| Name | pyrokinetics JSON |
| Version |
0.6.1
JSON |
| download |
| home_page | |
| Summary | Python package for running and analysing gyrokinetic simulations |
| upload_time | 2023-12-07 12:34:43 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A "Combined Work" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the "Linked Version". The "Minimal Corresponding Source" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. The "Corresponding Application Code" for a Combined Work means the object code and/or source code for the Application, including any data and utility programs needed for reproducing the Combined Work from the Application, but excluding the System Libraries of the Combined Work. 1. Exception to Section 3 of the GNU GPL. You may convey a covered work under sections 3 and 4 of this License without being bound by section 3 of the GNU GPL. 2. Conveying Modified Versions. If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (a) uses at run time a copy of the Library already present on the user's computer system, and (b) will operate properly with a modified version of the Library that is interface-compatible with the Linked Version. e) Provide Installation Information, but only if you would otherwise be required to provide such information under section 6 of the GNU GPL, and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version. (If you use option 4d0, the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code. If you use option 4d1, you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source.) 5. Combined Libraries. You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. |
| keywords |
gyrokinetics
analysis
plasma
research
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://pyrokinetics.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/pyro-kinetics/pyrokinetics/actions?query=workflow%3Atests)
[](https://pypi.org/project/pyrokinetics/)
[](https://github.com/python/black)
[](https://codecov.io/gh/pyro-kinetics/pyrokinetics)
# Pyrokinetics
This project aims to standardise gyrokinetic analysis.
A general pyro object can be loaded either from simulation/experimental data or from an existing gyrokinetics file.
In general pyrokinetics can do the following
* Read data in from:
* Gyrokinetic input files
* Simulations outputs
* Write input files for various GK codes
* Generate N-D pyro object for scans
* Read in gyrokinetic outputs
* Standardise analysis of gk outputs
At a minimum pyrokinetics needs the local geometry and species data. Example scripts can be found in the examples folder
## Documentation
Documentation can be found at [readthedocs](https://pyrokinetics.readthedocs.io/en/latest/).
## Installation
Pyrokinetics requires a minimum Python version of 3.8. It may be necessary to upgrade
`pip` to install:
```bash
$ pip install --upgrade pip
```
To install the latest release:
```bash
$ pip install pyrokinetics
```
Otherwise, to install from source:
```bash
$ git clone https://github.com/pyro-kinetics/pyrokinetics.git
$ cd pyrokinetics
$ pip install .
```
If you are planning on developing pyrokinetics use the following instead to install:
```bash
$ pip install -e .[docs,tests]
```
Note that currently the installation of pyrokinetics requires an available Fortran compiler
## Testing
To run the tests:
```bash
$ pip install -e .[tests]
$ pytest --cov .
```
## Basic Usage
The simplest action in Pyrokinetics is to convert a gyrokinetics input file for code
'X' into an equivalent input file for code 'Y'. The easiest way to achieve this is to
use a `Pyro` object, which manages the various other classes in the API. For example,
to convert a GS2 input file to a CGYRO input file:
```python
>>> from pyrokinetics import Pyro
>>> pyro = Pyro(gk_file="my_gs2_file.in") # file type is automatically inferred
>>> pyro.write_gk_file("input.cgyro", gk_code="CGYRO")
```
There are many other features in Pyrokinetics, such as methods for building gyrokinetics
input files using global plasma equilibria and/or kinetics profiles. There are also
methods for analysing and comparing the results from gyrokinetics code runs. Please
[read the docs](https://pyrokinetics.readthedocs.io/en/latest/#) for more information.
## Command Line Interface
After installing, simple pyrokinetics operations can be performed on the command line
using either of the following methods:
```bash
$ python3 -m pyrokinetics {args...}
$ pyro {args...}
```
For example, to convert a GS2 input file to CGYRO:
```bash
$ pyro convert CGYRO "my_gs2_file.in" -o "input.cgyro"
```
You can get help on how to use the command line interface or any of its subcommands
by providing `-h` or `--help`:
```bash
$ pyro --help
$ pyro convert --help
```
## Docker
Pyrokinetics provides a `Dockerfile` from which you can build and run Docker containers.
To do so, you must have [Docker](https://docs.docker.com/engine/install/) installed on
your system. To build a local container:
```bash
$ docker build . -t pyrokinetics
```
It can then be run using:
```bash
$ docker run -it --rm -v ./path/to/local:/mymount pyrokinetics
```
where:
- `-it` runs an interactive shell.
- `--rm` deletes the Docker instance after use.
- `-v ./path/to/local:/mymount` mounts the local directory `./path/to/local` to the
directory `/mymount` within the Docker container.
The container runs an IPython interpreter, with Pyrokinetics already installed. Note
that you will need to `import` Pyrokinetics before it can be used.
