i#HdZddlZ ddlZddlZdZnO#e$rGdZddlZGddZej dZej de_ eej _ YnwxYwd d l m Z dd lmZGd d e jZGddej j ZddedefdZdS)aTGSD trajectory reader --- :mod:`MDAnalysis.coordinates.GSD` ============================================================ Class to read the GSD trajectory, output of `HOOMD-blue`_. The GSD format specifies both the topology and the trajectory of the particles in the simulation. The topology is read by the :class:`~MDAnalysis.topology.GSDParser.GSDParser` class. The GSD format was developed having in mind the possibility of changing number of particles, particle types, particle identities and changing topology. Currently this class has limited functionality, due to the fact that the number of particles and the topology are kept fixed in most MD simulations. The user will get an error only if at any time step the number of particles is detected to be different to the one that was set at the first time step. No check on changes in particle identity or topology is currently implemented. .. _`HOOMD-blue`: https://glotzerlab.engin.umich.edu/hoomd-blue/ Classes ------- .. autoclass:: GSDReader :inherited-members: .. autoclass:: GSDPicklable :members: .. autofunction:: gsd_pickle_open NTFceZdZdS)MockHOOMDTrajectoryN)__name__ __module__ __qualname__d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/GSD.pyrr>s r rgsdhoomd)base)store_init_argumentscteZdZdZdZdddZefdZdZdZ e dZ d Z d Z d ZxZS) GSDReaderzReader for the GSD format.GSDN)timelengthc Jtsd}t|tt|j|fi|||_||jdjj |_ |j |j fi|j |_ |dS)a Parameters ---------- filename : str trajectory filename **kwargs : dict General reader arguments. .. versionadded:: 0.17.0 .. versionchanged:: 2.0.0 Now use a picklable :class:`gsd.hoomd.HOOMDTrajectory`-- :class:`GSDPicklable` .. versionchanged:: 2.6.0 Support for GSD versions below 3.0.1 have been dropped. This includes support for schema 1.3. z0GSDReader: To read GSD files, please install gsdrN)HAS_GSD ImportErrorsuperr__init__filenameopen_trajectory_file particlesNn_atoms _Timestep _ts_kwargsts_read_next_timestep)selfrkwargserrmsg __class__s r rzGSDReader.__init__Qs& &GFf%% %'i';;F;;;   z!}.0  $.AAAA   """""r cJd|_t|jd|_dS)z0opens the trajectory file using gsd.hoomd moduler)modeN)_framegsd_pickle_openrrr$s r rzGSDReader.open_trajectoryos# $T]=== r cB|jjdS)z close readerN)rfilecloser.s r r1zGSDReader.closets r c*t|jS)znumber of frames in trajectory)lenrr.s r n_frameszGSDReader.n_framesxs4:r cV||dS)zreopen trajectoryN)r1rr.s r _reopenzGSDReader._reopen}s'  r c |j|}n#t$r tdwxYw||_||j_|jj|jjd<|jj |j_ tj tj |jj dd|jj dd<|jj}|jd}||jkrt%d|||jfz||j_|jS)NsteprznFrame %d has %d atoms but the initial frame has %d atoms. MDAnalysis in unable to deal with variable topology!)r IndexErrorIOErrorr,r"frame configurationr8databox dimensionsnprad2degarccosrpositionshaper ValueError positions)r$r<myframeframe_positions n_atoms_nows r _read_framezGSDReader._read_frames  $j'GG $ $ $t # $  &49 V%26!