Commit 9f4dfd6d authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Added central stellar heating source.

parent 069b51f7

etl/assets/commons/__init__.py

+1 −0
Original line number Diff line number Diff line
@@ -220,6 +220,7 @@ def extract_grid_metadata(config: dict) -> dict: 
    grid_metadata['distance_matrix'] = get_distance_matrix(grid_metadata, grid_metadata['centered_indices'])



    grid_metadata['grid_edges'] = get_grid_edges(grid_metadata)

    grid_metadata['continuum_lambdas'] = 100

    return grid_metadata

etl/assets/constants/__init__.py

+1 −0
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ radmc_input_headers = { 
    'wavelength_micron.inp': ['continuum_lambdas'],

    'numberdens_mol.inp': ['iformat', 'ncells'],

    'escprob_lengthscale.inp': ['iformat', 'ncells'],

    'stars.inp': ['iformat', 'nstars', 'continuum_lambdas', 'stars_properties', 'lambdas']

}

etl/mdl/mdl_execute_radmc_command.py

+12 −1
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ import sys 
from itertools import product

from typing import Union

import sqlalchemy

import shutil

from astropy import units as u

from datetime import datetime

from radmc3dPy import image
@@ -190,7 +191,8 @@ def populate_line_table(config_lines: dict, 
def main(grid_tarfile: str,

         run_id: str,

         override_config: Union[dict, None] = None,

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

         radmc_input_path: Union[str, None] = None,

         compute_dust_temperature: bool = True) -> 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
@@ -215,8 +217,17 @@ def main(grid_tarfile: str, 
    engine = get_pg_engine(logger=logger)



    # Execute radmc

    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')

        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/config/config.yml

+10 −0
Original line number Diff line number Diff line
@@ -20,6 +20,16 @@ grid: 
    velocity_gradient: 2

    velocity_gradient_unit: "km/(s pc)"



stars:

    nstars: 1

    rstars: [6.96e10, ]

    mstars: [1.99e36, ]

    star_positions: [[0, 0, 0]]

    star_fluxes: [[-32000,], ]

    nlambdas: 300

    spacing: 'log'

    lambdas_micron_limits: [0.001, 1300]



lines:

    species_to_include: ['e-ch3oh']

    molecular_abundances: {

etl/stg/stg_radmc_input_generator.py

+51 −8
Original line number Diff line number Diff line
@@ -34,7 +34,8 @@ def write_radmc_input(filename, 
                      quantity,

                      grid_metadata,

                      path: Union[None, str] = None,

                      override_defaults: Union[None, dict] = None):

                      override_defaults: Union[None, dict] = None,

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

    rt_metadata_default = {

        'iformat': 1,

        'grid_type': grid_metadata['grid_type'],
@@ -45,10 +46,11 @@ def write_radmc_input(filename, 
        'ncells_per_axis': ' '.join([str(axis_size) for axis_size in grid_metadata['grid_shape']]),

        'dust_species': 1,  ##

        'active_axes': ' '.join(['1'] * len(grid_metadata['grid_shape'])),

        'continuum_lambdas': 100,  ##

        'continuum_lambdas': grid_metadata['continuum_lambdas'],  ##

    }

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

    _filename = 'numberdens_mol.inp' if filename.startswith('numberdens_') else filename

    _flatten_style = validate_parameter(flatten_style, default='F')

    with open(os.path.join(_path, filename), "w") as outfile:

        for key in radmc_input_headers[_filename]:

            try:
@@ -56,7 +58,7 @@ def write_radmc_input(filename, 
            except (KeyError, TypeError):

                header_line = rt_metadata_default[key]

            outfile.write(f'{header_line}\n')

        outfile.write('\n'.join(quantity.flatten('F').astype(str)))

        outfile.write('\n'.join(quantity.flatten(_flatten_style).astype(str)))





def write_radmc_lines_input(line_config: dict,
@@ -217,12 +219,9 @@ def get_reference_value(grid_metadata: dict, 


def write_grid_input_files(profiles: dict,

                           grid_metadata: dict,

                           wavelengths_micron: np.array,

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

    _path = validate_parameter(path, default=os.path.join('mdl', 'radmc_files'))

    n_wavelengths = 100

    start_wavelength = 5

    end_wavelength = 1300

    wavelengths_micron = np.logspace(np.log10(start_wavelength), np.log10(end_wavelength), n_wavelengths)



    quantity_mapping = {

        'amr_grid.inp': {
@@ -402,6 +401,27 @@ def populate_grid_files(quantity: str, 
    )





def write_stellar_input_file(stars_metadata: dict,

                             grid_metadata: dict,

                             path: str,

                             wavelengths_micron: np.array):

    star_properties = [' '.join([str(rstar), str(mstar), str(pos[0]), str(pos[1]), str(pos[2])]) for rstar, mstar, pos in

                       zip(stars_metadata['rstars'], stars_metadata['mstars'], stars_metadata['star_positions'])]

    override_defaults = {

        'iformat': 2,

        'nstars': stars_metadata['nstars'],

        'continuum_lambdas': stars_metadata['nlambdas'],

        'stars_properties': '\n'.join(star_properties),

        'lambdas': ' \n'.join(wavelengths_micron.astype(str)),

    }

    write_radmc_input(filename='stars.inp',

                      path=path,

                      quantity=np.array(stars_metadata['star_fluxes']),

                      grid_metadata=grid_metadata,

                      override_defaults=override_defaults,

                      flatten_style='C')





def main(run_id: str,

         override_config: Union[dict, None] = None,

         path_radmc_files: Union[str, None] = None) -> str:
@@ -415,10 +435,33 @@ def main(run_id: str, 
    copy_additional_files(dst_path=input_files_dir)



    grid_metadata = extract_grid_metadata(config=config)

    if 'stars' in config:

        stars_metadata = config['stars']

        if stars_metadata['spacing'] == 'log':

            wavelengths_micron = np.logspace(np.log10(stars_metadata['lambdas_micron_limits'][0]),

                                             np.log10(stars_metadata['lambdas_micron_limits'][1]),

                                             stars_metadata['nlambdas'])

        elif stars_metadata['spacing'] == 'linear':

            wavelengths_micron = np.linspace(stars_metadata['lambdas_micron_limits'][0],

                                             stars_metadata['lambdas_micron_limits'][1],

                                             stars_metadata['nlambdas'])

        else:

            raise (NotImplemented('Spacing not defined. Choose between {linear, log}'))

        write_stellar_input_file(stars_metadata=stars_metadata,

                                 grid_metadata=grid_metadata,

                                 path=input_files_dir,

                                 wavelengths_micron=wavelengths_micron)

    else:

        wavelengths_micron = np.logspace(np.log10(5),

                                         np.log10(1300),

                                         100)

    grid_metadata['continuum_lambdas'] = len(wavelengths_micron)



    profiles = get_profiles(grid_metadata=grid_metadata)

    write_grid_input_files(grid_metadata=grid_metadata,

                           profiles=profiles,

                           path=input_files_dir)

                           path=input_files_dir,

                           wavelengths_micron=wavelengths_micron)

    get_moldata(species_names=config['lines']['species_to_include'],

                logger=logger,

                path=input_files_dir)