added new files for simulation.

.gitignore

config.toml

config.yaml

environment_setup/Dockerfile

legacy_scripts/find_s1.py

legacy_scripts/find_s2.py

legacy_scripts/main.cpp

legacy_scripts/src/main.cpp

results.csv

simulations/input/basic.par

simulations/input/generate_mesh.py

simulations/input/s1.par

simulations/input/s2.par

simulations/input/tests/new_basic.par

simulations/input/tests/s1_s2.par

yaml-cpp