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rewording of doc page

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This commit is contained in:
Steve Plimpton
2023-03-27 16:39:37 -06:00
parent 5b37ff8160
commit 7460cc682d
1 changed files with 51 additions and 37 deletions
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88
doc/src/set.rst
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@ -11,7 +11,16 @@ Syntax
set style ID keyword values ...
* style = *atom* or *type* or *mol* or *group* or *region*
* ID = atom ID range or type range or mol ID range or group ID or region ID
* ID = depends on style
.. parsed-literal::
for style = *atom*, ID = a range of atom IDs
for style = *type*, ID = a range of numeric types or a single type label
for style = *mol*, ID = a range of molecule IDs
for style = *group*, ID = a group ID
for style = *region*, ID = a region ID
* one or more keyword/value pairs may be appended
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
@ -28,22 +37,22 @@ Syntax
.. parsed-literal::
*type* value = atom type or type label
*type* value = numeric atom type or type label
value can be an atom-style variable (see below)
*type/fraction* values = type fraction seed
type = new atom type or type label
type = numeric atom type or type label
fraction = approximate fraction of selected atoms to set to new atom type
seed = random # seed (positive integer)
*type/ratio* values = type fraction seed
type = new atom type or type label
type = numeric atom type or type label
fraction = exact fraction of selected atoms to set to new atom type
seed = random # seed (positive integer)
*type/subset* values = type Nsubset seed
type = new atom type or type label
type = numeric atom type or type label
Nsubset = exact number of selected atoms to set to new atom type
seed = random # seed (positive integer)
*mol* value = molecule ID
value can be an atom-style variable (see below)
value can be an atom-style variable (see below)
*x*,\ *y*,\ *z* value = atom coordinate (distance units)
value can be an atom-style variable (see below)
*vx*,\ *vy*,\ *vz* value = atom velocity (velocity units)
@ -107,10 +116,10 @@ Syntax
*image* nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
any of nx,ny,nz can be an atom-style variable (see below)
*bond* value = bond type or bond type label for all bonds between selected atoms
*angle* value = angle type or angle type label for all angles between selected atoms
*dihedral* value = dihedral type or dihedral type label for all dihedrals between selected atoms
*improper* value = improper type or improper type label for all impropers between selected atoms
*bond* value = numeric bond type or bond type label, for all bonds between selected atoms
*angle* value = numeric angle type or angle type label, for all angles between selected atoms
*dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
*improper* value = numeric improper type or improper type label, for all impropers between selected atoms
*sph/e* value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/cv* value = heat capacity of SPH particles (need units)
@ -191,9 +200,13 @@ the properties of, via the *style* and *ID* arguments.
Support for type labels was added for selecting atoms by type
The style *atom* selects all the atoms in a range of atom IDs. The
style *type* selects all the atoms in a range of types or type labels.
The style *mol* selects all the atoms in a range of molecule IDs.
The style *atom* selects all the atoms in a range of atom IDs.
The style *type* selects all the atoms in a range of types or type
labels. The style *type* selects atoms in one of two ways. A range
of numeric atom types can be specified. Or a single atom type label
can be specified, e.g. "C". The style *mol* selects all the atoms in
a range of molecule IDs.
In each of the range cases, the range can be specified as a single
numeric value, or a wildcard asterisk can be used to specify a range
@ -250,15 +263,15 @@ from a file.
Support for type labels was added for setting atom, bond, angle,
dihedral, and improper types
Keyword *type* sets the atom type for all selected atoms. A specified value
can be a type id or a type label for atom type. When using a
type id, the specified value must be from 1 to ntypes, where ntypes was set
by the :doc:`create_box <create_box>` command or the *atom types* field in the
header of the data file read by the :doc:`read_data <read_data>`
command. In the case of the specified type label, it must have been defined
before use via an alphanumeric type label. See the
:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed syntax
of type labels and a general discussion of how type labels can be used.
Keyword *type* sets the atom type for all selected atoms. A specified
value can be either a numeric atom type or an atom type label. When
using a numeric type, the specified value must be from 1 to ntypes,
where ntypes was set by the :doc:`create_box <create_box>` command or
the *atom types* field in the header of the data file read by the
:doc:`read_data <read_data>` command. When using a type label it must
have been defined previously. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
Keyword *type/fraction* sets the atom type for a fraction of the selected
atoms. The actual number of atoms changed is not guaranteed
@ -268,10 +281,10 @@ that a particular atom is changed or not changed, regardless of how
many processors are being used. This keyword does not allow use of an
atom-style variable.
Keywords *type/ratio* and *type/subset* also set the atom type for
a fraction of the selected atoms. The actual number of
atoms changed will be exactly the requested number. For *type/ratio* the
specified fraction (0 <= *fraction* <= 1) determines the number. For
Keywords *type/ratio* and *type/subset* also set the atom type for a
fraction of the selected atoms. The actual number of atoms changed
will be exactly the requested number. For *type/ratio* the specified
fraction (0 <= *fraction* <= 1) determines the number. For
*type/subset*, the specified *Nsubset* is the number. An iterative
algorithm is used which ensures the correct number of atoms are
selected, in a perfectly random fashion. Which atoms are selected
@ -480,17 +493,18 @@ simulation, but may mess up analysis of the trajectories if a LAMMPS
diagnostic or your own analysis relies on the image flags to unwrap a
molecule which straddles the periodic box.
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type
(angle type, etc) of all bonds (angles, etc) of selected atoms to the
specified value from 1 to nbondtypes (nangletypes, etc). One can also use
a specified type label. See the :doc:`Howto type labels <Howto_type_labels>`
doc page for the allowed syntax of type labels and a general discussion of
how type labels can be used. All atoms in a
particular bond (angle, etc) must be selected atoms in order for the
change to be made. The value of nbondtype (nangletypes, etc) was set by
the *bond types* (\ *angle types*, etc) field in the header of the data
file read by the :doc:`read_data <read_data>` command. These keywords
do not allow use of an atom-style variable.
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value. The value can be a numeric type from 1 to
nbondtypes (nangletypes, etc). Or it can be a type label (bond type
label, angle type lable, etc). See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used. All atoms in
a particular bond (angle, etc) must be selected atoms in order for the
change to be made. The value of nbondtypes (nangletypes, etc) was set
by the *bond types* (\ *angle types*, etc) field in the header of the
data file read by the :doc:`read_data <read_data>` command. These
keywords do not allow use of an atom-style variable.
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
and density of smoothed particle hydrodynamics (SPH) particles. See