General simulation data file format.
Project description
GSD
GSD (General Simulation Data) is a file format specification and a library to read and write it. The package also contains a python module that reads and writes hoomd schema gsd files.
See the full GSD documentation at readthedocs.io.
Overview
GSD files:
- Efficiently store many frames of data from simulation runs.
- High performance file read and write.
- Support arbitrary chunks of data in each frame (position, orientation, type, etc...).
- Append frames to an existing file with a monotonically increasing frame number.
- Resilient to job kills.
- Variable number of named chunks in each frame.
- Variable size of chunks in each frame.
- Each chunk identifies data type.
- Common use cases: NxM arrays in double, float, int, char types.
- Generic use case: binary blob of N bytes.
- Can be integrated into other tools with python, or a C API (< 1k lines).
- Fast random access to frames.
HOOMD examples
Create a hoomd gsd file.
>>> s = gsd.hoomd.Snapshot()
>>> 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='wb')
>>> traj.append(s)
Append frames to a gsd file:
>>> def create_frame(i):
... s = gsd.hoomd.Snapshot();
... 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', 'ab') 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', 'rb') as t:
... snap = t[5]
... print(snap.configuration.step)
4
... print(snap.particles.N)
8
... print(snap.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', 'rb') 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='wb') 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='rb') as f:
for i in range(1,f.nframes):
position = f.read_chunk(frame=i, name='position');
do_something(position);
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