FACS: Flu And Coronavirus Simulator

Full documentation can be found at: http://facs.readthedocs.io

How to run the code

To run a simple simulation of a basic test dataset, type: python3 run.py --location=test --output_dir=.

To run it in parallel, type (for four core runs): mpirun -np 4 python3 run.py --location=test --output_dir=.

To do a run of custom length (with -t flag), and with a generically named out.csv output file, type: mpirun -np 1 python3 run.py -t=10 -g --location=test --output_dir=.

To run a simulation of the Borough of Brent, type: python3 run.py --location=brent --output_dir=.

To run a simulation of Brunel University London, type: python3 run_campus.py --location=brunel --output_dir=.

Outputs are written as CSV files in the output_dir. E.g. for the test run you will get: covid_out_infections.csv test-extend-lockdown-62.csv

There is a hardcoded lockdown in run.py which is representative for the UK. This can be disabled by selecting the transition scenario "no-measures".

We also included a simple plotting script. This can be called e.g. as follows: python3 PlotSEIR.py test-extend-lockdown-62.csv test

Advanced usage

Running with a specific data directory

Flacs can be run with a different input data directory as follows: python3 run.py --location=brent --output_dir=. --data_dir=/home/derek/covid19-postprocess/facs_input_private

Performing quick tests

Quick tests can be triggered with the '-q' flag. This sets the house ratio to 100 (default is 2), which means that households will be less well distributed. However, as a number of calculations are performed on the house level (not the household level), this setting speeds up the code by up to an order of magnitude. python3 run.py -q --location=brent --output_dir=.

Submitting jobs to the GridPP via HTCondor

Facs directory contains four additional files: script_grid.sh (bash script for job submission automation) run_grid.py (python script equivalent to run.py for job submission) joblist_grid.txt (list of jobs with facs arguments for job queuing) job_grid.submit (contains the configuration for facs simulations)

After initiating the python environment, the pyinstaller package can be used to create an executable from 'run_grid.py'. pyinstaller run_grid.py --onefile

There are currently 18 locations (jobs) in the 'joblist_grid.txt' file. (optional) The jobs are submitted with the command: condor_submit job_grid.submit

The results are transferred back to the local machine and placed in 'output_dir'.