Computational Ellipsometry

Tutorial Created with Software Release: 2025-1
Topics: Organic Electronics
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, MS Maestro

Tutorial files

13 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will learn how to compute the refractive index and extinction coefficient of  systems of organic optoelectronics.

 

Tutorial Content

  1. Introduction to Ellipsometry

  1. Creating Projects and Importing Structures

  1. Calculating and Analyzing the Ellipsometry of an Amorphous Film

  1. Calculating and Analyzing the Ellipsometry of a Deposited Film

  1. Calculating and Analyzing the Ellipsometry of a Crystal Structure

  1. Conclusion and References

  1. Glossary of Terms

     

1. Introduction to Ellipsometry

Ellipsometry is a powerful, non-destructive optical technique used to characterize the optical and structural properties of thin films and surfaces. In the context of organic electronics, computational approaches to ellipsometry are vital tools for predicting and optimizing the optical properties of materials, including refractive index and extinction coefficient, using molecular dynamics simulations and first-principles calculations. These optical properties are critical in understanding how light interacts with materials, influencing the performance and efficiency of optoelectronic devices.

Molecular alignment in organic thin films plays a crucial role in determining their optoelectronic properties. Organic materials can exhibit isotropic or anisotropic behavior depending on their molecular organization and processing conditions. Anisotropic materials, for instance, display direction-dependent optical properties due to molecular alignment, such as in oriented thin films, crystals, or layered structures. Processing-induced anisotropy, resulting from deposition techniques or post-processing treatments, can lead to significant variations of refractive index and extinction coefficient in different directions (e.g., x, y, z), which are essential for optimizing device performance in applications like OLEDs.

The refractive index and extinction coefficient directly impact light management and material optimization in organic electronics. Computational ellipsometry, leveraging techniques like density functional theory (DFT) and molecular dynamics (MD), provides a robust framework for predicting these properties. By integrating electronic structure calculations with realistic film morphologies, it enables accurate predictions and supports the design of high-performance organic electronic devices. In this tutorial, the refractive index and extinction coefficient for two carbazole-based compounds, including CBP (4,4′-Bis(9H-carbazol-9-yl)biphenyl) and oCBP (9,9'-Biphenyl-2,2'-diylbis-9H-carbazole), will be calculated using the Optoelectronic Film Properties panel and analyzed using the Optoelectronic Film Properties Viewer.

This tutorial does not cover building the CBP systems. See the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial for practice building an optoelectronic film morphology system. If interested in calculating other properties from the Optoelectronic Film Properties panel, see the Calculating Transition Dipole Moments (TDM), TDM Distributions, and Order Parameter tutorial and the Singlet Excitation Energy Transfer tutorial.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro and are added to the Entry List and Project Table. The Entry List is located to the left of the Workspace. The Project Table can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated input files are included for running jobs. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/ellipsometry.zip
  4. After downloading the zip file, unzip the contents in your Working Directory for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to ellipsometry_tutorial, click Save
    • The project is now named ellipsometry_tutorial.prj

Figure 2-3. The input structure entry.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose inputs.maegz and click Open

The imported file contains 3 entries. CBP_amorphous_film is an amorphous system composed of 1000 molecules of CBP. CBP_deposited_film is a system of 200 CBP molecules deposited on a graphene sheet. oCBP_crystal_structure is the oCBP experimental crystal structure.

3. Calculating and Analyzing the Ellipsometry of an Amorphous Film

We will calculate the refractive index and extinction coefficient for an MD equilibrated system containing 1000 CBP molecules using the Optoelectronic Film Properties panel and visualize the results with the Optoelectronic Film Properties Viewer panel.

Figure 3-1. Opening the Optoelectronic Film Properties panel.

  1. In the entry list, includethe entry is represented in the Workspace, the circle in the In column is blue and selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries the CBP_amorphous_film entry
  2. Go to Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties

This panel allows you to determine various optoelectronic film properties.

Refractive index tab: Specify the parameters for the refractive index calculation.

