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update read_dump docs with respect to reading xyz style dump files

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Axel Kohlmeyer
2024-09-30 14:54:35 -04:00
parent ec392d5613
commit a31f083bab
1 changed files with 11 additions and 10 deletions
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doc/src/read_dump.rst
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@ -241,17 +241,18 @@ ignore the second (title) line, and then read one line for each atom in the form
<label> <x coordinate> <y coordinate> <z coordinate>
If label is an integer number as label (like with XYZ files created by
If the atom label is a numeric integer (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.
number will be used as the atom type. If the atom label is a string,
then a type map must be 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