Source code for sloop.models.hycom3d.__init__

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
HYCOM utilities

"""
import logging
import os

from ...__init__ import SLOOP_SRC_DIR, SloopError



[docs]class SloopHycomError(SloopError):
    pass



LOGGER = logging.getLogger(__name__)

_THISDIR = os.path.dirname(__file__)

#: HYCOM vconf
HYCOM3D_VCONF = ["manga", "med", "indien", "gijon"]

#: HYCOM platform root dir
HYCOM3D_DIR = os.path.join(SLOOP_SRC_DIR, 'HYCOM')

#: HYCOM initial and open boundary root dir
HYCOM3D_IBC_DIR = os.path.join(HYCOM3D_DIR, 'ChaineFrontieresOuvertes')

#: HYCOM gen_inicon_hycom.F file
HYCOM3D_IBC_GEN_INICON = os.path.join(
    HYCOM3D_IBC_DIR, 'INTERP-VER/gen_inicon_hycom.F')

#: HYCOM vconf which needs particular gen_inicon_hycom.F file
HYCOM3D_IBC_GEN_INICON_VCONF = ["med", "indien"]

#: HYCOM inicon executable
HYCOM3D_IBC_INICON = os.path.join(HYCOM3D_IBC_DIR, 'INTERP-VER/inicon')

#: HYCOM regridcdf executable
HYCOM3D_IBC_REGRIDCDF = os.path.join(HYCOM3D_IBC_DIR, 'INTERP-HOR/regridcdf')

#: HYCOM 3D model directory
HYCOM3D_MODEL_DIR = os.path.join(HYCOM3D_DIR, 'Modele3D')

#: HYCOM 3D model executable
HYCOM3D_MODEL_EXE = os.path.join(
    HYCOM3D_MODEL_DIR, 'MAKELIB.', 'main')

#: HYCOM 3D model dimensions.h.template
HYCOM3D_MODEL_DIMENSIONSH_TEMPLATE = os.path.join(
    HYCOM3D_MODEL_DIR, 'COMMUNS./dimensions.h.template')

#: HYCOM rivers directory
HYCOM3D_RIVERS_DIR = os.path.join(HYCOM3D_DIR, 'Rivers')

#: HYCOM rivers flow climatology
HYCOM3D_RIVERS_FLOW_CLIM = os.path.join(HYCOM3D_RIVERS_DIR, "hycom_rivers.d")

#: HYCOM rivers hydro climatology
HYCOM3D_RIVERS_HYDRO_CLIM = os.path.join(
    HYCOM3D_RIVERS_DIR, "fleuves_climato_hydro")

#: HYCOM 3D model defstretch.f/F
HYCOM3D_MODEL_DEFSTRETCH_FILES = {
    "generic": os.path.join(
        HYCOM3D_MODEL_DIR, 'UTIL./defstretch.f.generic'),
    "med": os.path.join(
        HYCOM3D_MODEL_DIR, 'UTIL./defstretch.F.med')
    }

#: HYCOM spnudge root dir
HYCOM3D_SPNUDGE_DIR = os.path.join(HYCOM3D_DIR, 'Assimilation', 'Spectral_Nudging')

#: HYCOM demerliac executable
HYCOM3D_SPNUDGE_DEMERLIAC = os.path.join(
    HYCOM3D_SPNUDGE_DIR, 'demerliac')

#: HYCOM filter executable
HYCOM3D_SPNUDGE_SPECTRAL = os.path.join(
    HYCOM3D_SPNUDGE_DIR, 'lissage_spectral_fft')

#: HYCOM postproduction root dir
HYCOM3D_POSTPROD_DIR = os.path.join(HYCOM3D_DIR, 'PostProduction')

#: HYCOM postproduction time filtering executable
HYCOM3D_POSTPROD_FILTER = os.path.join(
    HYCOM3D_POSTPROD_DIR, 'cdfTraitementTemporel3D')

#: HYCOM postproduction file conversion executable
HYCOM3D_POSTPROD_INTERPOLATION = os.path.join(
    HYCOM3D_POSTPROD_DIR, 'cdfHycomTodataSHOMouSOAP')

#: HYCOM postproduction temperature conversion executable
HYCOM3D_POSTPROD_TEMPCONVERSION = os.path.join(
    HYCOM3D_POSTPROD_DIR, 'temppot2tempis_postProd')

#: HYCOM postproduction traductions noms longs
HYCOM3D_POSTPROD_LONGNAMES = "PARAMETERS{rank}./traductions_noms_longs_{postprod}"

#: HYCOM postproduction traductions noms standards
HYCOM3D_POSTPROD_STDNAMES = "PARAMETERS{rank}./traductions_noms_standards_2"

#: HYCOM postproduction traductions units
HYCOM3D_POSTPROD_UNITS = "PARAMETERS{rank}./traductions_unites"

