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: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/crystal_morphology.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 crystal_morphology_tutorial, click Save
   • The project is now named crystal_morphology_tutorial.prj

Figure 2-3. The structure after directly importing the provided cif.

8. Go to File > Import Structures
9. Navigate to where you downloaded the provided tutorials, choose lamotrigine_EFEMUX01.cif and click Open
   • 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

Figure 2-4. Renaming and stylizing the structure.

10. Rename the entry lamotrigine (double-click on the entry name in the entry list to rename)
11. Select all of the atoms in the workspace (this can be done in several ways, including using Quick Select: All from the toolbar )
12. From the Style palette (), change to ball-and-stick with the Apply ball-and-stick representation button
    ()
13. From the Style palette (), change to Color Atoms Element by using the dropdown and selecting Element, then clicking Color Atoms Element in the palette
    • The atom coloring should be updated to match the figure

Figure 2-5. Building the unit cell.

Note, .cif files typically contain lattice parameters, the space group of the crystal and coordinates of the atoms of the asymmetric unit. At the same time, the crystal morphology workflow requires the full crystal unit cell as an input.  To convert the  asymmetric unit to the complete unit cell, we use the periodic structure tool:

14. Click on the button to open the Periodic Structure Tool Window
15. Go to Build Cell and click Apply
    • The workspace is updated to now show the entire unit cell
    • Next to the Periodic Structure Tool icon, the green text indicates CELL: 1 x 1 x 1

 

This structure is now ready for crystal morphology calculations. For a complete summary of periodic structure tools, see the Building and Manipulating Crystal Structures tutorial.

Figure 3-1. Selecting and including the entry and opening the panel.

1. Ensure that lamotrigine 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 > Crystal Morphology > Crystal Morphology Calculations
   • The Crystal Morphologyinterchangeably referred to as crystal habit or crystal shape; the set of planes that show on the crystal surface, given by the relative areas of the crystal faces; the macroscopic shape of the crystal panel opens

Figure 3-2. Loading the bulk structure and enumerating planes.

3. Click Load Bulk from Workspace
   • lamotrigine appears next to the button

In cases where you know in advance which Miller planes contribute most significantly to the crystal morphology (typically based on experimental data or previous calculations), you can input a Single plane by inputting the indices and clicking Add.

More commonly, in cases where you do not know which planes will contribute most significantly, the Enumerate planes tool can be used

4. Change the Min plane to -3, -3, -3 and the Max plane to 3, 3, 3 and click Enumerate
   • The planes table is populated with 99 unique Miller planes as well as their corresponding interplanar distance (d_HKL) and multiplicity (mult.)
   • Note that these planes are unique to the particular unit cell

Figure 3-3. Sorting by interplanar distance.

In general, planes with larger interplanar distances are more likely to have smaller interplanar interactions, and therefore are expected to be more stable surfaces. These planes are more likely to contribute to the Wulff construction (Bravais-Friedel-Dannay-Harker model (BFDH)).

5. Click on the d_HKL column header twice tosort the crystal planes by their interplanar distance, d_HKL, from the largest to the smallest 

Figure 3-4. Deleting planes with low interplanar distances.

Using the BFDH model argument, we can assume that the crystal facets with d_HKL below ~4 Å are unlikely to contribute to the crystal habit. These facets can be excluded from the subsequent MD simulation.

6. In the table, highlight rows 42-99 (be sure that these are the rows with d_HKL < 4 Å) and click Delete
   • The table should now contain 41 rows

Figure 3-5. Defining the slab geometries.

Next, we generate slab models for the selected crystal planes:

7. Change the Slab thickness to 4, the Vacuum buffer to 4 and the Cell extents to 4
   • n refers to the number of cells (n = 1 being the original cell size and slab thickness, etc.)
   • This will determine the geometry of the slabs; these values are reasonable. The thickness should ensure energy convergence, the vacuum buffer should avoid periodic image effects and the extents should give reasonable size cells for MD (see the Modeling Surfaces tutorial for more on preparing slabs)

Figure 3-6. Generating the 41 slabs.

As a general practice, you can view the slabs to be generated independent of the forthcoming MD simulation (i.e. view the slabs but do not perform the surface energy calculations). This is a good idea to confirm that all the slabs models are correct. For example, you want to avoid slabs with half monolayers on the top and bottom or cases of polar slabs with different termination at the top and bottom. In cases like these, you can adjust the slabs and then load them back into the panel.

