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enable per-atom custom arrays in addition to vectors

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This commit is contained in:
Steve Plimpton
2020-09-04 11:33:49 -06:00
parent d00807ee9a
commit d1442b0538
23 changed files with 1390 additions and 722 deletions
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18
doc/src/balance.rst
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@ -465,12 +465,18 @@ atom-style variables can reference the position of a particle, its
velocity, the volume of its Voronoi cell, etc.
The *store* weight style does not compute a weight factor. Instead it
stores the current accumulated weights in a custom per-atom property
specified by *name*\ . This must be a property defined as *d_name* via
the :doc:`fix property/atom <fix_property_atom>` command. Note that
these custom per-atom properties can be output in a :doc:`dump <dump>`
file, so this is a way to examine, debug, or visualize the
per-particle weights computed during the load-balancing operation.
stores the current accumulated weights in a custom per-atom vector
specified by *name*\ . This must be a vector defined as *d_name* via
the :doc:`fix property/atom <fix_property_atom>` command. This means
the values in the vector can be read as part of a data file with the
:doc:`read_data <read_data>` command or specified with the :doc:`set
<set>` command. These weights can also be output in a :doc:`dump
<dump>` file, so this is a way to examine, debug, or visualize the
per-particle weights used during the load-balancing operation.
Note that the name of the custom per-atom vector is specified just
as *name*, not as *d_name* as it is for other commands that use
different kinds of custom atom vectors or arrays as arguments.
----------

117
doc/src/compute_property_atom.rst
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@ -20,7 +20,8 @@ Syntax
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
sp, spx, spy, spz, fmx, fmy, fmz,
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
@ -29,42 +30,42 @@ Syntax
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
buckling,
vfrac, s0,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name
i_name, d_name, i2_name[I], d2_name[I],
vfrac, s0, spin, eradius, ervel, erforce,
rho, drho, e, de, cv, buckling
.. parsed-literal::
id = atom ID
mol = molecule ID
proc = ID of processor that owns atom
type = atom type
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
sp = atomic magnetic spin moment
spx, spy, spz = direction of the atomic magnetic spin
fmx, fmy, fmz = magnetic force
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on finite-size particles
end12x, end12y, end12z = end points of line segment
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds assigned to an atom
buckling = buckling flag used in mesoscopic simulation of nanotubes
*id* = atom ID
*mol* = molecule ID
*proc* = ID of processor that owns atom
*type* = atom type
*mass* = atom mass
*x,y,z* = unscaled atom coordinates
*xs,ys,zs* = scaled atom coordinates
*xu,yu,zu* = unwrapped atom coordinates
*ix,iy,iz* = box image that the atom is in
*vx,vy,vz* = atom velocities
*fx,fy,fz* = forces on atoms
*q* = atom charge
*mux,muy,muz* = orientation of dipole moment of atom
*mu* = magnitude of dipole moment of atom
*spx, spy, spz* = direction of the atomic magnetic spin
*sp* = magintude of atomic magnetic spin moment
*fmx, fmy, fmz* = magnetic force
*nbonds* = number of bonds assigned to an atom
*radius,diameter* = radius,diameter of spherical particle
*omegax,omegay,omegaz* = angular velocity of spherical particle
*angmomx,angmomy,angmomz* = angular momentum of aspherical particle
*shapex,shapey,shapez* = 3 diameters of aspherical particle
*quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles
*tqx,tqy,tqz* = torque on finite-size particles
*end12x, end12y, end12z* = end points of line segment
*corner123x, corner123y, corner123z* = corner points of triangle
*i_name* = custom integer vector with name
*d_name* = custom floating point vector with name
*i2_name[I]* = Ith column of custom integer array with name
*d2_name[I]* = Ith column of custom floating-point array with name
.. parsed-literal::
@ -91,9 +92,8 @@ Syntax
.. parsed-literal::
:doc:`fix property/atom <fix_property_atom>` per-atom properties:
i_name = custom integer vector with name
d_name = custom integer vector with name
USER-MESONT package per-atom properties:
buckling = buckling flag used in mesoscopic simulation of nanotubes
Examples
""""""""
@ -104,6 +104,7 @@ Examples
compute 2 all property/atom type
compute 1 all property/atom ix iy iz
compute 3 all property/atom sp spx spy spz
compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3]
Description
"""""""""""
@ -116,20 +117,37 @@ ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable
<variable>` commands.
