Defining a new SETUP

This section is a small tutorial on how to define a setup from scratch. In this tutorial we will implement a hydrodynamics setup. The setup we will define is “blob”, that comes implemented in the public version of FARGO3D.

Blob test

This is a 2D test characterized by a uniform fluid, with a denser fluid disk embedded. The system is force-balanced (ie in pressure equilibrium) if there is no velocity between the two fluids. The disk is moving at a supersonic speed. In order to compare our results, we will develop the same parameters as http://www.astrosim.net/code/doku.php?id=home:codetest:hydrotest:wengen:wengen3.

Parameters of the test:

  • Mach number: 2.7
  • Density jump: 10
  • Pressure equilibria
  • gamma: 5/3

We will do the test in the XY plane, and we will implement periodic boundaries in X and reflexive boundaries in Y. We will do a second test with free outflow boundaries in Y.

In order to implement this setup we need:

  1. A setup name: In this case will be “myblob”.
  2. Therefore a directory inside setups/ called myblob.
  3. the .bound file in that directory, called myblob.bound.
  4. the .par file in that directory, called myblob.par.
  5. the .opt file in that directory, called myblob.opt.
  6. the file called condinit.c in that directory. This is where the fields are initialized.

Optionally:

  • the .units file, called myblob.units.
  • the .mandatory file, called myblob.mandatory.
  • the .objects file, called myblob.objects.
  • A boundaries.txt file (if it is not present it will be taken from the std/ directory).

Making the setup directory:

We start by creating the setup directory myblob:

$: cd setups/
$: mkdir myblob

Defining boundaries:

We define from scratch all the boundaries in the setup. In order to do that we create a file called boundaries.txt inside setups/myblob/:

$: emacs boundaries.txt

Naturally, you may use your favorite editor instead of emacs...

Now, we write these lines:

SYMMETRIC:
           Centered:    |a|a|
           Staggered:   |a|a|a|

ANTISYMMETRIC:
           Staggered:   |-a|0|a|

We will use the SYMMETRIC boundary for both reflective and free outflow boundaries, and ANTISYMMETRIC only for the normal velocity Vy in the reflective case.

We must create the file myblob.bound:

$: emacs myblob.bound

And write this lines:

Density:
        Ymin: SYMMETRIC
        Ymax: SYMMETRIC

Energy:
        Ymin: SYMMETRIC
        Ymax: SYMMETRIC

Vx:
        Ymin:   SYMMETRIC
        Ymax:   SYMMETRIC

Vy:
        Ymin:   ANTISYMMETRIC
        Ymax:   ANTISYMMETRIC

We say that all our fields are symmetric, but vy should be reflected in Y. This set is the reflective boundary condition on Y. The free outflow is the same, except for:

Vy:
        Ymin:   SYMMETRIC
        Ymax:   SYMMETRIC

Defining the parameter file

The parameter file is very useful when we want to change a value inside the code but you do not want to recompile the code. It is used in much the same way as with the former FARGO code. Yet in that code, parameters were defined in a rather manual way, in a file called var.c. With FARGO3D we do not have to edit this file. Rather, we provide in the SETUP sub directory a template parameter file that has same name as the setup plus the .par extension. From this file, a Python script will automagically draw a list of all global variables and guess their type, and will make a var.c accordingly, in a manner transparent to the user. At run time the user is free to run the code either with this .par file, or any other .par file in another directory, without rebuilt.

There are a set of minimal requirement in a .par file, related with the mesh size, and output parameters. We will start with the basic parameters:

We edit the new file myblob.par:

$: touch myblob.par

and write inside something similar to:

Setup                   myblob

Nx                      400
Ny                      100
Xmin                   -2.0
Xmax                    2.0
Ymin                   -0.5
Ymax                    0.5

Ntot                    1000
Ninterm                 1
DT                      0.05
OutputDir               outputs/myblob

Warning

Because a Python script will automagically create a var.c file (similar to that of the former FARGO code) out of this newly created parameter file, we must help the script to guess correctly the type of each variable. For instance, if we write “Xmin -2” instead of “Xmin -2.0”, it will wrongly deduce that Xmin is an integer, not a floating point value, with highly unpleasant consequences at run time. Similarly, the figure “-0.5” is correctly recognized by the script, but “-.5” would not be.

Now, we will define the parameters specific to our setup. They are:

gamma                   1.666667
rho21                   10.0
mach                    2.7
rblob                   0.15
xblob                  -1.0
yblob                   0.0

where gamma is the adiabatic index, rho21 is the quotient between the density in the circle (2) and outside (1), and the same for the temperature; rblob is the radius of the initial blob, normalized by the vertical size of the box; [xy]blob is the initial position of the blob.

