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Computing natural tiling, dual net, determining combinatorial types of tiles for the zeolite SOD (sodalite)
Algorithm:
1. Go to the SOD record and open an ADS window. Check Dual Nets and Determine Tile Topology (The flags on the Common tab and on the Topology tab are the same that in the Example 1).
2. Run ADS. Reply "No" to append the information on the tiling to the LTA_SOD_3dt.cgd file.
3. Create the database LTA_SOD# to save the data on the dual net.
4. Overwrite the LTA_SOD_t.tnt file.
5. Choose all atoms in the Choose Central Atoms window.
6. Pay attention that a new database is created with the record SOD/sod;PPT 1 containing both initial sod and dual net. The nodes of the dual net are designated as ZA. The degree of the node is 14 (equal to the number of faces in the sodalite cage).
7. Determine the topology of the dual net. For this purpose, open one more ADS window, uncheck all Common options and check Classification flag. Run ADS. Select all atoms as central. You will get the output:
Pay attention that there are two structural units (interpenetrating 3D nets) of the topological types sod (initial net) and bcu-x (dual net).
8. Close the ADS window and look at the initial and dual nets in IsoCryst. Select the central node of the dual net and grow it one time to get all its neighbors. Pay attention that all edges of the dual net pass through the faces of the tile in the initial net.
9. Close the IsoCryst window and the database LTA_SOD#, then select both records in the database LTA_SOD. Uncheck Write Data to .tnt and Essential Rings for 3dt options and specify Topology and Tiling options as shown below. Uncheck Continuous/Standard Ring Limits option to speed up the calculation (the rings up to size 8 will be checked only). Specify Continuous/Central Atoms = El.
10. Run ADS. Pay attention that now ADS has determined the [46.68] combinatorial type (truncated octahedron) both in SOD and in LTA.
Exercise: compute the natural tiling and dual net for your own crystal structure simplified in Module 4.
Algorithm:
1. Go to the SOD record and open an ADS window. Check Dual Nets and Determine Tile Topology (The flags on the Common tab and on the Topology tab are the same that in the Example 1).
2. Run ADS. Reply "No" to append the information on the tiling to the LTA_SOD_3dt.cgd file.
3. Create the database LTA_SOD# to save the data on the dual net.
4. Overwrite the LTA_SOD_t.tnt file.
5. Choose all atoms in the Choose Central Atoms window.
6. Pay attention that a new database is created with the record SOD/sod;PPT 1 containing both initial sod and dual net. The nodes of the dual net are designated as ZA. The degree of the node is 14 (equal to the number of faces in the sodalite cage).
7. Determine the topology of the dual net. For this purpose, open one more ADS window, uncheck all Common options and check Classification flag. Run ADS. Select all atoms as central. You will get the output:
Pay attention that there are two structural units (interpenetrating 3D nets) of the topological types sod (initial net) and bcu-x (dual net).
8. Close the ADS window and look at the initial and dual nets in IsoCryst. Select the central node of the dual net and grow it one time to get all its neighbors. Pay attention that all edges of the dual net pass through the faces of the tile in the initial net.
9. Close the IsoCryst window and the database LTA_SOD#, then select both records in the database LTA_SOD. Uncheck Write Data to .tnt and Essential Rings for 3dt options and specify Topology and Tiling options as shown below. Uncheck Continuous/Standard Ring Limits option to speed up the calculation (the rings up to size 8 will be checked only). Specify Continuous/Central Atoms = El.
10. Run ADS. Pay attention that now ADS has determined the [46.68] combinatorial type (truncated octahedron) both in SOD and in LTA.
Exercise: compute the natural tiling and dual net for your own crystal structure simplified in Module 4.
