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 input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/aimd.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 AIMD_tutorial and click Save
   • The project is now named AIMD_tutorial.prj

Figure 2-3. Importing structure file.

8. Go to  File > Import Structures
9. Navigate to where you saved the tutorial files and Open Li3PS4.mae
   • The new entry 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 Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and is includedthe entry is represented in the Workspace, the circle in the In column is blue

Note: Please refer to the Glossary of Terms for the difference between includedthe entry is represented in the Workspace, the circle in the In column is blue and 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.

Figure 2-4. The entry list after importing.

The imported entry is now available in the workspace. This experimental crystal structure is available from The Materials Project Database and can be imported using the Query Materials Project Database panel where then the file can be downloaded. This structure has the ID mp-985583. This asymmetric unit does not need any further preparation and is ready for QE simulations.

Figure 3-1. QE Calculations panel settings.

For the convergence tests, we will use the structure imported in Section 2.

1. With Li₃PS₄ includedthe entry is represented in the Workspace, the circle in the In column is blue and 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, go to Tasks > Materials > Quantum Mechanics > Quantum ESPRESSO > Quantum ESPRESSO Calculations
   • The Quantum ESPRESSO Calculations panel opens
2. Ensure that Use structures from shows Project Table (1 selected entry)
3. Check the Convergence tests box
4. Click Pseudopotentials
   • Quantum ESPRESSO Calculations - Pseudopotentials panel opens

Figure 3-2. Pseudopotentials panel settings.

5. In Path click Browse
6. Navigate to where you saved the tutorial file and choose the all_pbe_UPF_v1.5 directory
   • The Pseudopotentials panel is automatically filled with the paths to the directory and recognizes the Li, P, and S specific pseudopotential files
7. Click OK to close the Pseudopotentials panel
   • A message appears that the energy cutoffs were not defined. Click OK to close the message as we will define the cutoffs in the next step

Note: Pseudopotentials are not included with the Quantum ESPRESSO installation and must be downloaded separately. There are several libraries available (see this link for more information). The pseudopotentials used in this tutorial can be downloaded from GBRV pseudopotential site.

Note: Pseudopotentials are usually generated for a specific type of density functional. It is therefore recommended to employ the same type of density functional, if possible, in all QE calculations used in generation of the pseudopotentials. The functional used for the generation of the pseudopotential is stated in the Pseudopotentials panel (see the Figure)

Figure 3-3. Opening the Advanced Options.

8. Click Advanced Options

Figure 3-4. Advanced Options, Theory tab settings.

9. In the Theory tab, ensure the following are selected:
   • Non-polarized for Spin treatment
   • Disabled for DFT+U treatment
   • GGA for Density functional type
   • PBE for Density functional
   • DFT-D3 for Dispersion correction
     1. Note that the inclusion of D3 dispersion is not critical for bulk solid state materials
   • Uncheck Use symmetry
10. Select Grid place distance and set to 0.08
11. Check the box to Include Γ-point and click Update K-point mesh
    • The number of k-points will update to 4

Figure 3-5. Advanced Options, SCF tab settings.

12. Switch to the SCF tab
13. For Max steps in SCF, input 200
14. Select Fixed for Occupations

Note: The values of the wavefunction and charge density cutoffs will be overwritten by the values provided in the Convergence tests tab

Figure 3-6. Advanced Options, Convergence tests tab settings.

15. Switch to the Convergence tests tab
16. Make the following selections:
    • Minimum energy cutoff to 20 Ry for wavefunctions
    • Maximum energy cutoff to 100 Ry for wavefunctions
    • Step size to 10 Ry
    • Charge density multiplier to 8
    • Check Grid plane distance, with the following settings:
    • Max: 0.08
    • Decrement:  0.01
    • Steps: 8
    • Check Include Γ-point
    • Click Update K-point mesh
17. Click Save to return to the Quantum ESPRESSO Calculations panel

Figure 3-7. Convergence job settings.

18. Change the job Name to convergence_Li3PS4
19. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in several days using 8 CPUs

Note: The QE parallel options -npools must be a divisor of the number of threads and is used to evaluate several k-points at once. Other systems might require different parallelization settings, for more information check this help topic

20. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next steps
21. Close the Quantum ESPRESSO Calculations panel

Figure 3-8. Importing Structures and using the WAM button.

22. From the main menu, choose File > Import Structures
23. Navigate to where you downloaded the tutorial file and choose Section_03 > convergence_Li3PS4.maegz file
24. Click Open
    • A new group with 72 structures 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 entire group is automatically 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 the first entry 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
    • Maintain the entire entry group selection
25. Use the WAM (workflow action menu) button () to open the Convergence Tests Viewer
    • Alternatively, go to Tasks > Materials > Quantum Mechanics > Quantum ESPRESSO > Convergence Tests Viewer
    • The Convergence Tests Viewer panel opens

Figure 3-9. Loading data from Workspace.

