| Name | matexp JSON |
| Version |
1.0.0
JSON |
| download |
| home_page | |
| Summary | Simulator for Linear Time-Invariant Kinetic Models using the NMODL file format. |
| upload_time | 2023-07-17 13:40:16 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
nmodl
neuron
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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](https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechanisms/nmodl.html)
(".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](./DETAILS.md).
### Installation
Prerequisites:
* Compiler for the target system.
+ CPU requires `g++`
+ Cuda requires the `cupy` python package.
```
$ 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
```
Raw data
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"description": "# matexp\n\nThis program solves systems of differential equations for the NEURON simulator\nusing the matrix-exponential method of integration. This is a new method of\nintegration. The solution is faster and more accurate than NEURONs built\nin \"sparse\" solver. This method is only applicable to systems which are linear\nand time-invariant, such as Markov kinetic models. This method is also limited\nto systems with one or two inputs.\n\nThis program uses the\n[NMODL file format](https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechanisms/nmodl.html)\n(\".mod\" files). \nThe input kinetic model is an NMODL file, and the solution is written to a new NMODL file.\n\nFor more information about how this program works see [DETAILS.md](./DETAILS.md).\n\n\n### Installation\n\nPrerequisites:\n* Compiler for the target system.\n + CPU requires `g++`\n + Cuda requires the `cupy` python package.\n\n```\n$ pip install matexp\n```\n\n\n### Usage\n\n```\n$ matexp --help\nusage: matexp [-h] [-v] [--plot] -t TIME_STEP [-c CELSIUS] [-e ERROR]\n [-i NAME MIN MAX] [--log [INPUT]] [--target {host,cuda}]\n [-f {32,64}]\n INPUT_PATH OUTPUT_PATH\n\npositional arguments:\n INPUT_PATH input filename for the unsolved NMODL file\n OUTPUT_PATH output filename for the solution\n\noptions:\n -h, --help show this help message and exit\n -v, --verbose print diagnostic information, give twice for trace mode\n --plot show the propagator matrix\n\nsimulation parameters:\n -t TIME_STEP, --time_step TIME_STEP\n -c CELSIUS, --celsius CELSIUS\n default: 37\u00b0\n -e ERROR, --error ERROR\n maximum error per time step. default: 10^-4\n\ninput specification:\n -i NAME MIN MAX, --input NAME MIN MAX\n --log [INPUT] scale input logarithmically, for chemical concentrations\n\ncomputer specification:\n --target {host,cuda} default: host\n -f {32,64}, --float {32,64}\n default: 64\n\n```\n\n",
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