tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add docs to mention using a type labels for xyz files with string labels

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-09-21 12:24:41 -04:00
parent d16d744550
commit 061c80104a
1 changed files with 12 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
doc/src/read_dump.rst
View File

@ -230,13 +230,18 @@ will then have a label corresponding to the fix-ID rather than "x" or
"xs". The *label* keyword can also be used to specify new column
labels for fields *id* and *type*\ .
For dump files in *xyz* format, only the *x*, *y*, and *z* fields are
supported. The 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 *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.
For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and
*vz* fields can be specified. However, not all molfile formats store