run_mech.py
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	# -- coding: utf-8 --
	# @Author: Theo Lemaire
	# @Email: theo.lemaire@epfl.ch
	# @Date: 2016-11-21 10:46:56
	# @Last Modified by: Theo Lemaire
	# @Last Modified time: 2019-06-17 14:23:50

	''' Run simulations of the NICE mechanical model. '''

	import matplotlib.pyplot as plt

	from PySONIC.core import BilayerSonophore, Batch
	from PySONIC.utils import logger
	from PySONIC.plt import GroupedTimeSeries
	from PySONIC.parsers import MechSimParser


	def main():
	# Parse command line arguments
	parser = MechSimParser()
	args = parser.parse()
	logger.setLevel(args['loglevel'])

	# Run MECH batch
	logger.info("Starting mechanical simulation batch")
	pkl_filepaths = []
	inputs = [args[k] for k in ['freq', 'amp', 'charge']]
	for a in args['radius']:
	for d in args['embedding']:
	for Cm0 in args['Cm0']:
	for Qm0 in args['Qm0']:
	bls = BilayerSonophore(a, Cm0, Qm0, embedding_depth=d)
	queue = bls.simQueue(*inputs, outputdir=args['outputdir'])
	batch = Batch(bls.runAndSave, queue)
	pkl_filepaths += batch(mpi=args['mpi'], loglevel=args['loglevel'])

	# Plot resulting profiles
	if args['plot'] is not None:
	GroupedTimeSeries(pkl_filepaths, pltscheme=args['pltscheme'])()
	plt.show()


	if __name__ == '__main__':
	main()