Crystal Colouring

Layer Colouring

• Do you want to colour crystals in layers?: By answering "yes" this function allows you to colour terraces on crystal surfaces which is useful to mimic the nanoscopic features seen in atomic force micrographs.  
• Find layers or colour them from an existing file: In order to colour the crystal surfaces you first have to generate a file that contains the crystal surfaces to be coloured. Therefore, if it is the first time that you are working on a new crystal you should enter "find". This will generate two output files after a crystal is grown.  One called prefix_facets_found.txt, which is a first estimate of the facets expressed on the crystal.  The other file is called ./filepath/prefix_facets_all.txt which is a list of all other possible facets with h,k,l index equal to or less than 4.  The file prefix_facets_found.txt will probably need some editing - see below.  Once you have a correct edited ./filepath/prefix_facets_found.txt then you can enter "colour".
• File path for crystal terrace colouring: only needed if "colour" checked above.  This should be the name of the edited layer colouring file.
• Max hkl to find: only needed if "find" checked above.  This denotes the maximum value of h, k and l to search when determining the facets in the crystal. It is best to keep this number as small as possible in order to limit incorrect hits. However, it should be large enough to find the all the higher index facets. For example, if you are expecting only (100) and (110) facets then set this value to one.

Edit colouring file

• File path for layer colouring file to be edited: this should be ./filepath/prefix_facets_found.txt. Browse to find this file then press "read layer file".  This will generate a list of all the crystal facets that have been found. You should uncheck the crystal facets that are incorrect or unwanted.  Families of planes will all have the same d-spacing. Very often you will have duplicates. For example, (100) and (200). These are the same facets but the d-spacing is different. Choose the one with the correct d-spacing for the terrace height. The edit routine also allows you to adjust the "Number of layers to colour" (default is 4).  For larger crystals with more terraces on a given face this number will need to be increased. You can also adjust the "Offset for colouring". This allows the plane in the unit cell at which there is a colour change to be fine tuned to make sure all the molecules are neatly contained within one colour block for a given terrace. This will have to be adjusted by trial and error.
• File path to save edited layer colouring file: after unchecking undesired layers and adjusting "Number of layers to colour" and "Offset for colouring" enter a suitable filepath and click "save changes".
• File path for the file containing all planes info: following a "find" operation this file will contain all facets up to Max hkl set above. With this file you can add facets or families of facets present on your crystal that were not identified by the "find" operation.

RECOLOURING TIP

• If you want to adjust the colouring in order to get everything correct the first time you work on a new system: (i) save a checkpoint file with a size large enough to see the facets of interest; (ii) setup your colouring file; (iii) do a simulation with only 2 iterations while loading the checkpointed file. This will run almost instantaneously and allow you to see whether your colouring file is correct.  If not, keep repeating (ii) & (iii) until you are happy with the colouring.