Docs submodule fix

.github/workflows/deploy-github-pages.yml

@@ -16,6 +16,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: recursive
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -42,6 +44,7 @@ jobs:
         sudo apt-get install gfortran swig libhdf5-serial-dev
         pip install -r requirements.txt
         pip install meson numpy
+
         python -m pip install .
 
     - name: Make dependencies

docs/conf.py

@@ -161,6 +161,8 @@ def setup(app):
 plot_pre_code = """
 from generate_default_bsedict import get_default_BSE_settings
 default_BSEDict = get_default_BSE_settings(to_python=True)
+default_SSEDict = {'stellar_engine': 'sse'}
+
 """
 
 

docs/create_params_ini.py

@@ -83,6 +83,8 @@ def construct_ini_from_json(config, include_comments=True):
                 if "default" in option and option["default"]:
                     if setting["type"] == "checkbox":
                         default.append(str(option["name"]))
+                    elif option["name"] == "":
+                        default = '""'
                     else:
                         default = str(option["name"])
 

docs/pages/evolve/interface.rst

@@ -30,12 +30,14 @@ samples ~100 binaries and evolving them.
 
 .. ipython:: python
 
+    SSEDict = {'stellar_engine': 'sse'}
+
     InitialBinaries, mass_singles, mass_binaries, n_singles, n_binaries = InitialBinaryTable.sampler(
         'independent', [13, 14], [13, 14], binfrac_model=0.5, primary_model='kroupa01',
         ecc_model='sana12', porb_model='sana12', qmin=-1, SF_start=13700.0, SF_duration=0.0,
         met=0.002, size=1000)
 
-    bpp, bcm, initC, kick_info = Evolve.evolve(initialbinarytable=InitialBinaries, BSEDict=BSEDict)
+    bpp, bcm, initC, kick_info = Evolve.evolve(initialbinarytable=InitialBinaries, BSEDict=BSEDict, SSEDict=SSEDict)
 
 Now we can create a ``COSMICOutput`` object quite easily (with an optional label):
 

docs/pages/evolve/multiple.rst

@@ -73,5 +73,5 @@ progenitor, we expect most of the evolution to take place in the first ~60 Myr.
     import numpy as np
     np.random.seed(5)
     binary_set = InitialBinaryTable.InitialBinaries(m1=[85.543645, 11.171469], m2=[84.99784, 9.67305], porb=[446.795757, 370.758343], ecc=[0.448872, 0.370], tphysf=[13700.0, 13700.0], kstar1=[1, 1], kstar2=[1, 1], metallicity=[0.002, 0.02])
-    fig = evolve_and_plot(binary_set, t_min=None, t_max=[6.0, 60.0], BSEDict=BSEDict, SSEDict=SSEDict, sys_obs={})
+    fig = evolve_and_plot(binary_set, t_min=None, t_max=[6.0, 60.0], BSEDict=default_BSEDict, SSEDict=default_SSEDict, sys_obs={})
 

docs/pages/evolve/rerun.rst

@@ -24,11 +24,14 @@ First, let's evolve a binary and save the initC table.
 
 .. ipython:: python
 
+
+    SSEDict = {'stellar_engine': 'sse'}
+
     binary = InitialBinaryTable.InitialBinaries(
         m1=20, m2=15, porb=100, ecc=0.1, tphysf=13700.0, kstar1=1, kstar2=1, metallicity=0.02
     )
 
-    bpp, bcm, initC, kick_info = Evolve.evolve(initialbinarytable=binary, BSEDict=BSEDict)
+    bpp, bcm, initC, kick_info = Evolve.evolve(initialbinarytable=binary, BSEDict=BSEDict, SSEDict=SSEDict)
 
 We can check some of the output for this binary so that we can see it's identical after we re-run it.
 
@@ -74,7 +77,7 @@ pass in a BSEDict this time, since we are modifying the physics assumptions dire
 
     # modify alpha1 in the initC table
     initC_modified = initC.copy()
-    initC_modified['alpha1'] = 10
+    initC_modified['alpha1_0'] = 10
 
     # re-run the binary with modified physics
     bpp_rerun_mod, bcm_rerun_mod, initC_rerun_mod, kick_info_rerun_mod = Evolve.evolve(
@@ -107,7 +110,7 @@ very small sigma value for both regular core-collapse supernovae and electron-ca
 
