FRUITY model handlers

Handler for FRUITY model files (from http://fruity.oa-teramo.inaf.it/).

This module provides some functions to work with the FRUITY nucleosynthesis models.

Import as:

from rttools.nucmod import fruity

drop_a_z(df)

Drop columns for A and Z for a dataframe.

Leaves only columns with compositions over from a FRUITY dataframe and removes columns labeled "A" and "Z". If these columns don't exist, no error will be raised.

Parameters:

Name	Type	Description	Default
df	DataFrame	FRUITY dataframe with columns "A" and "Z" present.	required

Returns:

Type	Description
DataFrame	same dataframe with those vectors dropped.

Source code in src/rttools/nucmod/fruity.py

def drop_a_z(df: pd.DataFrame) -> pd.DataFrame:
    """Drop columns for A and Z for a dataframe.

    Leaves only columns with compositions over from a FRUITY dataframe and removes
    columns labeled "A" and "Z". If these columns don't exist, no error will be raised.

    :param df: FRUITY dataframe with columns "A" and "Z" present.

    :return: same dataframe with those vectors dropped.
    """
    retval = df.copy()
    columns = ["A", "Z"]
    for col in columns:
        try:
            retval.drop(columns=[col], inplace=True)
        except KeyError:
            pass

    return retval

get_delta_isoratio(fname, iso1, iso2, norm_self=False)

Take a FRUITY file and return delta values for one isotope ratio.

Delta will be calculated with respect to current iniabu default database. The ratio is going to be iso1/iso2. Initial and first dredge up (FDU) columns are returned as well.

Parameters:

Name	Type	Description	Default
fname	Path	FRUITY file name.	required
iso1	str	Nominator isotope, any iniabu isotope name accepted.	required
iso2	str	Denominator isotope, any iniabu isotope name accepted.	required
norm_self	bool	Norm to itself, i.e., to the initial composition instead of using standard database by iniabu.	False

Returns:

Type	Description
Series	Series with delta ratio of the two.

Source code in src/rttools/nucmod/fruity.py

def get_delta_isoratio(
    fname: Path, iso1: str, iso2: str, norm_self: bool = False
) -> pd.Series:
    """Take a FRUITY file and return delta values for one isotope ratio.

    Delta will be calculated with respect to current iniabu default database. The ratio
    is going to be iso1/iso2. Initial and first dredge up (FDU) columns are returned as
    well.

    :param fname: FRUITY file name.
    :param iso1: Nominator isotope, any `iniabu` isotope name accepted.
    :param iso2: Denominator isotope, any `iniabu` isotope name accepted.
    :param norm_self: Norm to itself, i.e., to the initial composition instead of using
        standard database by `iniabu`.

    :return: Series with delta ratio of the two.
    """
    iso1f = make_fruity_isoname(iso1)
    iso2f = make_fruity_isoname(iso2)

    data = drop_a_z(reader(fname))
    ratios = data.loc[iso1f] / data.loc[iso2f]

    if norm_self:
        delta = (ratios / ratios.iloc[0] - 1.0) * 1000
    else:
        delta = ini.iso_delta(iso1, iso2, ratios)
        # fixme: this should be handled correctly by iniabu, but is not
        delta = pd.Series(delta, index=ratios.index)
    return delta

label_latex_mass(fname, prec=1)

Create a LaTeX label for only mass.

Parameters:

Name	Type	Description	Default
fname	str	Filename of data file.	required
prec	int	Precision of return value (at most).	1

Returns:

Type	Description
str	LaTeX label.

Source code in src/rttools/nucmod/fruity.py

def label_latex_mass(fname: str, prec: int = 1) -> str:
    """Create a LaTeX label for only mass.

    :param fname: Filename of data file.
    :param prec: Precision of return value (at most).

    :return: LaTeX label.
    """
    m, _, _, _ = label_parser(fname)
    return f"${reduce_decimal(m, prec)}\\,M_{{\\odot}}$"

label_latex_mass_z(fname, prec=2)

Create a LaTeX label for mass and metallicity.

Parameters:

Name	Type	Description	Default
fname	str	Filename of data file.	required
prec	int	Precision of return value (at most).	2

Returns:

Type	Description
str	LaTeX label.

Source code in src/rttools/nucmod/fruity.py

def label_latex_mass_z(fname: str, prec: int = 2) -> str:
    """Create a LaTeX label for mass and metallicity.

