inZdZddlZddlZddlmZddlmZmZm Z ddl m Z m Z ddl mZdd l mZdd lmZdd lmZdd l mZddlZd ddddZGddejZGddejZGddejZGddejZGddejZdS)uLAMMPS DCD trajectory and DATA I/O --- :mod:`MDAnalysis.coordinates.LAMMPS` =============================================================================== Classes to read and write LAMMPS_ DCD binary trajectories, LAMMPS DATA files and LAMMPS dump files. Trajectories can be read regardless of system-endianness as this is auto-detected. LAMMPS can `write DCD`_ trajectories but unlike a `CHARMM trajectory`_ (which is often called a DCD even though CHARMM itself calls them "trj") the time unit is not fixed to be the AKMA_ time unit (20 AKMA is 0.978 picoseconds or 1 AKMA = 4.888821e-14 s) but can depend on settings in LAMMPS. The most common case for biomolecular simulations appears to be that the time step is recorded in femtoseconds (command `units real`_ in the input file) and lengths in ångströms. Other cases are unit-less Lennard-Jones time units. This presents a problem for MDAnalysis because it cannot autodetect the unit from the file. By default we are assuming that the unit for length is the ångström and for the time is the femtosecond. If this is not true then the user *should supply the appropriate units* in the keywords *timeunit* and/or *lengthunit* to :class:`DCDWriter` and :class:`~MDAnalysis.core.universe.Universe` (which then calls :class:`DCDReader`). Data file formats ----------------- By default either the `atomic` or `full` atom styles are expected, however this can be customised, see :ref:`atom_style_kwarg`. Dump files ---------- The DumpReader expects ascii dump files written with the default `LAMMPS dump format`_ of 'atom' Example: Loading a LAMMPS simulation ------------------------------------ To load a LAMMPS simulation from a LAMMPS data file (using the :class:`~MDAnalysis.topology.LAMMPSParser.DATAParser`) together with a LAMMPS DCD with "*real*" provide the keyword *format="LAMMPS*":: >>> import MDAnalysis >>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2 >>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS") If the trajectory uses *units nano* then use >>> import MDAnalysis >>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2 >>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS", ... lengthunit="nm", timeunit="ns") To scan through a trajectory to find a desirable frame and write to a LAMMPS data file, >>> import MDAnalysis >>> from MDAnalysis.tests.datafiles import LAMMPSdata2, LAMMPSdcd2 >>> u = MDAnalysis.Universe(LAMMPSdata2, LAMMPSdcd2, format="LAMMPS", ... lengthunit="nm", timeunit="ns") >>> take_this_frame = False >>> for ts in u.trajectory: ... # analyze frame ... if ts.frame == 4: ... take_this_frame = True ... if take_this_frame == True: ... with MDAnalysis.Writer('frame.data') as W: ... W.write(u.atoms) ... break Note ---- Lennard-Jones units are not implemented. See :mod:`MDAnalysis.units` for other recognized values and the documentation for the LAMMPS `units command`_. See Also -------- For further discussion follow the reports for `Issue 84`_ and `Issue 64`_. .. _LAMMPS: https://www.lammps.org/ .. _write DCD: