Merge pull request #401 from LSSTDESC/sigma8_fix

replaced sigma_8 -> sigma8

examples/Distance Calculations Example.ipynb

@@ -11,9 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -55,18 +53,20 @@
       "        Omega_b: 0.045\n",
       "        Omega_m: 0.315\n",
       "        Omega_k: 0.0\n",
-      "        Omega_l: 0.684927855904\n",
+      "        Omega_l: 0.684906869231\n",
       "             w0: -1.0\n",
       "             wa: 0.0\n",
       "             H0: 67.0\n",
       "              h: 0.67\n",
       "            A_s: 2.1e-09\n",
       "            n_s: 0.96\n",
-      "       N_nu_rel: 3.046\n",
-      "      N_nu_mass: 0.0\n",
-      "            mnu: 0.0\n",
+      "    bcm_log10Mc: 14.079181246\n",
+      "       bcm_etab: 0.5\n",
+      "         bcm_ks: 55.0\n",
+      "           Neff: 3.046\n",
+      "            mnu: <Swig Object of type 'double *' at 0x7fe2c4abecc0>\n",
       "   Omega_n_mass: 0.0\n",
-      "    Omega_n_rel: 1.70947512533e-05\n",
+      "    Omega_n_rel: 3.80814240441e-05\n",
       "          T_CMB: 2.725\n",
       "        Omega_g: 5.50493446829e-05\n",
       "         z_star: nan\n",
@@ -81,7 +81,7 @@
       "\n",
       "Status\n",
       "------\n",
-      "status(0): C\n"
+      "status(0): \n"
      ]
     }
    ],
@@ -93,7 +93,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As you can see, a number of cosmological parameters have been set to default values, or derived from the input parameters. Some, like `sigma_8`, have been left undefined; this is because calculating them from the input parameters is non-trivial, so this will only be done if needed (or if the user explicitly requests it)."
+    "As you can see, a number of cosmological parameters have been set to default values, or derived from the input parameters. Some, like `sigma8`, have been left undefined; this is because calculating them from the input parameters is non-trivial, so this will only be done if needed (or if the user explicitly requests it)."
    ]
   },
   {
@@ -139,7 +139,7 @@
     {
      "data": {
       "text/plain": [
-       "1962.9612048132053"
+       "1962.9391106362025"
       ]
      },
      "execution_count": 5,
@@ -167,9 +167,9 @@
     {
      "data": {
       "text/plain": [
-       "array([    0.        ,   436.69947016,   851.39817459,  1243.79753712,\n",
-       "        1614.11360802,  1962.96120481,  2291.23813831,  2600.02282463,\n",
-       "        2890.49121176,  3163.8538544 ])"
+       "array([   0.        ,  436.6985085 ,  851.39441823, 1243.7892696 ,\n",
+       "       1614.09913239, 1962.93911064, 2291.20727173, 2599.98206626,\n",
+       "       2890.43969486, 3163.7908473 ])"
       ]
      },
      "execution_count": 6,
@@ -197,7 +197,7 @@
     {
      "data": {
       "text/plain": [
-       "1962.9612048132053"
+       "1962.9391106362025"
       ]
      },
      "execution_count": 7,
@@ -225,7 +225,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Radial Dist. = 1992.55 Mpc \t Angular Dist. = 1999.14 Mpc\n"
+      "Radial Dist. = 1992.53 Mpc \t Angular Dist. = 1999.12 Mpc\n"
      ]
     }
    ],
@@ -254,7 +254,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Luminosity Dist = 2944.44 Mpc \t Distance Modulus = 42.35 \n"
+      "Luminosity Dist = 2944.41 Mpc \t Distance Modulus = 42.34 \n"
      ]
     }
    ],
@@ -279,7 +279,7 @@
     {
      "data": {
       "text/plain": [
-       "0.6666668249534857"
+       "0.6666639271123571"
       ]
      },
      "execution_count": 10,
@@ -294,9 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": []
   }
@@ -317,7 +315,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.10"
+   "version": "2.7.12"
   }
  },
  "nbformat": 4,

examples/MCMC Likelihood Analysis.ipynb

@@ -50,9 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "z = np.linspace(0., 3., 200)\n",
@@ -440,7 +438,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.10"
+   "version": "2.7.12"
   }
  },
  "nbformat": 4,