## Code structure
Pyro object comprised of
* Equilibrium
* LocalGeometry
* Miller
* Fourier (to be added)
* Kinetics
* LocalSpecies
* Numerics
* GKCodes
* GKOutput
* For nonlinear simulations
* Fields (field, kx, ky, theta, time)
* Fluxes (field, species, moment, ky, theta, time)
* For linear simulations
* Fields (field, kx, ky, theta, time)
* Fluxes (field, species, moment, ky, theta, time)
* Eigenfunctions (field, ky, theta, time)
* Eigenvalues - growth rate and mode freq (ky, time)
There also exists the PyroScan object which allows you to make a N-D parameter scan of Pyro objects
## Supports sources of Equilibrium data
pyrokinetics currently supports
* [GEQDSK](https://w3.pppl.gov/ntcc/TORAY/G_EQDSK.pdf)
* [TRANSP](https://w3.pppl.gov/~pshare/help/body_transp_hlp.html#outfile56.html)
Future formats to be added are
* CHEASE
## Supported sources of Kinetic data
Sources of kinetic profile data currently supported are
* SCENE
* JETTO
* TRANSP
Future codes to be add
* SimDB
* OMFIT
## Supported GK codes
The following gk codes are supported in pyrokinetics
* CGYRO
* GS2
* GENE
* TGLF
Codes to be added in the future
* Stella
* GX
## Note on units
The pyro object uses standardised reference values to normalise the results. It will automatically handle converting to a GK codes standard units.
Note any scans/parameter changes made will be in standard pyro units so please account for this.
Reference values
- $T_{ref} = T_e$ Electron temperature at flux surface
- $n_{ref} = n_e$ Electron density at flux surface
- $m_{ref} = m_D$ Deuterium mass
- $v_{ref} = c_s = \sqrt{T_e/m_D}$ Ion sound speed at flux surface
- $B_{ref} = B_0$ Toroidal field at centre of the flux surface
- $L_{ref} = a$ Minor radius of the last closed flux surface
- $t_{ref} = a/c_s$ Ion sound time at flux surface
- $\rho_{ref} = \frac{c_s}{eB_0/m_D}$ Ion Larmor radius at flux surface
It is possible to change the reference units but proceed with caution
## Used By
This project is used by the following institutions
- CCFE
- University of York
Copyright owned by UKAEA. Pyrokinetics is licensed under LGPL-3.0, and is free to use, modify, and distribute.
Raw data
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"author_email": "Bhavin Patel <bhavin.s.patel@ukaea.uk>",
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"description": "[](https://pyrokinetics.readthedocs.io/en/latest/?badge=latest)\n[](https://github.com/pyro-kinetics/pyrokinetics/actions?query=workflow%3Atests)\n[](https://pypi.org/project/pyrokinetics/)\n[](https://github.com/python/black)\n[](https://codecov.io/gh/pyro-kinetics/pyrokinetics)\n\n\n# Pyrokinetics\n\nThis project aims to standardise gyrokinetic analysis. \n\nA general pyro object can be loaded either from simulation/experimental data or from an existing gyrokinetics file. \n\nIn general pyrokinetics can do the following\n\n* Read data in from:\n * Gyrokinetic input files\n * Simulations outputs\n* Write input files for various GK codes\n* Generate N-D pyro object for scans\n* Read in gyrokinetic outputs\n* Standardise analysis of gk outputs\n\nAt a minimum pyrokinetics needs the local geometry and species data. Example scripts can be found in the examples folder\n\n## Documentation\n\nDocumentation can be found at [readthedocs](https://pyrokinetics.readthedocs.io/en/latest/).\n\n## Installation \n\nPyrokinetics requires a minimum Python version of 3.8. It may be necessary to upgrade\n`pip` to install:\n\n```bash\n$ pip install --upgrade pip\n```\n\nTo install the latest release:\n\n```bash\n$ pip install pyrokinetics\n```\n\nOtherwise, to install from source:\n\n```bash \n$ git clone https://github.com/pyro-kinetics/pyrokinetics.git\n$ cd pyrokinetics\n$ pip install .\n```\n\nIf you are planning on developing pyrokinetics use the following instead to install:\n\n```bash \n$ pip install -e .[docs,tests]\n```\n\nNote that currently the installation of pyrokinetics requires an available Fortran compiler\n\n## Testing\n\nTo run the tests:\n\n```bash\n$ pip install -e .[tests]\n$ pytest --cov .\n```\n\n## Basic Usage\n\nThe simplest action in Pyrokinetics is to convert a gyrokinetics input file for code\n'X' into an equivalent input file for code 'Y'. The easiest way to achieve this is to\nuse a `Pyro` object, which manages the various other classes in the API. For example,\nto convert a GS2 input file to a CGYRO input file:\n\n```python\n>>> from pyrokinetics import Pyro\n>>> pyro = Pyro(gk_file=\"my_gs2_file.in\") # file type is automatically inferred\n>>> pyro.write_gk_file(\"input.cgyro\", gk_code=\"CGYRO\")\n```\n\nThere are many other features in Pyrokinetics, such as methods for building gyrokinetics\ninput files using global plasma equilibria and/or kinetics profiles. There are also\nmethods for analysing and comparing the results from gyrokinetics code runs. Please\n[read the docs](https://pyrokinetics.readthedocs.io/en/latest/#) for more information.\n\n## Command Line Interface\n\nAfter installing, simple pyrokinetics operations can be performed on the command line\nusing either of the following methods:\n\n```bash\n$ python3 -m pyrokinetics {args...}\n$ pyro {args...