From b5c988f7005c99fbb7436f8b5187e3351af3dfc6 Mon Sep 17 00:00:00 2001 From: Carl Rodriguez Date: Mon, 25 May 2026 17:44:43 -0400 Subject: [PATCH] Fix docs build and update parameter reference Restore the GitHub Pages docs build, which had been failing on two counts: the IPython directive promoted a pandas chained-assignment warning (raised inside the COSMIC InitialCMCTable.write call) to a hard error, and the newly-added sphinx-copybutton extension was missing from requirements.txt. Set ipython_warning_is_error = False and add the dependency. Also expand the Params.ini flag reference (new flags, ADS citation links, corrected defaults), repair the broken Fork-me-on-GitHub ribbon by self-hosting the image instead of the dead S3 URL, and tidy the KingProfile/PlummerSphere examples. Co-Authored-By: Claude Opus 4.7 --- docs/sphinx/source/_static/forkme_ribbon.png | Bin 0 -> 7791 bytes docs/sphinx/source/_templates/layout.html | 2 +- docs/sphinx/source/conf.py | 15 ++ docs/sphinx/source/inifile/index.rst | 154 +++++++++++++------ examples/KingProfile.ini | 10 +- examples/PlummerSphere.ini | 8 +- requirements.txt | 1 + 7 files changed, 133 insertions(+), 57 deletions(-) create mode 100644 docs/sphinx/source/_static/forkme_ribbon.png diff --git a/docs/sphinx/source/_static/forkme_ribbon.png b/docs/sphinx/source/_static/forkme_ribbon.png new file mode 100644 index 0000000000000000000000000000000000000000..146ef8a800602169cf78c686fc5a6d138a76bc0a GIT binary patch literal 7791 zcmV-#9+2UQP)O>+M%?x9Q-Aclg+SU{aR>iZ-V5ENM}s?g?o3TCz>p076pgIvo9@XSFn67!Z(L}aTexp zAcOn{GYF{63{x3Y|KXge7Rgs|WVGqumV|_UKRatZba(eaMP)S%4i5UolZ=m#gN&6H zmI^z-ZZEFv>uz~$@a{kh`_f(c8kBDZWBCYFpnBH^sV@HRRs-u`N=owgva>frJ9_~y z=NB-xxa}8DG&D36Hs@wTUtd2CdUUM)X%#d;KqN)YP2# 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-------------------------- +# Strip IPython "In [1]:" / "Out[1]:" prompts and shell prompts from copied +# code blocks so users can paste snippets directly into a Python shell. +copybutton_prompt_text = r"In \[\d*\]: |\s*\.{3,}: |Out\[\d*\]: |\$ |> " +copybutton_prompt_is_regexp = True +copybutton_only_copy_prompt_lines = False +copybutton_remove_prompts = True + +# -- IPython directive -------------------------- +# Don't fail the build when an executed example emits a stray warning. Newer +# pandas raises chained-assignment warnings from inside COSMIC's +# InitialCMCTable.write, which would otherwise abort the whole docs build. +ipython_warning_is_error = False + # -- Extensions --------------------------------------------------------------- # -- autodoc ------------------------------------ diff --git a/docs/sphinx/source/inifile/index.rst b/docs/sphinx/source/inifile/index.rst index 74b530f3..4dd7e722 100644 --- a/docs/sphinx/source/inifile/index.rst +++ b/docs/sphinx/source/inifile/index.rst @@ -62,11 +62,13 @@ SNAPSHOT FLAGS **SNAPSHOT_CORE_COLLAPSE = 0** -``SNAPSHOT_WINDOWS`` write snapshots every X units of time into the .window.snapshots.h5 file. Format is: +``SNAPSHOT_WINDOWS`` write snapshots every X units of time into the .window.snapshots.h5 file. Note that ``SNAPSHOTTING`` must be on. Format is: start_w0,step_w0,end_w0:start_w1,step_w1,stop_w1 ... etc - **SNAPSHOT_WINDOWS = "0,0.1,13.8"** (will write one snapshot to snapshot.h5 every 100 Myr) + ``NULL`` : no window snapshots + + **SNAPSHOT_WINDOWS = 0,0.1,13.8** (will write one snapshot every 100 Myr) ``SNAPSHOT_WINDOW_UNITS`` What