    :param fname: Filename of data file.
    :param prec: Precision of return value (at most).

    :return: LaTeX label.
    """
    m, z, _, _ = label_parser(fname)
    return (
        f"${reduce_decimal(m, prec)}\\,M_{{\\odot}}$, "
        f"${reduce_decimal(z, prec)}\\,Z_{{\\odot}}$"
    )

label_latex_mass_z_pocket(fname, prec=2)

Create a LaTeX label for mass and metallicity.

Parameters:

Name	Type	Description	Default
fname	str	Filename of data file.	required
prec	int	Precision of return value (at most).	2

Returns:

Type	Description
str	LaTeX label.

Source code in src/rttools/nucmod/fruity.py

def label_latex_mass_z_pocket(fname: str, prec: int = 2) -> str:
    """Create a LaTeX label for mass and metallicity.

    :param fname: Filename of data file.
    :param prec: Precision of return value (at most).

    :return: LaTeX label.
    """
    m, z, _, pocket = label_parser(fname)
    return (
        f"${reduce_decimal(m, prec)}\\,M_{{\\odot}}$, "
        f"${reduce_decimal(z, prec)}\\,Z_{{\\odot}}$, "
        f"{pocket}"
    )

label_latex_mass_z_pocket_rot(fname, prec=2)

Create a LaTeX label for mass and metallicity.

Parameters:

Name	Type	Description	Default
fname	str	Filename of data file.	required
prec	int	Precision of return value (at most).	2

Returns:

Type	Description
str	LaTeX label.

Source code in src/rttools/nucmod/fruity.py

def label_latex_mass_z_pocket_rot(fname: str, prec: int = 2) -> str:
    """Create a LaTeX label for mass and metallicity.

    :param fname: Filename of data file.
    :param prec: Precision of return value (at most).

    :return: LaTeX label.
    """
    m, z, rot, pocket = label_parser(fname)
    return (
        f"${reduce_decimal(m, prec)}\\,M_{{\\odot}}$, "
        f"${reduce_decimal(z, prec)}\\,Z_{{\\odot}}$, "
        f"{pocket}, "
        f"IRV: ${reduce_decimal(rot, prec)}\\,$km\\,s$^{{-1}}$"
    )

label_parser(fname)

Label parser for FRUITY models.

Take a FRUITY filename and return various parameters as numbers.

Parameters:

Name	Type	Description	Default
fname	Union[str, Path]	File name of the FRUITY file.	required

Returns:

Type	Description
Tuple[float, float, float, str]	Mass (M_sun), Metallicity (Z_sun), Rotation (km/s), C13 pocket (std / ext)

Source code in src/rttools/nucmod/fruity.py

def label_parser(fname: Union[str, Path]) -> Tuple[float, float, float, str]:
    """Label parser for FRUITY models.

    Take a FRUITY filename and return various parameters as numbers.

    :param fname: File name of the FRUITY file.

    :return: Mass (M_sun), Metallicity (Z_sun), Rotation (km/s), C13 pocket (std / ext)
    """
    if isinstance(fname, Path):
        fname = str(fname.name)

    # remove 'isotopi_'
    fname = fname.replace("isotopi_", "")

    # now break by '_' and use first two
    fname = fname.split("_")[:2]

    # mass and metallicity
    z_start = fname[0].find("z")
    mass = float(fname[0][1:z_start].replace("p", "."))
    z = fname[0][z_start + 1 :].replace("m", "e-")
    if z == "sun":
        z = 1
    else:
        z = float(z) / 1.4e-2

    # pocket and rotation
    if fname[1][0] == "T":
        pocket = "ext"
    else:
        pocket = "std"
    rot = float(fname[1][1:])
    return mass, z, rot, pocket

make_fruity_isoname(iso)

Pass an isotope through iniabu and then parse a FRUITY isotope name.

Parameters:

Name	Type	Description	Default
iso	str	Isotope, e.g., "28Si", "Si-28", "Si28"	required

Returns:

Type	Description
str	FRUITY name, e.g., "Si28"

Source code in src/rttools/nucmod/fruity.py

def make_fruity_isoname(iso: str) -> str:
    """Pass an isotope through `iniabu` and then parse a FRUITY isotope name.

