Source code for pycif.plugins.models.chimere.io.inputs.make_endconcs

import filecmp
import os
import shutil
import pathlib
import numpy as np
from netCDF4 import Dataset
import xarray as xr
from logging import warning

from ......utils import path




def make_endconcs(
        self, datastore, runsubdir, mode, datei, datef, onlyinit,
        check_transforms=False
):
    """Link concentration restart files into the CHIMERE period run directory.

    Handles four cases depending on *mode* and *onlyinit*:

    * **Forward / TL, not onlyinit** — links the end-concentrations produced
      by the previous period as ``INI_CONCS.0.nc`` for the current period.
    * **Adjoint, onlyinit** — same as above (links forward end-concs as
      initial state for the backward adjoint).
    * **Adjoint, not onlyinit** — links the adjoint initial conditions
      (from the forward reference run stored in ``self.adj_refdir``) as
      ``aini.nc``.

    Args:
        self: CHIMERE model plugin instance (carries ``adj_refdir`` for
            adjoint runs).
        datastore (dict): mapping of tracer IDs to their data-store entries,
            each containing ``fileorig`` paths.
        runsubdir (str): path to the period run directory.
        mode (str): ``'fwd'``, ``'tl'``, or ``'adj'``.
        datei (datetime): period start date.
        datef (datetime): period end date.
        onlyinit (bool): ``True`` during the adjoint initialisation pass.
        check_transforms (bool): unused, kept for API compatibility.
    """
    
    # If adjoint and only init, fetching initial concentrations from forward
    # If fwd or tl and not only init, fetch initial concentrations from end
    # of previous simulation
    if (onlyinit and mode == "adj") or (not onlyinit and mode != "adj"):
        for trid in datastore:
            fileout = f"{runsubdir}/INI_CONCS.0.nc"
            fileorig = f"{self.adj_refdir}/{datastore[trid]['data'][datei]['fileorig']}"
            path.link(fileorig, fileout)
            
    if not onlyinit and mode == "adj":
        # Fixed name for INI_CONCS files
        fileout = f"{runsubdir}/aini.nc"
        
        for trid in datastore:
            fileorig = f"{runsubdir}/../{datastore[trid][max(datei, datef)]['fileorig']}"
            path.link(fileorig, fileout)