Simulation Options

Output Files

• File prefix for simulation results: this is a prefix that will be attached to all files associated with the simulation.
• Path to output files: this is the file path where all the output files will be stored under a timestamped folder.
• How do you wish to store visualiser (.xyz) files?: "together in a separate folder" stores all (.xyz) files in their own folder separate from other simulation data; "separately at data file locations" stores each (.xyz) file in a folder with other related simulation data; "in both locations" stores (.xyz) files according to both the previous options.
• Path to log file: this is the file path to save a logfile. Every time a simulation is run, a lot of useful information about the simulation is saved to a logfile called CrystalGrower_log.csv. The information is appended at the end of any existing logfile with this name in the directory identified here. The information is comma delimited and can be opened in, for example, Microsoft Excel.

Simulation Setup

• Do you want species grouped: this option will only appear for net type simulations.  In the structure file each molecule is given both a name and a number. If "yes" is checked the molecules will be treated the same if they have the same name. If "no" is checked then all molecules will be treated differently according to both name and number. Grouping molecules improves efficiency of the calculation and decreases other information required.
• Temperature in celcius?: temperature at which crystal is grown.
• Number of iterations?: how many (growth + dissolution) steps in the simulation.

Memory

• Do you want to calculate memory for the simulation?: With "yes" checked CrystalGrower will first grow a small crystal and then try to determine how much memory is required to complete the entire simulation. It is not absolutely foolproof but works for most situations and optimises memory allocation. With "no" checked the user will be asked to allocate memory (see next section).
• Max memory you wish to use (MBytes)? Default=10000: this option will only appear if users request for memory to be calculated automatically and prevents too much memory being allocated by the automatic memory function should users request a simulation of a very large crystal.
• Size of simulation in the x/y/z direction (Must be odd): Only asked if users request for memory to not be automatically calculated. This is the number of unit cells to be assigned to memory in the a, b and c directions of the primitive cell. If this is too small then the simulation will terminate early and save the grown crystal at that point. If a checkpointed file is read in then the size of the simulation will need to be entered.

Output Frames

• Movie output or single frame?: "single frame" records the simulations after the final iteration. "movie" records the simulation at multiple points.
• MOVIE - Number of frames?: only asked for a movie. The number of equally spaced frames in the movie.
• MOVIE - Iteration at initial frame? (default = 1): only asked for a movie. The starting point for the movie.
• MOVIE - Set final frame equal to the number of iterations: only asked for a movie. "yes" or "no".
• MOVIE - Iteration at final frame?: only asked for a movie if previous question answered "no". The end point for the movie.