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R4670/sim/MECH_run.py
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MECH_run.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2018-03-15 18:33:59
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-03-16 12:02:26
""" Script to run MECH simulations from command line. """
import sys
import os
import logging
from argparse import ArgumentParser
from PointNICE.utils import logger, InputError
from PointNICE.bls import BilayerSonophore
from PointNICE.solvers import checkBatchLog, runMech
from PointNICE.plt import plotBatch
# Default parameters
default = {
'a': 32.0, # nm
'd': 0.0, # um
'f': 500.0, # kHz
'A': 100.0, # kPa
'Cm0': 1.0, # uF/cm2
'Qm0': 0.0, # nC/cm2
'Qm': 0.0, # nC/cm2
}
def main():
# Define argument parser
ap = ArgumentParser()
# ASTIM parameters
ap.add_argument('-a', '--diameter', type=float, default=default['a'],
help='Sonophore diameter (nm)')
ap.add_argument('-d', '--embedding', type=float, default=default['d'],
help='Embedding depth (um)')
ap.add_argument('-f', '--frequency', type=float, default=default['f'],
help='Acoustic drive frequency (kHz)')
ap.add_argument('-A', '--amplitude', type=float, default=default['A'],
help='Acoustic pressure amplitude (kPa)')
ap.add_argument('-Cm0', '--restcapct', type=float, default=default['Cm0'],
help='Membrane resting capacitance (uF/cm2)')
ap.add_argument('-Qm0', '--restcharge', type=float, default=default['Qm0'],
help='Membrane resting charge density (nC/cm2)')
ap.add_argument('-Qm', '--charge', type=float, default=default['Qm'],
help='Applied charge density (nC/cm2)')
ap.add_argument('-o', '--outputdir', type=str, default=os.getcwd(),
help='Output directory')
# Boolean parameters
ap.add_argument('-v', '--verbose', default=False, action='store_true',
help='Increase verbosity')
ap.add_argument('-p', '--plot', default=False, action='store_true',
help='Plot results')
# Parse arguments
args = ap.parse_args()
a = args.diameter * 1e-9 # m
d = args.embedding * 1e-6 # m
Fdrive = args.frequency * 1e3 # Hz
Adrive = args.amplitude * 1e3 # Pa
Cm0 = args.restcapct * 1e-2 # F/m2
Qm0 = args.restcharge * 1e-5 # C/m2
Qm = args.charge * 1e-5 # C/m2
output_dir = args.outputdir
if args.verbose:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
try:
log_filepath, _ = checkBatchLog(output_dir, 'MECH')
logger.info('Running MECH simulation: a = %.1f nm, f = %.2f kHz, A = %.2f kPa',
a * 1e9, Fdrive * 1e-3, Adrive * 1e-3)
bls = BilayerSonophore(a, Fdrive, Cm0, Qm0, d)
outfile = runMech(output_dir, log_filepath, bls, Fdrive, Adrive, Qm)
logger.info('Finished')
if args.plot:
plotBatch(output_dir, [outfile])
except InputError as err:
logger.error(err)
sys.exit(1)
if __name__ == '__main__':
main()
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