Merge pull request #46 from BlackHolePerturbationToolkit/dev

frequencies back, zero ecc, ode_base issues
BlackHolePerturbationToolkit · Nov 18, 2021 · 81c446e · 81c446e
2 parents 9fd853a + 1080c7c
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diff --git a/README.md b/README.md
@@ -136,7 +136,7 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags).
 
-Current Version: 1.4.3
+Current Version: 1.4.4
 
 ## Authors
 

diff --git a/docs/doctrees/README.doctree b/docs/doctrees/README.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/general/docs_main.doctree b/docs/doctrees/general/docs_main.doctree
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/nbsphinx/tutorial/FastEMRIWaveforms_tutorial.ipynb b/docs/doctrees/nbsphinx/tutorial/FastEMRIWaveforms_tutorial.ipynb
@@ -2608,7 +2608,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you want to implement a set of ODE equations in C/C++, you can add your function to `src/ode_base.cc`. When you run `python setup install`, the installer will build a full file of ODEs and take care of all of the backend aspects to the integration. **You only have to implement the ODE**. You identify the ODE functions with `__deriv__` decorator. `#define` is then used to give extra necessary information on the function. Options are:\n",
+    "If you want to implement a set of ODE equations in C/C++, you can add your function to `src/ode_base.cc`. You have to create the file if you have not already. Make sure it is in the `src/` directory. When you run `python setup install`, the installer will build a full file of ODEs and take care of all of the backend aspects to the integration. **You only have to implement the ODE**. You identify the ODE functions with `__deriv__` decorator. `#define` is then used to give extra necessary information on the function. Options are:\n",
     "\n",
     "* `#define {waveform function name}_num_add_args {number of added args}`: Number of additional arguments beyond the required arguments. \n",
     "* `#define {waveform function name}_spinless`: Indicated Schwarzschild background. \n",
@@ -2640,18 +2640,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If the ODE is purely analytic, a function will work. Here is an example with the 5PN trajectory:\n",
+    "If the ODE is purely analytic, a function will work. Here is an example with the 5PN trajectory (see`include/ode_base_example.cc`):\n",
     "\n",
     "````\n",
     "#define pn5_Y\n",
     "#define pn5_citation1 pn5_citation\n",
     "__deriv__\n",
     "void pn5(double* pdot, double* edot, double* Ydot,\n",
-    "                  double Omega_phi, double Omega_theta, double Omega_r,\n",
+    "                  double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
     "                  double epsilon, double a, double p, double e, double Y, double* additional_args)\n",
     "{\n",
     "    // evaluate ODEs\n",
     "\n",
+    "    // the frequency variables are pointers!\n",
+    "    double x = Y_to_xI(a, p, e, Y);\n",
+    "    KerrGeoCoordinateFrequencies(Omega_phi, Omega_theta, Omega_r, a, p, e, x);\n",
+    "\n",
     "\tint Nv = 10;\n",
     "    int ne = 10;\n",
     "    *pdot = epsilon * dpdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
@@ -2663,11 +2667,7 @@
     "\n",
     "    Nv = 7;\n",
     "    ne = 10;\n",
-    "    *Ydot = -epsilon * dYdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
-    "\n",
-    "    // convert to proper inclination input to fundamental frequencies\n",
-    "    double xI = Y_to_xI(a, p, e, Y);\n",
-    "    KerrGeoCoordinateFrequencies(Omega_phi, Omega_theta, Omega_r, a, p, e, xI);\n",
+    "    *Ydot = epsilon * dYdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
     "\n",
     "}\n",
     "````\n",
@@ -2689,7 +2689,7 @@
     "If your function requires the storage of files or interpolants, you can also build your ODE as a class. In this case, \n",
     "it must have a constructor, destructor, and method called `deriv_func` with the ODEs.\n",
     "\n",
-    "Here is the implementation for the flux driven trajectory:\n",
+    "Here is the implementation for the flux driven trajectory (see`include/ode_base_example.cc`):\n",
     "\n",
     "````\n",
     "\n",
@@ -2713,24 +2713,25 @@
     "#define SchwarzEccFlux_file1 FluxNewMinusPNScaled_fixed_y_order.dat\n",
     "__deriv__\n",
     "void SchwarzEccFlux::deriv_func(double* pdot, double* edot, double* xdot,\n",
-    "                  double Omega_phi, double Omega_theta, double Omega_r,\n",
