420 accretion disk tutorial

.github/workflows/build_docs.yml

@@ -53,7 +53,7 @@ jobs:
         python setup.py install
       shell: bash -l {0}
       env:
-        CC:   gcc-10
+        CC:   gcc-12
     - name : build docs
       run: | 
         make html

.github/workflows/ci_tests.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       max-parallel: 5
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -54,7 +54,7 @@ jobs:
         python setup.py install
       shell: bash -l {0}
       env:
-        CC:   gcc-10
+        CC:   gcc-12
 
     - name: Test with pytest
       run: |

docs/source/Start_here.rst

@@ -26,6 +26,8 @@ All tutorials listed below may be found as Jupyter notebooks under ``docs/source
 
 * :doc:`Emitting patterns 2D projection<Emitting_patterns_2Dprojection>` is a tutorial showing how to use the 2D projection tool for the hot emitting regions on the star's surface.
 
+* :doc:`Accretion disk<Accretion_disk>` is a tutorial showing how to set up and accretion disk and add its emission to the emission of a star.
+
 * :doc:`Importance sampling<Importance_sampling>` is a tutorial for importance sampling.
 
 * :doc:`Module generator tutorial<Module_generator_tutorial>` provides instructions on how to generate Python modules in an automated way to run X-PSI.

docs/source/index.rst

@@ -37,6 +37,7 @@
    Polarization
    Post-processing
    Emitting_patterns_2Dprojection
+   Accretion_disk
    Importance_sampling
    Module_generator_tutorial
    Example_script_and_modules

examples/examples_modeling_tutorial/TestRun_AMXP.py

@@ -309,13 +309,14 @@ def __call__(self, boundto, caller = None):
 T_in = get_T_in_log10_Kelvin(0.16845756373108872) #(0.29)
 R_in = 0.308122224729265000E+02 #55.0
 values = {'T_in':T_in,'R_in':R_in,'K_disk': k_disk}
-disk = Disk(bounds={}, values=values)
+bounds_disk = {'T_in': (3., 10.), 'R_in': (0., 1e3), 'K_disk': None}
+disk = Disk(bounds=bounds_disk, values=values)
 
 from modules.CustomPhotosphere import CustomPhotosphere_NumA5
 
-stokes = False
+stokes = True
 bounds = dict(spin_axis_position_angle = (None, None))
-photosphere = CustomPhotosphere_NumA5(hot = hot, elsewhere = elsewhere, stokes=stokes, disk=None, bounds=bounds,
+photosphere = CustomPhotosphere_NumA5(hot = hot, elsewhere = elsewhere, stokes=stokes, disk=disk, bounds=bounds,
                                 values=dict(mode_frequency = spacetime['frequency']))
 
 photosphere.hot_atmosphere = this_directory+'/model_data/Bobrikova_compton_slab_I.npz'
@@ -354,31 +355,22 @@ def __call__(self, boundto, caller = None):
 #Tbb = 1 keV <=> tbb = 0.002 (roughly)
 #Te = 50 keV <=>  te = 100 (roughly)
 
+p = [mass,  # grav mass
+     radius,  # coordinate equatorial radius
+     distance,  # earth distance kpc
+     cos_i,  # cosine of earth inclination
+     phase_shift,  # phase of hotregion
+     super_colatitude,  # colatitude of centre of superseding region
+     super_radius,  # angular radius superseding region
+     tbb,
+     te,
+     tau,
+     T_in,
+     R_in]
+
 if stokes:
-    p = [mass, #grav mass
-          radius, #coordinate equatorial radius
-          distance, # earth distance kpc
-          cos_i, #cosine of earth inclination
-          chi0, #spin axis position angle
-          phase_shift, #phase of hotregion
-          super_colatitude, #colatitude of centre of superseding region
-          super_radius,  #angular radius superceding region
-          tbb,
-          te,
-          tau
-          ]
-elif not stokes:
-    p = [mass, #grav mass
-          radius, #coordinate equatorial radius
-          distance, # earth distance kpc
-          cos_i, #cosine of earth inclination
-          phase_shift, #phase of hotregion
-          super_colatitude, #colatitude of centre of superseding region
-          super_radius,  #angular radius superceding region
-          tbb,
-          te,
-          tau
-          ]
+    p.insert(4, chi0)  # spin axis position angle
+
 
 # print(len(p))
 

examples/examples_modeling_tutorial/modules/CustomPhotosphere.py

@@ -85,6 +85,10 @@ def __init__(self,
                                    symbol = r'$f_{\rm mode}$',
                                    value = values.get('mode_frequency', None))
 
+        custom = []
+        if disk is not None:
+            custom.append(disk)
+
         if stokes:
             doc = """
             Spin axis position angle measured from the north counterclock-