Ionic Conductivity

Tutorial Created with Software Release: 2025-4
Topics: Energy Capture & Storage
Methodology: All-Atom Molecular Dynamics
Products Used: Desmond, MS Maestro

Tutorial files

505 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 to calculate the ionic conductivity for a 1M LiPF6 system.

 

Tutorial Content

  1. Introduction to Ionic Conductivity

  1. Creating Projects and Importing Structures

  1. Running a Molecular Dynamics Simulation

  1. Performing Ionic Conductivity Calculations

  1. Analyzing Ionic Conductivity Calculations

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Ionic Conductivity

Atomistic modeling has emerged as a crucial tool in the development of new battery technologies over the last few decades, complementing experimental characterization. The broad adoption of computational methods depends on their ability to accurately predict key properties essential for material design. One such experimental property is ionic conductivity, which is modeled to predict, understand, and optimize ion movement within materials.

This tutorial outlines a process for calculating ionic conductivity using molecular dynamics (MD) on a liquid electrolyte system composed of lithium cations, an ethylene carbonate (EC) electrolyte, and PF6 anions. The initial step involves utilizing the MD Multistage Workflow panel to equilibrate the electrolyte system. Following this, the Ionic Conductivity and Ionic Conductivity Results panels will be used to calculate and analyze the ionic conductivity through three distinct methods.

The workflow is summarized in the following schematic:

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: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/ionic_conductivity.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 ionic_conductivity_tutorial, click Save
    • The project is now named ionic_conductivity_tutorial.prj

Figure 2-3. The entry list after importing.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose disordered_system_Li_PF6_EC_system-out.cms and click Open
    • A new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The system contains three components: lithium cations, PF6 anions, and amorphous ethylene carbonate (EC).

If you would prefer to practice preparing the system yourself, see Section 3 in the Liquid Electrolyte Properties: Part 2 tutorial. Before building the system, custom electrostatic potential (ESP) charges were assigned to the ionic components of the system. Then, the Disordered System Builder panel was used to construct a 1M LiPF6 system.

3. Running a Molecular Dynamics Simulation

This section details using the MD Multistage Workflow panel to conduct a molecular dynamics simulation. The simulation aims to relax the system before proceeding with ionic conductivity calculations.

Figure 3-1. Output of the Disordered System Build.

  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

Figure 3-2. Setting up the MD Multistage Workflow.

  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 Trajectory 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 (9)
  4. Change the Temperature to 298 K
  5. Click Append Stage
  6. For Stage (9), change to Average Cell
  7. Click Append Stage
  8. For Stage (10), change to Molecular Dynamics
  9. Change the Simulation time to 5 ns and the Trajectory Recording interval to 5 ps
  10. Change the Ensemble class to NVT
  11. Change the Temperature to 298 K
  12. Change the Job name to MD_Li_PF6_EC
  13. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 90 minutes on a GPU host
  14. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated MD_Li_PF6_EC-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
  15. Close the MD Multistage Workflow panel

 

Note: MLFF methods can be used to prepare the MD system as well. Learn more in the Machine Learning Force Field tutorial.

Figure 3-3. Output of the MD simulation.

  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_Li_PF6_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

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

4. Performing Ionic Conductivity Calculations

This section details the calculation of Ionic Conductivity using three distinct methods: MS1, MS2, and MS3, which are based on Maxwell-Stefan diffusion. The trajectory derived from the MS1 calculation is subsequently used for the MS2 and MS3 ionic conductivity calculations.

Figure 4-1. Opening the Ionic Conductivity panel.

  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 equilibrated MD structure disordered_system_Li_PF6_EC_all_components_amorphous entry, and navigate to Tasks > Materials > Classical Mechanics > Ionic Conductivity >  Ionic Conductivity Calculations
  2. Click on the Simulation Protocols tab
    • Leave all default settings in the Method tab for this calculation

Before we prepare this job submission, let’s learn a bit more about the general capabilities of the Ionic Conductivity panel.

 

Ionic conductivity can be determined using three methods: MS1, MS2, and MS3. All three methods are based on Maxwell-Stefan diffusion but differ in how they calculate the Onsager coefficients, leading to varying ionic conductivity values. For further details, refer to the works of Krishna et al. (MS1), Wheeler et al. (MS2), and Mistry et al. (MS3).

 

With respect to the trajectory to analyze, you can either use the panel to set up a MD simulation, or you can use the panel on a previously simulated trajectory by choosing Use existing.

 

You must set an initial Fitting range, but note that this range can be changed in the analysis stage with the viewer panel.

 

On the Simulation Protocols tab, set up the MD if you are running a new simulation at this stage.

 

Visit the help documentation to read more about using the panel.

Figure 4-2. Setting the Ionic Conductivity parameters.

  1. Change the Ensemble class to NVT
  2. Change the Initial temperature to 298 K
  3. Change the Simulation time to 10 ns
  4. Change the Trajectory recording interval to 5 ps
  5. Click Save trajectory
  6. Change the Job name to ionic_conductivity_MS1
  7. Adjust the job settings () as needed
    • This job runs on a CPU host and GPU subhost. The job can be completed in about 40 minutes
  8. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated ionic_conductivity_MS1_out.cms file from the provided tutorial files via File > Import Structures
  9. Close the Ionic Conductivity panel

 

Figure 4-3. The ionic conductivity MS1 output structure.

This output structure (and trajectory) can now be used as the input for calculating the ionic conductivity with the MS2 and MS3 methods.

  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 output structure from the ionic conductivity calculation titled disordered_system_Li_PF6_EC_all_components_amorphous entry
  2. Return to Tasks > Materials > Classical Mechanics > Ionic Conductivity >  Ionic Conductivity Calculations

Figure 4-4. Setting up an MS2 and MS3 ionic conductivity calculation.

In the previous ionic conductivity simulation, an MD simulation trajectory was generated prior to calculating the ionic conductivity. The same trajectory will be used in the MS2 and MS3 ionic conductivity calculations.

  1. Change the Trajectory to Use existing
  2. Change the Method to MS2 and MS3
  3. Change the Initial temperature to 298 K
  4. Change the Job name to ionic_conductivity_MS2_MS3
  5. Adjust the job settings () as needed
    • This job runs on a CPU host and GPU subhost. The job can be completed in about 3 hours
  6. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated ionic_conductivity_MS2_MS3_out.cms file from the provided tutorial files via File > Import Structures

 

Note: This particular job setup demonstrates how to calculate the ionic conductivity using an  existing trajectory. However, ionic conductivity can be calculated for all three methods through a single calculation.

Figure 4-6. The completed ionic conductivity calculations.

All output systems are now in the project workspace. Feel free to visualize, stylize, or rename the entries.

5. Analyzing Ionic Conductivity Calculations

In this section, we will use the Ionic Conductivity Results panel to analyze the ionic conductivity simulation from the three methods.

Figure 5-1. Selecting and including the MS1 output system.

  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 equilibrated structure output from the MS1 Ionic conductivity simulation and  disordered_system_Li_PF6_EC_all_components_amorphous
  2. Use the WAM () button in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to access the Ionic Conductivity Results panel
    • Alternatively, go to Tasks > Materials > Classical Mechanics > Ionic Conductivity >  Ionic Conductivity Results
    • The Ionic Conductivity Results panel opens

The Ionic Conductivity tab displays values for the ionic conductivity, ambipolar diffusivity, and the cation transference number.

You can manually adjust the bounds of the linear fit using the interactive sliders in the plot. The ionic conductivity value based on these modified bounds is computed in real-time below. In general, you should fit into the linear region of the curve. There is no consensus method for choosing the bounds of the fit, therefore it’s important to report these bounds for the sake of reproducibility.

The Diffusion Parameters tab displays values of diffusion coefficients and includes a plot of the mean square distance (MSD) against simulation time difference (Tau).

The Diffusion Trace tab shows the trace for a specified Mass center (by default 1, the first lithium ion) is shown in three 2D plots. These plots trace the movement of a single species over the course of the trajectory. They are a visual tool that can help identify anisotropic diffusive behavior as well as deviations from Brownian motion. The 2D plots show projections of the coordinates in each of the three planes: XY, XZ and YZ. For more information on analyzing diffusion calculations see the Diffusion tutorial.

Figure 5-2. Ionic conductivity results from the MS1 method.

  1. The calculated ionic conductivity is 4.6994 mS/cm for the MS1 method
    • At 298K, the experimental ionic conductivity for a 1M LiPF6 system is 6.9 mS/cm (see References)
  2. Close the Ionic Conductivity panel

 

Note: This example used only one replicate, but for optimal results, we recommend running additional replicates.

Figure 5-3. Ionic conductivity results from the MS2 method.

Let’s view the results for the other two ionic conductivity methods.

  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 output from the MS2 and MS3 calculation disordered_system_Li_PF6_EC_all_components_amorphous
  2. Use the WAM () button in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to access the Ionic Conductivity Results panel
  3. The calculated ionic conductivity is 4.6994 mS/cm for the MS2 method
    • An identical value as the MS1 method

Figure 5-4. Ionic conductivity results from the MS3 method.

  1. Click on a row using the MS3 method
  2. The calculated ionic conductivity is 5.0502 mS/cm for the MS3 method
    • A similar values compared to the MS1 and MS2 method
  3. Close the Ionic Conductivity panel

This study evaluated and compared the MS1, MS2, and MS3 methods. Additional calculations could explore temperature dependencies, as experimental data from Borodin et al. indicates that ionic conductivity increases with temperature.

 

6. Conclusion and References

In this tutorial, the ionic conductivity was calculated for a 1M LiPF6 system in an EC electrolyte using three different methods.

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 100+ 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:
  • See the help documentation
  • The Darken Relation for Multicomponent Diffusion in Liquid Mixtures of Linear Alkanes:  An Investigation Using Molecular Dynamics (MD) Simulations. DOI: 10.1021/ie050146c
  • Molecular Dynamics Simulations of Multicomponent Diffusion. 1. Equilibrium MethodClick to copy article link. DOI: 10.1021/jp047850b
  • On Relative Importance of Vehicular and Structural Motions in Defining Electrolyte Transport. DOI: 10.1149/1945-7111/ad0c66
  • Quantum Chemistry and Molecular Dynamics Simulation Study of Dimethyl Carbonate: Ethylene Carbonate Electrolytes Doped with LiPF6. DOI: 10.1021/jp809614h

 

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

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