matexp
This program solves systems of differential equations for the NEURON simulator using the matrix-exponential method of integration. This is a new method of integration. The solution is faster and more accurate than NEURONs built in "sparse" solver. This method is only applicable to systems which are linear and time-invariant, such as Markov kinetic models. This method is also limited to systems with one or two inputs.
This program uses the NMODL file format (".mod" files). The input kinetic model is an NMODL file, and the solution is written to a new NMODL file.
For more information about how this program works see DETAILS.md.
Installation
Prerequisites:
- Compiler for the target system.
- CPU requires
g++ - Cuda requires the
cupypython package.
- CPU requires
$ pip install matexp
Usage
$ matexp --help
usage: matexp [-h] [-v] [--plot] -t TIME_STEP [-c CELSIUS] [-e ERROR]
[-i NAME MIN MAX] [--log [INPUT]] [--target {host,cuda}]
[-f {32,64}]
INPUT_PATH OUTPUT_PATH
positional arguments:
INPUT_PATH input filename for the unsolved NMODL file
OUTPUT_PATH output filename for the solution
options:
-h, --help show this help message and exit
-v, --verbose print diagnostic information, give twice for trace mode
--plot show the propagator matrix
simulation parameters:
-t TIME_STEP, --time_step TIME_STEP
-c CELSIUS, --celsius CELSIUS
default: 37°
-e ERROR, --error ERROR
maximum error per time step. default: 10^-4
input specification:
-i NAME MIN MAX, --input NAME MIN MAX
--log [INPUT] scale input logarithmically, for chemical concentrations
computer specification:
--target {host,cuda} default: host
-f {32,64}, --float {32,64}
default: 64
