Merge d1c24be into c5fec94

docs/overview.rst

@@ -30,6 +30,7 @@ The following data are currently supported by *species* (support for other data
 - Photometry from `Sandy Leggett <http://www.gemini.edu/staff/sleggett>`_
 - Photometry of directly imaged planets and brown dwarfs (see dictionary in :class:`~species.data.companions`)
 - Calibration spectrum of `Vega <http://ssb.stsci.edu/cdbs/calspec/>`_
+- Optical constants compiled by `Mollière et al. (2019) <https://ui.adsabs.harvard.edu/abs/2019A%26A...627A..67M/abstract>`_ (see :func:`~species.data.database.Database.add_dust`)
 
 Please give credit to the relevant authors when using these data in a publication. More information is available on the respective websites.
 

docs/species.data.rst

@@ -60,6 +60,14 @@ species.data.drift\_phoenix module
    :undoc-members:
    :show-inheritance:
 
+species.data.dust module
+------------------------
+
+.. automodule:: species.data.dust
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.data.exo\_rem module
 ----------------------------
 

requirements.txt

@@ -6,9 +6,10 @@ h5py ~= 2.10
 matplotlib ~= 3.2
 numpy ~= 1.18
 pandas ~= 0.25
+PyMieScatt ~= 1.7
 pymultinest ~= 2.9
 scipy ~= 1.4
 spectres ~= 2.1
-tqdm ~= 4.45
+tqdm ~= 4.46
 typeguard ~= 2.7
 xlrd ~= 1.2

species/analysis/photometry.py

@@ -39,7 +39,7 @@ def __init__(self,
         self.filter_interp = None
         self.wavel_range = None
 
-        self.vega_mag = 0.03  # [mag]
+        self.vega_mag = 0.03  # (mag)
 
         config_file = os.path.join(os.getcwd(), 'species_config.ini')
 

species/data/companions.py

@@ -104,9 +104,9 @@ def get_data():
                                      'Paranal/SPHERE.IRDIS_D_H23_3': (17.95, 0.17),  # Keppler et al. 2018
                                      'Paranal/SPHERE.IRDIS_D_K12_1': [(16.78, 0.31), (16.72, 0.05)],  # Stolker et al. in prep.
                                      'Paranal/SPHERE.IRDIS_D_K12_2': [(16.23, 0.32), (16.38, 0.06)], # Stolker et al. in prep.
-                                     # 'Paranal/NACO.Lp': (14.08, 0.33),  # Stolker et al. in prep.
-                                     # 'Paranal/NACO.NB405': (13.91, 0.34),  # Stolker et al. in prep.
-                                     # 'Paranal/NACO.Mp': (13.64, 0.22),  # Stolker et al. in prep.
+                                     'Paranal/NACO.Lp': (14.08, 0.33),  # Stolker et al. in prep.
+                                     'Paranal/NACO.NB405': (13.91, 0.34),  # Stolker et al. in prep.
+                                     'Paranal/NACO.Mp': (13.64, 0.22),  # Stolker et al. in prep.
                                      'Keck/NIRC2.Lp': (14.64, 0.18)}},  # Wang et al. 2020
 
             'PDS 70 c': {'distance': (113.43, 0.52),

species/data/database.py

@@ -25,7 +25,7 @@
 from species.core import box, constants
 from species.data import drift_phoenix, btnextgen, vega, irtf, spex, vlm_plx, leggett, \
                          companions, filters, btsettl, ames_dusty, ames_cond, \
-                         isochrones, petitcode, exo_rem
+                         isochrones, petitcode, exo_rem, dust
 from species.read import read_model, read_calibration, read_planck
 from species.util import data_util
 # from species.util import data_util, retrieval_util
@@ -164,6 +164,43 @@ def add_companion(self,
                             distance=data[item]['distance'],
                             app_mag=data[item]['app_mag'])
 
