Merge pull request #341 from lukasmerten/Misc

Miscellaneous

doc/pages/Basic-concepts.md

@@ -30,7 +30,7 @@ the parallel sections of the code. If they do, a change by thread A is likely
 to mess with the correct calculation in thread B. Most importantly, the
 simulation modules which are in the current parallelization layout shared among
 the threads cannot store information on the cosmic ray. Instead the information
-has be stored on the cosmic ray itself.
+has to be stored on the cosmic ray itself.
 
 Program parts in which "thread-safety" cannot be ensured need to be put inside
 a "critical region". If a thread reaches a critical region that is occupied by

doc/pages/example_notebooks/Diffusion/DiffusionValidationI.v4.ipynb

@@ -2038,7 +2038,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

doc/pages/example_notebooks/acceleration/first_order_fermi_acceleration.ipynb

@@ -209,7 +209,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

doc/pages/example_notebooks/acceleration/second_order_fermi.ipynb

@@ -265,7 +265,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

doc/pages/example_notebooks/density/densitys_easy_example.ipynb

@@ -18,9 +18,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {
-    "collapsed": true,
     "jupyter": {
      "outputs_hidden": true
     }
@@ -40,9 +39,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -68,9 +66,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -110,14 +107,13 @@
    "metadata": {},
    "source": [
     "#### The ConstantDensity can be adjusted to new values and the usage of several parts can be chosen.\n",
-    "For this purpose methodes are available to change and activate (set-function) and methodes to see the actual configuration (getisfor-functions)."
+    "For this purpose methods are available to change and activate (set-function) and methodes to see the actual configuration (getisfor-functions)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 4,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -130,7 +126,10 @@
       "HI: True, HII: True, H2: True, \n",
       " \n",
       "\n",
-      "ConstantDensity:HI component is not activ and has a density of 1e+06 cm^-3      HII component is not activ and  has a density of 1.5e+06 cm^-3      H2 component is activ and  has a density of 1.3e+06 cm^-3\n"
+      "ConstantDensity:\n",
+      "HI component is not active and has a density of 1e+06 cm^-3\n",
+      "HII component is not active and has a density of 1.5e+06 cm^-3\n",
+      "H2 component is active and has a density of 1.3e+06 cm^-3\n"
      ]
     }
    ],
@@ -160,9 +159,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -206,9 +204,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 6,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -269,9 +266,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 7,
    "metadata": {
-    "collapsed": false,
     "jupyter": {
      "outputs_hidden": false
     }
@@ -314,18 +310,6 @@
     "print('H2 density n_H2 = %f' %n_H2)\n",
     "print('nucleon density n_nucl = %f' %n_nucl)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 12,
-   "metadata": {
-    "collapsed": true,
-    "jupyter": {
-     "outputs_hidden": true
-    }
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -344,7 +328,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

doc/pages/example_notebooks/galactic_trajectories/galactic_trajectories.v4.ipynb

@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Galactic trajectories\n",
-    "The following codes performs a backtracking simulation in the JF2012 Galactic magnetic field model and visualizes the trajectories.\n",
+    "The following code performs a backtracking simulation in the JF2012 Galactic magnetic field model and visualizes the trajectories.\n",
     "A custom simulation module is used for a numbered trajectory output, that simplifies separating the individual trajectories for plotting later on."
    ]
   },
@@ -153,7 +153,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

doc/pages/example_notebooks/secondaries/photons.v4.ipynb

@@ -139,7 +139,7 @@
    "source": [
     "## Photons from Proton Propagation\n",
     "\n",
-    "The generaton of photons has to be enabled for the individual energy-loss processes in the module chain. Also, separate photon output can be added:"
+    "The generation of photons has to be enabled for the individual energy-loss processes in the module chain. Also, separate photon output can be added:"
    ]
   },
   {

doc/pages/example_notebooks/sim1D/sim1D.v4.ipynb

@@ -13,7 +13,7 @@
     "\n",
     "To include cosmological effects in this 1D simulation we need two things:\n",
     "\n",
-    "First, the ```Redshift``` module updates the current redshift of the particle in each propagation step. It is best added directly after the propagation module, although the postion shouldn't matter much for the typically small propagation steps.\n",
+    "First, the ```Redshift``` module updates the current redshift of the particle in each propagation step. It is best added directly after the propagation module, although the position shouldn't matter much for the typically small propagation steps.\n",
     "\n",
     "Second, we need to set the initial redshift of the particles.\n",
     "In 1D simulations the intial redshift is determined by the source distance. To have the source automatically set the redshift we add ```SourceRedshift1D```. **Please note** that it has to be added after the source property that defines the source position.\n",

doc/pages/example_notebooks/sim4D/sim4D.v4.ipynb

@@ -11,7 +11,7 @@
     "**Note:** In CRPropa, time is always expressed in terms of redshift $z$, whereas positions are always expressed in terms of comoving coordinates as Cartesian 3-vectors.\n",
     "\n",
     "### Simulation setup\n",
-    "The simulation setup is that of a 3D simulation with a few addition:\n",
+    "The simulation setup is that of a 3D simulation with a few additions:\n",
     "1. We add a source property for the redshift at emission. This can be either ```SourceRedshift```, ```SourceUniformRedshift``` or ```SourceRedshiftEvolution```.\n",
     "2. The simulation module ```FutureRedshift``` implements adiabatic energy loss and updates the redshift. In contrast to ```Redshift``` it allows particles to be propagated into the future $z < 0$ which enables faster convergence for finite observation windows.\n",
     "3. The observer feature ```ObserverRedshiftWindow``` specifies a time window $z_\\rm{min} < z < z_\\rm{max}$ in which particles are detected if they hit the observer. Note that this can also be done after the simulation by cutting on the redshifts at observation. For this we also output the current redshift at observation.\n",

src/module/NuclearDecay.cpp

@@ -215,6 +215,8 @@ void NuclearDecay::betaDecay(Candidate *candidate, bool isBetaPlus) const {
 
 	// generate cdf of electron energy, neglecting Coulomb correction
 	// see Basdevant, Fundamentals in Nuclear Physics, eq. (4.92)
+	// This leads to deviations from theoretical expectations at low 
+	// primary energies.
 	std::vector<double> energies;
 	std::vector<double> densities; // cdf(E), unnormalized
 
@@ -231,6 +233,9 @@ void NuclearDecay::betaDecay(Candidate *candidate, bool isBetaPlus) const {
 	}
 
 	// draw random electron energy and angle
+	// assumption of ultra-relativistic particles 
+	// leads to deviations from theoretical predictions
+	// is not problematic for usual CRPropa energies E>~TeV
 	Random &random = Random::instance();
 	double E = interpolate(random.rand() * cdf, densities, energies);
 	double p = sqrt(E * E - me * me);  // p*c