finish (for now) the summary of the data file format
This commit is contained in:
Axel Kohlmeyer
@ -167,19 +167,38 @@ from the :doc:`command line <Run_options>`.
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The file is generally structured into a header section at the very
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beginning of the file and multiple titled sections like "Atoms",
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Masses", "Pair Coeffs", and so on. The data file **always** starts
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with a "title" line, which will be **ignored** by LAMMPS. Omitting
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the title line can lead to unexpected behavior as then a line of
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the header with an actual setting may be ignored. This is often a
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line with the "atoms" keyword, which results in LAMMPS assuming that
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there are no atoms in the data file and thus throwing an error on the
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contents of the "Atoms" section. The title line may contain some
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keywords that can be used by external programs to convey information
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about the system, that is not required and not read by LAMMPS.
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Masses", "Pair Coeffs", and so on. Header keywords can only be used
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*before* the first title section.
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The data file **always** starts with a "title" line, which will be
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**ignored** by LAMMPS. Omitting the title line can lead to unexpected
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behavior as then a line of the header with an actual setting may be
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ignored. This is often a line with the "atoms" keyword, which results
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in LAMMPS assuming that there are no atoms in the data file and thus
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throwing an error on the contents of the "Atoms" section. The title
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line may contain some keywords that can be used by external programs to
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convey information about the system (included as comments), that is not
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required and not read by LAMMPS.
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The line following a section title is also **ignored**. Skipping it
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will lead to short reads and thus errors. The number of lines in titled
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sections depends on header keywords, like the number of atom types, the
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number of atoms, the number of bond types, or the number of bonds and so
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on. The data in those sections has to be complete. A special case are
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the "Pair Coeffs" and "PairIJ Coeffs" sections; the former is for force
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fields and pair styles that use mixing of non-bonded potential
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parameters, the latter for pair styles and force fields requiring
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explicit coefficients. Thus with *N* being the number of atom types,
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the "Pair Coeffs" section has *N* entries while "PairIJ Coeffs" has
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:math:`N \cdot (N-1)` entries. Internally, these sections will be
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converted to :doc:`pair_coeff <pair_coeff>` commands. Thus the
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corresponding :doc:`pair style <pair_style>` must have been set *before*
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the :doc:`read_data command <read_data>` reads the data file.
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Data files may contain comments, which start with the pound sign '#'.
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There must be at least one blank between a valid keyword and the pound
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sign.
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sign. Below is a simple example case of a data file for :doc:`atom style
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full <atom_style>`.
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.. code-block:: bash
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@ -200,7 +219,7 @@ sign.
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3 15.9990
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4 1.0080
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Pair Coeffs
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Pair Coeffs # this section is optional
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1 0.110000 3.563595 0.110000 3.563595
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2 0.080000 3.670503 0.010000 3.385415
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@ -219,11 +238,69 @@ sign.
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8 1 4 0.070 42.07157 57.45486 37.62418 0 0 0
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9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0
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10 1 1 0.510 41.88641 58.62251 39.70398 0 0 0
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# ^^atomID ^^molID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord ^^image^^flags
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# ^^atomID ^^molID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord ^^image^^flags (optional)
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Velocities # this section is optional
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1 0.0050731 -0.00398928 0.00391473
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2 -0.0175184 0.0173484 -0.00489207
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3 0.00597225 -0.00202006 0.00166454
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4 -0.010395 -0.0082582 0.00316419
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5 -0.00390877 0.00470331 -0.00226911
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6 -0.00111157 -0.00374545 -0.0169374
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7 0.00209054 -0.00594936 -0.000124563
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8 0.00635002 -0.0120093 -0.0110999
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9 -0.004955 -0.0123375 0.000403422
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10 0.00265028 -0.00189329 -0.00293198
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The common problem is processing the "Atoms" section, since its format depends
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on the :doc:`atom style <atom_style>` used and that setting must be done in the
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input file *before* reading the data file. To assist with detecting incompatible
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data files, a comment is appended to the "Atoms" title indicating the atom style
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used (or intended) when *writing* the data file. For example below is the same
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section for :doc:`atom style charge <atom_style>`, which omits the molecule ID
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column.
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.. code-block:: bash
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Atoms # charge
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1 1 0.560 43.99993 58.52678 36.78550
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2 2 -0.270 45.10395 58.23499 35.86693
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3 3 -0.510 43.81519 59.54928 37.43995
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4 4 0.090 45.71714 57.34797 36.13434
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5 4 0.090 45.72261 59.13657 35.67007
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6 4 0.090 44.66624 58.09539 34.85538
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7 3 -0.470 43.28193 57.47427 36.91953
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8 4 0.070 42.07157 57.45486 37.62418
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9 1 0.510 42.19985 57.57789 39.12163
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10 1 0.510 41.88641 58.62251 39.70398
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# ^^atomID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord
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Another source of confusion about the "Atoms" section format is the
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ordering of columns. The three atom style variants `atom_style full`,
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`atom_style hybrid charge molecular`, and `atom_style hybrid molecular
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charge` all carry the same per-atom information, but in the data file
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the Atoms section has the columns 'Atom-ID Molecule-ID Atom-type Charge
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X Y Z' for atom style full, but hybrid atom styles the first columns are
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always 'Atom-ID Atom-type X Y Z' and then followed by any *additional*
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data added by the hybrid styles, and thus 'Charge Molecule-ID' for the
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first hybrid style and 'Molecule-ID Charge' in the second hybrid style
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variant. Finally, an alternative to a hybrid atom style is to use fix
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property/atom, e.g. to add molecule IDs to atom style charge. In this
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case the "Atoms" section is formatted according to atom style charge and
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a new section, "Molecules" is added that contains lines with 'Atom-ID
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Molecule-ID', one for each atom in the system. For adding charges
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to atom style molecular with fix property/atom, the "Atoms" section is
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now formatted according to the atom style and a "Charges" section is
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added.
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Molecule file
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^^^^^^^^^^^^^
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Molecule files look quite similar to data files but they do not have a
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compatible format, i.e. one cannot use a data file as molecule file and
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vice versa.
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Potential file
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^^^^^^^^^^^^^^
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