File layer examples

The file layer python module gsd.fl allows direct low level access to read and write GSD files of any schema. The HOOMD reader (gsd.hoomd) provides higher level access to HOOMD schema files, see HOOMD examples.

View the page source to find unformatted example code.

Import the module

In [1]: import gsd.fl

Open a gsd file

In [2]: f = gsd.fl.open(name="file.gsd",
   ...:                 mode='w',
   ...:                 application="My application",
   ...:                 schema="My Schema",
   ...:                 schema_version=[1,0])
   ...: 

Use gsd.fl.open to open a gsd file.

Note

When creating a new file, you must specify the application name, schema name, and schema version.

Warning

Opening a gsd file with a ‘w’ or ‘x’ mode overwrites any existing file with the given name.

Close a gsd file

In [3]: f.close()

Call the close method to close the file.

Write data

In [4]: f = gsd.fl.open(name="file.gsd",
   ...:                 mode='w',
   ...:                 application="My application",
   ...:                 schema="My Schema",
   ...:                 schema_version=[1,0]);
   ...: 

In [5]: f.write_chunk(name='chunk1', data=numpy.array([1,2,3,4], dtype=numpy.float32))

In [6]: f.write_chunk(name='chunk2', data=numpy.array([[5,6],[7,8]], dtype=numpy.float32))

In [7]: f.end_frame()

In [8]: f.write_chunk(name='chunk1', data=numpy.array([9,10,11,12], dtype=numpy.float32))

In [9]: f.write_chunk(name='chunk2', data=numpy.array([[13,14],[15,16]], dtype=numpy.float32))

In [10]: f.end_frame()

In [11]: f.close()

Add any number of named data chunks to each frame in the file with write_chunk. The data must be a 1 or 2 dimensional numpy array of a simple numeric type (or a data type that will automatically convert when passed to numpy.array(data). Call end_frame to end the frame and start the next one.

Note

While supported, implicit conversion to numpy arrays creates a copy of the data in memory and adds conversion overhead.

Warning

Call end_frame to write the last frame before closing the file.

Read data

In [12]: f = gsd.fl.open(name="file.gsd", mode='r')

In [13]: f.read_chunk(frame=0, name='chunk1')
Out[13]: array([1., 2., 3., 4.], dtype=float32)

In [14]: f.read_chunk(frame=1, name='chunk2')
Out[14]: 
array([[13., 14.],
       [15., 16.]], dtype=float32)

In [15]: f.close()

read_chunk reads the named chunk at the given frame index in the file and returns it as a numpy array.

Test if a chunk exists

In [16]: f = gsd.fl.open(name="file.gsd", mode='r')

In [17]: f.chunk_exists(frame=0, name='chunk1')
Out[17]: True

In [18]: f.chunk_exists(frame=1, name='chunk2')
Out[18]: True

In [19]: f.chunk_exists(frame=2, name='chunk1')
Out[19]: False

In [20]: f.close()

chunk_exists tests to see if a chunk by the given name exists in the file at the given frame.

Discover chunk names

In [21]: f = gsd.fl.open(name="file.gsd", mode='r')

In [22]: f.find_matching_chunk_names('')
Out[22]: ['chunk1', 'chunk2']

In [23]: f.find_matching_chunk_names('chunk')
Out[23]: ['chunk1', 'chunk2']

In [24]: f.find_matching_chunk_names('chunk1')
Out[24]: ['chunk1']

In [25]: f.find_matching_chunk_names('other')
Out[25]: []

find_matching_chunk_names finds all chunk names present in a GSD file that start with the given string.