#: HYCOM sigma to stmt_fns*.h files
HYCOM3D_SIGMA_TO_STMT_FNS = {
    '0': os.path.join(HYCOM3D_MODEL_DIR, 'COMMUNS./stmt_fns_SIGMA0_7term.h'),
    '2': os.path.join(HYCOM3D_MODEL_DIR, 'COMMUNS./stmt_fns_SIGMA2_17term.h'),
}

#: HYCOM mapping for stmt_fns.h files
HYCOM3D_CONTEXT_TO_STMT_FNS = {
    'ibc_hor': os.path.join(HYCOM3D_IBC_DIR, 'INTERP-HOR/stmt_fns.h'),
    'ibc_ver': os.path.join(HYCOM3D_IBC_DIR, 'INTERP-VER/stmt_fns.h'),
    'model': os.path.join(HYCOM3D_MODEL_DIR, 'COMMUNS./stmt_fns.h')
    }

#: HYCOM mask file
HYCOM3D_MASK_FILE = 'FORCING{rank}./regional.mask.nc'

#: HYCOM grid a file
HYCOM3D_GRID_AFILE = 'FORCING{rank}./regional.grid.a'

#: HYCOM grid b file
HYCOM3D_GRID_BFILE = 'FORCING{rank}./regional.grid.b'

#: HYCOM depth a file
HYCOM3D_DEPTH_AFILE = "FORCING{rank}./regional.depth.a"

#: HYCOM depth b file
HYCOM3D_DEPTH_BFILE = "FORCING{rank}./regional.depth.b"

#: HYCOM isosigma a file
HYCOM3D_ISOSIGMA_AFILE = 'FORCING{rank}./iso.sigma.a'

#: HYCOM isosigma b file
HYCOM3D_ISOSIGMA_BFILE = 'FORCING{rank}./iso.sigma.b'

#: HYCOM regricdf tabindicesT
HYCOM3D_REGRIDCDF_TABINDICEST = 'FORCING{rank}./tabindicesT'

#: HYCOM blkdat.input parameters file
HYCOM3D_BLKDAT_INPUT_FILE = "PARAMETERS{rank}./blkdat.input"

#: HYCOM blkdat.input parameters file
HYCOM3D_BLKDAT_CMO_INPUT_FILE = "PARAMETERS{rank}./blkdat_cmo.input"

#: HYCOM blkdat_cmo.input parameters file
HYCOM3D_BLKDAT_CMO_INPUT_FILES = {
            "spinup":"PARAMETERS{rank}./blkdat_cmo_A.input",
            "forecast":"PARAMETERS{rank}./blkdat_cmo_P.input",
            "spnudge_free":"PARAMETERS{rank}./blkdat_cmo_spnudge_free.input",
            "spnudge_relax":"PARAMETERS{rank}./blkdat_cmo_spnudge_relax.input",
            "free": "PARAMETERS{rank}./blkdat_cmo_A.input",
            }

#: HYCOM savefield.input parameters file
HYCOM3D_SAVEFIELD_INPUT_FILE = "PARAMETERS{rank}./savefield.input"

#: HYCOM blkdat_cmo.input parameters file
HYCOM3D_SAVEFIELD_INPUT_FILES = {
            "spinup":["PARAMETERS{rank}./savefield_C.input",
                      "PARAMETERS{rank}./savefield_A.input"],
            "forecast":["PARAMETERS{rank}./savefield_C.input",
                        "PARAMETERS{rank}./savefield_P.input"],
            "spnudge_free":["PARAMETERS{rank}./savefield_Assim_SN.input"],
            "spnudge_relax":["PARAMETERS{rank}./savefield_C.input",
                             "PARAMETERS{rank}./savefield_A.input"],
            "free":["PARAMETERS{rank}./savefield_C.input",
                    "PARAMETERS{rank}./savefield_A.input"],
            }

#: HYCOM defstrech.input parameters file
HYCOM3D_DEFSTRECH_INPUT_FILE = "PARAMETERS{rank}./defstrech*.input"

#: HYCOM MPI tiling file
HYCOM3D_PATCH_INPUT_FILE = "SPLIT{rank}./patch.input"

#: HYCOM ports.input parameters file
HYCOM3D_PORTS_INPUT_FILE = "PARAMETERS{rank}./ports.input"

#: HYCOM run.input.tpl parameters file
HYCOM3D_RUN_INPUT_TPL_FILE = "PARAMETERS{rank}./run.input.tpl"

#: HYCOM post-production configuration files
HYCOM3D_POSTPROD_CFG_FILE = "PARAMETERS{rank}./postprod.cfg"

#: HYCOM post-production configuration specs file
HYCOM3D_POSTPROD_INI_FILE = os.path.join(_THISDIR, "postprod.ini")

