.TH neurite 7 "March 2014" "Public version"
.SH NAME
Neurite - a parallel program for simulating electrophysiological signal propagation in neurites under mechanical loading
.SH SYNOPSIS
.B ./Neurite [Options] [output file] [log file]
.SH DESCRIPTION
Neurite is a finite difference program that simulates the electrophysiological signal propagation in myelinated and unmyelinated axons, and in dendritic trees under mechanical loading. The program has two different solvers---explicit and implicit---that can be executed with the sequential CPU processor or with GPU accelerators to run parallel simulations. The discretization must be defined as a function in space.cpp file
.SH MANDATORY
.IP -log
Set the name for the log file
.IP -out
Set the name for the output file
.SH INPUTS
Input_data.txt file: this file must be given to Neurite in case the mechanical model is used. For more information about this file, please see the mechanical_model.cpp file

neuron_for_neurite.txt file: this file must be given to Neurite when a segmented neuron is being loaded by the program
.SH OPTIONS
.IP General:
.IP -Tt
Total time of the simulation
.IP -dtf
Critical time step factor (Default value = 1)
.IP Solver:
.IP -E
Explicit solver
.IP -I
Implicit solver
.IP EXTRA:
.IP -xspan
Total length. N/A in a branched structure
.IP -MAXE
Maximum microscopic membrane axial strain
.IP -nu
Strain distribution coefficient between IR and NR
.IP -str
Microscopic membrane axial strain
.IP -IRE
Number of elements in each IR
.IP -HHE
Number of elements in each NR
.SH BUGS
None that I know of
.SH AUTHOR
Julian Andres Garcia-Grajales, under the supervision of Antoine Jerusalem
." .SH SEE ALSO
.SH