     # modify alpha1 in the initC table
     initC_modified_kick = initC.copy()
-    initC_modified_kick['alpha1'] = 10
+    initC_modified_kick['alpha1_0'] = 10
     initC_modified_kick['sigma'] = 1.0
     initC_modified_kick['sigmadiv'] = -1.0
     initC_modified_kick['kickflag'] = 1

docs/pages/evolve/resolution.rst

@@ -44,17 +44,14 @@ First, print all time steps during mass transfer
 
 .. include:: ../../_generated/default_bsedict.rst
 
-    bpp, bcm, initC, kick_info = Evolve.evolve(initialbinarytable=single_binary, BSEDict=BSEDict,
-                                                SSEDict=SSEDict, timestep_conditions=timestep_conditions)
-
 .. ipython:: python
     :okwarning:
 
     # Define the condition for the time step
     timestep_conditions = [['RRLO_1>=1', 'dtp=0.0'], ['RRLO_2>=1', 'dtp=0.0']]
 
     bpp, bcm, initC, kick_info = Evolve.evolve(
-        initialbinarytable=single_binary, BSEDict=BSEDict,
+        initialbinarytable=single_binary, BSEDict=BSEDict, SSEDict=SSEDict,
         timestep_conditions=timestep_conditions
     )
     print(bcm[['tphys', 'kstar_1', 'kstar_2', 'mass_1', 'mass_2', 'RRLO_1', 'RRLO_2']])

docs/pages/evolve/single.rst

@@ -183,8 +183,7 @@ You can also use the built-in plotting function to see how the system evolves:
     from cosmic.sample.initialbinarytable import InitialBinaryTable
     from cosmic.plotting import evolve_and_plot
     single_binary = InitialBinaryTable.InitialBinaries(m1=85.543645, m2=84.99784, porb=446.795757, ecc=0.448872, tphysf=13700.0, kstar1=1, kstar2=1, metallicity=0.002)
-    SSEDict = {'stellar_engine': 'sse'}
-    fig = evolve_and_plot(single_binary, t_min=None, t_max=None, BSEDict=default_BSEDict, SSEDict=SSEDict, sys_obs={})
+    fig = evolve_and_plot(single_binary, t_min=None, t_max=None, BSEDict=default_BSEDict, SSEDict=default_SSEDict, sys_obs={})
 
 
 In this case, all the action happens in the first few Myr, so let's specify a t_max:
@@ -199,5 +198,4 @@ In this case, all the action happens in the first few Myr, so let's specify a t_
     from cosmic.sample.initialbinarytable import InitialBinaryTable
     from cosmic.plotting import evolve_and_plot
     single_binary = InitialBinaryTable.InitialBinaries(m1=85.543645, m2=84.99784, porb=446.795757, ecc=0.448872, tphysf=13700.0, kstar1=1, kstar2=1, metallicity=0.002)
-    SSEDict = {'stellar_engine': 'sse'}
-    fig = evolve_and_plot(single_binary, t_min=None, t_max=6.0, BSEDict=default_BSEDict, SSEDict=SSEDict, sys_obs={})
+    fig = evolve_and_plot(single_binary, t_min=None, t_max=6.0, BSEDict=default_BSEDict, SSEDict=default_SSEDict, sys_obs={})

docs/pages/inifile.rst

@@ -63,6 +63,13 @@ Random Seed
     :file: ../_generated/config_insert_rand_seed.html
 
 
+Single star evolution
+---------------------
+
+.. raw:: html
+    :file: ../_generated/config_insert_sse.html
+
+
 Binary physics
 --------------
 

examples/Params.ini

@@ -204,6 +204,53 @@ match = -5.0
 ; Default: 42
 seed = 42
 
+[sse]
+
+; stellar_engine
+; Select which stellar evolution engine to use for single star evolution
+; 
+; Options: 
+;    sse - Use SSE for single star evolution which will apply the fitting formulae from Hurley+2000 for the single star evolution
+;    metisse - Use METISSE for single star evolution, must supply ``path_to_tracks`` and ``path_to_he_tracks``
+; Default: sse
+stellar_engine = sse
+
+; path_to_tracks
+; Path to the METISSE tracks for single star evolution. Must be supplied if ``stellar_engine`` is set to ``metisse``
+; 
+; Options: 
+;    path/to/tracks - This specifies the absolute path to the EEP tracks for single star evolution. Leave the string empty if not using METISSE for single star evolution.
+;     - Default value (not using METISSE for single star evolution)
+; Default: ""
+path_to_tracks = ""
+
+; path_to_he_tracks
+; Path to the METISSE tracks for helium star evolution. Must be supplied if ``stellar_engine`` is set to ``metisse``
+; 
+; Options: 
+;    path/to/he_tracks - This specifies the absolute path to the EEP tracks for helium star evolution. Leave the string empty if not using METISSE for single star evolution.
+;     - Default value (not using METISSE for single star evolution)
+; Default: ""
+path_to_he_tracks = ""
+
+; z_accuracy_limit
+; Sets the maximum allowed relative difference between the supplied metallicity and the tracks used by METISSE. If cosmic throws an error due to metallicity, increasing this slightly may help. Must be supplied if ``stellar_engine`` is set to ``metisse``
+; 
+; Options: 
+;    positive values - Minimum metallicity
+;    0.01 - Recommended value
+; Default: 0.01
+z_accuracy_limit = 0.01
+
+; metisse_verbose
+; Whether to print verbose output from METISSE when using METISSE for single star evolution.
+; 
+; Options: 
+;    True - Print verbose output from METISSE when using METISSE for single star evolution.
+;    False - Do not print verbose output from METISSE when using METISSE for single star evolution.
+; Default: False
+metisse_verbose = False
+
 [bse]
 
 ;;;;;;;;;;;;;;;;;

src/cosmic/data/cosmic-settings.json

@@ -459,6 +459,100 @@
             }
         ]
     },
+    {
+        "category": "sse", 
+        "category_label": "Single star evolution",
+        "category_description": "Settings that control the single star evolution in the simulation",
+        "docs-colour": "lightsteelblue",
+        "settings": [
+            {
+                "name": "stellar_engine",
+                "description": "Select which stellar evolution engine to use for single star evolution",
+                "type": "dropdown",
+                "options-preface": "",
+                "options": [
+                    {
+                        "name": "sse",
+                        "description": "Use SSE for single star evolution which will apply the fitting formulae from <a href='https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract'>Hurley+2000</a> for the single star evolution",
+                        "default": true
+
+                    },
+                    {
+                        "name": "metisse",
+                        "description": "Use METISSE for single star evolution, must supply <code>path_to_tracks</code> and <code>path_to_he_tracks</code>"
+                    }
+                ]
+            }, 
+            {
+                "name": "path_to_tracks",
+                "description": "Path to the METISSE tracks for single star evolution. Must be supplied if <code>stellar_engine</code> is set to <code>metisse</code>",
+                "type": "string",
+                "options-preface": "",
+                "options": [
+                    {
+                        "name": "path/to/tracks",
+                        "description": "This specifies the absolute path to the EEP tracks for single star evolution. Leave the string empty if not using METISSE for single star evolution."
+                    },
+                    {
+                        "name": "",
+                        "description": "Default value (not using METISSE for single star evolution)",
+                        "default": true
+                    }
+                ]
+            },
+            {
+                "name": "path_to_he_tracks",
+                "description": "Path to the METISSE tracks for helium star evolution. Must be supplied if <code>stellar_engine</code> is set to <code>metisse</code>",
+                "type": "string",
+                "options-preface": "",
+                "options": [
+                    {
+                        "name": "path/to/he_tracks",
+                        "description": "This specifies the absolute path to the EEP tracks for helium star evolution. Leave the string empty if not using METISSE for single star evolution."
+                    },
+                    {
+                        "name": "",
+                        "description": "Default value (not using METISSE for single star evolution)",
+                        "default": true
+                    }
+                ]
+            },
+            {
+                "name": "z_accuracy_limit",
+                "description": "Sets the maximum allowed relative difference between the supplied metallicity and the tracks used by METISSE. If cosmic throws an error due to metallicity, increasing this slightly may help. Must be supplied if <code>stellar_engine</code> is set to <code>metisse</code>",
+                "type": "number",
+                "options-preface": "",
+                "options": [
+                    {
+                        "name": "positive values",
+                        "description": "Minimum metallicity"
+                    },
+                    {
+                        "name": 0.01,
+                        "description": "Recommended value",
+                        "default": true
+                    }
+                ]
+            },
+            {
+                "name": "metisse_verbose",
+                "description": "Whether to print verbose output from METISSE when using METISSE for single star evolution.",
+                "type": "dropdown",
+                "options-preface": "",
+                "options": [
+                    {
+                        "name": "True",
+                        "description": "Print verbose output from METISSE when using METISSE for single star evolution."
+                    },
+                    {
+                        "name": "False",
+                        "description": "Do not print verbose output from METISSE when using METISSE for single star evolution.",
+                        "default": true
+                    }
+                ]
+            }
+        ]
+    },
     {
         "category": "bse",
         "category_label": "Binary physics",