#: HYCOM post-production configuration output files
HYCOM3D_POSTPROD_CONFIG_FILE = "PARAMETERS{rank}./postprod_{postprod}.cfg"

#: HYCOM check promises
HYCOM3D_PROMISES = "PARAMETERS{rank}./promises.cfg"

#: HYCOM rivers configuration specs file
HYCOM3D_RIVERS_INI = os.path.join(_THISDIR, "rivers.ini")

#: HYCOM rivers configuration file
HYCOM3D_RIVERS_CFG = 'FORCING{rank}./nest/rivers.cfg'

#: HYCOM spectral nudging parameters json file
HYCOM3D_SPNUDGE_JSON_FILE = "PARAMETERS{rank}./spnudging_parameters.json"

#: From standard_name to name
HYCOM3D_STANDARD_NAME_TO_NAME = {
    'sea_water_potential_temperature': 'temp',
    'sea_water_salinity': 'saln',
    'sea_surface_height_above_geoid': 'ssh',
    }

#: Required environment variables for each context
REQUIRED_ENV_VARIABLES = {
    # Pre- and post-processing tasks
    'prepost': [
        'FC', 'LDF', 'CC', 'FFLAGS', 'LDFLAGS', 'CPPFLAGS', 'MAKE',
        'MODEL_FFLAGS', 'MODEL_CFLAGS', 'MODEL_LDFLAGS'
        ],
    # Model
    'modelcompile': [
        'HOME_MODELE_SRC', 'MPIDIR',
        'FFLAGS', 'CPP', 'CPPFLAGS', 'LDFLAGS', 'CCFLAGS',
        'FC', 'CC', 'MAKE'
        ],
    'modelrun': [
        'HOME_MODELE_SRC', 'MPIDIR',
        ],
    }

REQUIRED_JOB_OPTIONS = {
    'prepost': [
        'submitcmd', 'queue', 'time'
        ],
    'modelrun': [
        'submitcmd', 'queue', 'time'
        ],
    'recdata': [
        'submitcmd', 'queue', 'refill', 'time'
        ],
    }

#: Patterns of geographic constant files
HYCOM3D_GEO_CONSTANT_PATTERNS = {
    "nest": [
        "FORCING{rank}./nest/debitmeso.list",
        HYCOM3D_RIVERS_CFG,
        "FORCING{rank}./nest/rivers.list",
        "FORCING{rank}./nest/rmu.[ab]"
    ],
    "tide": [
        "FORCING{rank}./tide/tide.list",
        "FORCING{rank}./tide/forcing.*tide.[ab]"
    ],
    "regional": [
        HYCOM3D_GRID_AFILE,
        HYCOM3D_GRID_BFILE,
        HYCOM3D_DEPTH_AFILE,
        HYCOM3D_DEPTH_BFILE,
        HYCOM3D_MASK_FILE,
        HYCOM3D_REGRIDCDF_TABINDICEST,
        HYCOM3D_ISOSIGMA_AFILE,
        HYCOM3D_ISOSIGMA_BFILE
    ],
    "run": ([
        HYCOM3D_BLKDAT_INPUT_FILE,
        HYCOM3D_BLKDAT_CMO_INPUT_FILE,
        HYCOM3D_DEFSTRECH_INPUT_FILE,
        HYCOM3D_PORTS_INPUT_FILE,
        HYCOM3D_RUN_INPUT_TPL_FILE,
        HYCOM3D_SPNUDGE_JSON_FILE
        ]+list(HYCOM3D_BLKDAT_CMO_INPUT_FILES.values())),
    "postprod": [
        HYCOM3D_POSTPROD_CFG_FILE,
        HYCOM3D_POSTPROD_CONFIG_FILE.format(
            rank="{rank}", postprod="*")
    ],
    "savefield": (
        [HYCOM3D_SAVEFIELD_INPUT_FILE] +
        list(set(p for pp in HYCOM3D_SAVEFIELD_INPUT_FILES.values()
                 for p in pp))
    ),
    "split": [
        HYCOM3D_PATCH_INPUT_FILE
    ],
    "promises": [
        HYCOM3D_PROMISES
    ],
}

#: Patterns of non-geographic constant files
HYCOM3D_NOT_GEO_CONSTANT_PATTERNS = {
    "naming": [
        "PARAMETERS{rank}./traductions_*",
    ]
}


#: Hycom3d specifications for the :mod:`xoa.cf` module use
HYCOM3D_CF_SPECS = {
    "data_vars": {
        "temp": {
            "name": "temp"
        },
        "sal": {
            "name": "saln"
        },
        "ssh": {
            "name": "ssh"
        },
        "sigmatheta": {
            "name": "thdd",
        },
        "ps": {
            "alt_name": ["preatm", "prmsl"],
            "attrs": {
                "standard_name": ["air_pressure_at_mean_sea_level"],
                "long_name": ["Pressure reduced to MSL"],
                "header": "pression atmospherique"
            }
        },
        "tair": {
            "alt_name": ["airtmp", "t2m"],
            "attrs": {
                "units": "degree Celsius",
                "standard_name": [
                    "air_temperature",
                    "air_temperature_at_2m"
                ],
                "long_name": "2 metre temperature",
                "header": "temperature de surface"
            }
        },

