Update documentation, rename some files

Ensor-code · Oct 18, 2024 · d179e0f · d179e0f
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diff --git a/...reating_figures_package/0_SliceLine.ipynb → ...0_creating_sliceFigures/0_SliceLine.ipynb b/...reating_figures_package/0_SliceLine.ipynb → ...0_creating_sliceFigures/0_SliceLine.ipynb
diff --git a/...ures_package/1_SlicePlot (beginner).ipynb → ...sliceFigures/1_SlicePlot (beginner).ipynb b/...ures_package/1_SlicePlot (beginner).ipynb → ...sliceFigures/1_SlicePlot (beginner).ipynb
diff --git a/...ures_package/2_SlicePlot (advanced).ipynb → ...sliceFigures/2_SlicePlot (advanced).ipynb b/...ures_package/2_SlicePlot (advanced).ipynb → ...sliceFigures/2_SlicePlot (advanced).ipynb
diff --git a/...ures_package/3_SliceLine Animations.ipynb → ...sliceFigures/3_SliceLine Animations.ipynb b/...ures_package/3_SliceLine Animations.ipynb → ...sliceFigures/3_SliceLine Animations.ipynb
diff --git a/...ures_package/4_SlicePlot Animations.ipynb → ...sliceFigures/4_SlicePlot Animations.ipynb b/...ures_package/4_SlicePlot Animations.ipynb → ...sliceFigures/4_SlicePlot Animations.ipynb
diff --git a/...ating_figures_package/5_SlicePlot Disk.py → ...creating_sliceFigures/5_SlicePlot Disk.py b/...ating_figures_package/5_SlicePlot Disk.py → ...creating_sliceFigures/5_SlicePlot Disk.py
diff --git a/...ples/0_creating_figures_package/index.rst → ...xamples/0_creating_sliceFigures/index.rst b/...ples/0_creating_figures_package/index.rst → ...xamples/0_creating_sliceFigures/index.rst
@@ -1,5 +1,5 @@
-Creating figures using the package
-##################################
+Creating 2D slice figures and animations, and 1D slice plots using the package
+#############################################################
 
 The following examples show how to create figures using plons.
 

