iURdZddlZddlZddlZddlZddlmZddlm Z ddl m Z ddl m Z dd lmZmZdd lmZmZGd d ejZGd dejZdS)aTRZ trajectory I/O --- :mod:`MDAnalysis.coordinates.TRZ` ============================================================ Classes to read `IBIsCO`_ / `YASP`_ TRZ binary trajectories, including coordinates, velocities and more (see attributes of the :class:`Timestep`). Data are read and written in binary representation but because this depends on the machine hardware architecture, MDAnalysis *always* reads and writes TRZ trajectories in *little-endian* byte order. .. _IBIsCO: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21717 .. _YASP: https://www.sciencedirect.com/science/article/abs/pii/0010465593901442 Classes ------- .. autoclass:: TRZReader :members: .. autoclass:: TRZWriter :members: N)base) NoDataError)Timestep)util)cachedstore_init_arguments) triclinic_boxtriclinic_vectorscBeZdZdZdZddddZedfd Zd Zdd Z e d Z e e d d Z dZdZe e ddZe e ddZdZdZdZdZddZdZxZS) TRZReaderaLReads an IBIsCO or YASP trajectory file Attributes ---------- ts : timestep.Timestep :class:`~MDAnalysis.coordinates.timestep.Timestep` object containing coordinates of current frame Note ---- Binary TRZ trajectories are *always* assumed to be written in *little-endian* byte order and are read as such. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based. Extra data (Temperature, Energies, Pressures, etc) now read into ts.data dictionary. Now passes a weakref of self to ts (ts._reader). .. versionchanged:: 1.0.1 Now checks for the correct `n_atoms` on reading and can raise :exc:`ValueError`. .. versionchanged:: 2.1.0 TRZReader now returns a default :attr:`dt` of 1.0 when it cannot be obtained from the difference between two frames. .. versionchanged:: 2.3.0 _frame attribute moved to `ts.data` dictionary. .. deprecated:: 2.7.0 The TRZ Reader and Writer are deprecated as of version 2.7.0 and will be removed in version 3.0.0. TRZpsnmnm/pstimelengthvelocityNc d}tj|ttt|j|fi||t dtj|j d|_ t|_ ||_ |t|jfd|j|d|j|_t)|dz}dd d d d d ddddddddddd|fdd|fdd|fdd|fdd |fd!d"|fg}|js|d#gz }n|d$d%|fd&d'|fd(d)|fd*gz }t+j||_|dS)+aCreates a TRZ Reader Parameters ---------- trzfilename : str name of input file n_atoms : int number of atoms in trajectory, must be taken from topology file! convert_units : bool (optional) converts units to MDAnalysis defaults Raises ------ ValueError If `n_atoms` or the number of atoms in the topology file do not match the number of atoms in the trajectory. zLThe TRZ reader is deprecated and will be removed in MDAnalysis version 3.0.0Nz&TRZReader requires the n_atoms keywordrbT) velocitiesforcesreaderz-TRZReader._read_trz_header..s.II1QXXg..IIIIIIrmrprrr FTN) rarb _headerdtypefromfilerWjoinstriprpr]IOError)redatas rlr[zTRZReader._read_trz_headersH&&& {4>Df=A\?K?KLLLH~a(1,BH#F|ABGG 7mA&BG)DK,?,?1,E,EGBM"&z"2BGJ )-iBG% &&*6lBGN #*.v,BG& '(,T BG$ %%)#YBGM "DzBE!!!HDzBE!!!HDzBE!!!H#':BN111a4 #':BN111a4 #':BN111a4 ~ .