i-dZddlZddlZddlZddlZddlmZddlm Z m Z ddl m Z ddl mZdd l mZGd d ejZGd d ejZdS)u FHI-AIMS file format --- :mod:`MDAnalysis.coordinates.FHIAIMS` ============================================================== Classes to read and write `FHI-AIMS`_ coordinate files. The cell vectors are specified by the (optional) lines with the ``lattice_vector`` tag:: lattice_vector x y z where x, y, and z are expressed in ångström (Å). .. Note:: In the original `FHI-AIMS format`_, up to three lines with ``lattice_vector`` are allowed (order matters) where the absent line implies no periodicity in that direction. In MDAnalysis, only the case of no ``lattice_vector`` or three ``lattice_vector`` lines are allowed. Atomic positions and names are specified either by the ``atom`` or by the ``atom_frac`` tags:: atom x y z name atom_frac nx ny nz name where x, y, and z are expressed in ångström, and nx, ny and nz are real numbers in [0, 1] and are used to compute the atomic positions in units of the basic cell. Atomic velocities can be added on the line right after the corresponding ``atom`` in units of Å/ps using the ``velocity`` tag:: velocity vx vy vz The field name is a string identifying the atomic species. See also the specifications in the official `FHI-AIMS format`_. Classes ------- .. autoclass:: FHIAIMSReader :members: :inherited-members: .. autoclass:: FHIAIMSWriter :members: :inherited-members: Developer notes: ``FHIAIMSWriter`` format strings ------------------------------------------------- The :class:`FHIAIMSWriter` class has a :attr:`FHIAIMSWriter.fmt` attribute, which is a dictionary of different strings for writing lines in ``.in`` files. These are as follows: ``xyz`` An atom line without velocities. Requires that the `name` and `pos` keys be supplied. E.g.:: fmt['xyz'].format(pos=(0.0, 1.0, 2.0), name='O') ``vel`` An line that specifies velocities:: fmt['xyz'].format(vel=(0.1, 0.2, 0.3)) ``box_triclinic`` The (optional) initial lines of the file which gives box dimensions. Requires the `box` keyword, as a length 9 vector. This is a flattened version of the (3, 3) triclinic vector representation of the unit cell. .. Links .. _FHI-AIMS: https://aimsclub.fhi-berlin.mpg.de/ .. _FHI-AIMS format: https://doi.org/10.6084/m9.figshare.12413477.v1 N)base) triclinic_boxtriclinic_vectors) NoDataError)util)mdamathc4eZdZdZddgZddddZdZd d Zd S) FHIAIMSReaderaReader for the FHIAIMS geometry format. Single frame reader for the `FHI-AIMS`_ input file format. Reads geometry (3D and molecules only), positions (absolut or fractional), velocities if given, all according to the `FHI-AIMS format`_ specifications INFHIAIMSpsAngstrom Angstrom/pstimelengthvelocitycj tj|jd5}ggggf\}}}}ddg}d}|D]u  drI| dd|d v }u d r^d|vr(td  |j| dd } d r3| dd }0t fd |Dr }Otd  |j dddn #1swxYwYtj |tj }t|dt|fvr=tdt|t|t|dvrtdt|dkrt|rtdt|x|_}|j|fi|jx|_} || _t|dkr6t'|| _tj| j||| j|<t|dkr|| _d|j_dS)Nrt#initial_momentatomr atom_fracrzPNon-conforming line (velocity must follow atom): ({0})in FHI-AIMS input file {0}latticec:g|]}|S) startswith).0taglines h/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/FHIAIMS.py z3FHIAIMSReader._read_first_frame..s%BBB,,BBBz4Non-conforming line: ({0})in FHI-AIMS input file {0})dtyperzRFound incorrect number of velocity tags ({0}) in the FHI-AIMS file, should be {1}.)rzQFound partial periodicity in FHI-AIMS file. This cannot be handled by MDAnalysis.zAFound relative coordinates in FHI-AIMS file without lattice info.)r openanyfilenamestripr!appendsplit ValueErrorformatanynpasarrayfloat32lenn_atoms _Timestep _ts_kwargsts positionsr dimensionsmatmul velocitiesframe) self fhiaimsfilerelativer:r=lattice_vectors skip_tagsoldliner6r9r$s @r%_read_first_framezFHIAIMSReader._read_first_frames \$- . . +?A2r2~ >>B?>B? DD'&D'I)EI)E1.I)0E11C*I))I-0I-)TN) rJrKrLrMr0rNrnrWrzr r'r%rGrGs|I FZ] K KE PHS   C    IIIIIr'rG)rMrerdrgnumpyr2rrcorerr exceptionsrlibr r SingleFrameReaderBaser WriterBaserGr r'r%rs0PPb 22222222$$$$$$cBcBcBcBcBD.cBcBcBLnnnnnDOnnnnnr'