ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

small tweaks

Browse Source
This commit is contained in:
Axel Kohlmeyer
2025-03-29 15:56:34 -04:00
parent 990007c87b
commit 7ff9ee51e5
1 changed files with 15 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
doc/src/Run_formats.rst
View File

@ -314,23 +314,25 @@ there is no information about the number of types or the box dimensions.
These parameters are set when the simulation box is created. Thus the
header only has the count of atoms, bonds, and so on.
Molecule files have a header followed by sections, but the section names
are different than those of a data file. There is no "Atoms" section
and the section format is independent of the atom style. Its
information is split across multiple sections, like "Coords", "Types",
and "Charges". Note that no "Masses" section is needed here. The atom
masses are by default tied to the atom type and set with a data file or
the :doc:`mass command <mass>`. A "Masses" section would only be
required for atom styles with per-atom masses, e.g. atom style sphere.
Molecule files have a header followed by sections (just as in data
files), but the section names are different than those of a data file.
There is no "Atoms" section and the section formats in molecule files is
independent of the atom style. Its information is split across multiple
sections, like "Coords", "Types", and "Charges". Note that no "Masses"
section is needed here. The atom masses are by default tied to the atom
type and set with a data file or the :doc:`mass command <mass>`. A
"Masses" section would only be required for atom styles with per-atom
masses, e.g. atom style sphere, where in data files you would provide
the density and the diameter instead of the mass.
Since the entire file is a 'molecule', LAMMPS will assign a new
molecule-ID (if supported by the atom style) when atoms are instantiated
from a molecule file, e.g. with the :doc:`create_atoms command
<create_atoms>`. It is possible to include a "Molecules" section in
case the atoms belong to multiple 'molecules'. Atom-IDs and
molecule-IDs in the molecule file are relative for the file (starting
from 1) and will be translated into actual atom-IDs also when the
molecule is created.
<create_atoms>`. It is possible to include a "Molecules" section to
indicate that the atoms belong to multiple 'molecules'. Atom-IDs and
molecule-IDs in the molecule file are relative for the file
(i.e. starting from 1) and will be translated into actual atom-IDs also
when the atoms from the molecule are created.
.. code-block:: bash
@ -407,7 +409,6 @@ are in the ``lmprestart.h`` header file.
LAMMPS restart files are not expected to be portable between platforms
or LAMMPS versions, but changes to the file format are rare.
.. Native Dump file
.. ^^^^^^^^^^^^^^^^
..