In this example, the generated slabs are all sufficient for the MD simulation, but we will generate them anyway for visual inspection:

8. Highlight all of the rows in the table and click Generate Slabs
   • When a Question appears, simply click OK. At this stage, some additional duplicates will be identified and removed
   • This process may take a minute or so

Figure 3-7. The bulk structure and some of the slabs tiled in the workspace.

A new entry group is added to the entry list titled morphology_1-surfaces (41) containing the bulk structure and the generated slabs.

Feel free to visualize any of the slabs. In the Figure we show the bulk structure and five of the slabs tiled.

In this case, we do not need to alter any of the slabs. In cases in which slab manipulation is necessary, you can Delete slabs from the table in the panel and use the Load Selected Entries button to load manipulated slabs back into the panel.

For background on manipulating slabs, visit the Modeling Surfaces tutorial

Figure 3-8. Setting the MD parameters.

Return to the panel to now define the Brownie simulation protocols:

9. Change the Simulation time to 2000.0 ps
   • We recommend a minimum of 2 ns for the molecular dynamics simulation. Note, longer runs may be required to converge cohesive energy (see Section 4)
10. Check Save intermediate data and maintain CMS files from the dropdown
    • This will provide the surfaces slabs after relaxation (useful for visualization and troubleshooting), but will not include the complete trajectories (disk-space intensive)

Figure 3-9. Naming and running the job.

11. Change the Job name to morphology_lamotrigine
12. This job takes about 4 hours on an 8 GPU Host. If you would like to run the job yourself, adjust your Job settings () as needed and click Run.
    • To run from the command line, use the Write option from the Job settings dropdown. Note that parallel calculation on multiple GPUs is supported for simultaneous calculation of surface energies for multiple slabs.
13. Alternatively, if you would prefer to proceed with pre-generated structures, skip directly to Section 4 where you will be guided to import a provided output.

Figure 4-1. The entry list after running the job or importing (note that the output has been translated into the unit cell).

If you ran the job yourself, you can skip the importing step. Otherwise:

1. Go to File > Import Structures
2. Navigate to where you downloaded the provided tutorials, choose Section_04 > morphology_lamotrigine > morphology_lamotrigine-out.maegz and click Open
   • 41 entries are added to the entry list
   • These entries are the outputs of the MD simulations for the bulk crystal cell and each surface slab

Note: It is possible that some outputs may appear outside of the unit cell. This is purely visual, but can be adjusted with the Translate to First Unit Cell option in the Periodic Structure Tools ()

Figure 4-2. Viewing the cohesive energy for the bulk structure.

It is good practice to perform a trajectory analysis for the bulk or any of the slabs. For example, we might be interested in viewing the cohesive energy, the key output for the Wulff crystal shape prediction, to confirm convergence

3. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
   • The MS MD Trajectory Analysis panel opens
4. Go to the Bulk Properties tab
5. Click Load
6. Navigate to the morphology_lamotrigine_bulk-out.eaf file in the provided tutorial files and click Open
   • The top plot shows Volume (or Density from the dropdown), which is constant as expected (NVT calculation was performed).
   • The bottom plot shows the parameter of interest, Cohesive Energy. We can confirm that the running average of the energy is converged in the last 20% of the trajectory. This part of the trajectory will be used for calculation of the crystal morphology.

Figure 4-3. Viewing the cohesive energy for one of the slab structures.

7. In the MS MD Trajectory Analysis, view an additional .eaf file, for example the {1,1,-1} slab as shown in the Figure

 

 

In this case, the cohesive energy is clearly converged before the final 20% of the trajectory. If this were not the case, a longer simulation time would be recommended in the initial Crystal Morphology calculations.

 

 

8. Close the MS MD Trajectory Analysis panel

Figure 4-4. Including the lamotrigine unit cell and selecting the MD outputs.

Now, we can proceed to use the Wulff Viewer panel to predict the crystal morphology:

9. Includethe entry is represented in the Workspace, the circle in the In column is blue the original lamotrigine entry in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed 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 41 entries output from the MD simulations
   • Recall that includethe entry is represented in the Workspace, the circle in the In column is blue means to fill the blue circle to show the structure in the workspace 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 means to highlight the row in the entry list

Figure 4-5. The Wulff Viewer panel after loading the bulk and the slabs.

10. Go to Tasks > Materials > Classical Mechanics > Crystal Morphology > Wulff Viewer
    • Alternatively, use the Workflow Action Menu (WAM) button to open the Wulff Viewer panel.
    • The Wulff Viewer panel opens
11. If necessary, click Load Bulk from Workspace to load the unit cell into the panel, and Load Selected Entries to load the slabs into the Miller plane table
    • Your panel may already be populated, in which case, confirm it matches the one shown in the Figure and proceed. If the bulk is loaded, lamotrigine will appear next to the button, and if the slabs are loaded, the table will be populated

 

Before proceeding, note that the table looks similar to our input table, but now includes Energy J/m² and Area Ų which are the cohesive energies and physical surface areas of the slabs. These columns are sortable.

Figure 4-6. The structure after plotting with the table sorted by Relative Area.

12. Click Plot
    • The viewer is updated with the macroscopic structure
13. Click on the Relative Area column header twice to sort in descending order to see the planes with the greatest contribution to the structure

 

Note that lower surface energy slabs contribute more to the overall structure, but that symmetry and multiplicity can result in some slabs with slightly higher energies contributing more to the crystal.

Figure 4-7. The workspace view.

In addition to visualizing the macroscopic structure in the Wulff Viewer, we can view the plot in the workspace.

14. Maintain Show in Workspace (or click the check if it is not selected)
15. Check Show Miller indices
16. Adjust your view so that you can see the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, the plot is shown as well as the indices corresponding with the various planes

Figure 4-8. Turning on planes view.

It can be useful to view {hkl} crystal planes in the workspace.

17. Open the Show Workspace Configuration panel ()
18. Click Planes
    • The default {1,1,0} plane is shown in the workspace
19. Click on the 3-dot icon to the right of Planes ()
    • The Crystal Planes panel opens

Figure 4-9. Viewing the {2,1,0} plane.

20. For Plane 0, input 2, 1, 0 for h, k and l, respectively
    • The {2,1,0} plane is shown in the workspace

 

Feel free to explore adding and viewing additional planes in the workspace.

Figure 4-10. Viewing the crystal habit based solely on the interplanar distance.

It is useful to also be aware that the Wulff Viewer can be used to construct crystal habits without actually performing any molecular dynamics simulation. Recall that in general, planes with larger interplanar distances are more likely to have smaller interplanar interactions, and therefore are expected to be more stable surfaces. These planes are more likely to contribute to the Wulff construction according to the BFDH model.

 

21. Return to the Wulff Viewer panel and check Use interplanar distance
    • The Wulff Viewer updates to display the predicted crystal habit using the simplest BFDH model
    • Clearly, without accounting for surface energy, the crystal habit prediction is too oversimplified

 

Note: In addition to viewing the output based on interplanar distance alone, if we were interested in simply generating a crystal habit for planes that we suspect will contribute, we can manually add those planes and Plot the resultant output. Use the Add, Delete and Plot buttons to explore this further.

Figure 4-11. Deleting the 0 0 2 entry.

22. Return the viewer to the original output (uncheck Use interplanar distance and, if you added or deleted any planes, reload the entries from the workspace; or simply repeat steps 9-12).

Another way the Wulff Viewer can be used in a predictive fashion is by changing the Energy associated with any of the surfaces and viewing the expected crystal habit. In this way, we can consider strategies for altering our crystallization approach or formulation entirely towards some desired outcome. For example, let’s change the Energy of the {0 0 2} entry and see the effect on the crystal habit.

23. Click to highlight the  0 0 2 row in the table
24. Click Delete
    • The 0 0 2 row is removed from the table
    • Of course, we can always load the original data back in from the entry list

Figure 4-12. Manually changing the energy of a plane.

25. In the Miller plane input at the top of the panel, enter 0 0 2 and click Add
    • The 0 0 2 row is added back to the table at the end
26. Change the Energy to 0.1 by double-clicking on the default 1.0 energy and typing in the new energy
27. Click Plot
    • The crystal habit is updated to demonstrate the effect of lowering the energy of the {0 0 2} slab

 

Feel free to explore manually utilizing the Wulff Viewer to study the effect of different slab contributions with different energy values. Such exploration may be useful for predictive efforts.