Source code for pycif.plugins.models.lmdz_acc.io.inputs.make_auxiliary

from ......utils import path
from .params import make_totinput
from logging import info, warning
import os
import shutil
from ......utils.check.errclass import CifError




def make_auxiliary(self, ddi, runsubdir,
                   onlyinit=False, do_simu=True, mode="fwd",
                   **kwargs):
    """Set up the LMDZ-ACC executable and input configuration for one sub-period.

    Symlinks the correct LMDZ binary into *runsubdir* and calls
    :func:`make_totinput` to write the LMDZ total-input configuration file.
    Returns immediately when ``do_simu=False`` or ``onlyinit=True``.

    Args:
        self: LMDZ-ACC model plugin instance with ``workdir`` set.
        ddi (datetime): sub-simulation period start.
        runsubdir (str): path to the period run directory.
        onlyinit (bool): skip if ``True`` (adjoint initialisation pass).
        do_simu (bool): skip if ``False``.
        mode (str): ``'fwd'``, ``'tl'``, or ``'adj'``.
        **kwargs: unused.
    """
    
    # If mode is "fwd" or "tl" but onlyinit is True,
    # it means that we are initializing an adjoint by running backward
    # the adjoint pipeline
    if mode in ["tl", "fwd"] and onlyinit:
        mode = "adj"
    
    if not do_simu or onlyinit:
        return
    
    # Linking executable
    source = f"{self.workdir}/model/dispersion.e"
    target = f"{runsubdir}/dispersion.e"
    path.link(source, target)
    
    # Dump totinput depending on parameters
    make_totinput(self, runsubdir, ddi, mode)
    
    # Link to trajq from corresponding forward simulation
    if mode == "adj":
        if not hasattr(self, "adj_refdir"):
            info(
                "Adjoint LMDZ couldn't be initialized "
                "with forward trajq.bin files"
            )
            raise CifError
    
        else:
            for spec in self.chemistry.acspecies.attributes:
                traj_file = f"trajq_{spec}_%Y%m%d%H%M.bin"
                source = ddi.strftime(
                    f"{self.adj_refdir}/chain/{traj_file}"
                )
                target = f"{runsubdir}/trajq_{spec}.bin"
            
                path.link(source, target)

    # TODO: at the moment, no satellite observation
    os.system(f"echo 0 > {runsubdir}/infousedsat.txt")
    
    # Remove restart TL if not running a tangent-linear run
    # TODO: Check whether it is still useful?
    if mode != "tl":
        shutil.rmtree(
            f"{runsubdir}/*start_tl.bin", ignore_errors=True
        )
    
    # Deal with chemical scheme and deposition
    if hasattr(self, "chemistry"):
        # Linking to pre-computed INCA fields for deposition
        if hasattr(self.chemistry, "deposition"):
            warning("TODO: move deposition to the datavect paragraph")
            for spec in self.chemistry.deposition.attributes:
                tracer = getattr(self.chemistry.deposition, spec)
                source = ddi.strftime(
                    f"{tracer.dir}/{tracer.file}"
                )
                target = f"{runsubdir}/dep_{spec}.nc"
                path.link(source, target)
    
        finf = f"{self.chemistry.dirchem_ref}/chemical_scheme.nml"
        target = f"{runsubdir}/chemical_scheme.nml"
        path.link(finf, target)

    return

    #
    # elif mod_input == "chem_fields":
    #     if hasattr(self, "chemistry"):
    #         # Linking to pre-computed INCA fields for deposition
    #         if hasattr(self.chemistry, "deposition"):
    #             for spec in self.chemistry.deposition.attributes:
    #                 tracer = getattr(self.chemistry.deposition, spec)
    #                 source = datei.strftime(
    #                     "{}/{}".format(tracer.dir, tracer.file)
    #                 )
    #                 target = "{}/dep_{}.nc".format(runsubdir, spec)
    #                 path.link(source, target)
    #
    #         finf = "{}/chemical_scheme.nml".format(self.chemistry.dirchem_ref)
    #         target = "{}/chemical_scheme.nml".format(runsubdir)
    #         path.link(finf, target)