Commit 0a625674 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Moved computation of dust temperature based on the presence of a central... 

Moved computation of dust temperature based on the presence of a central heating source to STG. TO BE TESTED!
parent 781b25ce

etl/mdl/mdl_execute_radmc_command.py

+1 −61
Original line number Diff line number Diff line
@@ -25,22 +25,6 @@ from assets.constants import (radmc_options_mapping, 
logger = setup_logger(name='MDL')





def write_radmc_main_input_file(config_mdl: dict,

                                config_lines: dict,

                                path: Union[None, str] = None):

    """

    Creates the main input file for RADMC, which is later used for execution

    :param config_mdl: the model configuration

    :param config_lines: te line configuration, from the STG layer

    :param path: the path where to put the input file

    """

    _path = validate_parameter(path, default='.')

    with open(os.path.join(_path, 'radmc3d.inp'), "w") as outfile:

        for parameter in config_mdl["radmc_postprocessing"]:

            outfile.write(f'{parameter} = {config_mdl["radmc_postprocessing"][parameter]}\n')

        outfile.write(f'lines_mode = {radmc_lines_mode_mapping[config_lines["lines_mode"]]}\n')





def save_cube_as_fits(cube_out_name: Union[str, None] = None,

                      cube_out_path: Union[str, None] = None,

                      path_radmc_files: Union[str, None] = None):
@@ -189,37 +173,10 @@ def populate_line_table(config_lines: dict, 
    )





def populate_stars_table(config_stars: dict,

                         engine: sqlalchemy.engine,

                         executed_on: datetime.timestamp,

                         grid_zipfile: str,

                         run_id: str):

    """

    Populate the stars table in the DB

    :param config_stars: the dictionary containing the stars configurations

    :param engine: the SQLAlchemy engine to use

    :param executed_on: the timestamp of execution, to add to the record

    :param grid_zipfile: the grid tarfile name, to be used as key

    :param run_id: the run unique identifier

    """

    _config_stars = config_stars.copy()

    _config_stars['zipped_grid_name'] = grid_zipfile

    _config_stars['created_on'] = executed_on

    _config_stars['run_id'] = run_id



    upsert(

        table_object=StarsPars,

        row_dict=_config_stars,

        conflict_keys=[StarsPars.zipped_grid_name, StarsPars.run_id],

        engine=engine

    )





def main(grid_zipfile: str,

         run_id: str,

         override_config: Union[dict, None] = None,

         radmc_input_path: Union[str, None] = None,

         compute_dust_temperature: bool = True) -> str:

         radmc_input_path: Union[str, None] = None) -> str:

    # This is necessary, because the lines_mode is needed both in the lines.inp and radmc3d.inp files

    # The reason for splitting the main input file from the rest is that some parameters can be changed

    # independently of the grid for the modeling. The mdl hash should depend on all the mdl parameters, not a subset
@@ -231,9 +188,6 @@ def main(grid_zipfile: str, 
    config_lines = config_stg['lines']

    config_mdl = load_config_file(os.path.join('mdl', 'config', 'config.yml'),

                                  override_config=_override_config['model'])

    write_radmc_main_input_file(config_mdl=config_mdl,

                                config_lines=config_lines,

                                path=_radmc_input_path)

    assert check_config(config=config_mdl['radmc_observation'])

    with open(os.path.join('mdl', 'radmc3d_postprocessing.sh'), 'w') as outfile:

        outfile.write(f'cd {_radmc_input_path}\n')
@@ -247,20 +201,6 @@ def main(grid_zipfile: str, 
    logger.debug(f'Executing command: {radmc_command}')

    execution_dir = os.getcwd()

    os.chdir(_radmc_input_path)

    if 'stars' in config_stg:

        if compute_dust_temperature is True:

            logger.info('Computing dust temperature distribution using the stars in the configuration file')

            os.system('radmc3d mctherm setthreads 16')

            os.system(f'zip -ur {os.path.join(execution_dir, "stg", "archive", grid_zipfile)} dust_temperature.dat')

            populate_stars_table(config_stars=config_stg['stars'],

                                 engine=engine,

                                 executed_on=executed_on,

                                 grid_zipfile=grid_zipfile,

                                 run_id=run_id)

        else:

            logger.info('Using cached dust temperature distribution')

            shutil.copy(os.path.join(execution_dir, 'model', 'data', 'dust_temperature.dat'),

                        os.path.join('.', 'dust_temperature.dat'))

    os.system(radmc_command)

    os.chdir(execution_dir)

    logger.debug(f'Checking presence of file: {os.path.join(_radmc_input_path, "image.out")}')

etl/stg/stg_radmc_input_generator.py

+63 −9
Original line number Diff line number Diff line
@@ -22,7 +22,7 @@ from assets.commons import (compute_power_law_radial_profile, 
from assets.constants import (mean_molecular_mass,