+    "                  double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
     "                  double epsilon, double a, double p, double e, double x, double* additional_args)\n",
     "{\n",
     "    if ((6.0 + 2. * e) > p)\n",
     "    {\n",
     "        *pdot = 0.0;\n",
     "        *edot = 0.0;\n",
     "        *xdot = 0.0;\n",
-    "\n",
     "        return;\n",
     "    }\n",
+    "\n",
+    "    SchwarzschildGeoCoordinateFrequencies(Omega_phi, Omega_r, p, e);\n",
+    "    *Omega_theta = *Omega_phi;\n",
+    "\n",
     "    double y1 = log((p -2.*e - 2.1));\n",
     "\n",
     "    // evaluate ODEs, starting with PN contribution, then interpolating over remaining flux contribution\n",
     "\n",
-    "    SchwarzschildGeoCoordinateFrequencies(Omega_phi, Omega_r, p, e);\n",
-    "\n",
-    "\tdouble yPN = pow((Omega_phi),2./3.);\n",
+    "\tdouble yPN = pow((*Omega_phi),2./3.);\n",
     "\n",
     "\tdouble EdotPN = (96 + 292*Power(e,2) + 37*Power(e,4))/(15.*Power(1 - Power(e,2),3.5)) * pow(yPN, 5);\n",
     "\tdouble LdotPN = (4*(8 + 7*Power(e,2)))/(5.*Power(-1 + Power(e,2),2)) * pow(yPN, 7./2.);\n",
@@ -2757,7 +2758,6 @@
     "    *xdot = 0.0;\n",
     "}\n",
     "\n",
-    "\n",
     "// When interfacing with cython, it helps to have  dealloc function to explicitly call\n",
     "// rather than the deconstructor\n",
     "SchwarzEccFlux::~SchwarzEccFlux()\n",
@@ -2773,6 +2773,39 @@
     "````"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this case, where the functions are implemented in a class, you will have to add the class to the header file: `include/ode_base.hh`. You do not need to add anything to the header file if you are working with functions and not classes. You will need to create this file if you have not already. Make sure it is in the `include/` directory. Here is an example of what is placed in the header file when working with classes (see `include/ode_base_example.hh`):\n",
+    "\n",
+    "````\n",
+    "#include \"Interpolant.h\"\n",
+    "\n",
+    "// Used to pass the interpolants to the ODE solver\n",
+    "struct interp_params{\n",
+    "\tdouble epsilon;\n",
+    "\tInterpolant *Edot;\n",
+    "\tInterpolant *Ldot;\n",
+    "};\n",
+    "\n",
+    "class SchwarzEccFlux{\n",
+    "public:\n",
+    "    interp_params *interps;\n",
+    "    Interpolant *amp_vec_norm_interp;\n",
+    "    double test;\n",
+    "\n",
+    "    SchwarzEccFlux(std::string few_dir);\n",
+    "\n",
+    "    void deriv_func(double* pdot, double* edot, double* Ydot,\n",
+    "                      double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
+    "                      double epsilon, double a, double p, double e, double Y, double* additional_args);\n",
+    "    ~SchwarzEccFlux();\n",
+    "};\n",
+    "\n",
+    "````"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_131_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_131_1.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_135_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_135_1.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_138_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_138_1.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_143_0.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_143_0.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_147_0.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_147_0.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_151_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_151_1.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_152_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_152_1.png
diff --git a/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_154_1.png b/docs/doctrees/nbsphinx/tutorial_FastEMRIWaveforms_tutorial_154_1.png
diff --git a/docs/doctrees/tutorial/FastEMRIWaveforms_tutorial.doctree b/docs/doctrees/tutorial/FastEMRIWaveforms_tutorial.doctree
diff --git a/docs/html/README.html b/docs/html/README.html
@@ -382,7 +382,7 @@ <h2>Versioning<a class="headerlink" href="#versioning" title="Permalink to this
 <p>We use <a class="reference external" href="http://semver.org/">SemVer</a> for versioning. For the versions
 available, see the <a class="reference external" href="https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags">tags on this
 repository</a>.</p>
-<p>Current Version: 1.4.3</p>
+<p>Current Version: 1.4.4</p>
 </div>
 <div class="section" id="authors">
 <h2>Authors<a class="headerlink" href="#authors" title="Permalink to this headline">¶</a></h2>

diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_131_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_131_1.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_135_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_135_1.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_138_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_138_1.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_143_0.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_143_0.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_147_0.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_147_0.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_151_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_151_1.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_152_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_152_1.png
diff --git a/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_154_1.png b/docs/html/_images/tutorial_FastEMRIWaveforms_tutorial_154_1.png
diff --git a/docs/html/_sources/README.rst.txt b/docs/html/_sources/README.rst.txt
@@ -199,7 +199,7 @@ We use `SemVer <http://semver.org/>`__ for versioning. For the versions
 available, see the `tags on this
 repository <https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags>`__.
 
-Current Version: 1.4.3
+Current Version: 1.4.4
 
 Authors
 -------

diff --git a/docs/html/_sources/general/docs_main.rst.txt b/docs/html/_sources/general/docs_main.rst.txt
@@ -34,6 +34,7 @@ Package TODOs
 Change Log
 ===========
 
+- 1.4.4: Bug fix at zero eccentricity. Frequencies back in ODE. Fix for git pull issue with ode_base files.
 - 1.4.3: Bug fixes for additional arguments in SchEcc waveform base.
 - 1.4.2: Bug fixes for additional arguments in AAK waveform.
 - 1.4.1: Bug fixes.

diff --git a/docs/html/_sources/tutorial/FastEMRIWaveforms_tutorial.ipynb.txt b/docs/html/_sources/tutorial/FastEMRIWaveforms_tutorial.ipynb.txt
@@ -2608,7 +2608,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you want to implement a set of ODE equations in C/C++, you can add your function to `src/ode_base.cc`. When you run `python setup install`, the installer will build a full file of ODEs and take care of all of the backend aspects to the integration. **You only have to implement the ODE**. You identify the ODE functions with `__deriv__` decorator. `#define` is then used to give extra necessary information on the function. Options are:\n",
+    "If you want to implement a set of ODE equations in C/C++, you can add your function to `src/ode_base.cc`. You have to create the file if you have not already. Make sure it is in the `src/` directory. When you run `python setup install`, the installer will build a full file of ODEs and take care of all of the backend aspects to the integration. **You only have to implement the ODE**. You identify the ODE functions with `__deriv__` decorator. `#define` is then used to give extra necessary information on the function. Options are:\n",
     "\n",
     "* `#define {waveform function name}_num_add_args {number of added args}`: Number of additional arguments beyond the required arguments. \n",
     "* `#define {waveform function name}_spinless`: Indicated Schwarzschild background. \n",
@@ -2640,18 +2640,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If the ODE is purely analytic, a function will work. Here is an example with the 5PN trajectory:\n",
+    "If the ODE is purely analytic, a function will work. Here is an example with the 5PN trajectory (see`include/ode_base_example.cc`):\n",
     "\n",
     "````\n",
     "#define pn5_Y\n",
     "#define pn5_citation1 pn5_citation\n",
     "__deriv__\n",
     "void pn5(double* pdot, double* edot, double* Ydot,\n",
-    "                  double Omega_phi, double Omega_theta, double Omega_r,\n",
+    "                  double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
     "                  double epsilon, double a, double p, double e, double Y, double* additional_args)\n",
     "{\n",
     "    // evaluate ODEs\n",
     "\n",
+    "    // the frequency variables are pointers!\n",
+    "    double x = Y_to_xI(a, p, e, Y);\n",
+    "    KerrGeoCoordinateFrequencies(Omega_phi, Omega_theta, Omega_r, a, p, e, x);\n",
+    "\n",
     "\tint Nv = 10;\n",
     "    int ne = 10;\n",
     "    *pdot = epsilon * dpdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
@@ -2663,11 +2667,7 @@
     "\n",
     "    Nv = 7;\n",
     "    ne = 10;\n",
-    "    *Ydot = -epsilon * dYdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
-    "\n",
-    "    // convert to proper inclination input to fundamental frequencies\n",
-    "    double xI = Y_to_xI(a, p, e, Y);\n",
-    "    KerrGeoCoordinateFrequencies(Omega_phi, Omega_theta, Omega_r, a, p, e, xI);\n",
+    "    *Ydot = epsilon * dYdt8H_5PNe10 (a, p, e, Y, Nv, ne);\n",
     "\n",
     "}\n",
     "````\n",
@@ -2689,7 +2689,7 @@
