i\ dZddlZddlZddlZddlZddlZddlmZm Z ddl m Z ddl m Z mZddlmZdd lmZmZmZmZmZmZmZmZmZmZmZmZdd lmZdd lm Z!ej"d Z#e$gd Z%e&e%D]PZ'e(e')dkr-e%*e')dQe$gdZ+Gdde Z,edej-deegde.dede/dedej0dede/dedej1ddZ2Gdde Z3ej4Gdde/Z5dS)a LAMMPSParser ============ Parses data_ or dump_ files produced by LAMMPS_. .. note:: By default, masses will be guessed on Universe creation if they are not read from the input file. This may change in release 3.0. See :ref:`Guessers` for more information. .. _LAMMPS: https://www.lammps.org/ .. _data: DATA file format: :https://docs.lammps.org/2001/data_format.html .. _dump: https://docs.lammps.org/dump.html .. versionchanged:: 1.0.0 Deprecated :class:`LAMMPSDataConverter` has now been removed. .. _atom_style_kwarg: Atom styles ----------- By default parsers and readers for Lammps data files expect either an *atomic* or *full* `atom_style`_. This can be customised by passing the `atom_style` keyword argument. This should be a space separated string indicating the position of the `id`, `type`, `resid`, `charge`, `x`, `y` and `z` fields. The `resid` and `charge` fields are optional and any other specified field will be ignored. For example to read a file with the following format, where there is no resid:: Atoms # atomic 1 1 3.7151744275286681e+01 1.8684434743140471e+01 1.9285127961842125e+01 0 0 0 The following code could be used:: >>> import MDAnalysis as mda >>> >>> u = mda.Universe('myfile.data', atom_style='id type x y z') .. _`atom_style`: https://docs.lammps.org/atom_style.html Classes ------- .. autoclass:: DATAParser :members: :inherited-members: .. autoclass:: LammpsDumpParser :members: N)openany conv_float) triclinic_box)TopologyReaderBase squash_by)Topology) AtomtypesAtomidsAnglesBondsCharges DihedralsElements ImpropersMassesResidsResnumsSegids)SYMB2Z)masseszMDAnalysis.topology.LAMMPS)Atoms Velocitiesr EllipsoidsLines TrianglesBodiesrr rrPairz Pair LJCoeffsz PairIJ Coeffsz Bond Coeffsz Angle CoeffszDihedral CoeffszImproper CoeffszBondBond CoeffszBondAngle CoeffszMiddleBondTorsion CoeffszEndBondTorsion CoeffszAngleTorsion CoeffszAngleAngleTorsion CoeffszBondBond13 CoeffszAngleAngle Coeffs)atomsbondsangles dihedrals impropersz atom typesz bond typesz angle typeszdihedral typeszimproper typeszextra bond per atomzextra angle per atomzextra dihedral per atomzextra improper per atomzextra special per atom ellipsoidslines trianglesbodiesxlo xhiylo yhizlo zhixy xz yzcneZdZdZdZdZdZedZdZ ddZ d Z d Z d Z dd Zd ZdZdS) DATAParserapParse a LAMMPS DATA file for topology and coordinates. Note that LAMMPS DATA files can be used standalone. Both topology and coordinate parsing functionality is kept in this class as the topology and coordinate reader share many common functions By default the parser expects either *atomic* or *full* `atom_style` however this can be by passing an `atom_style` keyword argument, see :ref:`atom_style_kwarg`. .. versionadded:: 0.9.0 .. versionchanged:: 2.8.0 Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). DATAc#Kt|j5}|D]5}|dd}|r|V6 ddddS#1swxYwYdS)N#r)rfilename partitionstrip)selfflines j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/LAMMPSParser.pyiterdatazDATAParser.iterdatas T] # # q  ~~c**1-3355JJJ                   s9AA"%A"c|t|dtDdgz i}ddD]@}tD]6}||r||d||<67AfdtddD}||fS)zSplit a data file into dict of header and sections Returns ------- header - dict of header section: value sections - dict of