The list of possible attributes is the same as that used by the
:doc:`dump custom <dump>` command, which describes their meaning, with
some additional quantities that are only defined for certain
:doc:`atom styles <atom_style>`. Basically, this augmented list gives
an input script access to any per-atom quantity stored by LAMMPS.
The list of possible attributes is essentially the same as that used
by the :doc:`dump custom <dump>` command, which describes their
meaning, with some additional quantities that are only defined for
certain :doc:`atom styles <atom_style>`. The goal of this augmented
list gives an input script access to any per-atom quantity stored by
LAMMPS.
The values are stored in a per-atom vector or array as discussed
below. Zeroes are stored for atoms not in the specified group or for
quantities that are not defined for a particular particle in the group
(e.g. *shapex* if the particle is not an ellipsoid).
Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these attributes. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.
*Nbonds* is available for all molecular atom styles and refers to the
number of explicit bonds assigned to an atom. Note that if the
:doc:`newton bond <newton>` command is set to *on*\ , which is the
default, then every bond in the system is assigned to only one of the
two atoms in the bond. Thus a bond between atoms I,J may be tallied
for either atom I or atom J. If :doc:`newton bond off <newton>` is
set, it will be tallied with both atom I and atom J.
*Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles
and define the 3d shape of each particle.
@ -146,19 +164,8 @@ line segment.
*corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for
triangular particles and define the corner points of each triangle.
*Nbonds* is available for all molecular atom styles and refers to the
number of explicit bonds assigned to an atom. Note that if the
:doc:`newton bond <newton>` command is set to *on*\ , which is the
default, then every bond in the system is assigned to only one of the
two atoms in the bond. Thus a bond between atoms I,J may be tallied
for either atom I or atom J. If :doc:`newton bond off <newton>` is
set, it will be tallied with both atom I and atom J.
The *i_name* and *d_name* attributes refer to custom integer and
floating-point properties that have been added to each atom via the
:doc:`fix property/atom <fix_property_atom>` command. When that
command is used specific names are given to each attribute which are
what is specified as the "name" portion of *i_name* or *d_name*.
In addition, the various per-atom quantities listed above for specific
packages are only accessible by this command.
Output info
"""""""""""

45
doc/src/dump.rst
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@ -78,7 +78,8 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
i_name, d_name, i2_name[I], d2_name[I]
.. parsed-literal::
@ -108,8 +109,10 @@ Syntax
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
d_name = per-atom floating point vector with name, managed by fix property/atom
i_name = per-atom integer vector with name, managed by fix property/atom
i_name = custom integer vector with name
d_name = custom floating point vector with name
i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below)
d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below)
* *local* args = list of local attributes
@ -134,7 +137,7 @@ Examples
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
@ -465,16 +468,15 @@ styles.
----------
Note that in the discussion which follows, for styles which can
reference values from a compute or fix, like the *custom*\ , *cfg*\ , or
*local* styles, the bracketed index I can be specified using a
wildcard asterisk with the index to effectively specify multiple
values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
size of the vector (for *mode* = scalar) or the number of columns in
the array (for *mode* = vector), then an asterisk with no numeric
values means all indices from 1 to N. A leading asterisk means all
indices from 1 to n (inclusive). A trailing asterisk means all
indices from n to N (inclusive). A middle asterisk means all indices
from m to n (inclusive).
reference values from a compute or fix or custom atom property, like
the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*"
or "m\*n". If N = the number of columns in the array, then an
asterisk with no numeric values means all column indices from 1 to N.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 dump commands are
@ -512,8 +514,9 @@ bonds and angles.
Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the :doc:`thermo_style custom <thermo_style>` command, and per-atom quantities can be
output by the dump custom command.
Instead, global quantities can be output by the :doc:`thermo_style
custom <thermo_style>` command, and per-atom quantities can be output
by the dump custom command.
If *c_ID* is used as a attribute, then the local vector calculated by
the compute is printed. If *c_ID[I]* is used, then I must be in the
@ -660,9 +663,13 @@ invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.