https://docs.lammps.org/dump.html .. _CHARMM trajectory: http://www.charmm.org/documentation/c36b1/dynamc.html#%20Trajectory .. _AKMA: http://www.charmm.org/documentation/c36b1/usage.html#%20AKMA .. _units real: https://docs.lammps.org/units.html .. _units command: https://docs.lammps.org/units.html .. _`Issue 64`: https://github.com/MDAnalysis/mdanalysis/issues/64 .. _`Issue 84`: https://github.com/MDAnalysis/mdanalysis/issues/84 .. _`LAMMPS dump format`: https://docs.lammps.org/dump.html Classes ------- .. autoclass:: DCDReader :members: :inherited-members: .. autoclass:: DCDWriter :members: :inherited-members: .. autoclass:: DATAReader :members: :inherited-members: .. autoclass:: DATAWriter :members: :inherited-members: .. autoclass:: DumpReader :members: :inherited-members: N)requires)utilmdamath distances)cachedstore_init_arguments)DCD)units) DATAParser) NoDataError)baseBondsAngles Dihedrals Impropers)bondangledihedralimproperc.eZdZdZdZdZdZfdZxZS) DCDWriterzWrite a LAMMPS_ DCD trajectory. The units can be set from the constructor with the keyword arguments *timeunit* and *lengthunit*. The defaults are "fs" and "Angstrom". See :mod:`MDAnalysis.units` for other recognized values. LAMMPSTcddd|_|d|jd|jd<|d|jd|jd<|jD]T\}} tj||krt d|d |2#t $rd |}t |dwxYwtt|j |i|dS) NfsAngstromtimelengthtimeunitr lengthunitr zLAMMPS DCDWriter: wrong unit  for unit type zLAMMPS DCDWriter: unknown unit ) r popitems unit_types TypeErrorKeyError ValueErrorsuperr__init__)selfargskwargs unit_typeuniterrmsg __class__s g/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/LAMMPS.pyr+zDCDWriter.__init__s-    $ZZ DJv4FGG 6%zz, 88LMM 8#z//11 3 3OIt 3#D)Y66#111%.117  3 3 3A4AA ((d2 3 (i'888888s =+B)) C ) __name__ __module__ __qualname____doc__format multiframeflavorr+ __classcell__r2s@r3rrsSFJ F999999999rc:eZdZdZdZdZefdZxZS) DCDReaderaaRead a LAMMPS_ DCD trajectory. The units can be set from the constructor with the keyword arguments *timeunit* and *lengthunit*. The defaults are "fs" and "Angstrom", corresponding to LAMMPS `units style`_ "**real**". See :mod:`MDAnalysis.units` for other recognized values. .. _units style: https://docs.lammps.org/units.html rc ddd|_|d|jd|jd<|d|jd|jd<|jD]Q\}} tj||krt d|d |2#t $rt d |wxYwtt|j |fi|dS) Nrrrr!rr"r zLAMMPS DCDReader: wrong unit r#zLAMMPS DCDReader: unknown unit ) r r$r%r&r'r(r)r*r?r+)r, dcdfilenamer.r/r0r2s r3r+zDCDReader.__init__s1    $ZZ DJv4FGG 6%zz, 88LMM 8#z//11 K KOIt K#D)Y66#111%.117  K K K !I4!I!IJJJ K'i' >>v>>>>>s =+B))C) r4r5r6r7r8r:r r+r;r<s@r3r?r?sYF F?????????r=r?cHeZdZdZdZddddZefdZdZxZ S) DATAReaderzReads a single frame of coordinate information from a LAMMPS DATA file. .. versionadded:: 0.9.0 .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based DATANrz Angstrom/fs)rr velocityc |dd}|td|dd|_tt|j|fd|i|dS)Nn_atomsz#DATAReader requires n_atoms keyword atom_style)r$r)rHr*rCr+)r,filenamer.rGr2s r3r+zDATAReader.__init__so**Y-- ?BCC C **\488(j$(MM7MfMMMMMr=ct|j5}||j|j|j|j|_dddn #1swxYwYd|j_|j rR| |jj  | |jj dS#t$rYdSwxYwdS)Nr)r rIread_DATA_timesteprG _Timestep _ts_kwargsrHtsframe convert_unitsconvert_pos_from_native_posconvert_velocities_from_native _velocitiesAttributeError)r,ps r3_read_first_framezDATAReader._read_first_frames  & & !