Appending a gsd file to another

[jude vishnu]

Dear all,

I would like to combine two gsd files, basically append one gsd file to another.  I have written the following code for this(see attachment). Is this the correct way to do it or is there a better way in which it can be done?

Kindly let me know.

Regards,

Jude

[Michael Howard]

Hi Jude,

I would use extend:

https://gsd.readthedocs.io/en/v2.5.2/python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory.extend

It works similarly to other python extend methods, something like:

traj1.extend(traj[start:25:step])

would work.

Regards,

Mike

[jude vishnu]

Dear Mike,

Should I open file in ab mode for appending always?

Because the file I opened (with wb) just now got overwritten when I tried extend method.

Regards,
Jude

[Michael Howard]

Yes, you would need to open the file you want to extend in append mode. It will be overwritten in write mode, which is the standard behavior of I/O modes.

Regards,

Mike

[jude vishnu]

Hi Mike,

I am still getting an error saying 

traj1=gsd.hoomd.open(name=filename1, mode='ab')
  File "/gpfs/fs1/home/jvishnu/vhoomd/lib/python3.7/site-packages/gsd/hoomd.py", line 1085, in open
    return HOOMDTrajectory(gsdfileobj)
  File "/gpfs/fs1/home/jvishnu/vhoomd/lib/python3.7/site-packages/gsd/hoomd.py", line 679, in __init__
    raise ValueError('Append mode not yet supported')

I am using gsd version 2.5.3.

Do you know what might be causing this issue?

Regards,

Jude

[Michael Howard]

Hi Jude,

I'm not sure why that would be the case based on the documentation:

https://gsd.readthedocs.io/en/v2.5.3/python-module-gsd.hoomd.html#gsd.hoomd.open

so someone else will need to jump in on that.

Regards,

Mike

[Joshua Anderson]

The error message is correct. I did not implement the 'ab` mode in the `hoomd` layer of the Python API. Only HOOMD supports this mode in hoomd.write.GSD - it is a very efficient low memory usage mode to add frames to an existing GSD file.

Use `rb+`to open an existing file for both reading and writing with the GSD Python API.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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