The *d_name* and *i_name* attributes allow to output custom per atom
floating point or integer properties that are managed by
:doc:`fix property/atom <fix_property_atom>`.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
See the :doc:`Modify <Modify>` doc page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

258
doc/src/fix_property_atom.rst
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@ -11,11 +11,11 @@ Syntax
.. parsed-literal::
fix ID group-ID property/atom vec1 vec2 ... keyword value ...
fix ID group-ID property/atom name1 name2 ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* property/atom = style name of this fix command
* vec1,vec2,... = *mol* or *q* or *rmass* or *i_name* or *d_name*
* name1,name2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* or *i2_name* or *d2_name*
.. parsed-literal::
@ -24,6 +24,10 @@ Syntax
*rmass* = per-atom mass
*i_name* = new integer vector referenced by name
*d_name* = new floating-point vector referenced by name
*i2_name* = new integer array referenced by name
i2_name arg = N = number of columns in the array
*d2_name* = new floating-point array referenced by name
d2_name arg = N = number of columns in the array
* zero of more keyword/value pairs may be appended
* keyword = *ghost*
@ -39,58 +43,64 @@ Examples
fix 1 all property/atom mol
fix 1 all property/atom i_myflag1 i_myflag2
fix 1 all property/atom d_sx d_sy d_sz
fix 1 all property/atom d2_sxyz 3 ghost yes
Description
"""""""""""
Create one or more additional per-atom vectors to store information
about atoms and to use during a simulation. The specified *group-ID*
is ignored by this fix.
Create one or more additional per-atom vectors or arrays to store
information about atoms and to use during a simulation. The specified
*group-ID* is ignored by this fix.
The atom style used for a simulation defines a set of per-atom
properties, as explained on the :doc:`atom_style <atom_style>` and
:doc:`read_data <read_data>` doc pages. The latter command allows these
properties to be defined for each atom in the system when a data file
is read. This fix will augment the set of properties with new custom
:doc:`read_data <read_data>` doc pages. The latter command defines
these properties for each atom in the system when a data file is read.
This fix augments the set of per-atom properties with new custom
ones. This can be useful in several scenarios.
If the atom style does not define molecule IDs, per-atom charge,
or per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
keywords. This can be useful, e.g, to define "molecules" to use as
rigid bodies with the :doc:`fix rigid <fix_rigid>` command, or just to
carry around an extra flag with the atoms (stored as a molecule ID)
that can be used to group atoms without having to use the group
If the atom style does not define molecule IDs, per-atom charge, or
per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
keywords. This ciykd be useful to define "molecules" to use as rigid
bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
around an extra flag with atoms (stored as a molecule ID) that can be
used by various commands like :doc:`compute chunk/atom
<compute_chunk_atom>` to group atoms without having to use the group
command (which is limited to a total of 32 groups including *all*\ ).
Another application would be to use the *rmass* flag in order to have
per-atom masses instead of per-type masses, for example this can be
useful to study isotope effects with partial isotope substitution.
Please :ref:`see below <isotopes>` for an example of simulating a mixture
of light and heavy water with the TIP4P water potential.
Another application is to use the *rmass* flag in order to have
per-atom masses instead of per-type masses. This could be used to
study isotope effects with partial isotope substitution. :ref:`See
below <isotopes>` for an example of simulating a mixture of light and
heavy water with the TIP4P water potential.
An alternative to using fix *property/atom* in these ways is to
An alternative to using fix *property/atom* for these examples is to
use an atom style that does define molecule IDs or charge or per-atom
mass (indirectly via diameter and density) or to use a hybrid atom
style that combines two or more atom styles
to provide the union of all atom properties. However, this has two
practical drawbacks: first, it typically necessitates changing the
format of the data file, which can be tedious for large systems;
and second, it may define additional properties that are not needed
such as bond lists, which has some overhead when there are no bonds.
style that combines two or more atom styles to provide the union of
all their atom properties. However, this has two practical drawbacks:
first, it typically necessitates changing the format of the Atoms
section in the data file and second, it may define additional
properties that are not needed such as bond lists, which incurs some
overhead when there are no bonds.
In the future, we may add additional per-atom properties similar to
*mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined
by some atom styles, so they can be used by atom styles that do not
define them.
In the future, we may add additional existing per-atom properties to
fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
"turn-on" specific properties defined by some atom styles, so they can
be easily used by atom styles that do not define them.