examples/ccl_sample_power.c

@@ -48,8 +48,8 @@ int main(int argc, char * argv[])
       return NAN;
     }
   }
-  printf("sigma_8 = %.6lE\n", ccl_sigmaR(cosmo,8./h,&status));
-  printf("Consistency check: sigma_8 = %.6lE\n", ccl_sigma8(cosmo,&status));
+  printf("sigma8 = %.6lE\n", ccl_sigmaR(cosmo,8./h,&status));
+  printf("Consistency check: sigma8 = %.6lE\n", ccl_sigma8(cosmo,&status));
   printf("Completed. Status = %d\n",status);
 
   ccl_cosmology_free(cosmo);

examples/ccl_sample_run.c

@@ -98,9 +98,9 @@ int main(int argc,char **argv)
   rhom = ccl_rho_x(cosmo, 1., ccl_species_m_label, isco, &status);
   printf("%i\t%.3f\t%.3f\t%.3f\t%.3e\t%.3e\t%.3e\n", 0, Om, OL, Or, rhoc, rhom, RHO_CRITICAL);
 
-  // Compute sigma_8
+  // Compute sigma8
   printf("Initializing power spectrum...\n");
-  printf("sigma_8 = %.3lf\n\n", ccl_sigma8(cosmo, &status));
+  printf("sigma8 = %.3lf\n\n", ccl_sigma8(cosmo, &status));
 
   //Create tracers for angular power spectra
   double z_arr_gc[NZ],z_arr_sh[NZ],nz_arr_gc[NZ],nz_arr_sh[NZ],bz_arr[NZ];

include/ccl_core.h

@@ -64,7 +64,7 @@ typedef struct ccl_parameters {
   double bcm_ks;
 
   // Derived parameters
-  double sigma_8;
+  double sigma8;
   double Omega_l;
   double z_star;
 
@@ -183,7 +183,7 @@ ccl_cosmology * ccl_cosmology_create_with_lcdm_params(
  * @param w0 Dark energy EoS parameter
  * @param wa Dark energy EoS parameter
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param bcm_log10Mc log10 cluster mass, one of the parameters of the BCM model
  * @param bcm_etab ejection radius parameter, one of the parameters of the BCM model
@@ -210,7 +210,7 @@ ccl_parameters ccl_parameters_create(double Omega_c, double Omega_b, double Omeg
  * @param Omega_c Omega_c 
  * @param Omega_b Omega_b 
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param status Status flag. 0 if there are no errors, nonzero otherwise.
  * For specific cases see documentation for ccl_error.c
@@ -223,7 +223,7 @@ ccl_parameters ccl_parameters_create_flat_lcdm(double Omega_c, double Omega_b, d
  * @param Omega_c Omega_c 
  * @param Omega_b Omega_b 
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param bcm_log10Mc log10 cluster mass, one of the parameters of the BCM model
  * @param bcm_etab ejection radius parameter, one of the parameters of the BCM model
@@ -242,7 +242,7 @@ ccl_parameters ccl_parameters_create_flat_lcdm_bar(double Omega_c, double Omega_
  * @param Omega_b Omega_b 
  * @param w0 Dark energy EoS parameter
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param status Status flag. 0 if there are no errors, nonzero otherwise.
  * For specific cases see documentation for ccl_error.c
@@ -257,7 +257,7 @@ ccl_parameters ccl_parameters_create_flat_wcdm(double Omega_c, double Omega_b, d
  * @param w0 Dark energy EoS parameter
  * @param wa Dark energy EoS parameter
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param status Status flag. 0 if there are no errors, nonzero otherwise.
  * For specific cases see documentation for ccl_error.c
@@ -273,7 +273,7 @@ ccl_parameters ccl_parameters_create_flat_wacdm(double Omega_c, double Omega_b,
  * @param w0 Dark energy EoS parameter
  * @param wa Dark energy EoS parameter
  * @param h Hubble constant in units of 100 km/s/Mpc
- * @param norm_pk the normalization of the power spectrum, either A_s or sigma_8
+ * @param norm_pk the normalization of the power spectrum, either A_s or sigma8
  * @param n_s the power-law index of the power spectrum
  * @param status Status flag. 0 if there are no errors, nonzero otherwise.
  * For specific cases see documentation for ccl_error.c

include/ccl_power.h

@@ -66,12 +66,12 @@ double ccl_nonlin_matter_power(ccl_cosmology * cosmo, double k, double a,int * s
 double ccl_sigmaR(ccl_cosmology *cosmo, double R, int * status);
 