#': 111a4 #': 111a4 #': 111a4 ! I,,TW\:::7%1001CBQB1GHHH33DG4GHHHI $ $ $t # $s GI I3c|jS)zNumber of atoms in a frame)rZres rlr\zTRZReader.n_atomss }rmn_framescZ ||jS#t$rYdSwxYw)z&Total number of frames in a trajectoryr)_read_trz_n_framesrWrrs rlrzTRZReader.n_framess? **4<88 8   11 s  **c tj|j}||jjz |jjzdkstdt||jjz |jjz }|S)zUses size of file and dtype information to determine how many frames exist .. versionchanged:: 0.9.0 Now is based on filesize rather than reading entire file rz Trajectory has incomplete frames) osfstatfilenost_sizer}itemsizercrint)rerWfsizenframess rlrzTRZReader._read_trz_n_framessv ))**2)22dk6JJaOO<== =ut099T[=QQRRrmc |jj} |jj}||jj}||z }|||S#t $rt wxYw#||wxYw)aThe amount of time between frames in ps Assumes that this step is constant (ie. 2 trajectories with different steps haven't been stitched together). Returns ``AttributeError`` in case of ``StopIteration`` (which makes :attr:`dt` return 1.0). .. versionchanged:: 2.1.0 Now returns an ``AttributeError`` if dt can't be obtained from the time difference between two frames. )r_rrnext _read_frame StopIterationAttributeError)re curr_framet0t1dts rl_get_dtzTRZReader._get_dtsW]  )B IIKKKBbB   Z ( ( ( (  ! ! !  !   Z ( ( ( (s1AA+A((A++Bdeltac |j|jz S)zMD integration timestep)r skip_timesteprs rlrzTRZReader.delta(sw+++rmrcD|jj} |jjd}||jjd}||z }|||S#t $rY||dSwxYw#||wxYw)z#Timesteps between trajectory framesrr)r_rrrrr)rerrrrs rlrzTRZReader.skip_timestep.sW]  )g&B IIKKKg&BGM!   Z ( ( ( (       Z ( ( ( ( (     Z ( ( ( (s)=A" B" B,BBBBc||jjz }||dz ||jS)zMove to *frame* and fill timestep with data. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based r)r_r_seekrd)rermoves rlrzTRZReader._read_frame?sA tw}$ 4!8   """wrmc|jj}||z}|dz}||krt|}||z}t||z }t||z}t |D]"}|jtd#|j|ddSt|}|j|ddS)zMove *nframes* in the trajectory Note that this doens't read the trajectory (ts remains unchanged) .. versionadded:: 0.9.0 rN)rcrlongrrangerWseekmaxint)rer framesizeseeksizemaxi_lnrepsrem_s rlrzTRZReader._seekKsK( w&A f  YI 7*H6)**Eh'((C5\\ - - !!&!,,,, L  c1 % % % % %8}}H L  h * * * * *rmc~|||dSN)closeopen_trajectoryr[rs rl_reopenzTRZReader._reopenhs9   rmc@|j ttjd|jt j|js ttjd|jtj |jd|_|j }d|_ |jS)zOpen the trajectory fileNzTRZ file already openedzTRZ file not foundr) rWrerrnoEALREADYrVrpathexistsENOENTrrUr_r)rer_s rlrzTRZReader.open_trajectoryms~ < #%.*CT]SS Sw~~dm,, M%,(| |jj}t||Sr)r_r\ TRZWriter)rerVr\s rlWriterzTRZReader.Writer|s ?goG7+++rmcX|j"|jd|_dSdS)zClose trz file if it was openNrWrrs rlrzTRZReader.closes1 < # L   DLLL $ #rmr)__name__ __module__ __qualname____doc__runitsr rSr[rdpropertyr\r rrrrrrrrrrr __classcell__)rks@rlrr=s@FTw ? ?EQ#Q#Q#Q#Q#Q#f"))))VX VJX   )))2 VG__,,_X, VO ) )X )   +++:     ,,,,        rmrc@eZdZdZdZdZddddZd dZd Zd Z d Z d S)raWrites a TRZ format trajectory. Note ---- Binary TRZ trajectories are *always* written in *little-endian* byte order. .. deprecated:: 2.7.0 The TRZ Reader and Writer are deprecated as of version 2.7.0 and will be removed in version 3.0.0. rTrrrrcjd}tj|t||_|t d|dkrt d||_t |dkrt d||_tj |jd|_ | |t|d z}tjgd d d d ddddddddddddddddddd |fd!d"d#|fd$d%d&|fd'd(d)|fd*d+d,|fd-d.d/|fd0|_dS)1aCreate a TRZWriter Parameters ---------- filename : str name of output file n_atoms : int number of atoms in trajectory title : str (optional) title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception. convert_units : bool (optional) units are converted to the MDAnalysis base format; [``True``] zLThe TRZ writer is deprecated and will be removed in MDAnalysis version 3.0.0Nz&TRZWriter requires the n_atoms keywordrz(TRZWriter: no atoms in output trajectoryPz3TRZWriter: 'title' must be 80 characters of shorterwbr)p1arr r"r$r&)p1br)p2arr,)p2br)p3arr/r1)p3br)p4ar)sixrr4r6r8r:)blanksz<2f8)p4br)p5arr=)p5br)p6arr?)p6br)p7arrA)p7br)p8arrC)p8br)p9arrE)p9br)p10arrG)p10br)rOrPrQrVrTr\lenrrrUrW _writeheaderr`rarb frameDtype)rerVr\rprrh floatsizes rlrSzTRZWriter.