diff --git a/docs/src/1_examples/1_creating_figures_pipeline/pipeline.rst b/docs/src/1_examples/1_creating_figures_pipeline/pipeline.rst
diff --git a/...les/1_creating_figures_pipeline/index.rst → docs/src/1_examples/1_pipeline/index.rst b/...les/1_creating_figures_pipeline/index.rst → docs/src/1_examples/1_pipeline/index.rst
diff --git a/docs/src/1_examples/1_pipeline/pipeline.rst b/docs/src/1_examples/1_pipeline/pipeline.rst
@@ -0,0 +1,68 @@
+Pipeline
+########
+
+PLONS contains a pipeline that produces useful output files with information about your simulation
+
+To use the pipeline, the pipeline needs to be :ref:`installed <link-installation-pipeline>` first.
+
+When running the pipeline, the user settings will be integrated, and models will be searched in the ``data_location``. All models found will be displayed, and the model for which the pipeline needs to run can be selected by typing the correct number. Multiple models can be selected by adding them with a space bar inbetween. When typing ``a`` or ``all``, all models will be used.
+
+Later a selection of the pipeline can be chosen to be executed. It currently contains the following options:
+
+1. 2D slice plots showing the density, temperature and velocity distribution of the last full dump of the model
+
+2. 1D line plots (radial structure) of the global structure of the last dump of the model along the x-, y- and z-axes
+
+3. Information and plots of the orbital evolution
+
+4. 1D spherical profiles, which are useful for single star models
+
+To run this pipeline, use the script 'main.py' in plons/scripts/ .
+To select a certain model and option, you can execute this script as python main.py -m ... -o ... (and filling in the model and option number instead of the ...).
+
+
+Pipeline - More detailed information
+------------------------------------
+
+This pipeline loads the wind.in and wind.setup files first. This is the general setup information
+of the model (configuration of the system, information of the thermodynamics, evolution time, wind
+outflow setup,...). Next the last full dump is loaded, and using this data, some other useful
+quantities are calculated (gas pressure/temperature, speed, sperical coordinates, sound speed of
+the gas,...).  Lastly, the data of the sink particle(s) is loaded. From this file, also the period
+and orbital velocity of the sink particles is calculated, if the system is a multiple, as a function of
+time. The last entry in the sink data corresponds to the full dump loaded. Therefore the
+position/velocity/mass/... of this last entry are also saved in the full dump data for easy usage.
+
+
+(1) 2D slice plots 
+___________________
+
+This option creates 2D sliceplots in the orbital plane (face-on view) and a perpendicular meridional plane (edge-on view) 
+at different scales. It shows the density, temperature and velocity distribution of your model in these 2 planes. 
+To get the data in these infinitely thin slices, the smoothing kernel from PHANTOM is used, and the calculations are done on a grid of n*n
+pixels, using the data of the m nearest neighbours (SPH particles) of those grid points. 
+These plots can be useful to get a first visual representation of the morphology in the AGB wind of the simulation, 
+and can be optimised according to your personal needs. 
+
+
+(2) 1D radial structure (line slice) plots 
+___________________________________________
+
+This option creates 1D radial line profiles of the density, velocity and temperature distribution along the x-, y- and z-axes.
+The data along these lines is achieved in the same way as explained in (1), but for a 1D grid. 
+These plots can be usefull as a more detailed and quantitive representation of the morphology, for example to identify global assymetries and non-spherical density distributions.
+For an example use case, see Appendix A of [Malfait et al. 2021](https://ui.adsabs.harvard.edu/abs/2021A%26A...652A..51M/abstract)
+
+
+(3) Information of the orbital evolution.
+_________________________________________
+
+This option produces several plots with usefull information about the orbital properties and orbital evolution of the simulation,
+such as the mass and angular momentum accretion by the companion.
+In order to get this information, the evolutionary sink files are used (.ev), which give relevant quantities of the sink particles as a function of time.
+
+
+(4) 1D spherical profiles for single star models
+________________________________________________
+
+This option should be used for single star simulations, and compares your 3D data to a 1D solution. It reads the wind_1D.dat data to plot the 1D solution.
diff --git a/docs/src/1_examples/2_accretion_disk/accrDisks_vrvtPlots_Plons.ipynb b/docs/src/1_examples/2_accretion_disk/accrDisks_vrvtPlots_Plons.ipynb
@@ -96,7 +96,7 @@
     "fig, axs = plt.subplots(nrows = 1, ncols= 3 , figsize=(28, 7))\n",
     "# you can optionally add limits for the density plot and draw a circle with the estimated radius of the disk\n",
     "limitsRho = [-16,-10]\n",
-    "r      = 0.78\n",
+    "r      = 0.7\n",
     "# ad.plot_vrvtRho(axs,smooth,zoom,r,limitsRho)  #r and limitsRho are optional arguments\n",
     "# ad.plot_vrvtRho(axs,smooth,zoom,limitsRho = limitsRho)\n",
     "ad.plot_vrvtRho(axs,smooth,zoom,r)\n",

diff --git a/src/plons/RadialStructurePlots1D.py b/src/plons/RadialStructurePlots1D.py
@@ -42,14 +42,14 @@ def getParamsLine(results_line, vec1, minT, gamma, vec2 = [], dumpData = None):
 definition used in plotParR, plots radial structure of given parameter (log(rho)/|v|/T) on the x- and y-axis
 '''
 def oneRadialStructurePlot(parX,parZ, X, Z, parName, axis, parMin, parMax, rcomp, bound, limX):
-    # print('bound is ',bound)
     axis.set_xlim(limX, bound)
+    # Uncomment if you want both sides
+    # axis.set_xlim(-bound,bound)
     axis.vlines(rcomp, parMin, parMax, 'black', linestyle='--', linewidth=1., label=r"$x_\mathrm{comp}$", zorder = 10)
 
     axis.plot(X/cgs.au, parX, color = 'C0', label = '$x$-axis', lw = 1)
     axis.plot(Z/cgs.au, parZ, color = 'C1', label = '$z$-axis', lw = 1)
 
-
     # ind_maxima = argrelextrema(parX,np.greater)
     # Xmax = X[ind_maxima]
     # RhoMax = parX[ind_maxima]
@@ -209,7 +209,6 @@ def radialStructPlots(run,loc, dumpData, setup):
         rhoMax           = 10 * max(rhoMaxX, rhoMaxZ)
         #print('rhomin en max zijn: ',rhoMin,rhoMax)
 
-
         vMinX, vMaxX = np.min(parX[1]), np.max(parX[1])
         vMinZ, vMaxZ = np.min(parZ[1]), np.max(parZ[1])
         vMin         = min(vMinX,vMinZ)