units should the snapshot windows be in. Options are: @@ -118,7 +120,16 @@ DYNAMICS FLAGS -------------- ================================== ===================================================== -``BINBIN`` Turn on Fewbody encounters between two binaries +``PERTURB`` Master switch for stellar dynamics. With this off, CMC is essentially a population synthesis code (that occasionally loses mass to tidal stripping). + + ``0`` : Off + + ``1`` : On + + **PERTURB = 1** + + +``BINBIN`` Turn on Fewbody encounters between two binaries ``0`` : Off @@ -149,7 +160,7 @@ DYNAMICS FLAGS **BH_RADIUS_MULTIPLYER = 5** -``THREEBODYBINARIES`` Turn on three-body binary formation semi-analytic treatment from Morscher et al., 2013 +``THREEBODYBINARIES`` Turn on three-body binary formation semi-analytic treatment from `Morscher et al., 2013 `_ ``0`` : Off @@ -183,6 +194,11 @@ DYNAMICS FLAGS **BINARY_BREAKING_MIN = 0** +``BINARY_DISTANCE_BREAKING`` If ``BINARY_BREAKING_MIN = 0``, what fraction of the interparticle seperation to break binaries at + + **BINARY_DISTANCE_BREAKING = 0.1** (10%) + + ``SS_COLLISION`` enable collisions between stars. NOTE: this activates collisions between single stars AND during fewbody encounters ``0`` : Off @@ -192,7 +208,7 @@ DYNAMICS FLAGS **SS_COLLISION = 1** -``TIDAL_CAPTURE`` Enable collisions bewteen giants and other individual stars. Can lead to binary formation. Uses cross sections from Lombardi et al., 2006. Only activated if SS_COLLISION = 1 +``TIDAL_CAPTURE`` Enable collisions bewteen giants and other individual stars. Can lead to binary formation. Uses cross sections from `Lombardi et al., 2006 `_. Only activated if SS_COLLISION = 1 ``0`` : Off @@ -201,21 +217,30 @@ DYNAMICS FLAGS **TIDAL_CAPTURE = 0** -``TC_POLYTROPE`` Enable tidal captures during single-single interactions. Uses polytropic stellar models for stars. Uses cross sections from Kim & Lee 1999. Only activated if SS_COLLISION = 1 - +``TC_POLYTROPE`` Enable tidal captures during single-single interactions. Uses polytropic stellar models for stars. Uses cross sections from `Kim & Lee, 1999 `_. Only activated if SS_COLLISION = 1. Do not turn this on at the same time as ``TC_FACTOR``. + ``0`` : Off - + ``1`` : On - + **TC_POLYTROPE = 0** - - + + +``TC_FACTOR`` Allow for tidal capture during single-single collisions, where the capture cross section is a multiple of the pericenter. Do not turn this on at the same time as ``TC_POLYTROPE``. + + ``1`` : Off + + ``>1`` : Set the multiplier on the pericenter + + **TC_FACTOR = 1** + + ``COLL_FACTOR`` Set the multiplying factor for direct collisions. Default = 1.0 (sticky sphere) **COLL_FACTOR = 1.0** -``CO_TDE`` Treat BH(NS,WD)--MS TDEs in TDE vs direct collision limit. Follows prescription in Kremer et al., 2020 +``CO_TDE`` Treat BH(NS,WD)--MS TDEs in TDE vs direct collision limit. Follows prescription in `Kremer et al., 2020 `_ ``0`` : collision @@ -224,7 +249,7 @@ DYNAMICS FLAGS **CO_TDE = 0** -``WD_TC`` Turn on wd-wd tidal capture in single-single and fewbody (0=off,>0=on). Follows prescription in Ye et al. 2024 +``WD_TC`` Turn on wd-wd tidal capture in single-single and fewbody (0=off,>0=on). Follows prescription in `Ye et al., 2024 `_ ``0`` : Off @@ -232,8 +257,7 @@ DYNAMICS FLAGS **WD_TC = 0** -``TDE_SPINUP`` Turn on NS-MS star TDE mass accretion onto the NS (1=on, 0=off). Follows prescription i -n Ye et al. 2024 +``TDE_SPINUP`` Turn on NS-MS star TDE mass accretion onto the NS (1=on, 0=off). Follows prescription in `Ye et al., 2024 `_ **TDE_SPINUP = 0** @@ -254,8 +278,16 @@ INPUT OPTIONS **INPUT_FILE = input.hdf5** +``OVERWRITE_RVIR`` Override the virial radius from the input file with a new value, in pc. A value of 0 keeps the input file's Rvir. + + **OVERWRITE_RVIR = 0** + =============================== ===================================================== +.. warning:: + + ``OVERWRITE_RVIR`` only rescales the cluster's physical units; it does **not** rescale the stellar radii (which were set when the initial conditions were generated). Shrinking the virial radius can therefore place the components of close binaries inside one another's stellar radii, putting them in a merger state during the first timestep, which breaks the code. If you need to shrink the cluster significantly, regenerate the initial conditions with the desired virial radius. + TIDAL FIELD OPTIONS ------------------- @@ -487,7 +519,7 @@ Parameters for controlling the CMC run. **DT_HARD_BINARIES = 0** -``HARD_BINARY_KT `` The minimum binary binding energy (in units of kT) for a binary to be considered 'hard' for the time step calculation. +``HARD_BINARY_KT`` The minimum binary binding energy (in units of kT) for a binary to be considered 'hard' for the time step calculation. **HARD_BINARY_KT = 0.7** @@ -514,28 +546,43 @@ Parameters for controlling the CMC run. the type of parameter or flag. +======================= ===================================================== +``STELLAR_EVOLUTION`` Master switch for stellar evolution in CMC. When off, all stars are treated as point masses (and most ``[bse]`` parameters below are ignored). + + ``0`` : Off + + ``1`` : On + + **STELLAR_EVOLUTION = 1** +======================= ===================================================== + + SAMPLING FLAGS -------------- -======================= ===================================================== -``pts1`` determines the timesteps chosen in each evolution phase as - decimal fractions of the time taken in that phase for - Main Sequence (MS) stars +========================== ===================================================== +``pts1`` determines the timesteps chosen in each evolution phase as + decimal fractions of the time taken in that phase for + Main Sequence (MS) stars - **pts1 = 0.001** following `Bannerjee+2019 `_ + **pts1 = 0.05** (use 0.001 for massive stars, following `Bannerjee+2019 `_, by setting ``pts1_highmass_cutoff``) -``pts2`` determines the timesteps chosen in each evolution phase as - decimal fractions of the time taken in that phase for - Giant Branch (GB, CHeB, AGB, HeGB) stars +``pts2`` determines the timesteps chosen in each evolution phase as + decimal fractions of the time taken in that phase for + Giant Branch (GB, CHeB, AGB, HeGB) stars - **pts2 = 0.01** following `Hurley+2000 `_ + **pts2 = 0.01** following `Hurley+2000 `_ -``pts3`` determines the timesteps chosen in each evolution phase as - decimal fractions of the time taken in that phase for - HG, HeMS stars +``pts3`` determines the timesteps chosen in each evolution phase as + decimal fractions of the time taken in that phase for + HG, HeMS stars - **pts3 = 0.02** following `Hurley+2000 `_ -======================= ===================================================== + **pts3 = 0.02** following `Hurley+2000 `_ + +``pts1_highmass_cutoff`` Above this ZAMS mass (in solar masses), reduce ``pts1`` by a factor of 10 for MS and HeMS stars. + + **pts1_highmass_cutoff = 5** +========================== ===================================================== @@ -568,13 +615,13 @@ WIND FLAGS **windflag = 3** -``eddlimflag`` Limits the mass-loss rate of low-metallicity stars near +``eddlimflag`` Adjusts the dependence of mass loss on metallicity for stars near the Eddington limit (see `Grafener+2011 `_, `Giacobbo+2018 `_). - ``0`` : does not apply Eddington limit + ``0`` : does not adjust metallicity dependence for stars near the Eddington limit - ``1`` : applies Eddington limit + ``1`` : adjusts metallicity dependence for stars near the Eddington limit as in `Giacobbo+2018 `_ **eddlimflag = 0** @@ -595,7 +642,7 @@ WIND FLAGS **bwind = 0, inactive for single** -``hewind`` Helium star mass loss parameter: 10\ :sup:`-13` *hewind* L\ :sup:`2/3` gives He star mass-loss. Equivalent to 1 - :math:`{\mu}` in the last equation on `page 19 of SSE `_. +``hewind`` Helium star mass loss parameter: 10\ :sup:`-13` *hewind* L\ :sup:`2/3` gives He star mass-loss. Equivalent to 1 - :math:`{\mu}` in the last equation on `page 19 of SSE `_. Only applies when ``windflag = 0``; otherwise it is overwritten by the chosen wind prescription. **hewind = 0.5** @@ -671,7 +718,7 @@ common envelope occurs regardless of the choices below: ``1`` : Uses the `de Kool 1990 `_ model - **ceflag = 0** + **ceflag = 1** ``cekickflag`` Selects which mass and separation values to use when a supernova occurs during the CE and a kick @@ -878,7 +925,7 @@ KICK FLAGS instability SN and sets the maximum mass of the allowed remnant - **pisn = 45.0** + **pisn = -2** ``bhsigmafrac`` Sets a fractional modification which scales down *sigma* for BHs. This works in addition to whatever is chosen for @@ -939,7 +986,7 @@ REMNANT MASS FLAGS ``4`` : delayed prescription from `Fryer+2012 `_ - **remnantflag = 3** + **remnantflag = 4** ``mxns`` Sets the boundary between the maximum NS mass and the minimum BH mass @@ -959,8 +1006,8 @@ REMNANT MASS FLAGS **rembar_massloss = 0.5** ``wd_mass_lim`` Determines if the maximum white dwarf mass is limited to - the chandraekhar mass during mic. 1 implements the limit. - + the chandrasekhar mass during merger induced collapse. 1 implements the limit, while 0 does not. + **wd_mass_lim = 1** =================== ===================================================== @@ -1042,7 +1089,9 @@ MASS TRANSFER FLAGS `Hurley+2002 `_ ``-2`` : donor mass loss rate is calculated following - `Claeys+2014 `_ + `Claeys+2014 `_ + + **don_lim = -1** ``acc_lim`` Limits the amount of mass accreted during Roche overflow @@ -1061,6 +1110,8 @@ MASS TRANSFER FLAGS ``>=0`` : sets overall accretion fraction of donor mass as in Belcyznski+2008 w/ acc_lim = 0.5 + **acc_lim = -1** + ======================= ===================================================== @@ -1152,7 +1203,7 @@ PULSAR FLAGS ``negative values`` : sets k in Myr from Equation 8 to -1 * *bconst* - **bconst = -3000** + **bconst = 3000** ``ck`` Sets the magnetic field decay time-scale for pulsars following Section 3 of `Kiel+2008 `_. @@ -1160,7 +1211,7 @@ PULSAR FLAGS ``negative values`` : sets :math:`{\tau}`\ :sub:`b` in Myr from Equation 2 to -1 * *ck* - **ck = -1000** + **ck = 1000** ======================= ===================================================== MIXING