                              radmc_input_headers,

                              radmc_lines_mode_mapping)

from stg.stg_build_db_structure import GridPars, GridFiles

from stg.stg_build_db_structure import GridPars, GridFiles, StarsPars

from astropy import units as u

from astropy import constants as cst

from astropy.io import fits
@@ -96,15 +96,20 @@ def copy_additional_files(files_to_transfer: Union[None, List[str]] = None, 
        shutil.copy2(os.path.join(_path, filename), _dst_path)





def write_radmc_main_input_file(config: dict,

def write_radmc_main_input_file(config_mdl: dict,

                                config_lines: dict,

                                path: Union[None, str] = None):

    """

    Creates the main input file for RADMC, which is later used for execution

    :param config_mdl: the model configuration

    :param config_lines: te line configuration, from the STG layer

    :param path: the path where to put the input file

    """

    _path = validate_parameter(path, default='.')

    with open(os.path.join(_path, 'radmc3d.inp'), "w") as outfile:

        outfile.write(f'nphot = {config["radmc_postprocessing"]["nphotons"]}\n')

        outfile.write(f'scattering_mode_max = {config["radmc_postprocessing"]["scattering_mode_max"]}\n')

        outfile.write(f'iranfreqmode = {config["radmc_postprocessing"]["iranfreqmode"]}\n')

        outfile.write(f'tgas_eq_tdust = {config["radmc_postprocessing"]["tgas_eq_tdust"]}\n')

        outfile.write(f'lines_mode = {radmc_lines_mode_mapping[config["lines"]["lines_mode"]]}\n')

        for parameter in config_mdl["radmc_postprocessing"]:

            outfile.write(f'{parameter} = {config_mdl["radmc_postprocessing"][parameter]}\n')

        outfile.write(f'lines_mode = {radmc_lines_mode_mapping[config_lines["lines_mode"]]}\n')





def get_solid_body_rotation_y(grid_metadata):
@@ -401,6 +406,31 @@ def populate_grid_files(quantity: str, 
    )





def populate_stars_table(config_stars: dict,

                         engine: sqla_engine,

                         grid_zipfile: str,

                         run_id: str):

    """

    Populate the stars table in the DB

    :param config_stars: the dictionary containing the stars configurations

    :param engine: the SQLAlchemy engine to use

    :param executed_on: the timestamp of execution, to add to the record

    :param grid_zipfile: the grid tarfile name, to be used as key

    :param run_id: the run unique identifier

    """

    _config_stars = config_stars.copy()

    _config_stars['zipped_grid_name'] = grid_zipfile

    _config_stars['created_on'] = datetime.now()

    _config_stars['run_id'] = run_id



    upsert(

        table_object=StarsPars,

        row_dict=_config_stars,

        conflict_keys=[StarsPars.zipped_grid_name, StarsPars.run_id],

        engine=engine

    )





def write_stellar_input_file(stars_metadata: dict,

                             grid_metadata: dict,

                             path: str,
@@ -424,9 +454,14 @@ def write_stellar_input_file(stars_metadata: dict, 


def main(run_id: str,

         override_config: Union[dict, None] = None,

         path_radmc_files: Union[str, None] = None) -> str:

         path_radmc_files: Union[str, None] = None,

         compute_dust_temperature: bool = True) -> str:

    _override_config = validate_parameter(override_config, default={'grid_lines': {}, 'model': {}})

    config = load_config_file(os.path.join('stg', 'config', 'config.yml'),

                              override_config=override_config)

                              override_config=_override_config)

    config_lines = config['lines']

    config_mdl = load_config_file(os.path.join('mdl', 'config', 'config.yml'),

                                  override_config=_override_config['model'])

    engine = get_pg_engine(logger=logger)



    input_files_dir = validate_parameter(path_radmc_files, default=os.path.join('mdl', 'radmc_files'))
@@ -490,6 +525,25 @@ def main(run_id: str, 
                        filename=grid_file_name,

                        run_id=run_id)



    write_radmc_main_input_file(config_mdl=config_mdl,

                                config_lines=config_lines,

                                path=input_files_dir)

    execution_dir = os.getcwd()

    os.chdir(input_files_dir)

    if 'stars' in config:

        if compute_dust_temperature is True:

            logger.info('Computing dust temperature distribution using the stars in the configuration file')

            os.system('radmc3d mctherm setthreads 16')

            populate_stars_table(config_stars=config['stars'],

                                 engine=engine,

                                 grid_zipfile=zip_filename,

                                 run_id=run_id)

        else:

            logger.info('Using cached dust temperature distribution')

            shutil.copy(os.path.join(execution_dir, 'model', 'data', 'dust_temperature.dat'),

                        os.path.join('.', 'dust_temperature.dat'))

    os.chdir(execution_dir)



    make_archive(output_filename=zip_filename,

                 source_dir=input_files_dir,

                 archive_path=os.path.join('stg', 'archive'))