    :param iso: Isotope, e.g., "28Si", "Si-28", "Si28"

    :return: FRUITY name, e.g., "Si28"
    """
    iso = ini.iso[iso].name.split("-")
    iso_fruity = iso[0] + iso[1][-2:]
    return iso_fruity

plot_mod(ax, fname, xisos, yisos, norm_self=False, marker='o', color='tab:blue', label=None, linestyle='-', **kwargs)

Plot FRUITY Model curve onto a plot.

Note that **kwargs are passed along to both plotting routines. For C/O < 1, the marker is set to 'None'.

Parameters:

Name	Type	Description	Default
ax	Axes	Matplotlib axis to plot on.	required
fname	Path	Filename of model data file	required
xisos	Tuple[str, str]	Tuple of two isotopes (nominator, denominator) for x axis.	required
yisos	Tuple[str, str]	Tuple of two isotopes (nominator, denominator) for y axis.	required
norm_self	bool	Norm to itself, i.e., to the initial composition instead of using standard database by iniabu.	False
marker	str	Marker of the plot, defaults to 'o'	'o'
color	str	Color of the plot, defaults to 'tab:blue'	'tab:blue'
linestyle	str	Linestyle of the plot, defaults to '-'	'-'

Returns:

Type	Description
None	Nothing

Source code in src/rttools/nucmod/fruity.py

def plot_mod(
    ax: plt.Axes,
    fname: Path,
    xisos: Tuple[str, str],
    yisos: Tuple[str, str],
    norm_self: bool = False,
    marker: str = "o",
    color: str = "tab:blue",
    label=None,
    linestyle: str = "-",
    **kwargs,
) -> None:
    """Plot FRUITY Model curve onto a plot.

    Note that **kwargs are passed along to both plotting routines. For C/O < 1, the
    marker is set to 'None'.

    :param ax: Matplotlib axis to plot on.
    :param fname: Filename of model data file
    :param xisos: Tuple of two isotopes (nominator, denominator) for x axis.
    :param yisos: Tuple of two isotopes (nominator, denominator) for y axis.
    :param norm_self: Norm to itself, i.e., to the initial composition instead of using
        standard database by `iniabu`.
    :param marker: Marker of the plot, defaults to 'o'
    :param color: Color of the plot, defaults to 'tab:blue'
    :param linestyle: Linestyle of the plot, defaults to '-'

    :return: Nothing
    """
    drop_cols = ["INI", "FDU"]
    xdat_all = get_delta_isoratio(fname, xisos[0], xisos[1], norm_self=norm_self).drop(
        columns=drop_cols
    )
    ydat_all = get_delta_isoratio(fname, yisos[0], yisos[1], norm_self=norm_self).drop(
        columns=drop_cols
    )
    co_ratio = drop_a_z(reader(fname).loc["CO_ratio"]).drop(columns=drop_cols)

    crich_mask = co_ratio >= 1

    # plot all
    ax.plot(
        xdat_all, ydat_all, marker="None", linestyle=linestyle, color=color, **kwargs
    )
    # plot c-rich
    ax.plot(
        xdat_all[crich_mask],
        ydat_all[crich_mask],
        marker=marker,
        color=color,
        linestyle="None",
        label=label,
        **kwargs,
    )

reader(fname)

Read in a FRUITY file and return values as DataFrame.

Source code in src/rttools/nucmod/fruity.py

def reader(fname: Path) -> pd.DataFrame:
    """Read in a FRUITY file and return values as DataFrame."""
    data = pd.read_csv(fname, sep=r" ", index_col=0, skipinitialspace=True)

    # drop nan columns
    data = data.dropna(axis=1, how="all")

    # set the column labels straight
    col_labels = ["A", "Z", "INI", "FDU"]  # the first four, isotope is index
    co_ratio_cols = ["INI", "FDU"]  # calculate CO ratios for these plus TDUs
    for it in range(data.shape[1] - len(col_labels)):
        tdu = f"TDU_{it+1}"
        col_labels.append(tdu)
        co_ratio_cols.append(tdu)
    data.columns = col_labels

    # create a new series with C/O ratio called CO_ratio
    co_ratio = data.loc[["C12", "C13"], co_ratio_cols].sum(axis=0) / data.loc[
        ["O16", "O17", "O18"], co_ratio_cols
    ].sum(axis=0)

    data.loc["CO_ratio"] = co_ratio

    return data