+    @typechecked
+    def add_dust(self) -> None:
+        """
+        Function for adding optical constants of MgSiO3 and Fe to the database. The optical
+        constants have been compiled by Mollière et al. (2019) for petitRADTRANS from the
+        following sources:
+
+        - MgSiO3, crystalline
+            - Scott & Duley (1996), ApJS, 105, 401
+            - Jäger et al. (1998), A&A, 339, 904
+
+        - MgSiO3, amorphous
+            - Jäger et al. (2003), A&A, 408, 193
+
+        - Fe, crystalline
+            - Henning & Stognienko (1996), A&A, 311, 291
+
+        - Fe, amorphous
+            - Pollack et al. (1994), ApJ, 421, 615
+
+        Returns
+        -------
+        NoneType
+            None
+        """
+
+        h5_file = h5py.File(self.database, 'a')
+
+        if 'dust' in h5_file:
+            del h5_file['dust']
+
+        h5_file.create_group('dust')
+
+        dust.add_optical_constants(self.input_path, h5_file)
+
+        h5_file.close()
+
     def add_filter(self,
                    filter_name,
                    filename=None):

species/data/dust.py

@@ -0,0 +1,92 @@
+"""
+Module for optical constants of dust grains.
+"""
+
+import os
+import zipfile
+import urllib.request
+
+import h5py
+import numpy as np
+
+from typeguard import typechecked
+
+
+@typechecked
+def add_optical_constants(input_path: str,
+                          database: h5py._hl.files.File) -> None:
+    """
+    Function for adding the optical constants of crystalline and amorphous MgSiO3 and Fe to the
+    database.
+
+    Parameters
+    ----------
+    input_path : str
+        Folder where the data is located.
+    database : h5py._hl.files.File
+        Database.
+
+    Returns
+    -------
+    None
+        NoneType
+    """
+
+    if not os.path.exists(input_path):
+        os.makedirs(input_path)
+
+    url = 'https://people.phys.ethz.ch/~stolkert/species/optical_constants.zip'
+
+    data_file = os.path.join(input_path, 'optical_constants.zip')
+
+    if not os.path.isfile(data_file):
+        print('Downloading optical constants (87 kB)...', end='', flush=True)
+        urllib.request.urlretrieve(url, data_file)
+        print(' [DONE]')
+
+    print('Unpacking optical constants...', end='', flush=True)
+
+    with zipfile.ZipFile(data_file, 'r') as zip_ref:
+        zip_ref.extractall(input_path)
+
+    print(' [DONE]')
+
+    print('Adding optical constants of MgSiO3...', end='')
+
+    nk_file = os.path.join(input_path, 'optical_constants/mgsio3/crystalline/'
+                           'mgsio3_jaeger_98_scott_96_axis1.dat')
+
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/mgsio3/crystalline/axis_1/', data=data)
+
+    nk_file = os.path.join(input_path, 'optical_constants/mgsio3/crystalline/'
+                           'mgsio3_jaeger_98_scott_96_axis2.dat')
+
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/mgsio3/crystalline/axis_2/', data=data)
+
+    nk_file = os.path.join(input_path, 'optical_constants/mgsio3/crystalline/'
+                           'mgsio3_jaeger_98_scott_96_axis3.dat')
+
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/mgsio3/crystalline/axis_3/', data=data)
+
+    nk_file = os.path.join(input_path, 'optical_constants/mgsio3/amorphous/'
+                           'mgsio3_jaeger_2003_reformat.dat')
+
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/mgsio3/amorphous', data=data)
+
+    print(' [DONE]')
+
+    print('Adding optical constants of Fe...', end='')
+
+    nk_file = os.path.join(input_path, 'optical_constants/fe/crystalline/fe_henning_1996.dat')
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/fe/crystalline', data=data)
+
+    nk_file = os.path.join(input_path, 'optical_constants/fe/amorphous/fe_pollack_1994.dat')
+    data = np.loadtxt(nk_file)
+    database.create_dataset('dust/fe/amorphous', data=data)
+
+    print(' [DONE]')