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doc page for write_data

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Steve Plimpton
2023-11-15 09:29:04 -07:00
parent a0a21fab64
commit fc5803188f
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doc/src/write_data.rst
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@ -19,6 +19,7 @@ Syntax
*nocoeff* = do not write out force field info *nocoeff* = do not write out force field info
*nofix* = do not write out extra sections read by fixes *nofix* = do not write out extra sections read by fixes
*nolabelmap* = do not write out type labels *nolabelmap* = do not write out type labels
*triclinic/general = write data file in general triclinic format
*types* value = *numeric* or *labels* *types* value = *numeric* or *labels*
*pair* value = *ii* or *ij* *pair* value = *ii* or *ij*
*ii* = write one line of pair coefficient info per atom type *ii* = write one line of pair coefficient info per atom type
@ -31,6 +32,7 @@ Examples
write_data data.polymer write_data data.polymer
write_data data.* write_data data.*
write_data data.solid triclinic/general
Description Description
""""""""""" """""""""""
@ -85,10 +87,11 @@ using the :doc:`-r command-line switch <Run_options>`.
:doc:`fixes <fix>` are stored. :doc:`Binary restart files <read_restart>` :doc:`fixes <fix>` are stored. :doc:`Binary restart files <read_restart>`
store more information. store more information.
Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command will Bond interactions (angle, etc) that have been turned off by the
be written to a data file as if they are turned on. This means they :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>`
will need to be turned off again in a new run after the data file is command will be written to a data file as if they are turned on. This
read. means they will need to be turned off again in a new run after the
data file is read.
Bonds that are broken (e.g. by a bond-breaking potential) are not Bonds that are broken (e.g. by a bond-breaking potential) are not
written to the data file. Thus these bonds will not exist when the written to the data file. Thus these bonds will not exist when the
@ -122,6 +125,23 @@ not written to the data file. By default, they are written if they
exist. A type label must be defined for every numeric type (within a exist. A type label must be defined for every numeric type (within a
given type-kind) to be written to the data file. given type-kind) to be written to the data file.
Use of the *triclinic/general* keyword will output a data file which
specifies a general triclinic simulation box as well as per-atom
quantities consistent with the general triclinic box. The latter
means that per-atom vectors, such as velocities and dipole moments
will be oriented conistent with the 3d rotation implied by the general
triclinic box (relative to the associated restricted triclinic box).
This option can only be requested if the simulation box was initially
defined to be general triclinic. If if was and the
*triclinic/general* keyword is not used, then the data file will
specify a restricted triclinic box, since that is the internal format
LAMMPS uses for both general and restricited triclinic simulations.
See the :doc:`Howto triclinic <Howto_triclinic>` doc page for more
explanation of how general triclinic simulation boxes are supported by
LAMMPS. And see the :doc:`read_data <read_data>` doc page for details
of how the format is altered for general triclinic data files.
The *types* keyword determines how atom types, bond types, angle The *types* keyword determines how atom types, bond types, angle
types, etc are written into these data file sections: Atoms, Bonds, types, etc are written into these data file sections: Atoms, Bonds,
Angles, etc. The default is the *numeric* setting, even if type label Angles, etc. The default is the *numeric* setting, even if type label