section name: content cZg|](\}}|dtv&|)S)r)splitSECTIONS).0ir7s r8 z,DATAParser.grab_datafile..s2OOO44::<<?h3N3N!3N3N3NNrcPi|]"\}}||dz|dz#S)r)r>r?lr6startss r8 z,DATAParser.grab_datafile..sF   /3q!AaD!AEF1q5M)*   rA)listr9 enumerateHEADERSendswithr<)r5headerr7tokensectsr6rEs @@r8 grab_datafilezDATAParser.grab_datafiles  ! !OO9Q<<OOO4&kq kN  D   ==''$(JJu$5$5a$8F5M       7@7M7M   u}rAc&i|}dD]-} ||}||<#t$rY*wxYwgd}fd|D}|r5tdd|S)aLTransform a string description of atom style into a dict Required fields: id, type, x, y, z Optional fields: resid, charge eg: "id resid type charge x y z" {'id': 0, 'resid': 1, 'type': 2, 'charge': 3, 'x': 4, 'y': 5, 'z': 6, } )idtyperesidchargexyz)rQrRrUrVrWcg|]}|v| SrCrC)r>attr style_dicts r8r@z4DATAParser._interpret_atom_style.. s#OOO$J8N8N8N8N8NrAz/atom_style string missing required field(s): {}z, )r<index ValueErrorformatjoin) atom_stylerYlocation reqd_attrs missing_attrsrZs @r8_interpret_atom_stylez DATAParser._interpret_atom_styles" %%'' D , ,D ,%++D11$, 4       322 OOOO*OOO  6$))M2233  s8 AAc  ||d|_n#t$r d|_YnwxYw|\}} ||d}n#t$rd}YnwxYwd|vrt d ||d|}n #t$rd}t |dwxYwdt|j j D}tdd ftd d ftd d ftdd ffD][\}} } ||| | |\} } n#t$rgg} } YnwxYw||| | \|S)ziParses a LAMMPS_ DATA file. Returns ------- MDAnalysis Topology object. r_Nrrz#Data file was missing Atoms sectionzFailed to parse atoms section. You can supply a description of the atom_style as a keyword argument, eg mda.Universe(..., atom_style='id resid x y z')ci|]\}}|| SrCrC)r>r?atom_ids r8rFz$DATAParser.parse..7sJJJ*!W7AJJJrArrr rr)rcrZKeyErrorrO _parse_massesr\ _parse_atoms ExceptionrIidsvaluesrr rr_parse_bond_sectionadd_TopologyAttr) r5kwargsheadrNrtoperrmsgmappingrYLnentriesrRsects r8parsezDATAParser.parses #"88 9MNNDOO # # #"DOOO #((** e ''h88FF   FFF  %  BCC C /##E'NF;;CC / / /D  V$$$ .  /KJ #'.0I0IJJJGQ  Xq !  Q '  Q ' " 3 3 D!X  $!55!Hh dd $ $ $d $  dD!1!1 2 2 2 2 s< #77A.. A=<A=B11C! EEENc|d|_n|||_|\}}||} ||d\}} n'#t $r} d| } t | dd} ~ wwxYwd|vr||d| } nd} |j|fd| i|} || _ | S)a)Read a DATA file and try and extract x, v, box. - positions - velocities (optional) - box information Fills this into the Timestep object and returns it .. versionadded:: 0.9.0 .. versionchanged:: 0.18.0 Added atom_style kwarg Nrz Position information not found: r velocities) rZrcrO _parse_box _parse_posriIOError _parse_velfrom_coordinates dimensions)r5n_atomsTS_class TS_kwargsr_rLrNunitcell positionsorderingerrrtr{tss r8read_DATA_timestepzDATAParser.read_DATA_timestepJs  "DOO"88DDDO**,, ??6** ,"&//%."A"A Ixx , , ,===F&//t + , 5 |)> $%AAA>> J ++  GAt::<rUrus r8r@z2DATAParser._parse_bond_section..s#GGG1ws1vvGGGrArr)r<appendtuple)r5rrwrusectionrRr7s ` r8rozDATAParser._parse_bond_sections& ! !D::<>>??@@@ Z%v    rActdi}|D]4}|}t|d||d<5|S)zpLammps defines mass on a per atom type basis. This reads mass for each type and stores in dict zDoing Masses sectionrr)rrr<float)r5rrr7s r8rjzDATAParser._parse_masses3sV  *+++ - -D::<$>??JBBHQKNHQKNHQKNHQKNHQKNHQKN$h/HHx444Ha7HRaRL+HQRRLrAN)__name__ __module__ __qualname____doc__r]r9rO staticmethodrcryrr}rrorkrjr|rCrAr8r.r.s&F4$$\$L333l8<((((TB2+++r?rYs r8rFz*LammpsDumpParser.parse..s/#At4<;O;Oa;O;O;OrArQzNo id column found in dump filerrzJNo mass column found in dump file. Using guessed masses from element info.zGuessed all Masses to 1.0rRzSet all atom types to 1rrrzUnknown element zF found for some atoms. 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