More generally, the *i_name* and *d_name* vectors allow one or more
new custom per-atom properties to be defined. Each name must be
unique and can use alphanumeric or underscore characters. These
vectors can store whatever values you decide are useful in your
simulation. As explained below there are several ways to initialize
and access and output these values, both via input script commands and
in new code that you add to LAMMPS.
More generally, the *i_name* and *d_name* options allow one or more
new custom per-atom vectors to be defined. Likewise the *i2_name* and
*d2_name* options allow one or more custom per-atom arrays to be
defined. The *i2_name* and *d2_name* options take an argument *N*
which specifies the number of columns in the per-atom array, i.e. the
number of attributes associated with each atom. *N* >= 1 is required.
Each name must be unique and can use alphanumeric or underscore
characters. These vectors and arrays can store whatever values you
decide are useful in your simulation. As explained below there are
several ways to initialize, access, and output these values, via input
script commands, data files, and in new code you add to LAMMPS.
This is effectively a simple way to add per-atom properties to a model
without needing to write code for a new :doc:`atom style <atom_style>`
@ -107,42 +117,38 @@ new properties are also defined for the ghost atoms.
.. note::
If you use this command with the *mol*\ , *q* or *rmass* vectors,
then you most likely want to set *ghost* yes, since these properties
are stored with ghost atoms if you use an :doc:`atom_style <atom_style>`
that defines them, and many LAMMPS operations that use molecule IDs or
charge, such as neighbor lists and pair styles, will expect ghost
atoms to have these values. LAMMPS will issue a warning it you define
those vectors but do not set *ghost* yes.
If you use the *mol*\ , *q* or *rmass* names, you most likely want
to set *ghost* yes, since these properties are stored with ghost
atoms if you use an :doc:`atom_style <atom_style>` that defines
them. Many LAMMPS operations that use molecule IDs or charge, such
as neighbor lists and pair styles, will expect ghost atoms to have
these values. LAMMPS will issue a warning it you define those
vectors but do not set *ghost* yes.
.. note::
The properties for ghost atoms are not updated every timestep,
but only once every few steps when neighbor lists are re-built. Thus
the *ghost* keyword is suitable for static properties, like molecule
IDs, but not for dynamic properties that change every step. For the
latter, the code you add to LAMMPS to change the properties will also
need to communicate their new values to/from ghost atoms, an operation
that can be invoked from within a :doc:`pair style <pair_style>` or
:doc:`fix <fix>` or :doc:`compute <compute>` that you write.
.. note::
If this fix is defined **after** the simulation box is created,
a 'run 0' command should be issued to properly initialize the storage
created by this fix.
The specified properties for ghost atoms are not updated every
timestep, but only once every few steps when neighbor lists are
re-built. Thus the *ghost* keyword is suitable for static
properties, like molecule IDs, but not for dynamic properties that
change every step. For the latter, the code you add to LAMMPS to
change the properties will also need to communicate their new
values to/from ghost atoms, an operation that can be invoked from
within a :doc:`pair style <pair_style>` or :doc:`fix <fix>` or
:doc:`compute <compute>` that you write.
----------
This fix is one of a small number that can be defined in an input
script before the simulation box is created or atoms are defined.
This is so it can be used with the :doc:`read_data <read_data>` command
as described below.
This is so it can be used with the :doc:`read_data <read_data>`
command as described next.
Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by
the :doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>`
Per-atom properties that are defined by the :doc:`atom style
<atom_style>` are initialized when atoms are created, e.g. by the
:doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>`
commands. The per-atom properties defined by this fix are not. So
you need to initialize them explicitly. This can be done by the
you need to initialize them explicitly. One way to do thisis
:doc:`read_data <read_data>` command, using its *fix* keyword and
passing it the fix-ID of this fix.
@ -167,15 +173,22 @@ would allow a data file to have a section like this:
...
N 763 4.5
where N is the number of atoms, and the first field on each line is
the atom-ID, followed by a molecule-ID and a floating point value that
will be stored in a new property called "flag". Note that the list of
per-atom properties can be in any order.
where N is the number of atoms, the first field on each line is the
atom-ID, the next two are a molecule-ID and a floating point value
that will be stored in a new property called "flag". If a per-atom
array was specified in the fix property/atom commmand then the *N*
values for that array must be specified consecutively for that
property on each line.