The observant reader will notice that gamma is already defined in std/stdpar.par, with the same value. Since both sets of parameters are used (those of std/stdpar.par and those of setups/myblob/myblob.par), the first line in the block above is actually redundant and could have been omitted.

.opt file.

Our setup is 2D, and we want to use the energy equation. In the code’s jargon, we refer to this as an adiabatic situation. We work in Cartesian coordinates:

$: emacs myblob.opt

The minimal .opt file should be similar to:

FARGO_OPT += -DX
FARGO_OPT += -DY
FARGO_OPT += -DADIABATIC
FARGO_OPT += -DCARTESIAN
ifeq (${GPU}, 1)
FARGO_OPT += -DBLOCK_X=16
FARGO_OPT += -DBLOCK_Y=16
FARGO_OPT += -DBLOCK_Z=1
endif

If you want to use simple precision, you can set:

FARGO_OPT += -DFLOAT

Initial state:

Now we must fill all the primitive fields with the initial conditions. The standard method is as follow, step by step:

  1. Make a file called condinit.c inside your setup directory. (setups/myblob/condinit.c).
  2. At the top of this file include the fargo3d.h header.
  3. Define a function called CondInit() that returns a void.
  4. Fill the Field_variable->field_cpu with the data, for each field of the problem.

step by step

  1. Start by opening the new file for initial conditions:

    $: emacs condinit.c
    
  2. In the top line include FARGO3D’s header file:

    #include "fargo3d.h"
    
  3. Subsequently add lines similar to these lines:

    void CondInit() {
    
    
    }
    
  4. Write inside the function something similar to:

    int i,j,k;
    
    real* rho = Density->field_cpu;
    real* vx  = Vx->field_cpu;
    real* vy  = Vy->field_cpu;
    real* e   = Energy->field_cpu;
    
    i = j = k = 0;
    
    for (k = 0; k<Nz+2*NGHZ; k++) {
      for (j = 0; j<Ny+2*NGHY; j++) {
        for (i = 0; i<Nx; i++) {
    
        The fields are filled here with the help of the "l" index.
    
        }
      }
    }
    

    This is the basic structure of a routine that works on fields. Note the pointers, and the triple-nested loop. For filling the fields, we will use the helper index “l”. In this case, the outer loop is not necessary, but when Z is not defined, by default NGHZ = 0 and Nz = 1, so there is only one external loop cycle. Also, in this particular case, we need to define a circle, and the size of the circle should be resolution-independent, so we will need to normalize it. We could add the following macrocommand lines above the initialization of the indices i,j,k

    #define Q1 (xmed(i) - XBLOB)
    #define Q2 (ymed(j) - YBLOB)
    

    (Remember, all the upper variables are taken from the .par file.)

    Now, inside the innermost loop, we will fill the field. First we need a condition about where the blob is:

    if(sqrt(Q1*Q1+Q2*Q2) < RBLOB/(YMAX-YMIN)) {
    
    }
    

    And inside these curly brackets, for example, the density must to be RHO21 times denser than the density outside. The inner loop should be similar to:

    rho[l] = 1.0;               // Constant value outside
    e[l]   = 1.0/(GAMMA-1.0);   // The isothermal soundspeed is equal to 1.0.
    vx[l]  = sqrt(e[l]*(GAMMA-1.0))*MACH;
    vy[l]  = 0.0;
    
    if(sqrt(Q1*Q1+Q2*Q2) < RBLOB/(YMAX-YMIN)) {
          rho[l] *= RHO21;
          vx[l] = 0.0;
    }
    

A complete view of the file condinit.c is:

#include "fargo3d.h"

void CondInit() {

  int i,j,k;

  real* rho = Density->field_cpu;
  real* vx  = Vx->field_cpu;
  real* vy  = Vy->field_cpu;
  real* e   = Energy->field_cpu;

  #define Q1 (xmed(i) - XBLOB)
  #define Q2 (ymed(j) - YBLOB)

  i = j = k = 0;

  for (k = 0; k<Nz+2*NGHZ; k++) {
    for (j = 0; j<Ny+2*NGHY; j++) {
      for (i = 0; i<Nx; i++) {

        rho[l] = 1.0;               // Constant value outside
        e[l]   = 1.0/(GAMMA-1.0);   // The isothermal soundspeed is equal to 1.0.
        vx[l]  = sqrt(e[l]*(GAMMA-1.0))*MACH;
        vy[l]  = 0.0;

        if(sqrt(Q1*Q1+Q2*Q2) < RBLOB/(YMAX-YMIN)) {
          rho[l] *= RHO21;
          vx[l] = 0.0;
        }
      }
    }
  }
}

Making the executable:

We are now ready to build the code:

$: make SETUP=myblob view

You may skip the final rule “view” if the build process fails (you need to install Python’s matplotlib for it to work).