     "If your function requires the storage of files or interpolants, you can also build your ODE as a class. In this case, \n",
     "it must have a constructor, destructor, and method called `deriv_func` with the ODEs.\n",
     "\n",
-    "Here is the implementation for the flux driven trajectory:\n",
+    "Here is the implementation for the flux driven trajectory (see`include/ode_base_example.cc`):\n",
     "\n",
     "````\n",
     "\n",
@@ -2713,24 +2713,25 @@
     "#define SchwarzEccFlux_file1 FluxNewMinusPNScaled_fixed_y_order.dat\n",
     "__deriv__\n",
     "void SchwarzEccFlux::deriv_func(double* pdot, double* edot, double* xdot,\n",
-    "                  double Omega_phi, double Omega_theta, double Omega_r,\n",
+    "                  double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
     "                  double epsilon, double a, double p, double e, double x, double* additional_args)\n",
     "{\n",
     "    if ((6.0 + 2. * e) > p)\n",
     "    {\n",
     "        *pdot = 0.0;\n",
     "        *edot = 0.0;\n",
     "        *xdot = 0.0;\n",
-    "\n",
     "        return;\n",
     "    }\n",
+    "\n",
+    "    SchwarzschildGeoCoordinateFrequencies(Omega_phi, Omega_r, p, e);\n",
+    "    *Omega_theta = *Omega_phi;\n",
+    "\n",
     "    double y1 = log((p -2.*e - 2.1));\n",
     "\n",
     "    // evaluate ODEs, starting with PN contribution, then interpolating over remaining flux contribution\n",
     "\n",
-    "    SchwarzschildGeoCoordinateFrequencies(Omega_phi, Omega_r, p, e);\n",
-    "\n",
-    "\tdouble yPN = pow((Omega_phi),2./3.);\n",
+    "\tdouble yPN = pow((*Omega_phi),2./3.);\n",
     "\n",
     "\tdouble EdotPN = (96 + 292*Power(e,2) + 37*Power(e,4))/(15.*Power(1 - Power(e,2),3.5)) * pow(yPN, 5);\n",
     "\tdouble LdotPN = (4*(8 + 7*Power(e,2)))/(5.*Power(-1 + Power(e,2),2)) * pow(yPN, 7./2.);\n",
@@ -2757,7 +2758,6 @@
     "    *xdot = 0.0;\n",
     "}\n",
     "\n",
-    "\n",
     "// When interfacing with cython, it helps to have  dealloc function to explicitly call\n",
     "// rather than the deconstructor\n",
     "SchwarzEccFlux::~SchwarzEccFlux()\n",
@@ -2773,6 +2773,39 @@
     "````"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this case, where the functions are implemented in a class, you will have to add the class to the header file: `include/ode_base.hh`. You do not need to add anything to the header file if you are working with functions and not classes. You will need to create this file if you have not already. Make sure it is in the `include/` directory. Here is an example of what is placed in the header file when working with classes (see `include/ode_base_example.hh`):\n",
+    "\n",
+    "````\n",
+    "#include \"Interpolant.h\"\n",
+    "\n",
+    "// Used to pass the interpolants to the ODE solver\n",
+    "struct interp_params{\n",
+    "\tdouble epsilon;\n",
+    "\tInterpolant *Edot;\n",
+    "\tInterpolant *Ldot;\n",
+    "};\n",
+    "\n",
+    "class SchwarzEccFlux{\n",
+    "public:\n",
+    "    interp_params *interps;\n",
+    "    Interpolant *amp_vec_norm_interp;\n",
+    "    double test;\n",
+    "\n",
+    "    SchwarzEccFlux(std::string few_dir);\n",
+    "\n",
+    "    void deriv_func(double* pdot, double* edot, double* Ydot,\n",
+    "                      double* Omega_phi, double* Omega_theta, double* Omega_r,\n",
+    "                      double epsilon, double a, double p, double e, double Y, double* additional_args);\n",
+    "    ~SchwarzEccFlux();\n",
+    "};\n",
+    "\n",
+    "````"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/docs/html/general/docs_main.html b/docs/html/general/docs_main.html
@@ -238,6 +238,7 @@ <h1>Package TODOs<a class="headerlink" href="#package-todos" title="Permalink to
 <div class="section" id="change-log">
 <h1>Change Log<a class="headerlink" href="#change-log" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
+<li><p>1.4.4: Bug fix at zero eccentricity. Frequencies back in ODE. Fix for git pull issue with ode_base files.</p></li>
 <li><p>1.4.3: Bug fixes for additional arguments in SchEcc waveform base.</p></li>
 <li><p>1.4.2: Bug fixes for additional arguments in AAK waveform.</p></li>
 <li><p>1.4.1: Bug fixes.</p></li>

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -390,7 +390,7 @@ <h2>Versioning<a class="headerlink" href="#versioning" title="Permalink to this
 <p>We use <a class="reference external" href="http://semver.org/">SemVer</a> for versioning. For the versions
 available, see the <a class="reference external" href="https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags">tags on this
 repository</a>.</p>
-<p>Current Version: 1.4.3</p>
+<p>Current Version: 1.4.4</p>
 </div>
 <div class="section" id="authors">
 <h2>Authors<a class="headerlink" href="#authors" title="Permalink to this headline">¶</a></h2>

diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js