.dev70
  • +
  • 1.9a1.dev71
  •  ·