** dndotDG                     ( ( 6 6 6 33G'"       s#2AAAB22 C?C) r4r5r6r7r8r r r+rWr;r<s@r3rCrCswFZ] K KENNNNNr=rCcheZdZdZdZddZdZdZdZdZ d Z e d d dd Z d S) DATAWriteraWrite out the current time step as a LAMMPS DATA file. This writer supports the sections Atoms, Masses, Velocities, Bonds, Angles, Dihedrals, and Impropers. This writer will write the header and these sections (if applicable). Atoms section is written in the "full" sub-style if charges are available or "molecular" sub-style if they are not. Molecule id is set to 0 for all atoms. Note ---- This writer assumes "conventional" or "real" LAMMPS units where length is measured in Angstroms and velocity is measured in Angstroms per femtosecond. To write in different units, specify `lengthunit` If atom types are not already positive integers, the user must set them to be positive integers, because the writer will not automatically assign new types. To preserve numerical atom types when writing a selection, the Masses section will have entries for each atom type up to the maximum atom type. If the universe does not contain atoms of some type in {1, ... max(atom_types)}, then the mass for that type will be set to 1. In order to write bonds, each selected bond type must be explicitly set to an integer >= 1. rDTc xtj|dd|_||_ddd|_|d|jd|jd<|d |jd |jd <|d |jdd z|jd z|jd <dS)zSet up a DATAWriter Parameters ---------- filename : str output filename convert_units : bool, optional units are converted to the MDAnalysis base format; [``True``] dataT)extkeeprrrr"r r!r velocityunit/rEN)rrIrPr r$)r,rIrPr.s r3r+zDATAWriter.__init__&s hFFFF *"j99 %zz, 88LMM 8#ZZ DJv4FGG 6!' DJx036F9KK" "  :r=c`|jd|jd|jd |j}d}n#ttf$rd}YnwxYw|jdz}|jtj }| dtj t|t}|jr||jd}|rZt#|||||D]D\} } } } } | \}}}|j| d d | d d | d d | d d |d d |d d |d dEdSt#||||D]?\} } } } | \}}}|j| d d | d d | d d |d d |d d |d d @dS) N zAtoms TFr molecule_tagdtypeinplaced fz.10f)riwritechargesrrUindicestypesastypenpint32getzeroslenintrPconvert_pos_to_native positionszip)r,atomsr[rk has_chargesrlrmmoltags coordinatesindexmoltagatypechargecoordsxyzs r3 _write_atomszDATAWriter._write_atoms;s}  T  Y  T mGKK^,   KKK -!# ""28,,((>28CJJc+J+J+JKK   445K  8;%+99  4vuff!1a @55@55E@55f@55455!"455*+4555   14%11  ,vuf!1a RRRRRRERRRaRRRqRRRRRRR   sAA0/A0c |jd|jd|jd|jdz}||jd}t ||D]H\}}|jd||d|d|d IdS) Nraz Velocities r Frez!{i:d} {x:.10f} {y:.10f} {z:.10f} rr)irrr)rirjrlconvert_velocities_to_native velocitiesrwr8)r,rxrlrr|vels r3_write_velocitieszDATAWriter._write_velocitiescs  T  ^$$$  T-!#66  e7  gz22  JE3 FLL4;;s1vQ3q6<      r=c|jd|jd|jdi}t|jt j}td|dzD]}t|j j d |j }t|dkrd||<n|||<|rt!d|D]3\}}|jd ||4dS) NrazMasses r z type {:d}rg?zOLAMMPS DATAWriter: to write data file, atoms with same type must have same massz {:d} {:f} )rirjmaxrmrnrorprangesetuniverserx select_atomsr8massesrsr$r)r%)r,rx mass_dictmax_typer~rmasss r3 _write_masseszDATAWriter._write_massesrsa  T  Z     T u{))"(33441hl++  E$11&&u--F 6{{a#& %  #)::<< %   A  %??,, < %+#>??