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clarify docs for XYZ file format

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This commit is contained in:
Axel Kohlmeyer
2024-09-23 14:44:16 -04:00
parent abb8b5ae45
commit d787ecdcb3
1 changed files with 25 additions and 15 deletions
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doc/src/read_dump.rst
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@ -115,10 +115,11 @@ to tell LAMMPS how many parallel files exist, via its specified
The format of the dump file is selected through the *format* keyword.
If specified, it must be the last keyword used, since all remaining
arguments are passed on to the dump reader. The *native* format is
for native LAMMPS dump files, written with a :doc:`dump atom <dump>`
or :doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
formatted dump files. These formats take no additional values.
arguments are passed on to the dump reader. The *native* format is for
native LAMMPS dump files, written with a :doc:`dump atom <dump>` or
:doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
formatted dump files (see details below). These formats take no
additional values.
The *molfile* format supports reading data through using the `VMD <vmd_>`_
molfile plugin interface. This dump reader format is only available,
@ -231,17 +232,26 @@ will then have a label corresponding to the fix-ID rather than "x" or
labels for fields *id* and *type*\ .
For dump files in *xyz* format, only the *type*, *x*, *y*, and *z*
fields are supported. If the atoms have an integer number as label
(like when they are created with default setting by :doc:`dump style
<dump>` *xyz*), that number will be used at atom type. The the atom
label is a string, it is required that a map is created using the
:doc:`labelmap command <labelmap>` that maps those labels to the
(numeric) atom types that LAMMPS uses. The xyz format dump file does
not store atom IDs, so these are assigned consecutively to the atoms as
they appear in the dump file, starting from 1. Thus you should ensure
that order of atoms is consistent from snapshot to snapshot in the XYZ
dump file. See the :doc:`dump_modify sort <dump_modify>` command if the
XYZ dump file was written by LAMMPS.
fields are supported. There are many variants of the XYZ file format.
LAMMPS will read the number of atoms from the first line of each frame,
ignore the second (title) line, and then read one line for each atom in the format:
.. parsed-literal::
<label> <x coordinate> <y coordinate> <z coordinate>
If label is an integer number as label (like with XYZ files created by
created with default settings by :doc:`dump style <dump>` *xyz*), that
number will be used at atom type. If the atom label is a string, then
it is required that a map is created using the :doc:`labelmap command
<labelmap>`. This map needs to associate each (numeric) atom type with
one string label and that numeric type is stored. The xyz format dump
file does not store atom IDs, so these are assigned consecutively to the
atoms as they appear in the dump file, starting from 1. Thus you should
ensure that order of atoms is consistent from snapshot to snapshot in
the XYZ dump file. See the :doc:`dump_modify sort <dump_modify>`
command if the XYZ dump file was written by LAMMPS.
For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and
*vz* fields can be specified. However, not all molfile formats store