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small tweaks

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