    }
}

HYCOM3D_PARAM = {
    "preatm": {
        "name": [
            "preatm",
            "prmsl"
        ],
        "attrs": {
            "units": "Pa",
            "standard_name": "air_pressure_at_mean_sea_level",
            "long_name": "Pressure reduced to MSL",
            "header": "pression atmospherique"
        }
    },
    "airtmp": {
        "name": [
            "airtmp",
            "t2m"
        ],
        "attrs": {
            "units": "degree Celsius",
            "standard_name": [
                "air_temperature",
                "air_temperature_at_2m"
            ],
            "long_name": "2 metre temperature",
            "header": "temperature de surface",
            "diurnal": "True"
        }
    },
    "vapmix": {
        "name": [
            "vapmix"
        ],
        "attrs": {
            "units": "kg kg-1",
            "standard_name": [
                "water_vapor_mixing_ratio"
            ],
            "long_name": "water vapor mixing ratio",
            "header": "vapeur"
        }
    },
    "shwflx": {
        "name": [
            "shwflx",
            "ssr"
        ],
        "attrs": {
            "units": "W m-2 s-1",
            "standard_name": [
                "short_wave_fluxes"
            ],
            "long_name": "surface net solar radiation",
            "header": "flux radiatifs Short Wave",
            "diurnal": "True"
        }
    },
    "radflx": {
        "name": [
            "radflx",
            "str",
       ],
        "attrs": {
            "units": "W m-2 s-1",
            "standard_name": [
                "radiative_fluxes"
            ],
            "long_name": "total radiative fluxes",
            "header": "flux radiatifs IR",
            "diurnal": "True"
        }
    },
    "precip": {
        "name": [
            "precip",
            "tp"
        ],
        "attrs": {
            "units": "m s-1",
            "standard_name": [
                "precipitations"
            ],
            "long_name": "Total Precipitation",
            "header": "precipitations"
        }
    },
    "wndspd": {
        "name": [
            "wndspd",
            "si10"
        ],
        "attrs": {
            "units": "m s-1",
            "standard_name": [
                "wind_speed"
            ],
            "long_name": "10 metre wind speed",
            "header": "module du vent"
        }
    },
    "tauewd": {
        "name": [
            "tauewd",
            "ewss"
        ],
        "attrs": {
            "units": "N m-2",
            "standard_name": [
                "zonal_wind_stress"
            ],
            "long_name": "zonal wind stress",
            "header": "vent - composante zonale"
        }
    },
    "taunwd": {
        "name": [
            "taunwd",
            "nsss"
        ],
        "attrs": {
            "units": "N m-2",
            "standard_name": [
                "meridional_wind_stress"
            ],
            "long_name": "meridional wind stress",
            "header": "vent - compostante meridienne"
        }
    }
}

RESTART_FIELDS = [
        "restdate",
        "saln", "temp", "th3d", 
        "h", "dpmixl", "umbbiais", 
        "vmbbiais", "ut", "vt", "ptide",
        "uflxbam", "vflxbam", "difs"
]


_CACHE = {}



[docs]def get_constant_patterns(geo):
    """Get dict of HYCOM3D constant file glob patterns for each pack

    A file pattern typically contains the `{rank}` subsitution pattern

    Parameters
    ----------
    geo: bool
        Bounded to a geograhpical area?
    """
    return HYCOM3D_GEO_CONSTANT_PATTERNS if geo else HYCOM3D_NOT_GEO_CONSTANT_PATTERNS




[docs]def get_cf_specs():
    """Get a :class:`xoa.cf.CFSpecs` object for Hycom3D"""
    if "cf_specs" not in _CACHE:
        import xoa.cf
        _CACHE["cf_specs"] = xoa.cf.CFSpecs(HYCOM3D_CF_SPECS)
    return _CACHE["cf_specs"]




[docs]def format_ds(ds):
    """Format all variables in a dataset or dataarray to be hycom compliant"""
    # Time units
    time = get_cf_specs().coords.get(ds, "time")
    if time is not None:
        ds[time.name].encoding["units"] = "days since 1950-01-01"

    # Other encodings
    for vname, var in ds.items():
        for attr in 'dtype', 'scale_factor', 'add_offset':
            if attr in ds[vname].encoding:
                del ds[vname].encoding[attr]
        if ds[vname].dtype.kind in "fd":
            ds[vname].encoding['_FillValue'] = -1e34

    return ds