If everything goes fine, you should see a message similar to:

      All objects are OK. Linking stage

                FARGO3D SUMMARY:
                ===============

      This built is SEQUENTIAL. Use "make para" to change that

      This built has a graphical output,
      which uses the python's matplotlib library.
      Use "make noview" to change that.


      SETUP:      'myblob'
      (Use "make SETUP=[valid_setup_string]" to change set up)
      (Use "make list" to see the list of setups implemented)
      (Use "make info" to see the current sticky build options)

And finally, we can execute the test:
  • $: ./fargo3d -m setups/myblob/myblob.par

If you want to change the boundaries, you must modify myblob.bound and recompile the code (make again).

Plotting your new setup:

If you have ipython+pylab working, plotting your new setup is very easy (see the first run section).

  • $: ipython –pylab
  • In [1]: rho = fromfile(“outputs/myblob/gasdens10.dat”,dtype=’float32’).reshape(100,400)
  • In [2]: imshow(rho)
_images/myblob.png

myblob setup at output number 10 (ie at date = OUTPUTNB * NINTERM * DT = 0.5 here)

Run time visualization.

FARGO3D has a visualization module, that can be activated for a specific setup by doing:

$:make SETUP=setup view

or the equivalent form:

$:make SETUP=setup FARGO_DISPLAY=MATPLOTLIB

In order to use it you need to have a python-development package (if you are using some package-manager) or simply a basic python installation (the file python.h is needed at compilation time). Also, it is mandatory to have installed matplotlib and numpy packages.

How does it work?

Run time visualization uses an embedded Python interpreter running at the same time as your simulation. All the related routines are in src/matplotlib.c. The scheme developed to visualize data allows you to make a visualization routine adapted to your needs. If you work with matplotlib, you will see that making an interactive plot from within FARGO3D is the same as working in an interactive session of python+matplotlib. By default there are three main routines, called plot1d(), plot2d() and plot3d(). The functionality of each one is obvious from the name. The most important line for the run time visualization is:

Py_InitializeEx(1);

Upon execution of this function, you are able to execute any python command inside FARGO3D. A helper function was developed for passing values from FARGO3D to the python interpreter:

void pyrun(const char *, ...);

The pyrun() function works identically to printf() (man 3 printf), but pyrun() returns a void. The main difference between printf() and pyrun() is that pyrun() prints on the python interpreter, and the text printed is interpreted as a python command. In the background, pyrun is only a wrapper to the function PyRun_SimpleString().

In the basic public implementation of the run time visualization, a set of helper parameters have been implemented. These parameters should be included in your .par files. You can see the standard value of each one in std/stdpar.par:

  • Field: Name of the field you want to plot. Eg: gasdens

  • Cmap: A matplotlib palette. Eg: cubehelix (related to cmap matplotlib karg)

  • Log: If you want to use a logarithmic scale for your color map. Values: Yes/No

  • Colorbar: If you want to see the colorbar. Values Yes/No

  • Autocolor: If you want a dynamic colorbar between the min and max of the field. Values: Yes/No

  • Aspect: The same as the aspect karg of matplotlib (imshow() method). Values: Auto, None

  • vmin: Min value for the colorbar. Only if Autocolor is No

  • vmax: Max value for the colorbar. Only if Autocolor is No

  • PlotLine: Allows to make an arbitrary plot when your simulation is 3D. The field is stored in a 3D numpy array called field. For example, if you want to plot the 2D Z-sum projection, you should do something similar to:

    PlotLine         np.sum(field,axis=0)
    

Also, you can make a z-slice doing something similar to:

PlotLine         field[k,:,:]

where k is an integer with 0<k<NZ.

Backends

Matplotlib uses the concept of backend to refer to some specific set of widgets used for rendering the plot (eg: qt, tkinter, wx, etc). This is very important for us because not all the backends (at least for now) are compatible with interactive non-blocking plots. If the main widget that appears after the execution of FARGO3D does not work for you, you can try with another backend. (More details can be found in the matplotlib official documentation). There is a file in the main directory of FARGO3D, called matplotibrc that contains all the useful configurations related with matplotlib that will be used at run time. This file is matplotlib-standard, and is version-dependent. If you want to modify the aspect of the widget, or change the backend, it is a good idea to start modifying this file. We work on a daily basis with the backend TKAgg.

If you want to use the default matplotlibrc configured in your environment instead of the one we provide, it should be enough to rename the matplotlibrc file provided with FARGO3D with any arbitrary name.