phasicFlow/tutorials/sphereGranFlow/binarySystemOfParticles/README.md

# Problem definition
A rotating drum with two particle sizes is randomly filled and let it rotate to see the segregation of particles.
The focus of this tutorial is to show how to use the pre-processing tool, `particlesPhasicFlow`, to create the initial mixture of small and large particles. 

**Note:** It is supposed that you have reviewed [simulating a rotating drum](https://github.com/PhasicFlow/phasicFlow/wiki/Simulating-a-rotating-drum) tutorial before starting this tutorial.

<div align="center"><b>
a view of the rotating drum with small and large particles after 7 seconds of rotation</b>
</div>
<div align="center">
<img src="https://github.com/PhasicFlow/phasicFlow/blob/media/media/rotating-drum-binary-system.png" width="400">
</div>

***

# Case setup
PhasicFlow simulation case setup is based on the text-based files that we provide in two folders located in the simulation case folder: `settings` and `caseSetup`. Here we will have a look at some important files and the rest can be found in the tutorial folder of this case setup. 

[Simulation case setup files can be found in tutorials/sphereGranFlow folder.](https://github.com/PhasicFlow/phasicFlow/tree/main/tutorials/sphereGranFlow/binarySystemOfParticles)
### Shape definition 
In file `caseSetup/sphereShape`, two particle types with names `smallSphere` and `largeSphere` and diameters 3 and 5 mm are defined. 

<div align="center"> 
in <b>caseSetup/sphereShape</b> file
</div>

```C++
names        (smallSphere largeSphere); // names of shapes 
diameters    (0.003     0.005);    // diameter of shapes (m)
materials    (prop1  prop1);       // material names for shapes 
```
### Positioning and initial mixture 

In dictionary `positionParticles` located in file `settings/particlesDict`, 30000 particles are located in a cylindrical region. These particles are positioned in order along `z`, `x` and then `y` axis with 0.005 m distance between their centers. 

<div align="center"> 
in <b>settings/particlesDict</b> file
</div>


```C++
// positions particles 
positionParticles
{
    method positionOrdered;     // ordered positioning

    maxNumberOfParticles 30001; // maximum number of particles in the simulation
    mortonSorting Yes;          // perform initial sorting based on morton code?   

    cylinder  // cylinder region for positioning particles 
    {
        p1 (0.0 0.0 0.003);     // begin point of cylinder axis (m m m)
        p2 (0.0 0.0 0.097);     // end point of cylinder axis (m m m)
        radius       0.117;     // radius of cylinder (m)
    }
        
    positionOrderedInfo
    {        
        diameter 0.005;     // minimum space between centers of particles
        numPoints 30000;    // number of particles in the simulation 
        axisOrder (z x y);  // axis order for filling the space with particles
    }
}
```

In dictionary `setFields` located in file `settings/particlesDict`, you define the initial `velocity`, `acceleration`, `rotVelocity`, and  `shapeName` fields for all 30000 particles in the simulation. In `selectors` dictionary, you can select  subsets of particles and set the field value for these subsets. In `shapeAssigne` sub-dictionary, the `selectRange` selector is defined. It defines a range with `begin` (begin index), `end` (end index) and `stride` to select particles. And in `fieldValue` sub-dictionary, the fields values for selected particles are set (any number of field values can be set here).

**Note:** Other selectors are: `selectBox` that selects particles inside a box and `randomSelect` that selects particles randomly from a given index range. 

<div align="center"> 
in <b>settings/particlesDict</b> file
</div>

```C++
setFields
{
    /*
        Default value for fields defined for particles
    These fields should always be defined for simulations with 
    spherical particles.*/

    defaultValue 
    {
        velocity        realx3     (0 0 0); // linear velocity (m/s)
        acceleration    realx3     (0 0 0); // linear acceleration (m/s2)
        rotVelocity     realx3     (0 0 0); // rotational velocity (rad/s)
        shapeName       word   smallSphere; // name of the particle shape 
    }

    selectors
    {
        shapeAssigne
        {
            selector     selectRange; // type of point selector
            selectRangeInfo
            {
                begin   0;            // begin index of points
                end     30000;        // end index of points 
                stride  3;            // stride for selector 
            }
            fieldValue  // fields that the selector is applied to 
            {
                /*
                sets shapeName of the selected points to largeSphere*/
                shapeName     word     largeSphere;
            }
        
    }
}

```

# Running the simulation 
Enter the following command in terminal:

`> geometryPhasicFlow`

`> particlesPhasicFlow`

`> sphereGranFlow`

  

### Note on using particlesPhasicFlow
Each executable in PhasicFlow comes with some command line options that you can see them by using flag `-h` in front of that command.

`> particlesPhasicFlow -h` prints out the following output:

```
Usage: particlesPhasicFlow [OPTIONS]

Options:
  -h,--help                   Help for using createParticles of phasicFlow v-0.1
  -v,--version                Program version information
  --discription               What does this app do?
  --positionParticles-only    Exectue the positionParticles part only and store the created pointStructure in the time folder.
  --setFields-only            Exectue the setFields part only. Read the pointStructure from time folder and setFields and save the result in the same time folder.
```

so, with flag `--setFields-only`, you can execute the `setFields` part of `particlesDict`. Now suppose that you have a simulation case which proceeded up to 2 seconds and for any reason you want to change some field value at time 3 s and continue the simulation from 3 s. To this end, you need to change `startTime` in settings dictionary to 3, execute `particlesPhasicFlow --setFields-only`, and start the simulation.