}\n```\n\nFor example, to convert a GS2 input file to CGYRO:\n\n```bash\n$ pyro convert CGYRO \"my_gs2_file.in\" -o \"input.cgyro\"\n```\n\nYou can get help on how to use the command line interface or any of its subcommands\nby providing `-h` or `--help`:\n\n```bash\n$ pyro --help\n$ pyro convert --help\n```\n\n## Docker\n\nPyrokinetics provides a `Dockerfile` from which you can build and run Docker containers.\nTo do so, you must have [Docker](https://docs.docker.com/engine/install/) installed on\nyour system. To build a local container:\n\n```bash\n$ docker build . -t pyrokinetics\n```\n\nIt can then be run using:\n\n```bash\n$ docker run -it --rm -v ./path/to/local:/mymount pyrokinetics\n```\n\nwhere:\n\n- `-it` runs an interactive shell.\n- `--rm` deletes the Docker instance after use.\n- `-v ./path/to/local:/mymount` mounts the local directory `./path/to/local` to the\n directory `/mymount` within the Docker container.\n\nThe container runs an IPython interpreter, with Pyrokinetics already installed. Note\nthat you will need to `import` Pyrokinetics before it can be used.\n\n## Code structure \n\nPyro object comprised of \n\n* Equilibrium\n * LocalGeometry\n * Miller\n * Fourier (to be added)\n* Kinetics\n * LocalSpecies \n* Numerics\n* GKCodes\n* GKOutput\n * For nonlinear simulations\n * Fields (field, kx, ky, theta, time)\n * Fluxes (field, species, moment, ky, theta, time)\n * For linear simulations\n * Fields (field, kx, ky, theta, time)\n * Fluxes (field, species, moment, ky, theta, time)\n * Eigenfunctions (field, ky, theta, time)\n * Eigenvalues - growth rate and mode freq (ky, time)\n\nThere also exists the PyroScan object which allows you to make a N-D parameter scan of Pyro objects\n\n\n## Supports sources of Equilibrium data\npyrokinetics currently supports\n* [GEQDSK](https://w3.pppl.gov/ntcc/TORAY/G_EQDSK.pdf)\n* [TRANSP](https://w3.pppl.gov/~pshare/help/body_transp_hlp.html#outfile56.html)\n\nFuture formats to be added are\n* CHEASE\n\n\n## Supported sources of Kinetic data\n\nSources of kinetic profile data currently supported are\n* SCENE\n* JETTO\n* TRANSP\n\nFuture codes to be add \n* SimDB\n* OMFIT\n\n## Supported GK codes\n\nThe following gk codes are supported in pyrokinetics\n\n* CGYRO\n* GS2\n* GENE\n* TGLF\n\nCodes to be added in the future\n* Stella\n* GX\n\n## Note on units\n\nThe pyro object uses standardised reference values to normalise the results. It will automatically handle converting to a GK codes standard units.\n\nNote any scans/parameter changes made will be in standard pyro units so please account for this.\n\nReference values\n- $T_{ref} = T_e$ Electron temperature at flux surface\n- $n_{ref} = n_e$ Electron density at flux surface\n- $m_{ref} = m_D$ Deuterium mass\n- $v_{ref} = c_s = \\sqrt{T_e/m_D}$ Ion sound speed at flux surface\n- $B_{ref} = B_0$ Toroidal field at centre of the flux surface\n- $L_{ref} = a$ Minor radius of the last closed flux surface\n- $t_{ref} = a/c_s$ Ion sound time at flux surface\n- $\\rho_{ref} = \\frac{c_s}{eB_0/m_D}$ Ion Larmor radius at flux surface\n\nIt is possible to change the reference units but proceed with caution\n \n## Used By\n\nThis project is used by the following institutions\n\n- CCFE\n- University of York\n\n\nCopyright owned by UKAEA. Pyrokinetics is licensed under LGPL-3.0, and is free to use, modify, and distribute.\n \n",
"bugtrack_url": null,
"license": "GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, \"this License\" refers to version 3 of the GNU Lesser General Public License, and the \"GNU GPL\" refers to version 3 of the GNU General Public License. \"The Library\" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An \"Application\" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A \"Combined Work\" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the \"Linked Version\". The \"Minimal Corresponding Source\" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. The \"Corresponding Application Code\" for a Combined Work means the object code and/or source code for the Application, including any data and utility programs needed for reproducing the Combined Work from the Application, but excluding the System Libraries of the Combined Work. 1. Exception to Section 3 of the GNU GPL. You may convey a covered work under sections 3 and 4 of this License without being bound by section 3 of the GNU GPL. 2. Conveying Modified Versions. If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (a) uses at run time a copy of the Library already present on the user's computer system, and (b) will operate properly with a modified version of the Library that is interface-compatible with the Linked Version. e) Provide Installation Information, but only if you would otherwise be required to provide such information under section 6 of the GNU GPL, and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version. (If you use option 4d0, the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code. If you use option 4d1, you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source.) 5. Combined Libraries. You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License \"or any later version\" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. ",
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