#BIdg6H6L,M,M!N!N122"+4%+A. $, & & %{DLAB  !0DG ws #c<||jdzS)zread next frame in trajectoryr )rKr,r.s r r#zGSDReader._read_next_timesteps a000r )rrr__doc__formatunitsrrrr1propertyr4r6rKr# __classcell__)r's@r rrKs$$ FT * *E#####:>>>    X <1111111r rceZdZdZdZdZdS) GSDPicklablea1Hoomd GSD file object (read-only) that can be pickled. This class provides a file-like object (as by :func:`gsd.hoomd.open`, namely :class:`gsd.hoodm.HOOMDTrajectory`) that, unlike file objects, can be pickled. Only read mode is supported. When the file is pickled, filename and mode of :class:`gsd.fl.GSDFile` in the file are saved. On unpickling, the file is opened by filename. This means that for a successful unpickle, the original file still has to be accessible with its filename. Note ---- Open hoomd GSD files with `gsd_pickle_open`. After pickling, the current frame is reset. `universe.trajectory[i]` has to be used to return to its original frame. Parameters ---------- file: :class:`gsd.fl.GSDFile` File to access. Example ------- :: gsdfileobj = gsd.fl.open(name=filename, mode='r', application='gsd.hoomd '+ gsd.version.version, schema='hoomd', schema_version=[1, 3]) file = GSDPicklable(gsdfileobj) file_pickled = pickle.loads(pickle.dumps(file)) See Also --------- :func:`MDAnalysis.lib.picklable_file_io.FileIOPicklable` :func:`MDAnalysis.lib.picklable_file_io.BufferIOPicklable` :func:`MDAnalysis.lib.picklable_file_io.TextIOPicklable` :func:`MDAnalysis.lib.picklable_file_io.GzipPicklable` :func:`MDAnalysis.lib.picklable_file_io.BZ2Picklable` .. versionadded:: 2.0.0 c2|jj|jjfS)N)r0namer+r.s r __getstate__zGSDPicklable.__getstate__sy~ty~--r ctjj}ddg}tj|d|dd|zd|}||dS)Nr r gsd.hoomd r rUr+ applicationschemaschema_version)r versionflopenr)r$args gsd_versionr] gsdfileobjs r __setstate__zGSDPicklable.__setstate__sek) QV[[aa${2) !   j!!!!!r N)rrrrMrVrdrr r rSrSs=,,\... " " " " "r rSr*rUr+ctjj}ddg}|dkrtdtj||d|zd|}t |S)aiOpen hoomd schema GSD file with pickle function implemented. This function returns a GSDPicklable object. It can be used as a context manager, and replace the built-in :func:`gsd.hoomd.open` function in read mode that only returns an unpicklable file object. Schema version will depend on the version of gsd module. Note ---- Can be only used with read mode. Parameters ---------- name : str a filename given a text or byte string. mode: str, optional 'r': open for reading. Returns ------- stream-like object: GSDPicklable Raises ------ ValueError if `mode` is not one of the allowed read modes Examples ------- open as context manager:: with gsd_pickle_open('filename') as f: line = f.readline() open as function:: f = gsd_pickle_open('filename') line = f.readline() f.close() See Also -------- :func:`MDAnalysis.lib.util.anyopen` :func:`MDAnalysis.lib.picklable_file_io.pickle_open` :func:`MDAnalysis.lib.picklable_file_io.bz2_pickle_open` :func:`MDAnalysis.lib.picklable_file_io.gzip_pickle_open` :func:`gsd.hoomd.open` .. versionadded:: 2.0.0 .. versionchanged:: 2.6.0 Only GSD versions 3.0.1+ are supported. 'rb' mode support has been replaced with 'r' mode. r rXr*z(Only read mode 'r' files can be pickled.rYr rZ)r r^rFr_r`rS)rUr+rbr]rcs r r-r-snp+%KVN s{{FGGG   ;.% J  # ##r )r*)rMnumpyrAr gsd.flrrtypesr ModuleTyper HOOMDTrajectoryrMDAnalysis.lib.utilr ReaderBaserrSstrr-rr r ros.<JJJMMMGG 4 4 4GLLL         % 5 ! !C  ))CI 3CI 4444444W1W1W1W1W1W1W1W1t<"<"<"<"<"39,<"<"<"~C$C$#C$SC$C$C$C$C$C$sA AA