__init__s+ d.///  ?EFF F a<<GHH H u::??RSS S*|DM488  %   LL5( ('$ '$ '$ '$  '$  '$  '$ '$ '$ '$ '$ '$ '$ '$ '$ '$ !'$" #'$$ %'$& ''$( )'$* +'$, -'$.9 /'$0 1'$2 3'$49 5'$6 7'$8 9'$:9 ;'$< ='$> ?'$@9 A'$B C'$D E'$F9 G'$H I'$J K'$L9 M'$N O'$''rmctjgd}tjd|}d\|d<|d<|ddt|z zz|d <d \|d <|d <d |d<||jdS)N))pad1rro)r>r)r@r)nrecr)rBrrb)rrrr> rrp)rr@rBr{r)rarbzerosrtofilerW)rerphdtouts rlrzTRZWriter._writeheadersh???@@hr%%%#) F S[sb3u::o66G #' F S[F  4<     rmc |j}n>#t$r1 |jj}n #t$rd}t|dwxYwYnwxYw|jj|jksd}t |i}g}dD]g} |j|||<#t$rG|dkr$tj dtj ||<nd||<| |YdwxYw |jd |d <n/#t$r"|j |d <| d YnwxYw |j|d <n<#t$r/t|j |d <| d YnwxYw|r:t!jd d ||j(t+|jd}n4t!jdtj dtj} |j}nL#t2$r?tj |jdftjd}t!jdYnwxYwtj d|j} d\| d<| d<|j dz| d<|d | d<|j| d<|d | d<d\| d<| d<||d !| d"<d#\| d$<| d%<|d&| d&<|d| d'<d(\| d)<| d*<d| d+<|d,| d-<|d.| d/<|d0| d1<|d2| d3<d4| d5<|jd6z} | | c| d7<| d8<||jd !| d9<| | c| d:<| d;<||jd !| d<<| | c| d=<| d><||jd !| d?<| | c| d@<| dA<||dddBfd !| dC<| | c| dD<| dE<||dddfd !| dF<| | c| dG<| dH<||dddIfd !| dJ<| |j!dS)KaWrite information associated with ``obj`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe .. versionchanged:: 1.0.0 Renamed from `write_next_timestep` to `_write_next_frame`. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. z-Input obj is neither an AtomGroup or UniverseNz1Number of atoms in ts different to initialisation)r0rrrrrrrrsteprzeTimestep didn't have the following attributes: '{0}', these will be set to 0 in the output trajectoryz, zSTimestep didn't have dimensions information, box will be written as all zero valuesrF)rborderzZTimestep didn't have velocity information, this will be set to zero in output trajectory. r)r|r|rrrr!r#r%r')Hr rrF)inplacer-)8r rrr0r2)<r rrrrr5rr7rr9rr;)rrrrrrr=rrr?rrrArrrrCrrrErrrrG)"r_r trajectory TypeErroratomsr\rTrKeyErrorrarfloat64appendrrfloatrOrPrrrr rfloat32rrrconvert_pos_to_nativerrrconvert_velocities_to_nativerrW) reobjr_errmsgr faked_attrsattunitcellvelsrsizes rl_write_next_framezTRZWriter._write_next_framesy 2BB 2 2 2 2^&! 2 2 2H''T1 2 2y DL00HFV$$ $ I ( (C (GCLS  ( ( (+++ ""* = = =DII #DI""3'''''  (  '77+DLL ' ' '8DL   v & & & & & ' '7DLL ' ' ' ??DL   v & & & & & '  = M#VDIIk$:$:;; = = = = $(77??BBHH MC D D Dx444H M=DD M M M8T\1-RZsKKKD ML M M M M M M hr111!'E CJ1 H 6lF  H F|G !'E CJ//%/HHE !'E CJz*J/0I!'E CJE >*F -.F )*D  &C H zA~!%tE CJ..rue.DDD !%tE CJ..rue.DDD !%tE CJ..rue.DDD !%tE CJ55d111a4j%5PPD !%tE CJ55d111a4j%5PPD #' F S[55d111a4j%5PPD  4<     sk A "A?AA7BACCC..)DD D))6E"!E"H AIIcX|jdS|jd|_dS)zClose if it was openNrrs rlrzTRZWriter.close[s. <  F  rmN)rT) rrrrr multiframerrSrrrrrmrlrrs  FJTw ? ?EKKKKZ ! ! !f!f!f!Prmr)rrOnumpyrarrrur exceptionsrtimesteprlibrlib.utilr r corer r ReaderBaser WriterBaserrrmrlr*s%2. $$$$$$3333333322222222I I I I I I I I X WWWWWWWWWWrm