Classification of the simplified CaCO3 polymorphs 

  1. Open the database CaCO3_c generated in Module 4 and open an ADS window for the first record. Go to the ADS Topology options and check the Classification flag. The following parameters will also be specified:

    Dimen. Calc. (Common tab) – to recognize all non-bonded (separated) structural components (molecules, chains, layers, 3D frameworks and interpenetration). This flag may be unchecked to speed the analysis if you are sure that the crystal structure consists of a single net.

    Point Symbol (Topology tab) – to calculate ES.

    Coord. Seq. (Topology tab) – to calculate CS (default number of coordination shells is 10).

    Other flags in Common and Topology tabs will be unchecked. Pay attention that you may not set a smaller value of Coord. Seq. and uncheck Point Symbol until the Classification flag is unchecked. You may specify non-zero Max. Ring parameter to use extended CS+ES+VS set of indices for classification. However, in most cases CS+ES set is sufficient to recognize nets and it works much faster than CS+ES+VS. We recommend to use the default set for the first time, then you may toggle to CS+ES+VS set and check the results of the first classification. See below.

  2. Run ADS and select all atoms in the Choose Central Atoms window. You will get the output like in Task 1, but the last line will contain the information about topological type:

    Topological type: nia {4^12;6^3}{4^9;6^6} - VS [*.*.*] [] (69712 types in 10 databases)

    You see that the topological type of the simplified aragonite is nia indeed. Pay attention that the size of rings in VS is not larger than 6. So you may check CS+ES+VS set with Max. Ring = 6.
  3. Return to ADS options, specify Max. Ring = 6 and run ADS again. Be sure that the CS+ES+VS set gives the same result.
  4. Repeat the procedure for the remaining two records in a batch mode. Select them, open an ADS window, specify Options/Continuous/Central Atoms = El and check Standard Ring Limits flag. This ensures that ToposPro will use standard Max. Ring values for different nets depending on the net coordination:

    CoordinationMax. RingCoordinationMax. Ring
    3- or 4-coordinated 26 7-coordinated 12
    5-coordinated 20 8- or 9-coordinated 10
    6-coordinated 16 >9-coordinated 8

    These values will be applied instead of the Max. Ring value specified in the Topology tab only if CS+ES+VS set is used (Max. Ring > 0). Pay attention that Standard Ring Limits flag as well as all other options on the Continuous tab are valid only in the batch mode, when there are selected records in the database and the flag Common/Cont. Calc. is checked.

    Run ADS.

  Go to the top