The Convergence Tests Viewer panel will be used to analyze the results of the convergence calculations

26. Click Load data from Workspace
    • This loads in the entry group from the previous calculation
27. Check Convert energy to eV
28. Check Show relative energy
    • Energy values are now displayed relative to the lowest energy value in the data set

Figure 3-10. Convergence with respect to the k-point grid.

29. In Wavefunction cutoffs (Ry) column, shift-click entries 40 through 100
    • The graph shows convergence with k-points for the different wavefunction cutoffs. We observe a fast convergence with the number of k-points already after 8 k-points. This means that we can use the 2 x 2 x 3 k-point grid.

Figure 3-11. Convergence with the wavefunction cutoff for a given k-point grid.

30. In # of k-points column, click 8 (2, 2, 3)
    • The graph shows the convergence with respect to the wavefunction cutoff for our chosen k-point grid. We observe a fast convergence after a wavefunction cutoff of 40 Ry.

Figure 4-1. Li₃PS₄ structure.

For the optimization calculation, we will use the structure imported in Section 2.

1. With Li₃PS₄ includedthe entry is represented in the Workspace, the circle in the In column is blue and 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, go to Tasks > Materials > Quantum Mechanics > Quantum ESPRESSO > Quantum ESPRESSO Calculations
   • The Quantum ESPRESSO Calculations panel opens

Figure 4-2. Quantum ESPRESSO Calculations panel settings.

2. Ensure that Use structures from shows Project Table (1 selected entry)
3. Check the Optimize atomic positions and cell box and uncheck all other boxes
4. Click Pseudopotentials
   • Quantum ESPRESSO Calculations - Pseudopotentials panel opens  

Figure 4-3. Selecting pseudopotentials.

The pseudopotential panel should have remembered the location of the pseudopotentials used in the convergence calculation. If this is not the case, use the next several steps to set them once again

5. In Path click Browse
6. Navigate to where you saved the tutorial file and choose the all_pbe_UPF_v1.5 directory
   • The Pseudopotentials panel is automatically filled with the paths to the directory and recognizes the Li, P, and S specific pseudopotential files
7. Click OK to close the Pseudopotentials panel
   • A message appears that the energy cutoffs were not defined. Click OK.

Figure 4-4. Opening the Advanced Options.

8. Click Advanced Options

Figure 4-5. Advanced Options, Theory tab.

9. In the Theory tab, ensure the following are selected:
   • Non-polarized for Spin treatment
   • Disabled for DFT+U treatment
   • GGA for Density functional type
   • PBE for Density functional
   • DFT-D3 for Dispersion correction
   • Uncheck Use symmetry
10. Set the Grid plane distance to 0.04000, check Include Γ-point, and click Update K-point mesh to update the Monkhorst-Pack grid values
    • The relationship between the density and the Monkhorst Pack definition can be checked with the Update K-point mesh option. This leads to the grid from the convergence test.

Figure 4-6. Advanced Options, SCF tab settings.

11. Go to the SCF tab
12. For Custom energy cutoff for wavefunctions, input 40
13. For Custom energy cutoff for charge density, input 320
14. For Max steps in SCF, input 200
15. Select Gaussian Smearing, input 0.003

Figure 4-7. Advanced Options, Optimization tab settings.

16. Go to the Optimization tab
17. Make the following selections:
    • Number of steps to 200
    • Total energy threshold to 1e-06 Ry
    • Force threshold to 0.00050 Ry/Bohr
18. Click Save to return to the Quantum ESPRESSO Calculations panel

Figure 4-8. Starting the optimization calculation.

19. Change the Job Name to optimization_Li3PS4
20. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in approximately 12 hours using 8 CPUs
21. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results
22. Close the Quantum ESPRESSO Calculations panel

Figure 4-9. DFT-relaxed Li₃PS₄ in the workspace.

23. To proceed with pre-generated files, from the main menu, choose File > Import Structures
24. Navigate to where you downloaded the tutorial file and choose the Section_04 > optimization_Li3PS4.maegz file
25. 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

Figure 4-10. Expanding the DFT-relaxed Li₃PS₄ system.

Let’s create a 128 atom supercell from our 32 atom DFT-relaxed structure before performing AIMD simulations.

26. Click on the periodic structure tools in the bottom right corner of the GUI,
27. Open the Build Cell panel
28. Click Extents
29. Increase the +B and +C extent to 1
30. Click Apply

Figure 4-11. Creating a P1 supercell.

A structure with 128 atoms is shown in the workspace. Now the simulation box needs to be adjusted to the extended structure to create the final supercell.

31. Once again, click on the periodic structure tools in the bottom right corner of the GUI,
32. Click Make P1 Cell

Figure 4-12. The Li₃PS₄ supercell.

Our cell now contains 128 atoms. Feel free to right click on the entry name and rename if you would like.

Figure 5-1. QE Calculations panel settings.

For the AIMD simulation, we will use the supercell.

1. With the new P1 supercell includedthe entry is represented in the Workspace, the circle in the In column is blue and 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, go to Tasks > Materials > Quantum Mechanics > Quantum ESPRESSO > Quantum ESPRESSO Calculations
   • The Quantum ESPRESSO Calculations panel opens
2. Ensure that Use structures from shows Project Table (1 selected entry)
3. Check the Molecular dynamics box
4. Click Pseudopotentials

Figure 5-2. Selecting pseudopotentials.

The pseudopotential panel should have remembered the location of the pseudopotentials used in the convergence and optimization calculations. If this is not the case, use the next several steps to set them once again

5. In Path click Browse
6. Navigate to where you saved the tutorial file and choose the all_pbe_UPF_v1.5 directory
   • The Pseudopotentials panel is automatically filled with the paths to the directory and recognizes the Li, P, and S specific pseudopotential files
7. Click OK to close the Pseudopotentials panel
   • A message appears that the energy cutoffs were not defined. Click OK.

Figure 5-3. Opening the Advanced Options.

8. Click Advanced Options

Figure 5-4. Advanced Options, Theory tab settings.

9. In the Theory tab, ensure the following are selected:
   • Non-polarized for Spin treatment
   • Disabled for DFT+U treatment
   • GGA for Density functional type
   • PBE for Density functional
   • DFT-D3 for Dispersion correction
   • Uncheck Use symmetry
   • Γ-point only (real wavefunctions) for the Brillouin zone partition options

Figure 5-5. Advanced Options, SCF tab settings.

10. Switch to the SCF tab
11. Keep all options the same as set for the optimization calculation

Figure 5-6. Advanced Options, Dynamics tab settings.

12. Switch to the Dynamics tab
13. Set the Time step to 2 fs
14. Set the temperature to 1000 K
    • This simulation needs to be performed at a higher temperature than the system's melting point. This means that the structure will become amorphous and we will investigate the diffusion coefficient in the final amorphous structure.

Note: AIMD simulation times should be fairly long to properly study the ion hoping in conductive materials. The 10 ps used here are just for the purpose of this tutorial, consider a production style run of >50 ps if resources allow.

15. Click Save to return to the Quantum ESPRESSO Calculations panel

Figure 5-7. AIMD job settings.

16. Change the job Name to AIMD_Li3PS4
17. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in approximately two weeks on 16 CPUs
18. If you would like to run the job, click Run. Otherwise, we will proceed with pre-generated results in the next section
19. Close the Quantum ESPRESSO Calculations panel

Figure 5-8. AIMD output in the workspace.

33. To proceed with pre-generated files, from the main menu, choose File > Import Structures
34. Navigate to where you downloaded the tutorial file and choose the Section_05 > AIMD_Li3PS4.maegz file
35. 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

Due to the vast amount of movement in the simulation the imported structure will look like the Figure.

Using the periodic structure tools in the bottom right corner of the GUI, you can translate your system to a first unit cell and recalculate connectivity to generate a cleaner looking structure.

Figure 6-1. Selecting and including the entry and opening the Diffusion Coefficient panel.

1. Ensure that AIMD_Li3PS4 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
   • The Diffusion Coefficient panel opens

Figure 6-2. Setting the Method settings.

3. In the Trajectory section, select Use existing
   • This will use the trajectory generated from the AIMD simulation
4. In the Fitting range section, change the Include Tau values from range from 0 to 0.01 ns (10 ps)
   • Since we will be adjusting the fitting boundaries, these Tau values are the linear region when the results are imported and can be changed interactively through the viewer panel

Figure 6-3. Setting Diffusion Parameters and running the job.

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

5. Go to the Diffusion Parameters tab
6. For Atoms for diffusion parameters, we must define the lithium ions. Clear the default () and type (atom.ele Li)
   • Other methods for selecting the lithium atoms are available including Pick or the other dropdowns in the panel
   • Read more about ASL
7. Change the Job name to diffusion_coefficient_Li

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

8. If you would prefer not to run the job, import Section_06 > diffusion_coefficient_Li > diffusion_coefficient_Li.maegz from the provided tutorial files via File > Import Structures in the diffusion_coefficient_Li directory. Otherwise, click Run
9. Close the Diffusion Coefficient panel

Figure 6-4. The output after running the job or importing.

When the job completes or after importing, 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 entitled diffusion_coefficient_Li

Figure 6-5. Opening the Diffusion Coefficient Viewer panel.

10. 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.
11. 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 6-6. 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.

The Diffusion Trace tab shows the trace for a specified Mass center 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. In this case, the atoms mainly vibrate with limited overall movement due to the small system size and short AIMD simulation time. Feel free to explore the Diffusion Trace tab.

For best practices, in addition to performing AIMD simulations >50 ps, multiple replicates should also be considered. Long trajectories and the usage of replicate systems is best for modeling the Li ion mobility in well conductive materials.

AIMD paired with diffusion coefficient calculations can be used to get the migration energy barrier by running simulations at multiple temperatures and fitting Arrhenius relationship to the data. This would generate the global migration energy for the system from the slope of the fitted line. However, it is not shown here due to the high computational expense of such simulations.