VARIABLES @@ -1192,7 +1243,11 @@ MIXING VARIABLES ``bhms_coll_flag`` If set to 1 then if BH+star collision and if Mstar > Mbh, do not destroy the star - **default = 0** + ``0`` : Off + + ``1`` : On + + **bhms_coll_flag = 0** ======================= ===================================================== @@ -1225,9 +1280,12 @@ MISC FLAGS **ST_cr = 1** ``rtmsflag`` Activates different prescriptions for stellar radius at main sequence turnoff - ``0`` : uses the SSE rtms for M < 200 Msun and extrapolation for z < 0.0008 and M > 200 Msun. - ``1`` : interpolates the rtms from Boost tracks (Szécsi et al. (2022)). Extrapolation is used after M > 575 Msun - ``2`` : uses the best-fit power law for rtms vs stellar mass from BPASSv2.2 tracks (Stanway & Eldridge (2018)). - Rtms data for BPASS tracks is available only till 300 Msun and beyond that we follow the fitted power law profile. - **rtmsflag = 0** + + ``0`` : uses the SSE rtms for M < 200 Msun and extrapolation for z < 0.0008 and M > 200 Msun + + ``1`` : interpolates the rtms from Boost tracks (Szécsi et al. 2022). Extrapolation is used after M > 575 Msun + + ``2`` : uses the best-fit power law for rtms vs stellar mass from BPASSv2.2 tracks (Stanway & Eldridge 2018). Rtms data for BPASS tracks is available only up to 300 Msun and beyond that we follow the fitted power law profile + + **rtmsflag = 0** ======================= ===================================================== diff --git a/examples/KingProfile.ini b/examples/KingProfile.ini index aa158080..8cb01372 100644 --- a/examples/KingProfile.ini +++ b/examples/KingProfile.ini @@ -133,11 +133,6 @@ COLL_FACTOR = 1.0 ; default = 0 (coll) CO_TDE = 0 -; Allow for tidal capture in single-single interactions for non-giant stars (0=off, 1=on) -; Follows prescription in Ye et al. 2022 -; default = 0 -TC_POLYTROPE = 0 - ; Allow for tidal capture (a multiple of the set factor of the pericenter) during single-single collision ; 1=off, greater than 1 sets different multiplyers ; Do not turn this on the same time as TC_POLYTROPE ; default = 1 @@ -563,6 +558,11 @@ mxns = 3.0 ; default = 0.5 rembar_massloss = 0.5 +; wd_mass_lim determines if the maximum white dwarf mass is limited to +; the chandraekhar mass during merger induced collapse. +; 1 implements the limit, while 0 does not +; default = 1 +wd_mass_lim = 1 ;;;;;;;;;;;;;;;;;;;;;;;;;; diff --git a/examples/PlummerSphere.ini b/examples/PlummerSphere.ini index eb0d4cf7..bcf6145b 100644 --- a/examples/PlummerSphere.ini +++ b/examples/PlummerSphere.ini @@ -124,9 +124,11 @@ TIDAL_CAPTURE = 0 ; default = 0 (coll) CO_TDE = 0 -; Allow for tidal capture in single-single interactions for non-giant stars (0=off, 1=on) -; Follows prescription in Ye et al. 2022 -; default = 0 +; Enable tidal captures during single-single interactions +; Uses polytropic stellar models for stars +; Uses cross sections from Kim & Lee, 1999 +; Only activated if SS_COLLISION = 1 +; default = 0 (off) TC_POLYTROPE = 0 ; Allow for tidal capture (a multiple of the set factor of the pericenter) during single-single collision ; 1=off, greater than 1 sets different multiplyers diff --git a/requirements.txt b/requirements.txt index 8770c39c..1e9fe7f8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,6 +5,7 @@ sphinx-bootstrap-theme >= 0.6 sphinxcontrib-programoutput sphinxcontrib-katex sphinx-automodapi +sphinx-copybutton ipython sphinx_rtd_theme breathe