Small updates before 3.3 (corrected notebooks, updated output files, …

…recompiled documentation) * all notebooks and scripts checked and corrected. Involved the definition of a new derived parameter conf_time_reio * updated doxygen documentation to v3.3.0 * updated output/explanatory00_* files to v3.3.0
lesgourg · Feb 17, 2025 · ea88b4a · ea88b4a
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diff --git a/doc/input/chap3.md b/doc/input/chap3.md
@@ -49,10 +49,14 @@ it can be interfaced with other codes, etc.
 
 - `external/` contains auxiliary or external algorithms used by `CLASS`, in particular:
 
-- `external/hyrec/` contains the recombination code HyRec (Lee and Ali-Haimoud 2020) that solves the recombinaiton equations by default.
+- `external/HyRec2020/` contains the recombination code HyRec (Lee and Ali-Haimoud 2020) that solves the recombinaiton equations by default.
 
 - `external/RecfastCLASS/` contains an modified version of the recombinaiton code RECFAST v1.5. It can be used as an alternative to solve the recombinaiton equations (with `recombination=recfast').
 
+- `external/Halofit/` contains the Halofit algorithm (including Takahashi-Bird updates)
+
+- `external/HMcode/` contains the HMcode algorithm (including the 2020 updates)
+
 - `external/heating/` contains additional peices of code and interpolation tables for the calculation of energy injection (relevant for CMB anisotropies and spectral distorsions).
 
 - `external/distortions/` contains interpolation tables relevant for the calculation of CMB spectral distortions with J.Chluba's Green function method.

diff --git a/doc/manual/CLASS_MANUAL.pdf b/doc/manual/CLASS_MANUAL.pdf
diff --git a/include/thermodynamics.h b/include/thermodynamics.h
@@ -264,6 +264,9 @@ struct thermodynamics
   double ds_d;    /**< physical sound horizon at baryon drag */
   double rs_d;    /**< comoving sound horizon at baryon drag */
 
+  double conf_time_reio; /**< conformal time at reionization,
+                              not to be confused with optical depth tau_reio */
+
   double tau_cut; /**< at at which the visibility goes below a fixed fraction of the maximum visibility, used for an approximation in perturbation module */
 
   double angular_rescaling;      /**< [ratio ra_rec / (tau0-tau_rec)]: gives CMB rescaling in angular space relative to flat model (=1 for curvature K=0) */