Polarizability options: Calculate the polarizability tensor for a single representative molecule of each type or for all molecules of all types in the system.

Starting frequency: Specify the starting frequency in eV for frequency-dependent polarizability calculations.

Step size: Specify the step size in frequency in eV for frequency-dependent polarizability calculations.

Number of frequencies: Specify the number of frequencies to calculate. This value along with the Starting frequency and Step size defines the end point of the range of frequencies used in the polarizability calculations.

Mass density: Specify the mass density of the material in g/cm3.

Refractive index axes: Specify the vectors (i, j, and k) along which the refractive index is calculated.

Extinction coefficient tab: Specify the parameters for the extinction coefficient calculation.

Extinction coefficient options: Calculate required transition dipole moments to plot extinction coefficient using either a single representative molecule of each type or for all molecules of all types in the system.

Extinction coefficient axes: Specify the vectors (i, j, and k) along which the extinction coefficient is calculated.

Frequency bin width: Specify a value in eV to bin the excited state energies of molecules to plot absorption spectrum.

For detailed information about the various parameters in the panel, see the help documentation.

Figure 3-2. Setting up the Optoelectronic Film Properties panel.

  1. Ensure that Use structures from shows Workspace (included entry)
  2. Uncheck the Transition dipole moment order parameter option
  3. Check the Refractive index and Extinction coefficient option
  4. Set the Mass density to 1.1 g/cm3
    • The mass density of small molecules based materials used in organic electronics, such as OLEDs, typically is ~1.1–1.4 g/cm³
  5. Click the Extinction Coefficient tab

Figure 3-3. Running the calculation.

All Extinction Coefficient default settings will be kept for the calculation.

 

  1. Change the Job name to CBP_amorphous_film
  2. Adjust the job settings () as needed
    • This job requires a CPU host and can be completed in about 2 hours on 1 processor
  3. If running the job, proceed to click Run. If you would prefer to proceed with imported files, please proceed to the next steps.
  4. Close the Optoelectronic Film Properties panel

Figure 3-4. The calculation output.

Let’s import the results:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose Section_03 > CBP_amorphous_film > CBP_amorphous_film-out.maegz
  3. Selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output in the entry list and workspace, respectively.
    • Note that the structure will resemble the input structure, but now also contains the data from the Optoelectronic Film Properties calculation
  4. Use the WAM (workflow action menu) button () to open the Optoelectronic Film Properties Viewer
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties Viewer

Figure 3-5. Viewing the Optoelectronic Film Properties result, Refractive index.

  1. Ensure that the Refractive Index tab is selected
  2. Click the Extinction Coefficient tab

 

Figure 3-6. Viewing the Optoelectronic Film Properties result, Extinction coefficient.

  1. Click the Oscillator strength spectrum tab

 

4. Calculating and Analyzing the Ellipsometry of a Deposited Film

We will calculate the refractive index and extinction coefficient for an MD equilibrated system containing 200 CBP molecules deposited on a graphene sheet using the Optoelectronic Film Properties panel and visualize the results with the Optoelectronic Film Properties Viewer panel.

Figure 4-1. Highlighting the graphene sheet.

Before we can calculate the refractive index and extinction coefficient on the CBP molecules deposited on a graphene sheet, we need to remove the graphene sheet from the system.

  1. In the entry list, includethe entry is represented in the Workspace, the circle in the In column is blue and selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries the CBP_deposited_film entry
  2. Double click on the graphene sheet to highlight all carbon atoms

Figure 4-2. Deleting the graphene sheet in the CBP deposited film structure.

  1. Click delete on the keyboard to remove the graphene sheet

Figure 4-3. Opening the Optoelectronic Film Properties panel.

  1. Go to Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties

Figure 4-4. Setting up the Optoelectronic Film Properties panel.

  1. Ensure that Use structures from shows Workspace (included entry)
  2. If the previous settings have reset, uncheck the Transition dipole moment order parameter option
  3. Check the Refractive index and Extinction coefficient option
  4. Set the Mass density to 1.1 g/cm3
  5. Click the Extinction Coefficient tab

Figure 4-5. Running the calculation.

All default settings will be kept for the calculation

  1. Change the Job name to CBP_deposited_film
  2. Adjust the job settings () as needed
    • This job requires a CPU host and can be completed in about 2 hours on 1 processor
  3. If running the job, proceed to click Run. If you would prefer to proceed with imported files, please proceed to the next steps.
  4. Close the Optoelectronic Film Properties panel

Figure 4-6. The calculation output.

Let’s import the results:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose Section_04 > CBP_deposited_film > CBP_deposited_film-out.maegz
  3. Selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output in the entry list and workspace, respectively.
    • Note that the structure will resemble the input structure, but now also contains the data from the Optoelectronic Film Properties calculation
  4. Use the WAM (workflow action menu) button () to open the Optoelectronic Film Properties Viewer
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties Viewer

Figure 4-7. Viewing the Optoelectronic Film Properties result, Refractive index.

  1. Ensure that the Refractive Index tab is selected
  2. Click the Extinction Coefficient tab

 

Figure 4-8. Viewing the Optoelectronic Film Properties result, Extinction coefficient.

  1. Click the Oscillator strength spectrum tab

 

5. Calculating and Analyzing the Ellipsometry of Crystal Structure

We will calculate the refractive index and extinction coefficient for an oCBP crystal structure using the Optoelectronic Film Properties panel and visualize the results with the Optoelectronic Film Properties Viewer panel.

Figure 5-1. Opening the Optoelectronic Film Properties panel.

  1. In the entry list, includethe entry is represented in the Workspace, the circle in the In column is blue and selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries the oCBP_amorphous_film entry
  2. Go to Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties

Figure 5-2. Setting up the Optoelectronic Film Properties panel.

  1. Ensure that Use structures from shows Workspace (included entry)
  2. If the previous settings have reset, uncheck the Transition dipole moment order parameter option
  3. Check the Refractive index and Extinction coefficient option
  4. Set the Mass density to 1.1 g/cm3
  5. Set the Refractive index axes to xyz
  6. Click the Extinction Coefficient tab

Figure 5-3. Running the calculation.

  1. Set the Extinction coefficient axes to xyz
  2. Change the Job name to oCBP_crystal_structure
  3. Adjust the job settings () as needed
    • This job requires a CPU host and can be completed in about 30 minutes on 1 processor
  4. If running the job, proceed to click Run. If you would prefer to proceed with imported files, please proceed to the next steps.
  5. Close the Optoelectronic Film Properties panel

Figure 5-4. The calculation output.

Let’s import the results:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose Section_05 > oCBP_crystal_structure > oCBP_crystal_structure-out.maegz
  3. Selectthe entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output in the entry list and workspace, respectively.
    • Note that the structure will resemble the input structure, but now also contains the data from the Optoelectronic Film Properties calculation
  4. Use the WAM (workflow action menu) button () to open the Optoelectronic Film Properties Viewer
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > Optoelectronic Film Properties > Optoelectronic Film Properties Viewer

Figure 5-5. Viewing the Optoelectronic Film Properties result, Refractive index.

  1. Ensure that the Refractive Index tab is selected
  2. Click the Extinction Coefficient tab

 

Figure 5-6. Viewing the Optoelectronic Film Properties result, Extinction coefficient.

  1. Click the Oscillator strength spectrum tab  

6. Conclusion and References

This tutorial demonstrated how to compute the refractive index and extinction coefficient for optoelectronic materials using MS Maestro.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com. 

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

If you are interested in running Jaguar calculations from the command line, please visit the documentation for example files and guidance.

For some related practice, proceed to explore other relevant tutorials:

For further reading:

7. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Included - the entry is represented in the Workspace, the circle in the In column is blue

Incorporated - once a job is finished, output files from the working directory are added to the project and shown in the Entry List and Project Table

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Selected - the entry is chosen in the Entry List (and Project Table), the row is highlighted; project operations are performed on all selected entries

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed