Liquid Electrolyte Properties: Part 1

Tutorial Created with Software Release: 2026-1
Topics: Energy Capture & Storage, Polymeric Materials
Methodology: All-Atom Molecular Dynamics
Products Used: Desmond, MS Dielectric, Jaguar, MS Maestro, MS Transport

Tutorial files

1.6 GB
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 to perform a variety of calculations on a liquid electrolyte system using Materials Science (MS) Maestro. These properties include: density, radial distribution function, viscosity, and dielectric properties such as polarizability, refractive index, and dielectric constant.

 

Tutorial Content

  1. Introduction to Liquid Electrolyte Properties

  1. Creating Projects and Importing Structures

  1. Building, Running and Analyzing a Molecular Dynamics Simulation

  1. Analyzing the Radial Distribution Function

  1. Calculating Viscosity

  1. Calculating Dielectric Properties

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Liquid Electrolyte Properties

The design and manufacturing of safer, less expensive, and more effective energy storage devices is a critical challenge in a wide variety of industries including the automotive, aviation, and energy sectors with societal and environmental implications. Atomic-scale materials modeling has become an essential tool for the development of novel battery components -- cathodes, anodes, and electrolytes -- that support higher power density, capacity, rate capability, faster charging, and improved degradation resilience.

In this tutorial, we will use several panels in the Materials Science (MS) Maestro interface to perform a variety of practical calculations for studying liquid electrolyte properties, which are essential in understanding and optimizing battery systems.

We will begin by using the Disordered System Builder panel and the MD Multistage Workflow panel to construct and equilibrate a model system. Then, using the equilibrated output, we will plot density, calculate the Radial Distribution Function, and predict the Viscosity. Finally, we will employ the Amorphous Dielectric Properties panel to predict key dielectric properties such as polarizability, refractive index, and dielectric constant.

The workflow is summarized in the following schematic:

Specifically, we will perform MD simulations on a system of pure ethylene carbonate (EC), a prototypical liquid electrolyte, at three different temperatures and explore several key properties. For additional practice running MD simulations, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial. For other relevant examples, visit the Viscosity and the Dielectric Properties tutorials.

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 Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new 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 or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data 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 files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/electrolyte_properties_1.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved 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 liquid_electrolye_tutorial_1, click Save
    • The project is now named liquid_electrolyte_tutorial_1.prj

3. Building, Running and Analyzing a Molecular Dynamics Simulation

In this section, we will build a single component box with the Disordered System Builder panel containing 750 molecules of ethylene carbonate (EC). We will then use the MD Multistage Workflow panel to perform a molecular dynamics simulation and subsequent analysis on the system. This workflow can be utilized for preparing a disordered box containing any organic molecule.

Figure 3-1. 2D Sketcher panel with EC drawn.

Let’s begin with sketching the ethylene carbonate (EC) molecule:

  1. Open the 2D Sketcher panel via Edit > 2D Sketcher
  2. Draw the 2D structure of EC as shown in the Figure

Now save the molecule to the MS Maestro project

  1. Click Save as New
  2. Type EC in the Entry Title dialog that appears
  3. Close the 2D Sketcher panel

Figure 3-2. View of the 3D structure of EC with the corresponding entry in the Entry List.

The 3D structure of EC is generated in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the corresponding entry is available in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion on the left. Stylize as you wish, here we show the ball-and-stick representation.

Figure 3-3. The Components tab.

  1. Go to Tasks > Materials > Structure Builders > Disordered System

In this case, we wish to construct a system of 750 EC molecules:

  1. For Initial state, choose Tangled chain
    • Visit the documentation for the differences between the choices. Typically, the tangled chain option allows for the quickest build.
  2. For Number of molecules, input 750
    • Typically, a system size of 10,000 atoms or more is used for MD. Systems of size 20,000-50,000 atoms are typical for ‘production’ runs. Larger systems are possible, but will take substantially longer to run. In this example, 750 molecules of EC will be a 7,500 atom system which is relatively small, but sufficient for such a simple example
  3. Skip the Cells tab and the Disorder tab

 

Note: The Cells tab is for specifying the type and number of boxes to create. It also includes the setting to ensure that the output is ‘prepared’ for MD. The Disorder tab is for specifying packing parameters like density etc. Note that the build is just a starting cell, it is going to be subsequently equilibrated with MD.

  1. Change the Job name to disordered_system_EC
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in just a couple of minutes on a CPU host
  3. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_03 > disordered_system_EC > disordered_system_EC_system-out.cms file from the provided tutorial files via File > Import Structures
  4. Close the Disordered System Builder

Note: In general, always close the Disordered System Builder after use. This panel is interactive with the workspace and leaving it open can cause slowdowns.

Figure 3-4. Output of the Disordered System Build.

  1. When the job is finished or after importing, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 disordered_system_EC_all_components_amorphous from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Feel free to style the system for easier visualization. Here we have colored the atoms by element using the style menu.

MD simulations in MS Maestro are performed with the MD Multistage Workflow panel.

  1. Use the WAM (workflow action menu) button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens

Here we will use a relatively standard simulation protocol to equilibrate the system. For this example we choose the Compressive relaxation protocol, which is a seven step workflow that is effective for compressing systems that are built to low density. This relaxation protocol includes a high pressure stage intended to densify the system. Subsequently, we will perform molecular dynamics in two different thermodynamic ensembles and for varying simulation time. Note that protocols for MD simulations always depend on the system at hand as well as computational resources available.

The Compressive relaxation protocol is carried out at 300 K which is close enough to the temperature used in the following MD steps (313 K, the experimentally relevant temperature). Note that if the experimentally relevant temperature is vastly different, then a simulating annealing step could be performed before proceeding to the first MD stage to more gradually introduce dynamics.

Our MD protocol uses two different ensembles:

  • Equilibration in the NPT ensemble to ensure that equilibrium density is obtained
  • Equilibration in the NVT ensemble, using the average equilibrated box vectors from the NPT simulation to equilibrate the temperature for a structure at average density

Figure 3-5. Setting up the MD Multistage Workflow (Stages 1-10).

  1. Check Relaxation protocol and choose Compressive from the dropdown list
  2. For Stage (8), change to Molecular Dynamics
  3. Change the Simulation time to 10 ns and the Recording interval to 200 ps
    • This recording interval was chosen to give a sufficient number of samples to the Average Cell stage that follows in Stage (10)
  4. Change the Temperature to 313 K
  5. Click Append Stage
  6. For Stage (9), change to Analysis
  7. Click Append Stage
  8. For Stage (10), change to Average Cell
  9. Click Append Stage

Figure 3-6. Setting up the MD Multistage Workflow (Stages 11-12).

  1. For Stage (11), change to Molecular Dynamics
  2. Change the Simulation time to 10 ns and the Ensemble class to NVT
  3. Change the Temperature to 313 K
  4. Click Append Stage
  5. For Stage (12), change to Molecular Dynamics
  6. Change the Simulation time to 50 ns and the Ensemble class to NVT
  7. Change the Temperature to 313 K
  8. Change the Job name to multistage_simulation_EC_313
  9. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 5 hours on a GPU host
  10. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_EC_313-out.cms file from the provided tutorial files via File > Import Structures
    • MD simulations have a number of files associated with the job, for a full description of each file type see the help documentation on Desmond Files
  11. Close the MD Multistage Workflow panel

Figure 3-7. Output of the MD simulation at 313 K - the entry name has been renamed to include _313.

  1. When the job is finished or after importing, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 new disordered_system_EC_all_components_amorphous entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • You may wish to add 313 to the entry title to remember that this was the MD simulation performed at 313 K as shown in the Figure
    • This structure will now be referred to as disordered_system_EC_all_components_amorphous_313 in this tutorial 

Feel free to visualize the trajectory and stylize as you wish. Shown in the Figure is the Maestro Default preset with the molecules in ball-and-stick styling.

In this type of electrolyte study, one might be interested in analyzing properties at a variety of relevant battery temperatures. In particular, later in the tutorial we will predict viscosity for analogous systems at 333 K and 353 K. While we have the MD workflow panel parameterized, let’s perform an MD simulation at 333 K and 353 K now so that these structures are ready. Repeat the above steps using the original disordered system build (disordered_system_EC_all_components_amorphous), but now at 333 K and 353 K. Or, simply, navigate to where you downloaded the tutorial files and import the provided files for equilibrated systems multistage_simulation_EC_333-out.cms and multistage_simulation_EC_353-out.cms

Figure 3-8. Opening the MS MD Trajectory Analysis panel.

 

Next, let’s analyze bulk properties of the MD simulation performed at 313 K. Such analysis can provide useful quantities and confirm that the system was well-equilibrated by the protocol. 

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 disordered_system_EC_all_components_amorphous_313 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Use the WAM (workflow action menu) button () to open the MD Trajectory Analysis panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
    • The MS MD Trajectory Analysis panel opens

Figure 3-9. Loading data into the MS MD Trajectory Analysis panel.

Let’s view the bulk properties of the system over the course of the trajectory:

 

  1. If the ethylene carbonate structure is not pre-loaded in the panel, click Load from Workspace
    • The Simulation Detail tab fills with information about the MD job and system
  2. Go to the Bulk Properties tab

Figure 3-10. Viewing bulk properties.

The dropdowns can be used to view the various properties as a function of time from the MD stage

 

  1. Change the first property to Density from the dropdown
    • The calculated density of 1.290 g/cm3 matches the experimental density within ~2%
    • Use the dropdowns to view other various properties as a function of time from the MD stage, such as Heat of vaporization and the Solubility parameter
  2. When finished, close the MS MD Trajectory Analysis panel

In practice, depending on your research goals, you may now wish to revisit your parameters for the MD Multistage Workflow. For example, you may wish to run a more ‘production’ level MD simulation with a longer simulation time or larger box. You may also proceed to use this equilibrated cell as a starting point for subsequent workflows. Feel free to refer to the help documentation when performing a new workflow.

4. Analyzing the Radial Distribution Function

In this section, we will calculate the Radial Distribution Function for the EC system. The radial distribution function (RDF) gives the probability of finding a particle at a distance r from another particle. It is also known as the pair distribution function. The function is calculated from a trajectory as a histogram, in which bins are created for each distance range, and the count of interparticle distances that lie in the range for each bin are accumulated from each frame of the trajectory. The results are then normalized to give a probability.

Figure 4-1. Opening the Radial Distribution Function and loading a file.

Now let’s load in our system of interest and calculate its RDF:

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue and Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the equilibrated MD structure disorded_system_EC_all_components_amorphous_313 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Radial Distribution Function
  3. Make sure that the Trajectory source has Workspace (included entry) selected from the dropdown.
  4. Click Load

Figure 4-2. Defining the selections.

 

  1. In the Atom Selection section of the panel, for Set 1, choose Group By Molecules and Calculate using Center of Mass
  2. Input res.pt  "M0" in the Atom selection query
    • M0 - 750 represent the 750 EC molecules

Note: The Selection inputs are ASL representations for the EC molecules. There are other ways to represent these molecules. One straightforward way to generate ASL representations is from Select > Define from the main menu. There is only 1 type of molecule in the system so all EC molecules are included in the selection.

Figure 4-3. Running the calculation.

 

  1. In Options, Change the Max distance for RDF (max r) to 20.00 Å
    • The Max r (Å) should be about half the length of the system. The size of each dimension in our cubic system is ~44 Å.
  2. Change the Job name to rdf_EC
  3. Adjust Job settings () as needed, and click Run
    • The job takes ~5 minutes on a CPU host

 

Do not close the Radial Distribution Function panel. We will use the same panel for viewing the results.

Figure 4-4. Viewing the radial distribution function output.

When the job is finished, the panel will automatically switch to the View Results tab.

If it does not do so, go to the View Results tab, click Import Results File and load the rdf_EC.dat file

 

The radial distribution function indicates that the center of mass of most of the EC molecules are within 7.5 Å of one another.

Figure 4-5. Viewing the radial distribution function integral output.

10. Check Show integral

  • You can use the integral to infer average coordination numbers
  • The average coordination number is defined by the value of the integral up to the first minima in the RDF plot, which for the box of EC molecules is up to ~7.5 Å

 

 

Note that we will compare this RDF plot of pure EC to a system with salt added in the Liquid Electrolyte Properties: Part 2 tutorial

5. Calculating Viscosity

In this section, we will run Viscosity calculations on the three equilibrated systems at three different temperatures, 313 K, 333 K, and 353 K. We will then compare the results with experimentally known values.

Figure 5-1. Output of the MD simulation at 313 K.

  1. When all three MD jobs from Section 3 are finished or after importing, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 disordered_system_EC_all_components_amorphous_313 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • An equilibrated structure from a previous MD simulation is the required input for performing Viscosity calculations

Figure 5-2. Opening the Viscosity panel.

  1. Go to Tasks > Materials > Classical Mechanics > Viscosity > Viscosity Calculations

 

Figure 5-3. Parameterizing the Viscosity panel.

  1. Change the Simulation time to 10 ns
    • For this example, a 10 ns simulation time is sufficient but longer simulation times will decrease the standard error
  2. Change the Temperature to be 313 K
    • The viscosity calculation needs to be performed at the same temperature as the MD simulation
  3. Change the Trajectory recording interval to 1000 ps
    • 10 frames will be generated
  4. Open the Advanced MD Options window

Figure 5-4. Editing the MD options in the Viscosity panel.

  1. Check Set random number seed
  2. Change the Energy group recording interval to 0.006 ps. Make sure to press Enter on your keyboard after updating the input to ensure that the panel updates to read yields 166666 records
  3. Click OK to close the Advanced MD Options

Figure 5-5. Parameterizing the Fitting option in the Viscosity panel.

  1. Go to the Fitting option tab
  2. Open the Advanced Options window

Figure 5-6. Viscosity - Advanced Options panel.

  1. Check Calculate viscosity via Einstein-Helfand method
    • In the Einstein-Helfand method, the viscosity is determined from the ensemble average of the mean square displacement (MSD) of the time integral of the pressure tensors at long tau values
    • Calculating the viscosity two different ways provides extra validation for the computed values
  2. Click OK to close the Viscosity - Advanced Options window

Figure 5-7. Naming and running the Viscosity job.

  1. Change the Job name to viscosity_gk_EC_313

 

This job takes about 3 hours on 1 CPU (for the driver) and 1 GPU Host (for the MD simulations), highly depending on your GPU resources. If you would like to run the job yourself, adjust your Job settings as needed and click Run

If you would prefer to proceed with pre-generated results, you can import the viscosity jobs via File > Import Structures. Navigate to where you downloaded the tutorial files and choose the  viscosity_gk_EC_313-out.cms file

 

  1. Close the Viscosity panel

 

Repeat the above steps in this section with the MD equilibrated structures at 333 K and 353 K. Ensure that the viscosity calculations are set up at the same temperature used in the MD simulations. Or navigate to where you downloaded the tutorial files and import the  viscosity_gk_EC_333-out.cms and viscosity_gk_EC_353-out.cms files

For a complete description of the Viscosity panel and some best practices, refer to the help documentation or the Viscosity tutorial.

Figure 5-8. Opening the Viscosity Viewer panel.

You may wish to change the name of the viscosity output structures in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. These structures were renamed to disordered_system_EC_all_components_amorphous_viscosity_n, where n is the temperature at which the calculation was performed (313, 333, or 353 K), as shown in the Figure.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 disordered_system_EC_all_components_amorphous_viscosity_313 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Use the WAM button () to open the Viscosity Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Viscosity > Viscosity Results
    • The Viscosity Viewer panel opens

Figure 5-9. Include and load the viscosity output.

  1. If the results do not automatically load click Load data from Workspace
    • The Viscosity Viewer Panel updates to show the output
    • The Shear Viscosity (cP) and Standard deviation of fit (cP) are shown below the results figure
    • Two fitting modes are available for the Green-Kubo Method, which can be selected by toggling between Exponential and Average

 

Note: By dragging the blue dashed vertical lines, the fitting region can be manually adjusted

Figure 5-10. The Einstein-Helfand method plotted.

  1. Toggle the Method options to select the Einstein-Helfand method
  2. Adjust the blue dashed vertical line so the Data and Fitting curves between the blue dashed vertical lines are in good agreement
  3. Take note of the Shear viscosity value

 

Feel free to repeat these steps with the disordered_system_EC_all_components_amorphous_viscosity_333 and disordered_system_EC_all_components_amorphous_viscosity_353 entries to predict the viscosity at the additional temperatures. Take note of the Shear viscosity values for the three different temperatures. Expectedly, as the temperature increases the shear viscosity value will decrease.

The data for all three temperatures (shear viscosity) are comparable to the experimentally known values (Industrial Solvents Handbook. 5th edition) with good agreement:

Chart

6. Calculating Dielectric Properties

In this section, we will calculate and analyze various dielectric properties of EC using an automated workflow driven by the Amorphous Dielectric Properties panel.

Figure 6-1. Ethylene carbonate.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 original EC entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

 

Note: Unlike the Viscosity workflow, the Dielectric Properties workflow requires only a single molecule as input.

 

Figure 6-2. Opening the dielectric panel.

  1. Go to Tasks > Materials > Classical Mechanics > Amorphous Dielectric Properties > Amorphous Dielectric Properties Calculations

Figure 6-3. Setting the parameters for the Amorphous Dielectric Properties calculation.

  1. For Use structures from, maintain Project Table (1 selected entry)
  2. Maintain all of the Property selections: Refractive index, Abbe number, Static dielectric constant and Complex permittivity
  3. In the Polarizability section, maintain the settings and check Over a range of wavelength between
    • This will initiate a frequency dependent polarizability calculation
  4. Change in steps of to 100 nm
    • For example purposes, we will only look at the 4 wavelengths designated by this range plus, by default when we select Abbe number, 486.1, 589.3 and 656.3 nm frequency dependent polarizability will be calculated 
  5. For Number of molecules, input 750
  6. For Number of replicates, input 10
  7. Input 10 ns for Permittivity production time
    • In practice, longer simulation times provide better accuracy for dipole autocorrelation functions. Here, we will use a shorter time for ease of demonstration. However, the results for small organic molecules like this will still be high-quality
  8. For Equilibration temperature, input 313
  9. Input 1 ps for Dipole recording interval
  10. Change the Job name to dielectric_prop_EC_313
  11. Adjust the job settings () as needed
    • This job takes 6 hours on a 12 CPU host / 1 GPU host
    • This workflow requires both CPU and GPU hosts for handling both density functional theory and MD
  12. If you would like to run the job, click Run. Otherwise, import the pre-generated dielectric_prop_EC_313-out.cms file from the provided tutorial files via File > Import Structures
  13. Close the Amorphous Dielectric Properties panel

Further information on running dielectric property calculations is available in the help documentation Amorphous Dielectric Properties and in the Dielectric Properties tutorial.

Figure 6-4. Accessing the results through the Working Action Menu (WAM) button.

  1. When the job is finished or after importing, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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 new disordered_system_builder_r7_all_components_amorphous entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to view the structure
    • This is the results entry from the amorphous dielectric properties calculation
  2. Use the WAM (workflow action menu) button () to open the Amorphous Dielectric Properties Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Amorphous Dielectric Properties > Amorphous Dielectric Properties Results
    • The Amorphous Dielectric Viewer panel opens

Figure 6-5. Property outputs from the workflow.

The panel includes a Summary tab and three viewers: Refractive Index, Complex Permittivity and Decay Function.

The top half of the Summary tab shows the system information: number of atoms, number of molecules, etc. It also shows the properties that are available for analysis.

In the bottom half of the panel, the polarizability, refractive index, Abbe number, static dielectric constant and high-frequency dielectric constant as a result of the complex permittivity workflow are shown.

Figure 6-6. Refractive Index

  1. Go to the Refractive Index tab

A plot is shown of the refractive index versus wavelength, including the data points associated with the specified wavelength range and the three wavelengths utilized to compute Abbe number (486.1, 589.31 and 656.31 nm)

Figure 6-7. Complex Permittivity function within the amorphous dielectric viewer.

  1. Go to the Complex Permittivity tab

The Epsilon(Real) vs Frequency and Epsilon(Imaginary) vs frequency spectrums are shown

The Type dropdown menu has options to display Complex Plane and Loss Tangent plots. The Dielectric loss peak position is printed.

 

For more information about the plots and terms shown in this tab, please visit the help documentation.

Figure 6-8. Dielectric decay function.

  1. Proceed to the Decay Function tab

The plot of the Dielectric Decay function vs. time (Tau in this case) is shown

The toolbar has tools for manipulating the plot and saving data or images

The lower and upper limits of tau can be changed (either by clicking and dragging on the blue dashed lines or inputting the quantities) for fitting the KWW function to obtain the complex permittivity function

  1. Close the Amorphous Dielectric Viewer

7. Conclusion and References

In this tutorial, we explored many properties of a bulk liquid electrolyte system. We used the Disordered System Builder panel and the MD Multistage Workflow panel to build and equilibrate our model system. Then using the equilibrated MD structures, we plotted Density, calculated the Radial Distribution Function, and calculated the Viscosity. Lastly, we performed a workflow to calculate the Amorphous Dielectric Properties of pure EC. To see how salt affects the properties of a liquid electrolyte system, continue to the Liquid Electrolyte Properties: Part 2 tutorial.

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.

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

 

For further reading:

8. 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

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

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry 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