@@@  T5%3u::>":":;; 2 2GD! 2  ''3ty>>::hh 2Q 6>>sCCDDE  2 2 2: I::: ''T1  2 2 2s &A>D%%&E c>|jr)|tj|d}|jd|jdd|dd|jdd|dd|jd d|d d t|dd|d d|d dgrT|jd |dd|d d|d d |jdd S)zConvert dimensions to triclinic vectors, convert lengths to native units and then write the dimensions section Freraz{:f} {:f} xlo xhi rz{:f} {:f} ylo yhi r z{:f} {:f} zlo zhi rz{xy:f} {xz:f} {yz:f} xy xz yz )xyxzyzN)rPrurtriclinic_vectorsrirjr8any)r, dimensionstrivs r3_write_dimensionszDATAWriter._write_dimensionssp   --)*55u.D  T  *11#tAwqzBBCCC  *11#tAwqzBBCCC  *11#tAwqzBBCCC Q DGAJQ 3 4 4  FLL188Awqzd1gajT!WQZ9     Tr=rmrNc |j}||j|n|jjj}|j} |jtjn #t$rd}t|dwxYw |j }d}n#ttf$rd}YnwxYwi}tj|jd5|_|jd|jd|jdt'|gd } | D]~\} } || || <|jd t'|| | || |d || <|jd|jd t-|jtj|D]R\} } |jd t'| | S||j|||||jjj|D]-} | t'| dkr|| .|r||ddddS#1swxYwYdS)aWrite selection at current trajectory frame to file. The sections for Atoms, Masses, Velocities, Bonds, Angles, Dihedrals, and Impropers (if these are defined) are written. The Atoms section is written in the "full" sub-style if charges are available or "molecular" sub-style if they are not. Molecule id in atoms section is set to to 0. No other sections are written to the DATA file. As of this writing, other sections are not parsed into the topology by the :class:`DATAReader`. Note ---- If the selection includes a partial fragment, then only the bonds, angles, etc. whose atoms are contained within the selection will be included. Parameters ---------- selection : AtomGroup or Universe MDAnalysis AtomGroup (selection or Universe.atoms) or also Universe frame : int (optional) optionally move to frame number `frame` Nz=LAMMPS.DATAWriter: atom types must be convertible to integersTFwtz LAMMPS data file via MDAnalysis raz{:>12d} atoms ))rr)rangles)r dihedrals)r impropersz {:>12d} {} )strictz{:>12d} atom types z{:>12d} {} types r) r trajectoryrNrOrxrmrnrorpr)rrrUropenanyrIrirjr8rs__getattribute__atomgroup_intersectionrr%rrrrr[valuesrr) r, selectionrOurxr1rhas_velocitiesfeaturesattrsr attr_nameattrs r3rjzDATAWriter.writes8     L   LO)E / K  rx ( ( ( ( / / / V$$$ .  / ")J"NN^, # # #"NNN #  \$- . .+ .$& FLL< = = = FLL    FLL+223u::>> ? ? ?E%*   y"'"8"8"C"C #**3x+?+?KK#+5/"H"H$#I## FLL    FLL'.. **284455    (~~//   t )00TZZ\\1B1BEJJ  " "5#3 4 4 4   u % % %   eQ\_%9 : : : )) ( (<3t99>>!!$'''' .&&u---W+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .+ .s0$AA37BBB6JMM  M )TN) r4r5r6r7r8r+rrrrrrrjr=r3rYrYs8F    *&&&P   <<<2222$(Xgx  a.a.a.! a.a.a.r=rYc8eZdZdZdZgdZgdgdgdgddZgd ZeD] Z eee z Ze dfd Z dZ e eddZe eddZdZdZdZxZS) DumpReaderu@Reads the default `LAMMPS dump format `__ Supports coordinates in the LAMMPS "unscaled" (x,y,z), "scaled" (xs,ys,zs), "unwrapped" (xu,yu,zu) and "scaled_unwrapped" (xsu,ysu,zsu) coordinate conventions (see https://docs.lammps.org/dump.html for more details). If `lammps_coordinate_convention='auto'` (default), one will be guessed. Guessing checks whether the coordinates fit each convention in the order "unscaled", "scaled", "unwrapped", "scaled_unwrapped" and whichever set of coordinates is detected first will be used. If coordinates are given in the scaled coordinate convention (xs,ys,zs) or scaled unwrapped coordinate convention (xsu,ysu,zsu) they will automatically be converted from their scaled/fractional