forked from lijiext/lammps
436 lines
22 KiB
Plaintext
436 lines
22 KiB
Plaintext
.. index:: set
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set command
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===========
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Syntax
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""""""
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.. parsed-literal::
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set style ID keyword values ...
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* style = *atom* or *type* or *mol* or *group* or *region*
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* ID = atom ID range or type range or mol ID range or group ID or region ID
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* one or more keyword/value pairs may be appended
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* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/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 *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *i_name* or *d_name*
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.. parsed-literal::
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*type* value = atom type
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value can be an atom-style variable (see below)
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*type/fraction* values = type fraction seed
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type = new atom type
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fraction = fraction of selected atoms to set to new atom type
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seed = random # seed (positive integer)
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*mol* value = molecule ID
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value can be an atom-style variable (see below)
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*x*\ ,\ *y*\ ,\ *z* value = atom coordinate (distance units)
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value can be an atom-style variable (see below)
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*charge* value = atomic charge (charge units)
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value can be an atom-style variable (see below)
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*dipole* values = x y z
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x,y,z = orientation of dipole moment vector
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any of x,y,z can be an atom-style variable (see below)
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*dipole/random* value = seed Dlen
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seed = random # seed (positive integer) for dipole moment orientations
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Dlen = magnitude of dipole moment (dipole units)
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*quat* values = a b c theta
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a,b,c = unit vector to rotate particle around via right-hand rule
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theta = rotation angle (degrees)
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any of a,b,c,theta can be an atom-style variable (see below)
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*quat/random* value = seed
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seed = random # seed (positive integer) for quaternion orientations
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*diameter* value = diameter of spherical particle (distance units)
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value can be an atom-style variable (see below)
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*shape* value = Sx Sy Sz
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Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
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*length* value = len
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len = length of line segment (distance units)
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len can be an atom-style variable (see below)
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*tri* value = side
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side = side length of equilateral triangle (distance units)
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side can be an atom-style variable (see below)
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*theta* value = angle (degrees)
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angle = orientation of line segment with respect to x-axis
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angle can be an atom-style variable (see below)
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*theta/random* value = seed
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seed = random # seed (positive integer) for line segment orienations
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*angmom* values = Lx Ly Lz
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Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
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any of Lx,Ly,Lz can be an atom-style variable (see below)
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*omega* values = Wx Wy Wz
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Wx,Wy,Wz = components of angular velocity vector (radians/time units)
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any of wx,wy,wz can be an atom-style variable (see below)
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*mass* value = per-atom mass (mass units)
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value can be an atom-style variable (see below)
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*density* value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
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value can be an atom-style variable (see below)
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*volume* value = particle volume for Peridynamic particle (distance^3 units)
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value can be an atom-style variable (see below)
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*image* nx ny nz
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nx,ny,nz = which periodic image of the simulation box the atom is in
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*bond* value = bond type for all bonds between selected atoms
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*angle* value = angle type for all angles between selected atoms
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*dihedral* value = dihedral type for all dihedrals between selected atoms
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*improper* value = improper type for all impropers between selected atoms
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*meso/e* value = energy of SPH particles (need units)
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value can be an atom-style variable (see below)
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*meso/cv* value = heat capacity of SPH particles (need units)
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value can be an atom-style variable (see below)
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*meso/rho* value = density of SPH particles (need units)
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value can be an atom-style variable (see below)
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*smd/contact/radius* = radius for short range interactions, i.e. contact and friction
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value can be an atom-style variable (see below)
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*smd/mass/density* = set particle mass based on volume by providing a mass density
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value can be an atom-style variable (see below)
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*dpd/theta* value = internal temperature of DPD particles (temperature units)
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value can be an atom-style variable (see below)
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value can be NULL which sets internal temp of each particle to KE temp
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*i_name* value = value for custom integer vector with name
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*d_name* value = value for custom floating-point vector with name
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Examples
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""""""""
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.. parsed-literal::
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set group solvent type 2
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set group solvent type/fraction 2 0.5 12393
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set group edge bond 4
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set region half charge 0.5
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set type 3 charge 0.5
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set type 1*3 charge 0.5
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set atom * charge v_atomfile
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set atom 100*200 x 0.5 y 1.0
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set atom 1492 type 3
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Description
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"""""""""""
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Set one or more properties of one or more atoms. Since atom
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properties are initially assigned by the :doc:`read_data <read_data>`,
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:doc:`read_restart <read_restart>` or :doc:`create_atoms <create_atoms>`
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commands, this command changes those assignments. This can be useful
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for overriding the default values assigned by the
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:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0). It can
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be useful for altering pairwise and molecular force interactions,
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since force-field coefficients are defined in terms of types. It can
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be used to change the labeling of atoms by atom type or molecule ID
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when they are output in :doc:`dump <dump>` files. It can also be useful
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for debugging purposes; i.e. positioning an atom at a precise location
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to compute subsequent forces or energy.
