General simulation data file format.

These details have not been verified by PyPI

Project links

Development Status
- 5 - Production/Stable
Intended Audience
- Developers
- Science/Research
License
- OSI Approved :: BSD License
Operating System
- MacOS :: MacOS X
- POSIX
Topic
- Scientific/Engineering :: Physics

Project description

GSD

The GSD file format is the native file format for 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: Tutorials, Python API, C API, usage information, and format specification.
Installation Guide: Instructions for installing and compiling GSD.
HOOMD-blue: Simulation engine that reads and writes GSD files.
GSD discussion board: Ask the GSD community for help.
freud: A powerful set of tools for analyzing trajectories.
OVITO: The Open Visualization Tool works with GSD files.
gsd-vmd plugin: VMD plugin to support GSD files.

HOOMD examples

Create a hoomd gsd file.

>>> 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:

>>> 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:

>>> 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:

>>> 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

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()

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);

Project details

These details have not been verified by PyPI

Project links

Development Status
- 5 - Production/Stable
Intended Audience
- Developers
- Science/Research
License
- OSI Approved :: BSD License
Operating System
- MacOS :: MacOS X
- POSIX
Topic
- Scientific/Engineering :: Physics

Release history Release notifications | RSS feed

This version

3.4.2

Nov 13, 2024

3.4.1

Oct 21, 2024

3.4.0

Oct 18, 2024

3.3.2

Sep 6, 2024

3.3.1

Aug 19, 2024

3.3.0

May 29, 2024

3.2.1

Jan 22, 2024

3.2.0

Sep 27, 2023

3.1.1

Aug 3, 2023

3.1.0

Jul 28, 2023

3.0.1

Jun 21, 2023

3.0.0

Jun 16, 2023

2.9.0

May 19, 2023

2.8.1

Apr 13, 2023

2.8.0

Feb 24, 2023

2.7.0

Nov 30, 2022

2.6.1

Nov 4, 2022

2.6.0

Aug 19, 2022

2.5.3

Jun 23, 2022

2.5.2

Apr 15, 2022

2.5.1

Nov 17, 2021

2.5.0

Oct 13, 2021

2.4.2

Apr 14, 2021

2.4.1

Mar 11, 2021

2.4.0

Nov 11, 2020

2.3.0

Oct 30, 2020

2.2.0

Aug 5, 2020

2.1.2

Jun 26, 2020

2.1.1

Apr 20, 2020

2.1.0

Feb 27, 2020

2.0.0

Feb 3, 2020

1.10.0

Nov 26, 2019

1.9.3

Oct 4, 2019

1.9.2

Oct 1, 2019

1.9.1

Sep 23, 2019

1.9.0

Sep 18, 2019

1.8.1

Aug 19, 2019

1.7.0

Apr 30, 2019

1.6.2

Apr 17, 2019

1.6.1

Mar 5, 2019

1.6.0

Dec 20, 2018

1.5.5

Nov 28, 2018

1.5.4

Oct 4, 2018

1.5.2

Apr 4, 2018

1.5.1

Feb 26, 2018

1.5.0

Jan 19, 2018

1.4.0

Dec 5, 2017

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gsd 3.4.2

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