| Name | gsd JSON |
| Version |
3.4.1
JSON |
| download |
| home_page | None |
| Summary | General simulation data file format. |
| upload_time | 2024-10-21 12:34:49 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.6 |
| license | BSD-2-Clause |
| keywords |
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| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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# GSD
The **GSD** file format is the native file format for [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/).
**GSD** files store trajectories of the **HOOMD-blue** system state in a binary file with efficient random access to
frames. **GSD** allows all particle and topology properties to vary from one frame to the next. Use the **GSD** Python
API to specify the initial condition for a **HOOMD-blue** simulation or analyze trajectory output with a script. Read a
**GSD** trajectory with a visualization tool to explore the behavior of the simulation.
## Resources
* [GSD documentation](http://gsd.readthedocs.io): Tutorials, Python API, C API, usage information, and format
specification.
* [Installation Guide](INSTALLING.rst): Instructions for installing and compiling **GSD**.
* [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/): Simulation engine that reads and writes **GSD** files.
* [GSD discussion board](https://github.com/glotzerlab/gsd/discussions/):
Ask the **GSD** community for help.
* [freud](https://freud.readthedocs.io): A powerful set of tools for analyzing trajectories.
* [OVITO](https://www.ovito.org/): The Open Visualization Tool works with **GSD** files.
* [gsd-vmd plugin](https://github.com/mphoward/gsd-vmd): VMD plugin to support **GSD** files.
## HOOMD examples
Create a hoomd gsd file.
```python
>>> s = gsd.hoomd.Frame()
>>> s.particles.N = 4
>>> s.particles.types = ['A', 'B']
>>> s.particles.typeid = [0,0,1,1]
>>> s.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]
>>> s.configuration.box = [3, 3, 3, 0, 0, 0]
>>> traj = gsd.hoomd.open(name='test.gsd', mode='w')
>>> traj.append(s)
```
Append frames to a gsd file:
```python
>>> def create_frame(i):
... s = gsd.hoomd.Frame();
... s.configuration.step = i;
... s.particles.N = 4+i;
... s.particles.position = numpy.random.random(size=(4+i,3))
... return s;
>>> with gsd.hoomd.open('test.gsd', 'a') as t:
... t.extend( (create_frame(i) for i in range(10)) )
... print(len(t))
11
```
Randomly index frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'r') as t:
... frame = t[5]
... print(frame.configuration.step)
4
... print(frame.particles.N)
8
... print(frame.particles.position)
[[ 0.56993282 0.42243481 0.5502916 ]
[ 0.36892486 0.38167036 0.27310368]
[ 0.04739023 0.13603486 0.196539 ]
[ 0.120232 0.91591144 0.99463677]
[ 0.79806316 0.16991436 0.15228257]
[ 0.13724308 0.14253527 0.02505 ]
[ 0.39287439 0.82519054 0.01613089]
[ 0.23150323 0.95167434 0.7715748 ]]
```
Slice frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'r') as t:
... for s in t[5:-2]:
... print(s.configuration.step, end=' ')
4 5 6 7
```
## File layer examples
```python
with gsd.fl.open(name='file.gsd', mode='w') as f:
f.write_chunk(name='position', data=numpy.array([[1,2,3],[4,5,6]], dtype=numpy.float32));
f.write_chunk(name='angle', data=numpy.array([0, 1], dtype=numpy.float32));
f.write_chunk(name='box', data=numpy.array([10, 10, 10], dtype=numpy.float32));
f.end_frame()
```
```python
with gsd.fl.open(name='file.gsd', mode='r') as f:
for i in range(1,f.nframes):
position = f.read_chunk(frame=i, name='position');
do_something(position);
```
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"description": "# GSD\n\nThe **GSD** file format is the native file format for [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/).\n**GSD** files store trajectories of the **HOOMD-blue** system state in a binary file with efficient random access to\nframes. **GSD** allows all particle and topology properties to vary from one frame to the next. Use the **GSD** Python\nAPI to specify the initial condition for a **HOOMD-blue** simulation or analyze trajectory output with a script. Read a\n**GSD** trajectory with a visualization tool to explore the behavior of the simulation.\n\n## Resources\n\n* [GSD documentation](http://gsd.readthedocs.io): Tutorials, Python API, C API, usage information, and format\n specification.\n* [Installation Guide](INSTALLING.rst): Instructions for installing and compiling **GSD**.\n* [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/): Simulation engine that reads and writes **GSD** files.\n* [GSD discussion board](https://github.com/glotzerlab/gsd/discussions/):\n Ask the **GSD** community for help.\n* [freud](https://freud.readthedocs.io): A powerful set of tools for analyzing trajectories.\n* [OVITO](https://www.ovito.org/): The Open Visualization Tool works with **GSD** files.\n* [gsd-vmd plugin](https://github.com/mphoward/gsd-vmd): VMD plugin to support **GSD** files.\n\n## HOOMD examples\n\nCreate a hoomd gsd file.\n```python\n>>> s = gsd.hoomd.Frame()\n>>> s.particles.N = 4\n>>> s.particles.types = ['A', 'B']\n>>> s.particles.typeid = [0,0,1,1]\n>>> s.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]\n>>> s.configuration.box = [3, 3, 3, 0, 0, 0]\n>>> traj = gsd.hoomd.open(name='test.gsd', mode='w')\n>>> traj.append(s)\n```\n\nAppend frames to a gsd file:\n```python\n>>> def create_frame(i):\n... s = gsd.hoomd.Frame();\n... s.configuration.step = i;\n... s.particles.N = 4+i;\n... s.particles.position = numpy.random.random(size=(4+i,3))\n... return s;\n>>> with gsd.hoomd.open('test.gsd', 'a') as t:\n... t.extend( (create_frame(i) for i in range(10)) )\n... print(len(t))\n11\n```\n\nRandomly index frames:\n```python\n>>> with gsd.hoomd.open('test.gsd', 'r') as t:\n... frame = t[5]\n... print(frame.configuration.step)\n4\n... print(frame.particles.N)\n8\n... print(frame.particles.position)\n[[ 0.56993282 0.42243481 0.5502916 ]\n [ 0.36892486 0.38167036 0.27310368]\n [ 0.04739023 0.13603486 0.196539 ]\n [ 0.120232 0.91591144 0.99463677]\n [ 0.79806316 0.16991436 0.15228257]\n [ 0.13724308 0.14253527 0.02505 ]\n [ 0.39287439 0.82519054 0.01613089]\n [ 0.23150323 0.95167434 0.7715748 ]]\n```\n\nSlice frames:\n```python\n>>> with gsd.hoomd.open('test.gsd', 'r') as t:\n... for s in t[5:-2]:\n... print(s.configuration.step, end=' ')\n4 5 6 7\n```\n\n## File layer examples\n\n```python\nwith gsd.fl.open(name='file.gsd', mode='w') as f:\n f.write_chunk(name='position', data=numpy.array([[1,2,3],[4,5,6]], dtype=numpy.float32));\n f.write_chunk(name='angle', data=numpy.array([0, 1], dtype=numpy.float32));\n f.write_chunk(name='box', data=numpy.array([10, 10, 10], dtype=numpy.float32));\n f.end_frame()\n```\n\n```python\nwith gsd.fl.open(name='file.gsd', mode='r') as f:\n for i in range(1,f.nframes):\n position = f.read_chunk(frame=i, name='position');\n do_something(position);\n```\n",
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