diff --git a/docs/notes.pdf b/docs/notes.pdf index 8e49bbed..6f6adb68 100644 Binary files a/docs/notes.pdf and b/docs/notes.pdf differ diff --git a/docs/notes.tex b/docs/notes.tex index bfe2c542..e9c75572 100644 --- a/docs/notes.tex +++ b/docs/notes.tex @@ -328,6 +328,7 @@ \subsection{Loading basis sets} \begin{lstlisting} atoms = ["H", "H"] coords = np.array([[0, 0, 0], [0, 0, 1]]) + coord_types = "spherical" \end{lstlisting} \begin{itemize} \item To build a basis set from gbs file for the given atoms and coordinates, @@ -335,16 +336,17 @@ \subsection{Loading basis sets} from gbasis.parsers import parse_gbs, make_contractions all_basis_dict = parse_gbs("./path/to/from_basissetexchange.gbs") -basis = make_contractions(all_basis_dict, atoms, coords) +basis = make_contractions(all_basis_dict, atoms, coords, coord_types) \end{lstlisting} \item To build a basis set from nwchem file for the given atoms and coordinates, \begin{lstlisting}[xleftmargin=-25pt] from gbasis.parsers import parse_nwchem, make_contractions all_basis_dict = parse_nwchem("./path/to/from_basissetexchange.nwchem") -basis = make_contractions(all_basis_dict, atoms, coords) +basis = make_contractions(all_basis_dict, atoms, coords, coord_types) \end{lstlisting} \end{itemize} +The last argument in the \verb|make_contractions| function, \verb|coord_types|, is the type of coordinate system used by the basis. Details about this variable can be found in the next section. \verb|gbasis| also interfaces to the module \verb|iodata|, which handles the inputs and outputs for different quantum chemistry formats, such as Gaussian @@ -386,10 +388,10 @@ \subsection{Loading basis sets} \subsection{Types of coordinate systems used by basis functions} In \verb|gbasis|, user can provide the coordinate system used by each shell of generalized contractions. -The function \verb|make_contractions| has the keyword argument \verb|coord_type| to +The function \verb|gbasis.parsers.make_contractions| has the positional argument \verb|coord_type| to specify the coordinate systems used by the basis. -If \verb|coord_type="spherical"|, all of the shells are treated to be spherical. -If \verb|coord_type="cartesian"|, all of the shells are treated to be +If \verb|coord_type| is \verb|"spherical"| (or \verb|"p"|), all of the shells are treated to be spherical. +If \verb|coord_type| is \verb|"cartesian"| (or \verb|"c"|), all of the shells are treated to be Cartesian. If different shells correspond to different coordinate system, then a list/tuple of the same length as the basis set must be provided with each entry being @@ -400,21 +402,17 @@ \subsection{Types of coordinate systems used by basis functions} \begin{itemize} \item To treat all contractions to be spherical \begin{lstlisting}[xleftmargin=-25pt] -basis = make_contractions(all_basis_dict, atoms, coords, coord_type="spherical") +basis = make_contractions(all_basis_dict, atoms, coords, "spherical") \end{lstlisting} \item To treat all contractions to be Cartesian \begin{lstlisting}[xleftmargin=-25pt] -basis = make_contractions(all_basis_dict, atoms, coords, coord_type="cartesian") +basis = make_contractions(all_basis_dict, atoms, coords, "cartesian") \end{lstlisting} \item To treat first shell of generalized contractions to be Cartesian and second shell to be spherical \begin{lstlisting}[xleftmargin=-25pt] -basis = make_contractions( - all_basis_dict, ["H", "H"], coords, coord_type=["cartesian", "spherical"] -) +basis = make_contractions(all_basis_dict, ["H", "H"], coords, ["c", "spherical"]) \end{lstlisting} -% In this case, the basis set must consist of exactly two shells of -% generalized contractions. Otherwise, an error will be raised. In this case, each hydrogen atom must contributes exactly one shell of generalized contractions. Otherwise, an error will be raised. \end{itemize}