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R4670 PySONIC (old)
constants.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-11-04 13:23:31
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2019-05-29 02:45:41
''' Algorithmic constants used in the package. '''
# Biophysical constants
FARADAY
=
9.64853e4
# Faraday constant (C/mol)
Rg
=
8.31342
# Universal gas constant (Pa.m^3.mol^-1.K^-1 or J.mol^-1.K^-1)
Z_Ca
=
2
# Calcium valence
Z_Na
=
1
# Sodium valence
Z_K
=
1
# Potassium valence
CELSIUS_2_KELVIN
=
273.15
# Celsius to Kelvin conversion constant
# Fitting and pre-processing
LJFIT_PM_MAX
=
1e8
# intermolecular pressure at the deflection lower bound for LJ fitting (Pa)
PNET_EQ_MAX
=
1e-1
# error threshold for net pressure at computed equilibrium position (Pa)
PMAVG_STD_ERR_MAX
=
3000
# error threshold in nonlinear fit of molecular pressure (Pa)
# Mechanical simulations
MAX_RMSE_PTP_RATIO
=
1e-4
# threshold RMSE / peak-to-peak ratio for periodic convergence
Z_ERR_MAX
=
1e-11
# periodic convergence threshold for deflection (m)
NG_ERR_MAX
=
1e-24
# periodic convergence threshold for gas content (mol)
NCYCLES_MAX
=
10
# max number of acoustic cycles in mechanical simulations
CHARGE_RANGE
=
(
-
200e-5
,
150e-5
)
# physiological charge range constraining the membrane (C/m2)
# E-STIM simulations
DT_ESTIM
=
5e-5
# A-STIM simulations
SOLVER_NSTEPS
=
1000
# maximum number of steps allowed during one call to the LSODA/DOP853 solvers
CLASSIC_TARGET_DT
=
1e-8
# target temporal resolution for output arrays of classic simulations
NPC_FULL
=
1000
# nb of samples per acoustic period in full system
NPC_HH
=
40
# nb of samples per acoustic period in HH system
DQ_UPDATE
=
1e-5
# charge evolution threshold between two hybrid integrations (C/m2)
DT_UPDATE
=
5e-4
# time interval between two hybrid integrations (s)
DT_EFF
=
5e-5
# time step for effective integration (s)
MIN_SAMPLES_PER_PULSE_INT
=
1
# minimal number of time points per pulse interval (TON of TOFF)
# Spike detection
SPIKE_MIN_QAMP
=
5e-5
# threshold amplitude for spike detection on charge signal (C/m2)
SPIKE_MIN_QPROM
=
20e-5
# threshold prominence for spike detection on charge signal (C/m2)
SPIKE_MIN_VAMP
=
10.0
# threshold amplitude for spike detection on potential signal (mV)
SPIKE_MIN_VPROM
=
20.0
# threshold prominence for spike detection on potential signal (mV)
SPIKE_MIN_DT
=
5e-4
# minimal time interval for spike detection on charge signal (s)
MIN_NSPIKES_SPECTRUM
=
3
# minimum number of spikes to compute firing rate spectrum
# Titrations
TITRATION_T_OFFSET
=
200e-3
# offset period for titration procedures (s)
TITRATION_ASTIM_DA_MAX
=
1e2
# acoustic pressure search range threshold for titration (Pa)
TITRATION_ESTIM_A_MAX
=
50.0
# initial current density upper bound for titration (mA/m2)
TITRATION_ESTIM_DA_MAX
=
0.1
# current density search range threshold for titration (mA/m2)
# QSS stability analysis
QSS_REL_OFFSET
=
.
05
QSS_HISTORY_INTERVAL
=
30e-3
# recent history interval (s)
QSS_INTEGRATION_INTERVAL
=
1e-3
# iterative integration interval (s)
QSS_MAX_INTEGRATION_DURATION
=
1000e-3
# iterative integration interval (s)
QSS_Q_CONV_THR
=
1e-7
# max. charge deviation to infer convergence (C/m2)
QSS_Q_DIV_THR
=
1e-4
# min. charge deviation to infer divergence (C/m2)
TMIN_STABILIZATION
=
500e-3
# time window for stabilization analysis (s)
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