Liquid Electrolyte Properties: Part 2

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

Tutorial files

1.7 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: determining the radial distribution function, performing cluster analysis, and calculating the diffusion coefficient.

 

Tutorial Content

  1. Introduction to Liquid Electrolyte Properties: Part 2

  1. Creating Projects and Importing Structures

  1. Preparing a Charged System for Molecular Dynamics Simulations

  1. Running a Molecular Dynamics Simulation for Radial Distribution Function and Cluster Analysis Determination

  1. Analyzing the Radial Distribution Function

  1. Performing Cluster Analysis

  1. Running a Molecular Dynamics Simulation for use in a Diffusion Coefficient Calculation

  1. Performing and Analyzing Diffusion Coefficient Calculations

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Liquid Electrolyte Properties: Part 2

Over the past few decades, atomistic modeling of battery materials has complemented experimental characterization techniques and become an important part of the development of new technologies. Widespread application of computational methods is contingent on their ability to quantitatively predict key properties that drive material design. In a previous tutorial, Liquid Electrolyte Properties: Part 1, a bulk ethylene carbonate (EC) system was studied. We plotted the Density, calculated the Radial Distribution Function, predicted the Viscosity, and calculated various Amorphous Dielectric Properties. We recommend reviewing that content before proceeding with this tutorial.

In this tutorial, we will explore a prototypical system of interest with respect to battery design using several panels in the Materials Science (MS) Maestro interface to perform a variety of practical calculations. Specifically, we will build a system containing lithium cations in an EC electrolyte mixed with PF6 anions and explore several key properties.

We will first use the Disordered System Builder panel to construct the system. Second, we will utilize the MD Multistage Workflow panel to execute an identical molecular dynamics (MD) protocol as performed in the Liquid Electrolyte Properties: Part 1 tutorial. Third, using the equilibrated MD structure, we will calculate the Radial Distribution Function and perform a Cluster Analysis. Next, we will return to the MD Multistage Workflow panel to execute an MD equilibration in preparation for a diffusion coefficient calculation. Then, we will use the Diffusion Coefficient calculation panel to run a production NVT simulation and collect diffusion data for the Li ions. Finally, we will employ the Diffusion Coefficient Results panel to analyze the results.

The workflow is summarized in the following schematic:

For additional practice running MD simulations, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial. To learn more about the properties studied in this tutorial, visit the Cluster Analysis and Diffusion 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: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/electrolyte_properties_2.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_2, click Save
    • The project is now named liquid_electrolyte_tutorial_2.prj

Figure 2-3. The entry list after importing.

We will construct a typical system containing three components: lithium cations, PF6 anions, and amorphous ethylene carbonate (EC). These components are provided:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose inputs_electrolyte2.mae 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 containing three entries

If you would prefer to practice preparing the components yourself, draw the ions in the 2D Sketcher and be sure to include charge. For background on using these tools, see the Introduction to Materials Science Maestro tutorial.

3. Preparing a Charged System for Molecular Dynamics Simulations

Before building the system, we will assign custom electrostatic potential (ESP) charges to the ionic components of the system. Then, we will build a multi-component box with the Disordered System Builder panel containing EC, Li ions, and PF6 ions. The constructed mixture will be a 1M LiPF6 solution. In Section 4 we will use this system to run an MD simulation with the MD Multistage Workflow panel, to determine radial distribution function (RDF) and clustering analysis. Note that in Section 7, we will perform a different MD simulation on the same system for diffusion coefficient calculations.

While we can proceed directly to construct a disordered system, it is worth noting that the current atomic charges (+1 for the lithium ion and -1 for the PF6 ion) may have a disproportionate effect on the system’s dynamics. To account for this, it is often practical to first scale the atomic charges on the ions to dampen their impact on the simulation and better match experiment.

 

To determine the quantities to assign as the partial charges, it is typical to perform a quantum mechanical calculation to calculate ESP charges for a small aperiodic system composed of one or more ion pairs in a relevant environment.

 

To learn how to perform an atomic charge calculation, visit the Computing Atomic Charges tutorial.

 

In this tutorial, we will provide the scaled atomic charges and learn how to designate them before performing any molecular dynamics simulations.

Figure 3-1. Including the lithium ion and opening the Change Atom Properties window.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the lithium ion in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Right-click on the atom and choose Additional Edits > Change Atom Properties

Figure 3-2. Setting a partial atomic charge.

  1. Choose Partial Charge from the dropdown
  2. Set the Partial charge to 0.7 and the Solvation charge to 0.7
  3. Click Apply
  4. Click Close

Figure 3-3. Confirming that the partial charge is set.

We can quickly confirm that the charge is set by viewing the labels in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

  1. From the Style palette, click the dropdown next to Apply Labels and choose Partial Charge
    • The ion is labeled with 0.700 in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

 

Note: To change the color or font size of the label right click on the label and click Change Preferences

Figure 3-4. The PF6 ion with its newly assigned partial charges labeled in the workspace.

Now we need to assign the atomic charges for PF6.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the PF6 entry in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Proceed to repeat the above steps for the 7 atoms in PF6. Note that you can select, for example, all six fluorine atoms at the same time, to set their charge simultaneously. Set the charges as follows:
    • P: 2.042
    • F: -0.457
  3. After updating the charges, view the labels in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed to confirm that your entry matches the Figure.

 

We have now scaled the ion charges to +/- 0.7.

 

These quantities are based on a quantum mechanical ESP calculation. There are many strategies for determining these charges, and exploring the effect of different charges on the subsequent simulations may be necessary in a study.

 

Note: An MD simulation is recommended to be performed on a neutral system. So, it is important to be sure that your overall system will be neutral once fully constructed.

Figure 3-5. Selecting the entries and opening the Disordered System Builder.

Now we can proceed to build our disordered 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 the entire inputs_electrolyte2 (3) entry group
    • Recall that 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 means to highlight the entries in 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 > Structure Builders > Disordered System

Figure 3-6. Setting the component table in the Disordered System Builder.

  1. Change the Initial state to Tangled chain
  2. Change the Number of molecules to 1278
  3. Change both the number of Li and PF6 molecules to 75
    • The number of EC molecules should update automatically to 1128
    • This system will contain an approximately 1 M LiPF6 salt concentration
  4. Change the Periodic Boundary Conditions (PBC) to Create new cubic PBC using the dropdown menu
  5. Check the Custom PBC dimensions box and set the box length to 50 Å
  6. Go to the Cells tab

Figure 3-7. Setting the Cells table in the Disordered System Builder.

Because we are using custom charges, we need to update the force field:

 

  1. Click Force Field
  2. Click Custom Charges
  3. Check Use custom charges
  4. For Charge property choose charge1 (Maestro)
    • These refer to the charges we just assigned
  5. For Apply to atoms click Select Atoms

Figure 3-8. Selecting the charged atoms.

  1. Select Element from the options on the left
  2. From the Element menu select Li, F, and P
    • This will indicate that the custom charges should only be used for the Li and PF6 ions
  3. Click Add to add the element selections
  4. Click OK to close the Atom Selection window
  5. Click OK to close the Custom Atom Charges Window and OK again to close the Force Field window

 

An option for a machine learning force field (MLFF) is available as an alternative. See the Disordered System Builder panel documentation to learn more.

Figure 3-9. Setting the Disorder tab and running the job.

  1. Change the Job name to disordered_system_Li_PF6_EC

 

Adjust the job settings () as needed. This job requires a CPU host. The job can be completed in about 5 minutes.

  1. If you would prefer not to run the job, import Section_03 > disordered_system_Li_PF6-EC > disordered_system_Li_PF6_EC_system-out.cms from the provided tutorial files via File > Import Structures. Otherwise, click Run
  2. Close the Disordered System Builder panel

 

Note: If the labels are still turned on and are cluttering the workspace, turn them off with the button in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Note: For general practice with the Disordered System Builder and more information about the various parameters, see the Disordered System Building and MD Multistage Workflows tutorial

4. Running a Molecular Dynamics Simulation for Radial Distribution Function and Cluster Analysis Determination

In this section, we will use the MD Multistage Workflow panel to perform a molecular dynamics simulation on the system. For direct comparison to the pure system, this MD protocol will be identical to the MD simulation performed in the Liquid Electrolytes Properties: Part 1 tutorial.

Figure 4-1. 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_Li_PF6_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

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

Here we will use the same simulation protocols from Liquid Electrolyte Properties: Part 1 to facilitate the comparison of the results. Please refer to Liquid Electrolyte Properties: Part 1 for details on the simulation protocol.

Figure 4-2. 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 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 (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 4-3. 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_Li_PF6_EC_313
  9. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 6 hours on a GPU host
  10. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_Li_PF6_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 4-4. 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.

5. Analyzing the Radial Distribution Function

In this section, we will calculate the Radial Distribution Function for the LiPF6 and 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 5-1. 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_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.
  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 5-2. 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. For Set 1 atoms, input the following ASL: (atom.ele Li)
  3. Check the box to include Set 2
  4. Choose Group By Molecules and Calculate using Center of Mass
  5. For Set 2 atoms, input the following ASL: (res.ptype "M0 ")

 

Note: The Selection inputs are ASL representations for the Li atoms and EC molecules. There are other ways to represent these. One straightforward way to generate ASL representations is from Select > Define from the main menu.

 

  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 our cubic system is ~44 Å on each side

Figure 5-3. Naming and running the job.

  1. Change the Job name to rdf_Li_EC
  2. 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 5-4. Viewing the radial distribution function output for Li-EC.

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_Li_EC.dat file

 

The radial distribution function indicates that the center of mass of most Li ions are within ~5 Å of the center of mass of the EC molecules

Figure 5-5. Viewing the radial distribution function integral output for Li-EC.

  1. 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 Li atoms and EC molecules is up to ~5 Å    

This RDF plot of Li-EC interactions can be compared to a plot of pure EC in the Liquid Electrolyte Properties: Part 1 tutorial

Let’s compare this RDF plot to the plot of pure EC in the Liquid Electrolyte Properties: Part 1 tutorial. We see that the RDF indicates that the center of mass between most Li atoms and EC molecules are within ~5 Å of one another, which are closer together than the center of mass from the EC molecules in a pure EC system.

Figure 5-6. Defining the selections and running the RDF job.

To explore the RDF panel further, we can plot the interaction between the center of mass of the Li and P atoms.

 

  1. To do this, 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_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.
  2. Make sure that the Trajectory source has Workspace (included entry) selected from the dropdown
  3. Maintain (atom.ele Li) for Set 1 atoms and change the Set 2 atoms to (atom.ele P)
  4. The Options menu should not have changed but verify that everything is the same as in Step 11
  5. Change the Job name to rdf_Li_P
  6. Adjust Job settings () as needed, and click Run
    • The job takes ~5 minutes on a CPU host

Figure 5-7. Viewing the radial distribution function integral output for Li-P.

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_Li_P.dat file

 

  1. 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 Li atoms and P atoms is up to ~5 Å, which is expectedly shorter than the distance between the Li atoms and EC molecules plotted above

6. Performing Cluster Analysis

In this section, we will analyze the trajectory and explore the clusters that emerge using the Cluster Analysis Panel. For a complete description of the cluster analysis workflow, see the Cluster Analysis tutorial. This workflow is useful for understanding and quantifying aggregation in a system. 

Figure 6-1. Opening the Cluster Analysis 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 return to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Calculations
    • The Cluster Analysis panel opens
  2. Click Load from Workspace
    • Be patient, loading can take a few seconds depending on the size of the trajectory
    • disordered_system_Li… appears next to the Load from Workspace button

Figure 6-2. Setting the Cluster Analysis parameters for the full trajectory.

  1. Keep the Maximum neighbor distance at 3.00 Å
    • This is the radius for defining a neighbor in the cluster-defining algorithm. 3.00 Å is recommended for atomistic systems, and 6.00-9.00 Å for coarse-grained systems.

Use the Cluster constituents section of the panel to decide which components can qualify as part of a cluster.

  1. From the Molecular species dropdown, deselect C3H4O3 Mols:1128 which are the EC molecules
    • This ensures that the EC molecules are excluded from the cluster analysis calculation

Figure 6-3. Setting the Cluster Analysis parameters for the full trajectory.

  1. Check Extract clusters at last frame
    • The output will include both the cluster analysis output entry as well as a standalone entry of the extracted cluster (or several entries in cases with several clusters)
  2. Change the Job name to cluster_analysis_Li_PF6
  3. Adjust the job settings () as needed
    • This job runs on a CPU host. The job can be completed in about 15 minutes
  4. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated cluster_analysis_Li_PF6_out.mae file from the provided tutorial files via File > Import Structures
  5. Close the Cluster Analysis panel

Figure 6-4. Visualizing the Cluster Analysis output in the workspace.

  1. Once the job is complete, or if you have imported the pregenerated results file, 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 file: disordered_system_Li_PF6_EC_all_components_amorphous
    • This is the last frame in the trajectory range
    • The clusters are automatically colored
    • Stylize the system as you wish, shown in the Figure is the CPK representation

Figure 6-5. The number of molecules over time for the two largest clusters.

  1. To analyze the results panel for the calculation, use WAM button () or go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Cluster Analysis Results

 

The top graph shows the number of clusters over time.