representation to their real values. Supports both orthogonal and triclinic simulation box dimensions (for more details see https://docs.lammps.org/Howto_triclinic.html). In either case, MDAnalysis will always use ``(*A*, *B*, *C*, *alpha*, *beta*, *gamma*)`` to represent the unit cell. Lengths *A*, *B*, *C* are in the MDAnalysis length unit (Å), and angles are in degrees. By using the keyword `additional_columns`, you can specify arbitrary data to be read. The keyword expects a list of the names of the columns or `True` to read all additional columns. The results are saved to :attr:`Timestep.data`. For example, if your LAMMPS dump looks like this .. code-block:: ITEM: ATOMS id x y z q l 1 2.84 8.17 -25 0.00258855 1.1 2 7.1 8.17 -25 6.91952e-05 1.2 Then you may parse the additional columns `q` and `l` via: .. code-block:: python u = mda.Universe('structure.data', 'traj.lammpsdump', additional_columns=['q', 'l']) The additional data is then available for each time step via: .. code-block:: python for ts in u.trajectory: charges = ts.data['q'] # Access additional data, sorted by the id ls = ts.data['l'] ... Parameters ---------- filename : str Filename of LAMMPS dump file lammps_coordinate_convention : str (optional) default="auto" Convention used in coordinates, can be one of the following according to the `LAMMPS documentation `__: - "auto" - Detect coordinate type from file column header. If auto detection is used, the guessing checks whether the coordinates fit each convention in the order "unscaled", "scaled", "unwrapped", "scaled_unwrapped" and whichever set of coordinates is detected first will be used. - "scaled" - Coordinates wrapped in box and scaled by box length (see note below), i.e., xs, ys, zs - "scaled_unwrapped" - Coordinates unwrapped and scaled by box length, (see note below) i.e., xsu, ysu, zsu - "unscaled" - Coordinates wrapped in box, i.e., x, y, z - "unwrapped" - Coordinates unwrapped, i.e., xu, yu, zu If coordinates are given in the scaled coordinate convention (xs,ys,zs) or scaled unwrapped coordinate convention (xsu,ysu,zsu) they will automatically be converted from their scaled/fractional representation to their real values. unwrap_images : bool (optional) default=False If `True` and the dump file contains image flags, the coordinates will be unwrapped. See `read_data `__ in the lammps documentation for more information. **kwargs Other keyword arguments used in :class:`~MDAnalysis.coordinates.base.ReaderBase` .. versionchanged:: 2.8.0 Reading of arbitrary, additional columns is now supported. (Issue `#3504 `__) .. versionchanged:: 2.4.0 Now imports velocities and forces, translates the box to the origin, and optionally unwraps trajectories with image flags upon loading. .. versionchanged:: 2.2.0 Triclinic simulation boxes are supported. (Issue `#3383 `__) .. versionchanged:: 2.0.0 Now parses coordinates in multiple lammps conventions (x,xs,xu,xsu) .. versionadded:: 0.19.0 LAMMPSDUMP)autounscaledscaled unwrappedscaled_unwrapped)rrr)xsyszs)xuyuzu)xsuysuzsu)rrrr)idvxvyvzfxfyfzrFNc tt|j|fi|tj|j\}}||jvr||_n5dd |jzdz}td|d|||_ tj |s||dur||_ntd|di|_||dS)N'z', 'zlammps_coordinate_convention='z.' is not a valid option. Please choose one of Tzadditional_columns=z[ is not a valid option. Please provide an iterable containing the additionalcolumn headers.)r*rr+ospathsplitextrI _conventionslammps_coordinate_conventionrr)_unwrapriterable_additional_columns_cache_reopen_read_next_timestep) r,rIr unwrap_imagesadditional_columnsr.rootr\ option_stringr2s r3r+zDumpReader.