fl-examples.rst

File layer

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

View the page source to find unformatted example code.

Open a gsd file

python

f = gsd.fl.open(name="file.gsd",

mode='wb', application="My application", schema="My Schema", schema_version=[1,0])

f.close()

Warning

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

Write data

python

f = gsd.fl.open(name="file.gsd",

mode='wb', application="My application", schema="My Schema", schema_version=[1,0]);

f.write_chunk(name='chunk1', data=numpy.array([1,2,3,4], dtype=numpy.float32)) f.write_chunk(name='chunk2', data=numpy.array([[5,6],[7,8]], dtype=numpy.float32)) f.end_frame() f.write_chunk(name='chunk1', data=numpy.array([9,10,11,12], dtype=numpy.float32)) f.write_chunk(name='chunk2', data=numpy.array([[13,14],[15,16]], dtype=numpy.float32)) f.end_frame() f.close()

Call :pygsd.fl.open to access gsd files on disk. Add any number of named data chunks to each frame in the file with :pygsd.fl.GSDFile.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 :pygsd.fl.GSDFile.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

Make sure to call end_frame() before closing the file, or the last frame will be lost.

Read data

python

f = gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0])

f.read_chunk(frame=0, name='chunk1') f.read_chunk(frame=1, name='chunk2') f.close()

:pygsd.fl.GSDFile.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

python

f = gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0])

f.chunk_exists(frame=0, name='chunk1') f.chunk_exists(frame=1, name='chunk2') f.chunk_exists(frame=2, name='chunk1') f.close()

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

Discover chunk names

python

f = gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0])

f.find_matching_chunk_names('') f.find_matching_chunk_names('chunk') f.find_matching_chunk_names('chunk1') f.find_matching_chunk_names('other')

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

Read-only access

python

f = gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0])

if f.chunk_exists(frame=0, name='chunk1'):

data = f.read_chunk(frame=0, name='chunk1')

data # Fails because the file is open read only @okexcept f.write_chunk(name='error', data=numpy.array([1])) f.close()

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

Access file metadata

python

f = gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0])

f.name f.mode f.gsd_version f.application f.schema f.schema_version f.nframes f.close()

File metadata are available as properties.

Open a file in read/write mode

python

f = gsd.fl.open(name="file.gsd",

mode='wb+', application="My application", schema="My Schema", schema_version=[1,0])

f.write_chunk(name='double', data=numpy.array([1,2,3,4], dtype=numpy.float64)); f.end_frame() f.nframes f.read_chunk(frame=0, name='double')

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

Write a file in append mode

python

f = gsd.fl.open(name="file.gsd",

mode='ab', application="My application", schema="My Schema", schema_version=[1,0])

f.write_chunk(name='int', data=numpy.array([10,20], dtype=numpy.int16)); f.end_frame() f.nframes # Reads fail in append mode @okexcept f.read_chunk(frame=2, name='double') f.close()

Open a file in append mode to write additional chunks to an existing file, but prevent reading.

Use as a context manager

python

with gsd.fl.open(name="file.gsd",

mode='rb', application="My application", schema="My Schema", schema_version=[1,0]) as f:

data = f.read_chunk(frame=0, name='double');

data

:pygsd.fl.GSDFile works as a context manager for guaranteed file closure and cleanup when exceptions occur.

Store string chunks

python

f = gsd.fl.open(name="file.gsd",

mode='wb+', application="My application", schema="My Schema", schema_version=[1,0])

f.mode s = "This is a string" b = numpy.array([s], dtype=numpy.dtype((bytes, len(s)+1))) b = b.view(dtype=numpy.int8) b f.write_chunk(name='string', data=b) f.end_frame() r = f.read_chunk(frame=0, name='string') r r = r.view(dtype=numpy.dtype((bytes, r.shape[0]))); r[0].decode('UTF-8') 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

python

f = gsd.fl.open(name="file.gsd",

mode='ab', application="My application", schema="My Schema", schema_version=[1,0])

f.nframes f.schema, f.schema_version, f.application f.truncate() f.nframes f.schema, f.schema_version, f.application

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.