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: 2019-07-01 15:49:33

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

	from PySONIC.core import BilayerSonophore, Batch
	from PySONIC.utils import logger
	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")
	queue = BilayerSonophore.simQueue(*parser.parseSimInputs(args), outputdir=args['outputdir'])
	output = []
	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)
	batch = Batch(bls.simAndSave if args['save'] else bls.simulate, queue)
	output += batch(mpi=args['mpi'], loglevel=args['loglevel'])

	# Plot resulting profiles
	if args['plot'] is not None:
	parser.parsePlot(args, output)


	if __name__ == '__main__':
	main()