__init__s@ )j$(<#tD$rtdwxYw|j |vrtd|j d||j }"|jr|"#|d+v}#|j$dur(tK,&|j'}$nQ|j$rHt7,fd|j$DstQj)d,fd|j$D}$ng}$|$D]#}%t!j*|j |j|%<$tW|j D]}&| -|#r-+d||&<t!j,-fd |"Dt j-}'|jr*|'d!d}(|'dd!}'|'|(|jdd!zz }'n |'dd!}'|'|j.|&<|jr-fd"| D|j/|&<|jr-fd#|!D|j0|&<|$D]})-+|)|j|)|&< t!j1|}*|j.|*|_.|jr|j/|*|_/|jr|j0|*|_0|$D]})|j|)|*|j|)<|j 2d$r$tgj4|j.|j|_.|xj.t!j,||| gdddfzc_.|S)%Nr steprzINumber of atoms in trajectory changed this is not supported in MDAnalysisrr)rrcrrgV@ci|]\}}|| Srr).0rrs r3 z2DumpReader._read_next_timestep..s<<<41a!Q<<z2DumpReader._read_next_timestep..s+111*+N1%111r=c g|] }| Srrrs r3rz2DumpReader._read_next_timestep..$sLLLAnQ/LLLr=)ixiyizz3Trajectory must have image flag in order to unwrap.c3 K|]}|vV dSrrrs r3 z1DumpReader._read_next_timestep..*s(MMQQ.0MMMMMMr=)rrrTc g|] }| Srrrs r3rz2DumpReader._read_next_timestep..-sFFFaq)FFFr=c3 K|]}|vV dSrrrs r3r z1DumpReader._read_next_timestep...s(OOqqN2OOOOOOr=)rrrc g|] }| Srrrs r3rz2DumpReader._read_next_timestep..1sHHH.+HHHr=rz"No coordinate information detectedz$No coordinates following convention z found in timesteprcg|]}|vSrrrkeyrs r3rz2DumpReader._read_next_timestep..RsIIIu IIIr=zPSome of the additional columns are not present in the file, they will be ignoredcg|]}|v| Srrrs r3rz2DumpReader._read_next_timestep..Ws%3%<<<<.es333333r=rc g|] }| Srrrs r3rz2DumpReader._read_next_timestep..qs#D#D#DCF3K#D#D#Dr=c g|] }| Srrrs r3rz2DumpReader._read_next_timestep..ssBBBs BBBr=r)5rrNrOrsEOFErrorrrtr[dtrGr)splitmapfloatminrrorrfloat64r triclinic_boxr enumerate_coordtype_column_namesr%r(rall _has_velsr _has_forces has_forcesrlist IndexErrorextendrr difference_parsable_columnswarningswarnemptyrarrayfloat32rvrforcesargsort startswithrtransform_StoR).r,rirNstep_numrG triclinic xlo_bound xhi_boundr ylo_bound yhi_boundrzlozhirxloxhiyloyhiboxxlenylenzlenalphabetagammarlatomlineconvention_to_col_ixcv_name cv_col_names image_colsvel_cols force_cols coord_colsidsadditional_keysrrrimages attribute_keyorderrrrs. @@@r3rzDumpReader._read_next_timesteps J W A  8s4yy N qzz||$$""RU* ajjll## dl " "6   **,,--2  ('*5!**,,2D2D2F2F'G'G $Iy"'*5!**,,2D2D2F2F'G'G $Iy"uajjll&8&8&:&:;;LCbc#r2rBw777Cc#r2rBw777Cc#rll*Cc#rll*C(6444C3YS(CFsC'CFS3Y&CF3:3H#3N 0D$eT555!**,,"4"4"6"677HC5!**,,"4"4"6"677HC5!**,,"4"4"6"677HC9D9D9D#' 'E 'D5dD%u< (4 G $B FFFF3EFFFHOOOO 1M%0BM   ) %(BI- C CM%'W]%;E%BBGM " "  , 7 7 A A $3 bmBL #sC11$'::  s*O11 O>=O> PP)0S S%)rFN)r4r5r6r7r8rr"r+keysrr r+rpropertyrrGrrrrr;r<s@r3rrs^^@FL$OO$$$'''111 CBB&++--::4S99&, *#*#*#*#*#*#X  VIX VJ " "X "*** kkkkkkkr=r)r7rnumpyro core.groupsrlibrrrlib.utilrr r r topology.LAMMPSParserr exceptionsrrr,rrr?SingleFrameReaderBaserC WriterBaserY ReaderBaserrr=r3ras2qqd """"""**********33333333......$$$$$$   99999 999B????? ???D!!!!!+!!!HL.L.L.L.L.L.L.L.^xxxxxxxxxxr=