 /**
- * Computes sigma_8, variance of the matter density field with (top-hat) smoothing scale R = 8 Mpc/h, from linear power spectrum.
- * Returns sigma_8 for specified cosmology.
+ * Computes sigma8, variance of the matter density field with (top-hat) smoothing scale R = 8 Mpc/h, from linear power spectrum.
+ * Returns sigma8 for specified cosmology.
  * @param cosmo Cosmology parameters and configurations
  * @param status Status flag. 0 if there are no errors, nonzero otherwise.
  * For specific cases see documentation for ccl_error.c
- * @return sigma_8.
+ * @return sigma8.
  */
 double ccl_sigma8(ccl_cosmology *cosmo, int * status);
 

src/ccl_core.c

@@ -40,8 +40,8 @@ const ccl_gsl_params default_gsl_params = {GSL_EPSREL,
    The following are the relevant global variables:
 */
 
-ccl_spline_params * ccl_splines; // Global variable
-ccl_gsl_params * ccl_gsl; // Global variable
+ccl_spline_params * ccl_splines=NULL; // Global variable
+ccl_gsl_params * ccl_gsl=NULL; // Global variable
 
 void ccl_cosmology_read_config(void)
 {
@@ -208,7 +208,7 @@ mnu_type: how the neutrino mass(es) should be treated
 w0: Dark energy eqn. of state parameter
 wa: Dark energy eqn. of state parameter, time variation
 h: Hubble's constant divided by (100 km/s/Mpc).
-norm_pk: amplitude of the primordial PS (either A_s or sigma_8)
+norm_pk: amplitude of the primordial PS (either A_s or sigma8)
 n_s: index of the primordial PS
 */
 ccl_cosmology * ccl_cosmology_create_with_params(double Omega_c, double Omega_b, double Omega_k,
@@ -247,7 +247,7 @@ Omega_c: cold dark matter
 Omega_b: baryons
 Omega_k: curvature
 h: Hubble's constant divided by (100 km/s/Mpc).
-norm_pk: amplitude of the primordial PS (either A_s or sigma_8)
+norm_pk: amplitude of the primordial PS (either A_s or sigma8)
 n_s: index of the primordial PS
 */
 ccl_cosmology * ccl_cosmology_create_with_lcdm_params(double Omega_c, double Omega_b, double Omega_k,
@@ -274,7 +274,7 @@ Omega_g = (Omega_g*h^2)/h^2 is the radiation parameter; "g" is for photons, as i
 T_CMB: CMB temperature in Kelvin
 Omega_l: Lambda 
 A_s: amplitude of the primordial PS, enforced here to initially set to NaN
-sigma_8: variance in 8 Mpc/h spheres for normalization of matter PS, enforced here to initially set to NaN
+sigma8: variance in 8 Mpc/h spheres for normalization of matter PS, enforced here to initially set to NaN
 z_star: recombination redshift
  */
 void ccl_parameters_fill_initial(ccl_parameters * params, int *status)
@@ -311,8 +311,8 @@ void ccl_parameters_fill_initial(ccl_parameters * params, int *status)
   params->Omega_l = 1.0 - params->Omega_m - params->Omega_g - params->Omega_n_rel -params->Omega_n_mass- params->Omega_k;
   // Initially undetermined parameters - set to nan to trigger
   // problems if they are mistakenly used.
-  if (isfinite(params->A_s)) {params->sigma_8 = NAN;}
-  if (isfinite(params->sigma_8)) {params->A_s = NAN;}
+  if (isfinite(params->A_s)) {params->sigma8 = NAN;}
+  if (isfinite(params->sigma8)) {params->A_s = NAN;}
   params->z_star = NAN;
 
   if(fabs(params->Omega_k)<1E-6)
@@ -362,7 +362,7 @@ ccl_parameters ccl_parameters_create(
   params.mnu = NULL;
   params.z_mgrowth=NULL;
   params.df_mgrowth=NULL;
-  params.sigma_8 = NAN;
+  params.sigma8 = NAN;
   params.A_s = NAN;
   params.Omega_c = Omega_c;
   params.Omega_b = Omega_b;
@@ -485,7 +485,7 @@ ccl_parameters ccl_parameters_create(
   if(norm_pk<1E-5)
     params.A_s=norm_pk;
   else
-    params.sigma_8=norm_pk;
+    params.sigma8=norm_pk;
   params.n_s = n_s;
 
   //Baryonic params

src/ccl_emu17.c

@@ -176,7 +176,7 @@ static void emu(double *xstar, double **ystar, int* status, ccl_cosmology* cosmo
                     break;
                 case 2:
                     sprintf(cosmo->status_message, 
-                            "ccl_pkemu(): sigma_8 must be between %f and %f.\n", 
+                            "ccl_pkemu(): sigma8 must be between %f and %f.\n", 
                             xmin[i], xmax[i]);
                     break;
                 case 3: