Tutorial ======== .. _installing_dependencies: Installing Dependencies ----------------------- 1. **Installing Java 11** The different ways to install **Java 11** on different distros are shown below: **Ubuntu** .. code-block:: console $ sudo apt-get install openjdk-11-jdk **Fedora** .. code-block:: console $ sudo dnf install java-11-openjdk -y **Mac** .. code-block:: console $ sudo port install openjdk11 2. **Installing PyVista** PyVista can be installed from `PyPI `_ using ``pip`` on Python >= 3.7:: pip install pyvista You can also visit `PyPI `_, `Anaconda `_, or `GitHub `_ to download the source. See the `Installation `_ for more details regarding optional dependencies or if the installation through pip doesn't work out. .. _input_parameters: Input Parameters ---------------- The basic input parameters for **REST** are listed below: 1. Type of structure * Strongly Damaged Sphere (SDS) * Rough Surface (RS) * Poked Structure (PS) * Rough Surface Super-ellipsoids (RS-SE) * Poked Structure Super-ellipsoids (PS-SE) * Rough Fractal Aggregates (RFA) 2. Radius of initial spherical structure R\ :sub:`d` (for the SDS, RS and PS structures) 3. Semi-axes *a*, *b* and *c* (for RS-SE and PS-SE structures) 4. East-west exponent *e* and north-south exponent *n* (for the RS-SE and PS-SE structures) 5. Coordinates in the format *[r, X, Y, Z, material_tag]* where *r* is the radius of each grain of a fractal aggregate and *material_tag* is 1 for homogeneous material and 1 or 2 for inhomogeneous material (for RFA structures) 6. Number of material seed cells *N*\ :sub:`m` 7. Number of space seed cells *N*\ :sub:`s` 8. Number of surface seed cells *N*\ :sub:`ss` 9. Thickness of surface layer *t* 10. Final structure file *name* .. _strongly_damaged_sphere: Strongly Damaged Sphere (SDS) [*Default Seeds*] -------------------------------------------- 1. Select the option **Strongly Damaged Sphere**. Upon selecting an option the input panel appears as shown below. .. image:: er3.png 2. Select the **Default Seeds** option from the input panel. Enter the *Radius* of initial structure in number of dipoles (e.g. R\ :sub:`d`\ = 32) and enter a filename for the final structre in the **File name** section of the input panel. Finally click the **Calculate** button to start the calculation. During calculation an **xterm** window will open and indicate the progress of calculation as shown below. .. image:: er4.png 3. Upon completion of the calculation, the control box will appear below the input panel having *pink* border. .. image:: er5.png 4. Click the **Final structure data** button to import the data calculated for generating the final **SDS** structure in the **Structure file** panel on the right-hand side. .. image:: er7.png 5. Finally, click the **3D Plot** button to convert all the structure data into *VTK* files and generate the 3D structures initial and final structure along with the distribution of the different seed cells within the initial structure. .. image:: e8.png 6. Save the structure data by clicking **Save data** button and save the 3D plot by clicking **Save plot** button. 7. Reset or clear the input and output entries by clicking **Clear & Reset** button. .. _strongly_damaged_sphere_custom: Strongly Damaged Sphere (SDS) [*Custom Seeds*] ---------------------------------------------- 1. In case of SDS (*Custom seed*) option select **Custom Seeds**. 2. Enter the values for **Intitial radius of the sphere** (R\ :sub:`d`\), **No. of Material seed cells** (N\ :sub:`m`\) and **No. of Space seed cells** (N\ :sub:`s`\). 3. Enter the **File name** and hit **Calculate** button. .. image:: sds_c.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _rough_surface: Rough Surface (RS) ------------------ 1. In case of RS option select **Rough Surface and Poked Sphere** option and then select **Rough Surface** option from the input panel. 2. Enter the values for **Intitial radius of the sphere** (R\ :sub:`d`\), **No. of Material seed cells** (N\ :sub:`m`\), **No. of Space seed cells** (N\ :sub:`s`\) and the **Thickness**. 3. Enter the **File name** and hit **Calculate** button. .. image:: rs1.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _poked_structures: Poked Structures (PS)[*Homogeneous*] --------------------- 1. In case of PS (*Homogenous*) option select **Rough Surface and Poked Sphere** option and then select **Poked sphere** option followed by **Homogeneous** option from the input panel. 2. Enter the values for **Intitial radius of the sphere** (R\ :sub:`d`\), **No. of Material seed cells** (N\ :sub:`m`\), **No. of Internal Space seed cells** (N\ :sub:`s`\), **No. of surface space seed cells** (N\ :sub:`ss`\) and the **Thickness**. 3. Enter the **File name** and hit **Calculate** button. .. image:: ps_h.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _poked_structures_inhomogeneous: Poked Structures (PS)[*Inhomogeneous*] --------------------- 1. In case of PS (*Homogenous*) option select **Rough Surface and Poked Sphere** option and then select **Poked sphere** option followed by **Inhomogeneous** option from the input panel. 2. Enter the values for **Intitial radius of the sphere** (R\ :sub:`d`\), **No. of Material seed cells** (N\ :sub:`m1` and N\ :sub:`m2`), **No. of Internal Space seed cells** (N\ :sub:`s`\), **No. of surface space seed cells** (N\ :sub:`ss`\) and the **Thickness**. 3. Enter the **File name** and hit **Calculate** button. .. image:: ps_inh.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _rough_surface_super-ellipsoids: Rough Surface Super-ellipsoids (RS-SE) -------------------------------------- 1. In case of RS option select **Rough Superellipsoids** option and then select **Rough Surface** option from the input panel. 2. Enter the values for **Semi-axes (a,b,c)**, **Exponents (e,n)**, **No. of Material seed cells** (N\ :sub:`m`\) and **No. of Space seed cells** (N\ :sub:`s`\). 3. Enter the **File name** and hit **Calculate** button. .. image:: rs_se.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _poked_structure_super-ellipsoids_homogeneous: Poked Structure Super-ellipsoids (PS-SE) [*Homogeneous*] ---------------------------------------- 1. In case of PS (*Homogenous*) option select **Rough Superellipsoids** option and then select **Poked sphere** option followed by **Homogeneous** option from the input panel. 2. Enter the values for **Semi-axes (a,b,c)**, **Exponents (e,n)**, **No. of Material seed cells** (N\ :sub:`m`\), **No. of Internal Space seed cells** (N\ :sub:`s`\) and **No. of surface space seed cells** (N\ :sub:`ss`\). 3. Enter the **File name** and hit **Calculate** button. .. image:: ps_se.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _poked_structure_super-ellipsoids_ihomogeneous: Poked Structure Super-ellipsoids (PS-SE) [*Inhomogeneous*] ---------------------------------------- 1. In case of PS (*Inhomogenous*) option select **Rough Superellipsoids** option and then select **Poked sphere** option followed by **Inhomogeneous** option from the input panel. 2. Enter the values for **Semi-axes (a,b,c)**, **Exponents (e,n)**, **No. of Material seed cells** (N\ :sub:`m` and N\ :sub:`m2`), **No. of Internal Space seed cells** (N\ :sub:`s`\) and **No. of surface space seed cells** (N\ :sub:`ss`\). 3. Enter the **File name** and hit **Calculate** button. .. image:: ps_se_inh.png 4. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre. .. _rough_fractal_aggregates: Rough Fractal Aggregates (RFA) ------------------------------ 1. Prepaper a fractal aggregate (FA) made up of *N* spheres each having radius *r* and coordinates (*X, Y, Z*). The format of the FA structure file is shown below: 0 r\ :sub:`0` X\ :sub:`0` Y\ :sub:`0` Z\ :sub:`0` mtag mtag 1 r\ :sub:`1` X\ :sub:`1` Y\ :sub:`1` Z\ :sub:`1` mtag mtag 2 r\ :sub:`2` X\ :sub:`2` Y\ :sub:`2` Z\ :sub:`2` mtag mtag . . . . . . . . . . . . . . . . . . . . . N r\ :sub:`N` X\ :sub:`N` Y\ :sub:`N` Z\ :sub:`N` mtag mtag where mtag represents either 1 or 2 for homogeneous or inhomogeneous composition respectively. 2. Click the **Rough Fractal Aggregate** option from the top panel. 3. Choose the *FA* structure file by clicking **Browse** button. 4. Select **Monomer size scale** between 1 to 10 which is required to scale the aggregate into an initial sphere and click **Save**. The radius of the initial sphere will be automatically setup depending on the scale factor. 5. Click the **Load** button to load the structure and scale it according to the size scale factor. 6. Enter the values for **No. of Material seed cells** (N\ :sub:`m`) and **No. of Surface Space seed cells** (N\ :sub:`ss`\). 7. Enter the **File name** and hit **Calculate** button. .. image:: rfa_h.png 8. For inhomogeneous RFA structures select **Mixed Composition** .. image:: rfa_inh.png 9. Follow the steps (3-7) from the **SDS** (*Default seeds*) section to generate the structre.