Another way of initializing the new properties is via the
:doc:`set <set>` command. For example, if you wanted molecules
defined for every set of 10 atoms, based on their atom-IDs,
these commands could be used:
Note that the the lines of per-atom properties can be listed in any
order. Also note that all the per-atom properties specified by the
fix ID (prop in this case) must be included on each line in the
specified data file section (Molecules in this case).
Another way of initializing the new properties is via the :doc:`set
<set>` command. For example, if you wanted molecules defined for
every set of 10 atoms, based on their atom-IDs, these commands could
be used:
.. code-block:: LAMMPS
@ -185,53 +198,59 @@ these commands could be used:
The :doc:`atom-style variable <variable>` will create values for atoms
with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
:doc:`set <set>` commands assigns them to the molecule ID for each atom,
they will be truncated to an integer value, so atoms 31-40 will all be
assigned a molecule ID of 4.
:doc:`set <set>` commands assigns them to the molecule ID for each
atom, they will be truncated to an integer value, so atoms 31-40 will
all be assigned a molecule ID of 4.
Note that :doc:`atomfile-style variables <variable>` can also be used in
place of atom-style variables, which means in this case that the
Note that :doc:`atomfile-style variables <variable>` can also be used
in place of atom-style variables, which means in this case that the
molecule IDs could be read-in from a separate file and assigned by the
:doc:`set <set>` command. This allows you to initialize new per-atom
properties in a completely general fashion.
----------
For new atom properties specified as *i_name* or *d_name*, the
:doc:`compute property/atom <compute_property_atom>` command can access
their values. This means that the values can be output via the :doc:`dump custom <dump>` command, accessed by fixes like :doc:`fix ave/atom <fix_ave_atom>`, accessed by other computes like :doc:`compute reduce <compute_reduce>`, or used in :doc:`atom-style variables <variable>`.
For new atom properties specified as *i_name*, *d_name*, *i2_name*, or
*d2_name*, the :doc:`dump custom <dump>` and :doc:`compute
property/atom <compute_property_atom>` commands can access their
values. This means that the values can be used accessed by fixes like
:doc:`fix ave/atom <fix_ave_atom>`, accessed by other computes like
:doc:`compute reduce <compute_reduce>`, or used in :doc:`atom-style
variables <variable>`.
For example, these commands will output two new properties to a custom
dump file:
For example, these commands will output both the instantanous and
time-averaged values of two new properties to a custom dump file:
.. code-block:: LAMMPS
fix prop all property/atom i_flag1 d_flag2
fix myprops all property/atom i_flag1 d_flag2
compute 1 all property/atom i_flag1 d_flag2
dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
fix 1 all ave/atom 10 10 100 c_1[1] c_1[2]
dump 1 all custom 100 tmp.dump id x y z i_flag1 d_flag2 f_1[1] f_1[2]
----------
If you wish to add new :doc:`pair styles <pair_style>`,
:doc:`fixes <fix>`, or :doc:`computes <compute>` that use the per-atom
properties defined by this fix, see the :doc:`Modify atom <Modify_atom>`
doc page which has details on how the properties can be accessed from
added classes.
If you wish to add new :doc:`pair styles <pair_style>`, :doc:`fixes
<fix>`, or :doc:`computes <compute>` that use the per-atom properties
defined by this fix, see the :doc:`Modify atom <Modify_atom>` doc page
which has details on how the custom properties of this fix can be
accessed from added classes.
----------
.. _isotopes:
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the :doc:`TIP4P pair styles <Howto_tip4p>` for water, you have to provide exactly
one atom type each to identify the water oxygen and hydrogen
atoms. Since the atom mass is normally tied to the atom type, this
makes it impossible to study multiple isotopes in the same simulation.