diff --git a/notebooks/check_PPF_approx.ipynb b/notebooks/check_PPF_approx.ipynb
@@ -124,7 +124,7 @@
     "h = {'PPF1':0.64,'PPF2':0.74,'FLD1':0.64}\n",
     "\n",
     "fig, axes = plt.subplots(1,2,figsize=(16,5))\n",
-    "for Omega_K in [-0.1, 0.0, 0.15]:\n",
+    "for Omega_K in [-0.1, 0.0, 0.1]:\n",
     "    for gauge in ['Synchronous','Newtonian']:\n",
     "        cosmo = {}\n",
     "        for M in models:\n",
@@ -196,7 +196,7 @@
     "\n",
     "fig, axes = plt.subplots(1,2,figsize=(18,8))\n",
     "\n",
-    "for Omega_K in [-0.1, 0.0, 0.15]:\n",
+    "for Omega_K in [-0.1, 0.0, 0.1]:\n",
     "    for ppfgauge in ['Synchronous','Newtonian']:\n",
     "        cosmo = {}\n",
     "        for M in models:\n",
@@ -253,21 +253,11 @@
     "\n",
     "fig.savefig('check_PPF_Omegak2.pdf')               "
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print (0.31*0.64**2-0.022)\n",
-    "print (0.26*0.74**2-0.022)"
-   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -281,9 +271,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/cl_ST.ipynb b/notebooks/cl_ST.ipynb
@@ -8,7 +8,10 @@
    "source": [
     "# import necessary modules\n",
     "from classy import Class\n",
-    "from math import pi"
+    "from math import pi\n",
+    "%matplotlib inline\n",
+    "import matplotlib\n",
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -97,27 +100,6 @@
     "cl_lensed = M.lensed_cl(l_max_scalars)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# modules and esthetic definitions for the plots\n",
-    "#\n",
-    "# uncomment to get plots displayed in notebook\n",
-    "%matplotlib inline\n",
-    "#\n",
-    "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
-    "#\n",
-    "font = {'size'   : 16, 'family':'STIXGeneral'}\n",
-    "axislabelfontsize='large'\n",
-    "matplotlib.rc('font', **font)\n",
-    "matplotlib.mathtext.rcParams['legend.fontsize']='medium'\n",
-    "plt.rcParams[\"figure.figsize\"] = [8.0,6.0]"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -148,22 +130,14 @@
     "plt.loglog(ellt,factort*clt['ee'],'b:',label=r'$\\mathrm{EE(t)}$')\n",
     "plt.loglog(ellt,factort*clt['bb'],'g:',label=r'$\\mathrm{BB(t)}$')\n",
     "plt.loglog(ell,factor*(cl_lensed['bb']-cl_tot['bb']),'g-',label=r'$\\mathrm{BB(lensing)}$')\n",
-    "plt.legend(loc='right',bbox_to_anchor=(1.4, 0.5))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "plt.legend(loc='right',bbox_to_anchor=(1.4, 0.5))\n",
     "plt.savefig('cl_ST.pdf',bbox_inches='tight')"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -177,9 +151,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/cltt_terms.ipynb b/notebooks/cltt_terms.ipynb
@@ -8,7 +8,10 @@
    "source": [
     "# import necessary modules\n",
     "from classy import Class\n",
-    "from math import pi"
+    "from math import pi\n",
+    "%matplotlib inline\n",
+    "import matplotlib\n",
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -72,26 +75,6 @@
     "M.empty()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# modules and settings for the plot\n",
-    "#\n",
-    "# uncomment to get plots displayed in notebook\n",
-    "%matplotlib inline\n",
-    "import matplotlib\n",
-    "import matplotlib.pyplot as plt\n",
-    "# esthetic definitions for the plots\n",
-    "font = {'size'   : 16, 'family':'STIXGeneral'}\n",
-    "axislabelfontsize='large'\n",
-    "matplotlib.rc('font', **font)\n",
-    "matplotlib.mathtext.rcParams['legend.fontsize']='medium'\n",
-    "plt.rcParams[\"figure.figsize\"] = [8.0,6.0]"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -118,22 +101,14 @@
     "plt.semilogx(ell,factor*cl_tot['tt'],'r-',label=r'$\\mathrm{total}$')\n",
     "plt.semilogx(ell,factor*cl_lensed['tt'],'k-',label=r'$\\mathrm{lensed}$')\n",
     "#\n",
-    "plt.legend(loc='right',bbox_to_anchor=(1.4, 0.5))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "plt.legend(loc='right',bbox_to_anchor=(1.4, 0.5))\n",
     "plt.savefig('cltt_terms.pdf',bbox_inches='tight')"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -147,9 +122,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/distances.ipynb b/notebooks/distances.ipynb
@@ -15,18 +15,6 @@
     "from classy import Class"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "font = {'size'   : 20, 'family':'STIXGeneral'}\n",
-    "axislabelfontsize='large'\n",
-    "matplotlib.rc('font', **font)\n",
-    "matplotlib.mathtext.rcParams['legend.fontsize']='medium'"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -100,22 +88,14 @@
     "\n",
     "plt.xlabel(r\"$z$\")\n",
     "plt.ylabel(r\"$\\mathrm{Distance}\\times H_0$\")\n",
-    "plt.tight_layout()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "plt.tight_layout()\n",
     "plt.savefig('distances.pdf')"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -129,9 +109,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/many_times.ipynb b/notebooks/many_times.ipynb
@@ -18,20 +18,6 @@
     "import math"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# esthetic definitions for the plots\n",
-    "font = {'size'   : 16, 'family':'STIXGeneral'}\n",
-    "axislabelfontsize='large'\n",
-    "matplotlib.rc('font', **font)\n",
-    "matplotlib.mathtext.rcParams['legend.fontsize']='medium'\n",
-    "plt.rcParams[\"figure.figsize\"] = [8.0,6.0]"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -74,7 +60,8 @@
     "                   'perturbations_sampling_stepsize':'0.05',\n",
     "                   'P_k_max_1/Mpc':P_k_max_inv_Mpc,\n",
     "                   'compute damping scale':'yes', # needed to output and plot Silk damping scale\n",
-    "                   'gauge':'newtonian'}\n",
+    "                   'gauge':'newtonian',\n",
+    "                   'matter_source_in_current_gauge':'yes'}\n",
     "\n",
     "###############\n",
     "#   \n",
@@ -281,7 +268,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -295,9 +282,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/neutrinohierarchy.ipynb b/notebooks/neutrinohierarchy.ipynb
@@ -16,19 +16,6 @@
     "from scipy.optimize import fsolve"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# esthetic definitions for the plots\n",
-    "font = {'size'   : 16, 'family':'STIXGeneral'}\n",
-    "axislabelfontsize='large'\n",
-    "matplotlib.rc('font', **font)\n",
-    "matplotlib.mathtext.rcParams['legend.fontsize']='medium'"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -128,22 +115,14 @@
     "plt.xlim(kvec[0]/h,kvec[-1]/h)\n",
     "plt.xlabel(r'$k [h \\mathrm{Mpc}^{-1}]$')\n",
     "plt.ylabel(r'$1-P(k)^\\mathrm{NH}/P(k)^\\mathrm{IH}$')\n",
-    "plt.legend(legarray)    "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "plt.legend(legarray)    \n",
     "plt.savefig('neutrinohierarchy.pdf')"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -157,9 +136,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }