A listing of files and the subroutines/functions contained within the Phage to Shark code.
Code written by: Jon Parsons
Primary investigators:
Dr. P. Katira
Dr. C. Silveira
Dr. A. Luque
P2Smain.f90
Contains the master loop. No subroutines or functions contained.
coral_subs.F90 Contains subroutines related to the coral layer.
- corpop: Sets initial coral distribution and health
- corexp: Sets new coral
- newcoral: Sets new coral during spawning season
- growth: Grows existing coral
- decay: Handles interaction between coral and algae
disasters.f90 Contains the subroutines for disastrous events.
- hurricane: Handles simulation of a hurricane or other similar event
- disease: Handles simulation of a disease or other similar event
fish_subs.F90 Contains the subroutines pertaining to the fish elements
- fishinteraction: Handles interaction of fish with algae
- shark: Handles simulation of piscivores
microbes_subs.f90 Contains the subroutines for the microbial community
- kgrid: Determines the microbial carrying capacity at each point
- diffuse: Allows the bacteria population to diffuse based on population differences
- bactgrowptw: Grows the microbial community. The ptw suffix is deprecated, the code non longer simulates a piggyback the winner model
- microbepopptw: Generates the initial population of the microbial layer. The ptw suffix is deprecated
nonlifesubs.f90 Contains the subroutines which do no pertain the the evolution of the system. Mainly data handling and user input.
- printtofile: Accepts a 2-D array(3,N) which is printed in xyz format
- dircheck: Checks to see if a directory exists and creates it if not
- datacollect: Handles data collection and output for the entire reef
- inputs: Handles user input
- chartoup: Turns a char variable into uppercase
- domainout: Handles data collection and output for specific regions (coral//algae//interface)
- var/_adjuster: Adjusts parameters at a predetermined time based on user input
P2Smod.f90 Contains the global variables and functions for the simulation
- fishdelta: Returns change in fish population
- percentcor: Returns percentage of floor with coral
- virpopptw: Returns phage population. The ptw suffix is deprecated
- tempratio: Returns the temperance ratio
- lysratio: Returns the lysogen to bacteria ratio
- bactouch: Returns the bacterial influence parameter