8.4 How to predict structures based on known fragments?

Sometimes you already know that your structure is based on packing of some well defined motifs. You can tell the program to generate only structures based on the packing ‘fake molecules’. Meanwhile, you still use the standard approach to generate child structures (such as heredity and mutation) which treat the structure as atomic crystals, and thus can break the predefined motif. To activate the function, you just prepare an ordinary INPUT.txt,


% atomType
B
% EndAtomType

% numSpecices
48
% EndNumSpecices

Suppose you want to generate structures base on boron icosahedra, an additional MOL_1 file is needed

B12_[4]
Number of atoms: 12
B  -1.591325  -0.618615  -0.217220     0 0 0   0
B  -0.574110  -0.095870  -1.619670     1 0 0   0
B  -1.211325   1.134555  -0.455665     2 1 0   0
B  -1.158010   0.414740   1.203810     3 2 1   0
B  -0.487865  -1.260560   1.065420     4 3 1   0
B  -0.126980  -1.576135  -0.679575     5 4 1   0
B   0.487845   1.260560  -1.065430     3 2 1   0
B   0.127000   1.576130   0.679585     4 3 1   0
B   0.574120   0.095870   1.619670     5 4 1   0
B   1.211315  -1.134555   0.455685     6 5 1   0
B   1.158015  -0.414735  -1.203800     2 6 1   0
B   1.591320   0.618615   0.217195     7 8 3   0

Its format has been described in Section 5.3. The only difference is that we need to put some additional information in the header. [4] here tells that 4 MOL_1 (B12) will be used, which is consistent with 48 B atoms described in INPUT.txt. The consistency is required. Otherwise, the fragment feature won’t be activated, even though you put addition MOL_x files in the INPUT.txt. If you set everything right, you will find the messages that this feature is used from OUTPUT.txt.

For 2D crystals, you need to specify two thicknesses in thic case.

4.0   : thicknessS (it specifies the overall thickness of 2D crystal )
0.0   : thicknessB (it specifies the thickness measured by the molecular centers)

Currently, one can use this feature in 300 and -200. Note that you cannot use single block and fragement feature simutaneously. It is highly recommended to use it with the fixed cell mode, when the cell parameters are available.