Read-only access

In [26]: f = gsd.fl.open(name="file.gsd", mode='r')

In [27]: if f.chunk_exists(frame=0, name='chunk1'):
   ....:     data = f.read_chunk(frame=0, name='chunk1')
   ....: 

In [28]: data
Out[28]: array([1., 2., 3., 4.], dtype=float32)

# Fails because the file is open read only
In [29]: f.write_chunk(name='error', data=numpy.array([1]))
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[29], line 1
----> 1 f.write_chunk(name='error', data=numpy.array([1]))

File ~/checkouts/readthedocs.org/user_builds/gsd/envs/stable/lib/python3.12/site-packages/gsd/fl.pyx:627, in gsd.fl.GSDFile.write_chunk()

File ~/checkouts/readthedocs.org/user_builds/gsd/envs/stable/lib/python3.12/site-packages/gsd/fl.pyx:55, in gsd.fl.__raise_on_error()

RuntimeError: File must be writable: file.gsd

In [30]: f.close()

Writes fail when a file is opened in a read only mode.

Access file metadata

In [31]: f = gsd.fl.open(name="file.gsd", mode='r')

In [32]: f.name
Out[32]: 'file.gsd'

In [33]: f.mode
Out[33]: 'r'

In [34]: f.gsd_version
Out[34]: (2, 0)

In [35]: f.application
Out[35]: 'My application'

In [36]: f.schema
Out[36]: 'My Schema'

In [37]: f.schema_version
Out[37]: (1, 0)

In [38]: f.nframes
Out[38]: 2

In [39]: f.close()

Read file metadata from properties of the file object.

Open a file in read/write mode

In [40]: f = gsd.fl.open(name="file.gsd",
   ....:                 mode='w',
   ....:                 application="My application",
   ....:                 schema="My Schema",
   ....:                 schema_version=[1,0])
   ....: 

In [41]: f.write_chunk(name='double', data=numpy.array([1,2,3,4], dtype=numpy.float64));

In [42]: f.end_frame()

In [43]: f.nframes
Out[43]: 1

In [44]: f.read_chunk(frame=0, name='double')
Out[44]: array([1., 2., 3., 4.])

Open a file in read/write mode to allow both reading and writing.

Use as a context manager

In [45]: with gsd.fl.open(name="file.gsd", mode='r') as f:
   ....:     data = f.read_chunk(frame=0, name='double');
   ....: 

In [46]: data
Out[46]: array([1., 2., 3., 4.])

Use gsd.fl.GSDFile as a context manager for guaranteed file closure and cleanup when exceptions occur.

Store string chunks

In [47]: f = gsd.fl.open(name="file.gsd",
   ....:                 mode='w',
   ....:                 application="My application",
   ....:                 schema="My Schema",
   ....:                 schema_version=[1,0])
   ....: 

In [48]: f.mode
Out[48]: 'w'

In [49]: s = "This is a string"

In [50]: b = numpy.array([s], dtype=numpy.dtype((bytes, len(s)+1)))

In [51]: b = b.view(dtype=numpy.int8)

In [52]: b
Out[52]: 
array([ 84, 104, 105, 115,  32, 105, 115,  32,  97,  32, 115, 116, 114,
       105, 110, 103,   0], dtype=int8)

In [53]: f.write_chunk(name='string', data=b)

In [54]: f.end_frame()

In [55]: r = f.read_chunk(frame=0, name='string')

In [56]: r
Out[56]: 
array([ 84, 104, 105, 115,  32, 105, 115,  32,  97,  32, 115, 116, 114,
       105, 110, 103,   0], dtype=int8)

In [57]: r = r.view(dtype=numpy.dtype((bytes, r.shape[0])));

In [58]: r[0].decode('UTF-8')
Out[58]: 'This is a string'

In [59]: f.close()

To store a string in a gsd file, convert it to a numpy array of bytes and store that data in the file. Decode the byte sequence to get back a string.

Truncate

In [60]: f = gsd.fl.open(name="file.gsd", mode='r+')

In [61]: f.nframes
Out[61]: 1

In [62]: f.schema, f.schema_version, f.application
Out[62]: ('My Schema', (1, 0), 'My application')

In [63]: f.truncate()

In [64]: f.nframes
Out[64]: 0

In [65]: f.schema, f.schema_version, f.application
Out[65]: ('My Schema', (1, 0), 'My application')

In [66]: f.close()

Truncating a gsd file removes all data chunks from it, but retains the same schema, schema version, and application name. The file is not closed during this process. This is useful when writing restart files on a Lustre file system when file open operations need to be kept to a minimum.