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Note that the *style* and *ID* arguments determine which atoms have
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their properties reset. The remaining keywords specify which
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properties to reset and what the new values are. Some strings like
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*type* or *mol* can be used as a style and/or a keyword.
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----------
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This section describes how to select which atoms to change
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the properties of, via the *style* and *ID* arguments.
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The style *atom* selects all the atoms in a range of atom IDs. The
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style *type* selects all the atoms in a range of types. The style
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*mol* selects all the atoms in a range of molecule IDs.
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In each of the range cases, the range can be specified as a single
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numeric value, or a wildcard asterisk can be used to specify a range
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of values. This takes the form "*" or "*n" or "n*" or "m*n". For
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example, for the style *type*\ , if N = the number of atom types, then
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an asterisk with no numeric values means all types from 1 to N. A
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leading asterisk means all types from 1 to n (inclusive). A trailing
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asterisk means all types from n to N (inclusive). A middle asterisk
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means all types from m to n (inclusive). For all the styles except
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*mol*\ , the lowest value for the wildcard is 1; for *mol* it is 0.
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The style *group* selects all the atoms in the specified group. The
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style *region* selects all the atoms in the specified geometric
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region. See the :doc:`group <group>` and :doc:`region <region>` commands
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for details of how to specify a group or region.
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----------
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This section describes the keyword options for which properties to
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change, for the selected atoms.
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Note that except where explicitly prohibited below, all of the
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keywords allow an :doc:`atom-style or atomfile-style variable <variable>` to be used as the specified value(s). If the
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value is a variable, it should be specified as v_name, where name is
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the variable name. In this case, the variable will be evaluated, and
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its resulting per-atom value used to determine the value assigned to
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each selected atom. Note that the per-atom value from the variable
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will be ignored for atoms that are not selected via the *style* and
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*ID* settings explained above. A simple way to use per-atom values
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from the variable to reset a property for all atoms is to use style
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*atom* with *ID* = "*"; this selects all atom IDs.
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Atom-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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keywords for the simulation box parameters and timestep and elapsed
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time. They can also include per-atom values, such as atom
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coordinates. Thus it is easy to specify a time-dependent or
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spatially-dependent set of per-atom values. As explained on the
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:doc:`variable <variable>` doc page, atomfile-style variables can be
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used in place of atom-style variables, and thus as arguments to the
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set command. Atomfile-style variables read their per-atoms values
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from a file.
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.. note::
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Atom-style and atomfile-style variables return floating point
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per-atom values. If the values are assigned to an integer variable,
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such as the molecule ID, then the floating point value is truncated to
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its integer portion, e.g. a value of 2.6 would become 2.
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Keyword *type* sets the atom type for all selected atoms. The
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specified value must be from 1 to ntypes, where ntypes was set by the
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:doc:`create_box <create_box>` command or the *atom types* field in the
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header of the data file read by the :doc:`read_data <read_data>`
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command.
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Keyword *type/fraction* sets the atom type for a fraction of the
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selected atoms. The actual number of atoms changed is not guaranteed
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to be exactly the requested fraction, but should be statistically
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close. Random numbers are used in such a way that a particular atom
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is changed or not changed, regardless of how many processors are being
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used. This keyword does not allow use of an atom-style variable.
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Keyword *mol* sets the molecule ID for all selected atoms. The :doc:`atom style <atom_style>` being used must support the use of molecule
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IDs.
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Keywords *x*\ , *y*\ , *z*\ , and *charge* set the coordinates or charge of
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all selected atoms. For *charge*\ , the :doc:`atom style <atom_style>`
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being used must support the use of atomic charge.
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Keyword *dipole* uses the specified x,y,z values as components of a
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vector to set as the orientation of the dipole moment vectors of the
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selected atoms. The magnitude of the dipole moment is set
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by the length of this orientation vector.
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Keyword *dipole/random* randomizes the orientation of the dipole
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moment vectors for the selected atoms and sets the magnitude of each
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to the specified *Dlen* value. For 2d systems, the z component of the
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orientation is set to 0.0. Random numbers are used in such a way that
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the orientation of a particular atom is the same, regardless of how
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many processors are being used. This keyword does not allow use of an
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atom-style variable.
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Keyword *quat* uses the specified values to create a quaternion
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(4-vector) that represents the orientation of the selected atoms. The
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particles must define a quaternion for their orientation
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(e.g. ellipsoids, triangles, body particles) as defined by the
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:doc:`atom_style <atom_style>` command. Note that particles defined by
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:doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters. The 3
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values must be non-zero for each particle set by this command. They
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are used to specify the aspect ratios of an ellipsoidal particle,
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which is oriented by default with its x-axis along the simulation
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box's x-axis, and similarly for y and z. If this body is rotated (via
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the right-hand rule) by an angle theta around a unit rotation vector
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(a,b,c), then the quaternion that represents its new orientation is
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given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
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c*sin(theta/2)). The theta and a,b,c values are the arguments to the
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*quat* keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
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not specified as a unit vector. For 2d systems, the a,b,c values are
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ignored, since a rotation vector of (0,0,1) is the only valid choice.
