Commit 4ec0c8ee authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Edited procedures for spherical model.

parent 1cb307e3

etl/assets/commons/__init__.py

+4 −0
Original line number Diff line number Diff line
@@ -128,6 +128,7 @@ def compute_power_law_radial_profile( 
        central_value: float,

        power_law_index: float,

        distance_matrix: np.array,

        maximum_radius: Union[float, None] = None,

        value_at_reference: Union[float, None] = None,

        distance_reference: Union[float, u.Quantity] = 1.0,

        fill_reference_pixel: bool = True) -> np.array:
@@ -136,6 +137,7 @@ def compute_power_law_radial_profile( 
    :param central_value: value in the center of the grid

    :param power_law_index: index of the power law used to scale the profile

    :param distance_matrix: the matrix of distances from the reference point

    :param maximum_radius: the maximum radius to populate with gas within the grid

    :param value_at_reference: value of the profile at the reference distance; defaults to central value if not provided

    :param distance_reference: value of the reference distance

    :param fill_reference_pixel: whether to fill the reference point with central_value and set this to the maximum in
@@ -153,6 +155,8 @@ def compute_power_law_radial_profile( 
    # If the routine fills the 0-distance point (the centre), it fixes the profile making the central value the maximum

    if fill_reference_pixel is True:

        profile = np.where(profile > central_value, central_value, profile)

    if maximum_radius is not None:

        profile = np.where(distance_matrix > maximum_radius + maximum_radius/1e5, 0, profile)

    return profile

etl/mdl/mdl_execute_radmc_command.py

+4 −3
Original line number Diff line number Diff line
@@ -181,12 +181,13 @@ def main(grid_tarfile: 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

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

    executed_on = datetime.now()

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

                                  override_config=override_config['grid_lines'])

                                  override_config=_override_config['grid_lines'])

    config_lines = config_stg['lines']

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

                                  override_config=override_config['model'])

                                  override_config=_override_config['model'])

    write_radmc_main_input_file(config_mdl=config_mdl,

                                config_lines=config_lines,

                                path=os.path.join('mdl', 'radmc_files'))
@@ -194,7 +195,7 @@ def main(grid_tarfile: str, 
    with open(os.path.join('mdl', 'radmc3d_postprocessing.sh'), 'w') as outfile:

        outfile.write('cd mdl/radmc_files\n')

        options_set = get_command_options(config_mdl)

        radmc_command = f'radmc3d image {" ".join(options_set)}'

        radmc_command = f'radmc3d image setthreads 4 {" ".join(options_set)}'

        outfile.write(radmc_command)



    engine = get_pg_engine(logger=logger)

etl/stg/config/config.yml

+7 −5
Original line number Diff line number Diff line 
grid:

    grid_type: regular

    coordinate_system: cartesian

    central_density: 1e6

    central_density: 1e8

    density_unit: "cm^-3"

    density_powerlaw_idx: 0

    density_powerlaw_idx: -1.5

    density_value_at_reference: 1e6

    maximum_radius: 1

    maximum_radius_unit: 'pc'

    distance_reference: 0.5

    distance_reference_unit: 'pc'

    dust_temperature: 15
@@ -12,7 +14,7 @@ grid: 
    dust_temperature_powerlaw_idx: 0

    microturbulence: 1.5

    microturbulence_unit: 'km/s'

    dim1: {"size":1, "size_units": "pc", "shape": 3, "refpix": 1}

    dim1: {"size":1.2, "size_units": "pc", "shape": 21, "refpix": 10}

    velocity_field: 'solid'

    velocity_gradient: 2

    velocity_gradient_unit: "km/(s pc)"
@@ -20,8 +22,8 @@ grid: 
lines:

    species_to_include: ['e-ch3oh']

    molecular_abundances: {

                              "e-ch3oh": 1e-8,

                              "p-h2": 0.25,

                              "e-ch3oh": 1e-10,

                              "p-h2": 1,

    }

    lines_mode: 'lvg'

    collision_partners: ['p-h2']

etl/stg/stg_radmc_input_generator.py

+4 −3
Original line number Diff line number Diff line
@@ -121,7 +121,7 @@ def get_profiles(grid_metadata): 
                (float(grid_metadata['density_value_at_reference']) * u.Unit(grid_metadata['density_unit']))

                .to(u.cm ** -3)).value,

            'distance_reference': (float(grid_metadata['distance_reference']) * u.Unit(

                grid_metadata['distance_reference_unit']).to(u.cm)).value

                grid_metadata['distance_reference_unit'])).to(u.cm).value

        }

    except (KeyError, AttributeError):

        density_ref = {
@@ -151,8 +151,8 @@ def get_profiles(grid_metadata): 
        },

        'escprob_lengthscale': {

            # FIXME: make the unit consistent with the max via indexing

            'central_value': (max(grid_metadata['grid_size']) * u.Unit(grid_metadata['grid_size_units'][0]))

            .to(u.cm).value,

            'central_value': min((max(grid_metadata['grid_size']) * u.Unit(grid_metadata['grid_size_units'][0]))

            .to(u.cm).value, (grid_metadata['maximum_radius'] * u.Unit(grid_metadata['maximum_radius_unit'])).to(u.cm).value),

            'power_law_index': 0,

            'value_at_reference': None,

            'distance_reference': 1.0
@@ -186,6 +186,7 @@ def get_profiles(grid_metadata): 
            distance_matrix=grid_metadata['distance_matrix'],

            value_at_reference=profiles_mapping[profile]['value_at_reference'],

            distance_reference=profiles_mapping[profile]['distance_reference'],

            maximum_radius=grid_metadata['maximum_radius'] * u.Unit(grid_metadata['maximum_radius_unit']).to(u.cm)

        )



    if grid_metadata['velocity_field'] == 'solid':

etl/tests/test_commons.py

+11 −1
Original line number Diff line number Diff line
@@ -163,6 +163,16 @@ class Test(TestCase): 
                                              indices=indices)

        self.assertTrue(np.array_equal(expected_results, distance_matrix))



    def test_get_distance_matrix_symmetric(self):

        grid_metadata = {

            'grid_shape': [5, 5, 5],

            'physical_px_size': [1 * u.cm, 1 * u.cm, 1 * u.cm]

        }

        indices = np.indices(grid_metadata['grid_shape']) - 3

        distance_matrix = get_distance_matrix(grid_metadata=grid_metadata,

                                              indices=indices)

        self.assertTrue(np.array_equal(distance_matrix, distance_matrix.T))



    def test_get_centered_indices(self):

        grid_metadata = {

            'grid_shape': [5, 3],
@@ -232,7 +242,7 @@ class Test(TestCase): 
            'DB_PORT': 5432,

        }

        credentials = get_credentials(logger=self.logger,

                                      credentials_filename=os.path.join('tests', 'test_files', 'credentials.yaml'),

                                      credentials_filename=os.path.join('test_files', 'credentials.yaml'),

                                      set_envs=True)

        self.assertDictEqual(credentials, expected_results)

        for key in expected_results: