1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. 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/sei.zip
5. 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.

6. Go to File > Save Project As
7. Change the File name to SEI_tutorial, click Save
   • The project is now named SEI_tutorial.prj

Figure 2-3. The entry list after importing.

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

8. Go to File > Import Structures
9. Navigate to where you downloaded the provided tutorial files, choose molecules.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.

Custom charges are assigned to all the atoms and come directly from the OPLS4 force field. The charges on Li⁺ and PF₆^- are scaled by a factor of 0.8 (so that the charges on Li, P and F are 0.8, 0.484, and -0.214, respectively).

To learn how to perform an atomic charge calculation, visit the Computing Atomic Charges tutorial. For more information about assigning charges to this particular system, visit the Liquid Electrolyte Properties: Part 2 tutorial.

Feel free to turn off labels at any time during this tutorial using the blue label icon in the bottom right corner.

Figure 3-1. Setting the parameters in the Nanostructure Builder panel.

1. Go to Tasks > Materials > Structure Builders > Nanostructures
   • The Nanostructure Builder panel opens
2. For Termination, keep Periodic selected
   • This generates an infinite sheet as opposed to a capped finite plane
3. For Dimensions (unit cells), input 7 x 12
   • This is the quantity of graphene unit cell translations in the a and b directions that will comprise the new P1 cell
4. For Number of bilayers, input 2
5. Change the Job name to layered_graphene
6. If you’d like to import the structure rather than run the job, import Section_03 > layered_graphene > layered_graphene.maegz from the tutorial files (via File > Import Structures). Otherwise, to run the job, click Run
   • The job should complete within a few minutes
7. Close the Nanostructure Builder panel

For more details on considerations for constructing the graphene bilayer see the Building a Polymer-Polymer Interface Model tutorial.

Figure 3-2. Viewing the layered graphene structure.

A new entry group titled layered_graphene is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 3-3. Setting the parameters in the Disordered System Builder panel.

Now we can proceed to build the disordered system:

8. 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 molecules (3) entry group and includethe entry is represented in the Workspace, the circle in the In column is blue the entry nanosheet
   • 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 list a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusionand includethe entry is represented in the Workspace, the circle in the In column is blue means to show the entry in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed
9. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
10. Change Number of molecules to 194
11. Change both the number of Li and PF₆ molecules to 12
    • The number of EC molecules should update automatically to 170
    • This system will contain an approximately 1 M LiPF₆ salt concentration after the system is equilibrated
12. Check the Substrate box
13. Select from the Structure drop down menu Included entry
14. Click Import
    • The included entry nanosheet has been imported as the substrate
15. Select Planar interface as the Substrate type
16. Click Define interface…

Figure 3-4. Viewing the interface.

17. Increase the Buffer between surface and components to 2
18. Increase the Buffer between components and surface mirror image in the periodic box to 2
    • This will aid the build and will be reconciled in the later MD stages
19. Click OK to close the panel

Figure 3-5. Setting the parameters in the Disordered System Builder panel.

20. Change the Periodic Boundary Conditions (PBC) to Use/expand substrate PBC using the dropdown menu
21. Go to the Cells tab

Figure 3-6. Setting the parameters in the Disordered System Builder panel in the Cells tab.

22. Click Force Field…

Figure 3-7. Including custom charges in the build.

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

23. Click Custom Charges…
24. Check the box to Use custom charges
25. Type all in the Apply to atoms box
26. Click OK to close the Custom Atom Charges panel
27. Click OK to close the Force Field panel

Figure 3-8. Running the Disordered System Builder panel.

28. Click Tangled chain
29. Change the Job name to disordered_system_SEI
30. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in just a couple minutes on a CPU host
31. Click Run
32. Close the Disordered System Builder panel

Figure 3-9. Viewing the disordered system.

33. Once the job is successfully completed, a new disordered_system_SEI_system (1)  group, with a single entry titled disordered_system_SEI_system_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 is 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
    • In this structure, the four graphene sheets are on the bottom of the cell and the Li (red), PF6 (green), and EC (red) molecules are built on top
34. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow or use the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The MD Multistage Workflow panel opens

Figure 3-10.Setting the parameters in the MD Multistage Workflow panel.

35. Ensure that Use structures from says Project Table (1 selected entry)
36. Ensure that Brownian Minimization is selected for the first Stage type
37. Click Append Stage
    • Stage 2 is added to the workflow
38. In Stage 2, for Stage Type, choose Brownian Minimization
39. For Temperature (K), set to 300
40. Click Append Stage
    • Stage 3 is added to the workflow
41. In Stage 3, for Stage Type, choose Molecular Dynamics
42. For Simulation time (ns), set to 5
43. For Approximate number of frames, set to 100
44. Click Advanced Options…

Figure 3-11. Changing the Coupling style.

45. Select Anisotropic for the Coupling Style
    • The anisotropic coupling style is selected because our x and y directions will not significant change due to the rigidity of the graphene, but there will be changes in the z direction
46. Click Apply
47. Click OK

Figure 3-12. Running the MD Multistage Workflow.

48. For Job name, enter MD_SEI
49. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about an hour
50. If you would like to run the job, click Run. Otherwise, pre-generated results are provided in the next step to view the structure
51. Once the job is successfully completed, a new group will appear in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, titled MD: disordered_system_SEI_system (1)
52. Close the MD Multistage Workflow panel

Figure 3-13. Viewing the MD simulation results.

53. If importing the files instead, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > MD_SEI > MD_SEI-out.cms
    • 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

Figure 3-14. Deleting the two bottom graphene sheets.

Next we need to delete the two bottom graphene sheets. Because of periodic boundary conditions one or more of the graphene layers may have moved to the opposite side simulation cell

54. To delete graphene sheets, hold the shift key and double click on the graphene sheets to select
    • Alternatively, typing M activates molecule selection to select an entire molecule
55. In the top toolbar, go to Build > Delete selected atoms

Figure 3-15. Redefining the c cell parameter.

Before making the system non-periodic, we need to ensure that there is enough vacuum space in our system between periodic images so we will increase our z direction slightly.

56. 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 MD: disordered_system_SEI_system go to Tasks > Materials > Tools > Redefine Lattice
    • The Redefine Lattice panel opens
57. Set the new c cell parameter to 43
    • We are expanding the c lattice parameter only by about 6 Å
58. For Transformation mode select Frame (only cell dimensions may change)
59. Click Run
    • This calculation finishes instantly
60. Close the Redefine Lattice panel

Figure 3-16. Preparing the structure for MD.

61. A new entry has appeared in the entry list titled disordered_system_SEI_all_components_amorphous.
    • This entry has the same name as the previous structure so feel free to rename if you would prefer
    • By altering the c lattice parameter, this system needs to be prepared for MD before we can perform an SEI simulation
62. 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 disordered_system_SEI_all_components_amorphous entry, go to Tasks > Materials > Classical Mechanics > MD Simulations > Prepare for Molecular Dynamics
    • The Prepare for MD panel opens
63. Click Force Field…

Figure 3-17. Setting custom charges.

Similar to building the disordered system, we need to set custom charges

64. Click Custom Charges…
65. Check the box to Use custom charges
66. Type all in the Apply to atoms box
67. Click OK to close the Custom Atom Charges panel
68. Click OK to close the Force Field panel

Figure 3-18. Running the Prepare for MD job.

69. For Job name, enter md_prep_SEI
70. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in just a couple of minutes.
71. Click Run
72. Once the job is successfully completed, a new group titled MD: disordered_system_SEI_all_components_amorphous, is now in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
73. Close the Prepare for MD panel

Figure 3-19. Viewing atom properties.

Lastly, before we can perform an SEI simulation we need to add a barrier to the opposite side of the simulation cell from the graphene layers. However, first we need to view the z coordinate of one of the topmost atoms in the cell to determine where to add the barrier.

74. Click on any of the topmost atoms
75. Go to Tasks and search for Show Atom Properties
    • Click on Show Atom Properties to open the panel
76. Click Choose Properties…
77. Click Add
78. Add the z coord
79. Click OK to close the Choose Atom Properties to Display box
    • The Z-coordinate is now populated in your Atom Properties panel
80. Close the Atom Properties panel

Note: Based on which atom is selected in the workspace will result in a slightly different Z-coordinate

Figure 3-20. Adding a barrier to the system.

Now that we know one of the atom’s Z-coordinate we are ready to add the barrier

81. Ensure that MD: disordered_system_SEI_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 and includedthe entry is represented in the Workspace, the circle in the In column is blue in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
82. Go to Tasks > Materials > Classical Mechanics > MD Simulations > Setup Barrier Potential for MD
    • The Set Barrier Potential for MD panel opens
83. Ensure that Use structures from says Workspace (included entry)
84. Click Add Barrier
85. Set the Offset to 7.50 Å
    • This value was determined from the equation: L_z/2 - (Z-coordinate of the selected atom in step 80). L_Z represents the Z-dimension of the simulation box (43.0 in this case) and L_z/2 = 21.5
    • Your Z-coordinate might be slightly different from the tutorial value so vary the offset amount if needed so the orange plane is in line with the top of the cell
86. Click Apply
    • The Save Desmond Model to File dialogue opens
87. For File name, enter SEI_wall_system.cms
88. Click Save
    • A file, SEI_wall_system.cms, will be saved to the working directory, and an entry will be imported into the entry list
    • For more details on adding a potential barrier see the Applying Barrier Potentials for Molecular Dynamics Simulations tutorial

Figure 4-1. Importing the barrier system.

If you would like to proceed with the completed constructed system, please import the provided structure. If you have generated your own SEI_wall_system.cms file in Section 3 please proceed to Step 3

1. Go to File > Import Structures
2. Navigate to where you downloaded the provided tutorial files, choose Section_04 > SEI_wall_system.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 once again titled MD: disordered_system_SEI_all_componets

Now we are ready to proceed with an SEI calculation

Figure 4-2. Opening the Solid Electrolyte Interphase (SEI) Calculation panel.

3. With the latest MD: disordered_system_SEI_all_componets group 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 and includedthe entry is represented in the Workspace, the circle in the In column is blue go to Tasks > Materials > Classical Mechanics > Solid Electrolyte Interphase Formation > Solid Electrolyte Interphase Formation Calculations
   • The Solid Electrolyte Interphase (SEI) Calculation panel opens

Figure 4-3. Setting up the Solid Electrolyte Interphase (SEI) Calculation panel Reactions tab.

4. Click Add All Reactions
5. Select Random for Sequence to perform reactions
   • This allows the reactions to happen in any order
   • When the Random option is selected the probability value is grayed out
6. Go to the Electrode and Electrolyte tab

Figure 4-4. Solid Electrolyte Interphase (SEI) Calculation panel Electrode and Electrolyte tab.

7. Ensure that Add cation to neutralize the system is checked
   • Four reactions occurring in this calculation are reduction reactions so we need to add cations (Li⁺) to neutralize the system
8. Decrease the Reduction zone width to 12 Å
   • The reduction zone width is the distance from the electrode center where the reduction reactions can occur
9. Click the button > Select to open the Atom Selection panel
   • We need to select the graphene sheets as the electrode

Figure 4-5. Selecting the graphene sheets.

There are multiple ways to select the graphene sheets, these next steps detail one way.

10. Go to the Molecules tab
11. Select Molecule list
12. For Molecule list select UNK 1 and UNK 2
    • UNK 1 and UNK 2 are the two sheets of graphene
    • The graphene sheets are now selected in the structure
13. Click Add
14. Ensure that (mol.num 1) OR  (mol.num 2) are listed in the ASL window
15. Click OK to close the Atom Selection panel

Figure 4-6. Adding charges in the Solid Electrolyte Interphase (SEI) Calculation panel.

16. (mol.num 1) OR  (mol.num 2) is now listed as the Electrode ASL
17. Check the Custom charges on the electrode box
18. Select Uniform
19. Change the Charge per atom to -0.0200
    • This negative charge mimics the electric field facilitating flow of cations towards the anode in a real battery system
20. Go to the Simulation Protocol tab

Figure 4-7. Setting up the Solid Electrolyte Interphase (SEI) Calculation panel Simulation Protocol tab.

21. Check the Add Relaxation box
    • This runs a short MD simulation to relax the system before performing reactions
22. Set the Simulation time to 25000 ps
23. Set the Temperature to 350 K
    • The temperature increase is ideal for EC and to accelerate the molecules
24. Set the Trajectory recording interval to 100 ps
25. Set the Coefficient to scale custom charges to 0.800
    • This is the scaling coefficient used for Li⁺ and PF₆^- in Section 2
26. For Job name, enter SEI_simulation
27. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 12 hours
28. If you would like to run the job, click Run. Otherwise, pre-generated results are provided to view the structure
29. Once the job is successfully completed, a new group will appear in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, titled MD: SEI_simulation_iter250_model_system (1)
30. Close the Solid Electrolyte Interphase (SEI) Calculation panel

Figure 4-8. Viewing the SEI calculations output structure.

31. If importing the files instead, go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > SEI_simulation > SEI_simulation-out.cms

Figure 5-1. Opening the Solid Electrolyte Interphase Formations Results panel.

1. With the MD: SEI_iter250_model_sysem (1) group 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 and includedthe entry is represented in the Workspace, the circle in the In column is blue go to Tasks > Materials > Classical Mechanics > Solid Electrolyte Interphase Formation > Solid Electrolyte Interphase Formation Results or use the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • The Solid Electrolyte Interphase Formation Results panel opens

Figure 5-2. Viewing the Solid Electrolyte Interphase (SEI) Viewer panel.

The plot shows selected species over the entire simulation.

Figure 5-3. Adjusting the species.

2. Under the Species drop down menu select All
3. Unselect C3H4O3
   • Feel free to add or remove various species

Figure 5-4. Viewing the Average Density along the Z axis.

4. Go to the Density Depth tab
5. Change the Axis to Z
   • This shows the mass density of selected species in the selected direction of the simulation cell.

Initially the plot will show a density of 0 g/cm³, but as time increases the various species start producing.

6. Move the time bar at the bottom of the panel to view the species’ density over time.

Figure 5-5. Viewing the Density Projection 2D density plot.

7. Go to the Density Projection tab
8. Once again, feel free to toggle the time bar and change the species and planes

Select various species and watch the planar density change over time in this 2D plot.