 

 

Data for the first two largest clusters over time appears in the graph window. Hover the mouse over the graph to view corresponding (x, y) coordinates.

Figure 6-6. Visualizing the Cluster Analysis output in the workspace for a 4 M LiPF6 salt concentration solution.

The constructed system contains 1 M LiPF6 salt concentration.

One could imagine systematically studying the effects of concentration on the size and shapes of the clusters. For example, shown in the Figure we have performed an analogous study on a 4 M LiPF6 salt concentration solution simply by increasing the number of both Li and PF6 ions to 301 and repeating Sections 4 and 6.

As the salt concentration increases, we observe large interconnected LiPF6 domains of clusters.

7. Running a Molecular Dynamics Simulation for use in a Diffusion Coefficient Calculation

In this section, we will use the MD Multistage Workflow panel to employ a best practice molecular dynamics (MD) protocol for preparing a system for diffusion calculations. Since we have already assigned custom ESP charges to the ionic components of the system we can proceed to the MD Multistage Workflow panel.

Figure 7-1. Selecting and including the disordered system.

  1. Go back to the structure output from the disordered builder 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 and includethe entry is represented in the Workspace, the circle in the In column is blue disordered_system_Li_PF6_EC_all_components_amorphous

It is recommended to use the following best practices for preparing a system for diffusion calculations:

  • Equilibrate the system in the NPT ensemble to ensure that equilibrium density is obtained.
  • Equilibrate the system in the NVT ensemble, using the average equilibrated box vectors from the NPT simulation to equilibrate the temperature for a structure at average density.
  • Perform a production run, this could be done at different ensembles, but for this system an NVT ensemble will be used.

In our case, we also want to study the system at 500 K, which is an experimentally relevant condition. As a result, before the first NPT equilibration, we will compress the cell and then use an annealing procedure to heat the system to 500 K.

For more information about best practices for diffusion calculations, see the Diffusion tutorial and the Diffusion Coefficient Panel documentation.

Figure 7-2. Setting up the MD Multistage Workflow (Stages 1-8).

  1. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens
    • Alternatively, 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 panel
  2. Check Relaxation protocol and choose Compressive from the dropdown list
  3. For Stage (8), change to Simulated Annealing
  4. Change the Number of stages to 2
  5. Set the Time to 0, 2000 and the Temperature to 300, 500
    • The system temperature will be linearly ramped from 300 to 500 K over the course of 2 ns
  6. Change the Simulation time to 2 ns and the trajectory Recording interval to 50 ps
  7. Change the Ensemble class to NPT

Figure 7-3. Setting up the MD Multistage Workflow (Stages 9-11).

  1. Click Append Stage
  2. For Stage (9), change to Molecular Dynamics
  3. Change the Simulation time to 50 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
  4. Change the Temperature to 500 K
  5. Click Append Stage
  6. For Stage (10), change to Average Cell
  7. Click Append Stage
  8. For Stage (11), change to Molecular Dynamics
  9. Change the Simulation time to 10 ns and the Trajectory Recording interval to 1000 ps
  10. Change the Ensemble class to NVT
  11. Change the Temperature to 500 K

Figure 7-4. Setting up the MD Multistage Workflow (Stage 12).

  1. Click Append Stage
  2. For Stage (12), change to Molecular Dynamics
  3. Change the Simulation time to 50 ns and the Trajectory Recording interval to 50 ps
  4. Change the Ensemble class to NVT
  5. Change the Temperature to 500 K
  6. Change the Job name to multistage_simulation_diffusion_Li_PF6_EC

 

Adjust the job settings () as needed. This job requires a GPU host and can be completed in about 9 hours.

  1. If you would prefer not to run the job, import multistage_simulation_diffusion_Li_PF6_EC-out.cms from the provided tutorial files via File > Import Structures. Otherwise, click Run
  2. Close the MD Multistage Workflow panel

Figure 7-5. 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, stylize as you wish, or rename the entry to distinguish it from the other MD simulation. Shown in the Figure is the Maestro Default preset with the ions in ball-and-stick styling.

8. Performing and Analyzing Diffusion Coefficient Calculation

Now that we have equilibrated the system with our prescribed protocol, we are ready to move towards the final NVT simulation to be used for the Diffusion Coefficient calculation. In this section, we will use the Diffusion Coefficient panel to run an NVT simulation and collect diffusion data for the Li ions, then we will use the Diffusion Coefficient Results panel to analyze the results.

Figure 8-1. Selecting and including the entry and opening the Diffusion Coefficient panel.

  1. Ensure that disordered_system_Li_PF6_EC_all_components_amorphous is 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Go to Tasks > Materials > Classical Mechanics > Diffusion Coefficient > Diffusion Coefficient Calculations

Figure 8-2. Setting the Simulation Protocols.

As mentioned earlier, we will use the Mean squared displacement method here, and we will run a production NVT simulation at this stage.

  1. Click on the Simulation Protocols tab
  2. Change the Ensemble class to NVT
    • An ensemble class of NVE would also produce the same Diffusion Coefficient results
  3. Change the Initial temperature to 500 K, the Simulation time to 20 ns, the Time step to 2 fs and the Trajectory recording interval to 10 ps
    • Note that it is important to yield a significant amount of frames for calculating the diffusion constant
  4. Click Save trajectory
    • This will take some extra memory, but can be useful if we want to visualize the NVT simulation or perform subsequent analysis beyond the diffusion calculation (for example, see the Polymer Electrolyte Analysis workflow)

Figure 8-3. Setting the Tau range.

  1. Return to the Method tab
  2. In the Fitting range section, change the Include Tau values from upper limit to 15 ns and the lower limit value to 5 ns  

Note: During the analysis stage, the Tau values can be adjusted again, and so there is no need to take care when selecting this range at this moment. However, if you were running a batch job (say, hundreds of systems at many temperatures) without the intention of using the viewer panel to analyze the diffusivity, you may want to use care when deciding this range initially. 

Figure 8-4. Setting Diffusion Parameters and running the job.

Now, we can specify the ions or molecules for which to calculate diffusion parameters.

  1. Go to the Diffusion Parameters tab
  2. For Atoms for diffusion parameters, we must define the lithium ions. Clear the default () and use the button to choose Metal Atoms
    • The panel updates to show metals and 75 atoms selected
    • Confirm that in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, the lithium ions are all selected
    • Other methods for selecting the lithium atoms are available including Pick or the other dropdowns in the panel
    • Read more about ASL
  3. Change the Job name to diffusion_coefficient_Li

 

Adjust the job settings () as needed. This job requires a CPU and GPU host (for the analysis and MD, respectively). The job can be completed in about 2 hours using 1 CPU and 1 GPU.

  1. If you would prefer not to run the job, import diffusion_coefficient_Li-out.cms from the provided tutorial files via File > Import Structures in the diffusion_coefficient_Li directory. Otherwise, click Run
  2. Close the Diffusion Coefficient panel

Figure 8-5. The output after running the job or importing.

When the job completes or after importing, a new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled diffusion_coeffient_Li_PF6_EC_all_components_amorphous

Feel free to edit the entry title to distinguish that this is the Li diffusion coefficient calculation

Figure 8-6. Opening the Diffusion Coefficient Viewer 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 output in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and workspacethe 3D display area in the center of the main window, where molecular structures are displayed, respectively
  2. Use the WAM (workflow action menu) button () to open the Diffusion Coefficient Viewer
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Diffusion Coefficient > Diffusion Coefficient Results
    • The Diffusion Coefficient Viewer panel opens

Figure 8-7. Opening the Diffusion Coefficient Viewer panel.

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

You can manually adjust the bounds of the linear fit using the interactive sliders in the plot. The diffusion coefficient 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. As a very loose recommendation, one should exclude the short timescale behavior, where the curve follows a ballistic trajectory and the atoms velocities have not been greatly impacted by interaction with surrounding atoms, as well as long times where the uncertainty is higher.

Figure 8-8. Viewing the 2D Diffusion Trace.

  1. Go to the Diffusion Trace tab

 

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.

Figure 8-9. Viewing the 3D Diffusion Trace.

  1. Change the Plot type to 3D

 

The trace for a specified Mass center (by default 1, the first lithium ion) is shown in a 3D plot.

 

Feel free to explore the various traces for additional Li ions by changing the Mass center input.

 

Note: The 3D plot can be rotated (left-click and drag) or zoomed (right-click and drag) similar to typical mouse actions in the MS Maestro workspacethe 3D display area in the center of the main window, where molecular structures are displayed

9. Conclusion and References

In this tutorial, we used the Disordered System Builder and MD Multistage Workflow panels to build and equilibrate model systems. We performed a workflow to calculate the Radial Distribution Function and performed a Cluster Analysis on the equilibrated MD structure. Then, we used the Diffusion Coefficient calculation panel and the Diffusion Coefficient Results panel to study the diffusion data for the Li ions.

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.

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

For further reading:

10. 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