Structure Options

Structure

• Is this a tile or net simulation?: "net" means that the structure is built of single units that are linked together (suitable for molecular and ionic crystals, MOFs and metals). In this case a new tab [Net Options] appears. "tile" means that the system is built from 3-dimensional tiles (suitable for zeolites and framework materials). In this case a new tab [Tile Options] will appear where information about the energies of the tiles can be entered.
• File path to structure file: use the browse box to input the file path to a structure file for your crystal. Then press "read structure file". The message "Structure file read successfully" will be displayed in the notification window if the file was read successfully.
• File path to net energy file: this question only appears for "net" type crystals and specifies the path to the file containing the crystallisation energies associated with the structure. Once the file path is specified, press "read net.txt". Users should see the message "Net file read successfully". A box will then appear that allows you to link the energies required for different molecules. If you wish different molecules to be treated the same then enter the same letter (e.g. both A). Press "Confirm interactions".

Optional Features

• Insert screw dislocation?: a single screw dislocation can be added to your crystal structure. If "yes" is checked then another tab [Screw Dislocation] will appear where you can enter the parameters for the required screw dislocation.
• Mode?: this refers to the type of simulation required. By default this is set to "normal". If you want to add growth modifiers to poison sites check "growth modifier". In that case a new tab [Growth Modifier] will appear where information about the sites to be poisoned is entered. Additional modes currently being tested are "ordered" - for consideration of the order of framework atoms in "tile" structures and "screw_stress" - to model the addition of stress at the screw core. Please enquire on the Contact Us page to arrange a possible collaboration using these modes.
• Energy penalty associated with ordered structure [kcal/mol]: this option will only appear if an "ordered" structure is selected in the previous question (currently under development). The value entered relates to the difference in energy of crystallisation for different components in a tile simulation – for example Al vs Si insertion in a zeolite structure.

Checkpoint file

• Do you want to load a checkpoint file?: a checkpoint file is a previous simulation (that must have been saved as a checkpoint file) that you can use as the starting point for a new simulation. There will be some restrictions placed on the subsequent simulation to be consistent with the checkpointed simulation. 
• Path to checkpoint file: If you check "yes" browse for a previously checkpointed file then click "read checkpoint file". Users should see the message "Checkpoint file read successfully".
• Do you want to save a checkpoint file?: If you check "yes" then a checkpoint file, which is a record of the simulation, will be saved. This file allows a subsequent simulation to be started from the end of this simulation.