With *fix property/atom rmass* however, the per-type masses are
replaced by per-atom masses. Asumming you have a working input deck
for regular TIP4P water, where water oxygen is atom type 1 and water
hydrogen is atom type 2, the following lines of input script convert
this to using per-atom masses:
Here is an example of using per-atom masses with TIP4P water to study
isotope effects. When setting up simulations with the :doc:`TIP4P pair
styles <Howto_tip4p>` for water, you have to provide exactly one atom
type each to identify the water oxygen and hydrogen atoms. Since the
atom mass is normally tied to the atom type, this makes it impossible
to study multiple isotopes in the same simulation. With *fix
property/atom rmass* however, the per-type masses are replaced by
per-atom masses. Asumming you have a working input deck for regular
TIP4P water, where water oxygen is atom type 1 and water hydrogen is
atom type 2, the following lines of input script convert this to using
per-atom masses:
.. code-block:: LAMMPS
@ -239,22 +258,22 @@ this to using per-atom masses:
set type 1 mass 15.9994
set type 2 mass 1.008
When writing out the system data with the :doc:`write_data <write_data>`
command, there will be a new section named with the fix-ID
(i.e. *Isotopes* in this case). Alternatively, you can take an
existing data file and just add this *Isotopes* section with
one line per atom containing atom-ID and mass. Either way, the
extended data file can be read back with:
When writing out the system data with the :doc:`write_data
<write_data>` command, there will be a new section named with the
fix-ID (i.e. *Isotopes* in this case). Alternatively, you can take an
existing data file and just add this *Isotopes* section with one line
per atom containing atom-ID and mass. Either way, the extended data
file can be read back with:
.. code-block:: LAMMPS
fix Isotopes all property/atom rmass ghost yes
read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
Please note that the first *Isotopes* refers to the fix-ID
and the second to the name of the section. The following input
script code will now change the first 100 water molecules in this
example to heavy water:
Please note that the first *Isotopes* refers to the fix-ID and the
second to the name of the section. The following input script code
will now change the first 100 water molecules in this example to heavy
water:
.. code-block:: LAMMPS
@ -271,17 +290,19 @@ example to heavy water:
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
simulation is restarted. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
This fix writes the per-atom values it stores to :doc:`binary restart
files <restart>`, so that the values can be restored when a simulation
is restarted. See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
None of the :doc:`fix_modify <fix_modify>` options are relevant to
this fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
:doc:`run <run>` command. This fix is not invoked during :doc:`energy
minimization <minimize>`.
Restrictions
""""""""""""
@ -290,9 +311,10 @@ Restrictions
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`set <set>`, :doc:`compute property/atom <compute_property_atom>`
:doc:`read_data <read_data>`, :doc:`set <set>`,
:doc:`compute property/atom <compute_property_atom>`
Default
"""""""
The default keyword values are ghost = no.
The default keyword value is ghost = no.

35
doc/src/fix_store_state.rst
View File

@ -23,8 +23,8 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID[N], f_ID, f_ID[N], v_name,
d_name, i_name
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
d_name, i_name, i2_name[I], d2_name[I],
.. parsed-literal::
@ -46,13 +46,15 @@ Syntax
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
d_name = per-atom floating point vector name, managed by fix property/atom
i_name = per-atom integer vector name, managed by fix property/atom
*c_ID* = per-atom vector calculated by a compute with ID
*c_ID[I]* = Ith column of per-atom array calculated by a compute with ID
*f_ID* = per-atom vector calculated by a fix with ID
*f_ID[I]* = Ith column of per-atom array calculated by a fix with ID
*v_name* = per-atom vector calculated by an atom-style variable with name
*i_name* = custom integer vector with name
*d_name* = custom floating point vector with name
*i2_name[I]* = Ith column of custom integer array with name
*d2_name[I]* = Ith column of custom floating-point array with name
* zero or more keyword/value pairs may be appended
* keyword = *com*
@ -92,7 +94,8 @@ steps.
those attributes may require quantities that are not defined in
between runs.
The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning.
The list of possible attributes is the same as that used by the
:doc:`dump custom <dump>` command, which describes their meaning.
If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu*
inputs store the position of each atom relative to the center-of-mass
@ -105,10 +108,11 @@ group.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
simulation is restarted. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
This fix writes the per-atom values it stores to :doc:`binary restart
files <restart>`, so that the values can be restored when a simulation
is restarted. See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
@ -121,7 +125,8 @@ can be accessed by various :doc:`output commands <Howto_output>`. The
per-atom values be accessed on any timestep.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

37
doc/src/group.rst
View File

@ -41,7 +41,7 @@ Syntax
keyword = *region* or *var* or *every*
*region* value = region-ID
*var* value = name of variable
*property* value = name of per-atom property
*property* value = name of custom integer or floating point vector
*every* value = N = update group every this many timesteps
*static* = no args
@ -226,18 +226,33 @@ simulation runs. This is in contrast to static groups where atoms are
permanently assigned to the group. The way the assignment occurs is
as follows. Only atoms in the group specified as the parent group via
the parent-ID are assigned to the dynamic group before the following
conditions are applied. If the *region* keyword is used, atoms not in
the specified region are removed from the dynamic group. If the *var*
keyword is used, the variable name must be an atom-style or
atomfile-style variable. The variable is evaluated and atoms whose
per-atom values are 0.0, are removed from the dynamic group. If the *property*
keyword is used, the per-atom property name must be a previously defined
per-atom property. The per-atom property is evaluated and atoms whose
values are 0.0 are removed from the dynamic group.
conditions are applied.
If the *region* keyword is used, atoms not in the specified region are
removed from the dynamic group.
If the *var* keyword is used, the variable name must be an atom-style
or atomfile-style variable. The variable is evaluated and atoms whose
per-atom values are 0.0, are removed from the dynamic group.
If the *property* keyword is used, the name refers to a custom integer
or floating point per-atom vector defined via the :doc:`fix
property/atom <fix_property_atom>` command. This means the values in
the vector can be read as part of a data file with the :doc:`read_data
<read_data>` command or specified with the :doc:`set <set>` command.
Or accessed and changed via the :doc:`library interface to LAMMPS
<Howto_library>`, or by styles you add to LAMMPS (pair, fix, compute,
etc) which access the custom vector and modify its values. Which
means the values can be modified between or during simulations. Atoms
whose values in the custom vector are zero are removed from the
dynamic group. Note that the name of the custom per-atom vector is
specified just as *name*, not as *i_name* or *d_name* as it is for
other commands that use different kinds of custom atom vectors or
arrays as arguments.
The assignment of atoms to a dynamic group is done at the beginning of
each run and on every timestep that is a multiple of *N*\ , which is the
argument for the *every* keyword (N = 1 is the default). For an
each run and on every timestep that is a multiple of *N*\ , which is
the argument for the *every* keyword (N = 1 is the default). For an
energy minimization, via the :doc:`minimize <minimize>` command, an
assignment is made at the beginning of the minimization, but not
during the iterations of the minimizer.

34
doc/src/set.rst
View File

@ -13,7 +13,17 @@ Syntax
* 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
* 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 *charge* or *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *density/disc* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *sph/e* or *sph/cv* or *sph/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name*
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
or *mol* or *x* or *y* or *z* or *charge* or *dipole* or
*dipole/random* or *quat* or *spin* or *spin/random* or
*quat* or *quat/random* or *diameter* or *shape* or
*length* or *tri* or *theta* or *theta/random* or *angmom* or
*omega* or *mass* or *density* or *density/disc* or
*volume* or *image* or *bond* or *angle* or *dihedral* or
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
*edpd/temp* or *edpd/cv* or *cc* or
*i_name* or *d_name* or *i2_name* or *d2_name*
.. parsed-literal::
@ -114,8 +124,12 @@ Syntax
*cc* values = index cc
index = index of a chemical species (1 to Nspecies)
cc = chemical concentration of tDPD particles for a species (mole/volume units)
*i_name* value = value for custom integer vector with name
*d_name* value = value for custom floating-point vector with name
*i_name* value = custom integer vector with name
*d_name* value = custom floating-point vector with name
*i2_name* value = column of a custom integer array with name
column specified as i2_name[N] where N is 1 to Ncol
*d2_name* value = column of a custom floating-point array with name
column specified as d2_name[N] where N is 1 to Ncol
Examples
""""""""
@ -132,6 +146,8 @@ Examples
set atom 100*200 x 0.5 y 1.0
set atom 100 vx 0.0 vy 0.0 vz -1.0
set atom 1492 type 3
set atom * i_myVal 5
set atom * d2_Sxyz[1] 6.4
Description
"""""""""""
@ -473,11 +489,13 @@ attribute. An integer for "index" selects a chemical species (1 to
Nspecies) where Nspecies is set by the atom_style command. The value
for the chemical concentration must be >= 0.0.
Keywords *i_name* and *d_name* refer to custom integer and
floating-point properties that have been added to each atom via the
:doc:`fix property/atom <fix_property_atom>` command. When that command
is used specific names are given to each attribute which are what is
specified as the "name" portion of *i_name* or *d_name*.
Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
Restrictions
""""""""""""