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Keyword *quat/random* randomizes the orientation of the quaternion for
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the selected atoms. The particles must define a quaternion for their
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orientation (e.g. ellipsoids, triangles, body particles) as defined by
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the :doc:`atom_style <atom_style>` command. Random numbers are used in
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such a way that the orientation of a particular atom is the same,
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regardless of how many processors are being used. For 2d systems,
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only orientations in the xy plane are generated. As with keyword
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*quat*\ , for ellipsoidal particles, the 3 shape values must be non-zero
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for each particle set by this command. This keyword does not allow
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use of an atom-style variable.
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Keyword *diameter* sets the size of the selected atoms. The particles
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must be finite-size spheres as defined by the :doc:`atom_style sphere <atom_style>` command. The diameter of a particle can be
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set to 0.0, which means they will be treated as point particles. Note
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that this command does not adjust the particle mass, even if it was
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defined with a density, e.g. via the :doc:`read_data <read_data>`
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command.
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Keyword *shape* sets the size and shape of the selected atoms. The
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particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_style>` command. The *Sx*\ , *Sy*\ , *Sz* settings are
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the 3 diameters of the ellipsoid in each direction. All 3 can be set
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to the same value, which means the ellipsoid is effectively a sphere.
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They can also all be set to 0.0 which means the particle will be
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treated as a point particle. Note that this command does not adjust
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the particle mass, even if it was defined with a density, e.g. via the
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:doc:`read_data <read_data>` command.
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Keyword *length* sets the length of selected atoms. The particles
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must be line segments as defined by the :doc:`atom_style line <atom_style>` command. If the specified value is non-zero the
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line segment is (re)set to a length = the specified value, centered
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around the particle position, with an orientation along the x-axis.
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If the specified value is 0.0, the particle will become a point
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particle. Note that this command does not adjust the particle mass,
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even if it was defined with a density, e.g. via the
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:doc:`read_data <read_data>` command.
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Keyword *tri* sets the size of selected atoms. The particles must be
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triangles as defined by the :doc:`atom_style tri <atom_style>` command.
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If the specified value is non-zero the triangle is (re)set to be an
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equilateral triangle in the xy plane with side length = the specified
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value, with a centroid at the particle position, with its base
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parallel to the x axis, and the y-axis running from the center of the
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base to the top point of the triangle. If the specified value is 0.0,
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the particle will become a point particle. Note that this command
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does not adjust the particle mass, even if it was defined with a
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density, e.g. via the :doc:`read_data <read_data>` command.
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Keyword *theta* sets the orientation of selected atoms. The particles
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must be line segments as defined by the :doc:`atom_style line <atom_style>` command. The specified value is used to set the
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orientation angle of the line segments with respect to the x axis.
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Keyword *theta/random* randomizes the orientation of theta for the
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selected atoms. The particles must be line segments as defined by the
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:doc:`atom_style line <atom_style>` command. Random numbers are used in
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such a way that the orientation of a particular atom is the same,
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regardless of how many processors are being used. This keyword does
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not allow use of an atom-style variable.
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Keyword *angmom* sets the angular momentum of selected atoms. The
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particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_style>` command or triangles as defined by the
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:doc:`atom_style tri <atom_style>` command. The angular momentum vector
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of the particles is set to the 3 specified components.
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Keyword *omega* sets the angular velocity of selected atoms. The
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particles must be spheres as defined by the "atom_style sphere"_
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atom_style.html command. The angular velocity vector of the particles
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is set to the 3 specified components.
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Keyword *mass* sets the mass of all selected particles. The particles
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must have a per-atom mass attribute, as defined by the
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:doc:`atom_style <atom_style>` command. See the "mass" command for how
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to set mass values on a per-type basis.
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Keyword *density* also sets the mass of all selected particles, but in
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a different way. The particles must have a per-atom mass attribute,
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as defined by the :doc:`atom_style <atom_style>` command. If the atom
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has a radius attribute (see :doc:`atom_style sphere <atom_style>`) and
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its radius is non-zero, its mass is set from the density and particle
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volume. If the atom has a shape attribute (see :doc:`atom_style ellipsoid <atom_style>`) and its 3 shape parameters are non-zero,
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then its mass is set from the density and particle volume. If the
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atom has a length attribute (see :doc:`atom_style line <atom_style>`)
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and its length is non-zero, then its mass is set from the density and
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line segment length (the input density is assumed to be in
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mass/distance units). If the atom has an area attribute (see
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:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
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mass is set from the density and triangle area (the input density is
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assumed to be in mass/distance^2 units). If none of these cases are
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valid, then the mass is set to the density value directly (the input
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density is assumed to be in mass units).
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Keyword *volume* sets the volume of all selected particles.
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Currently, only the :doc:`atom_style peri <atom_style>` command defines
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particles with a volume attribute. Note that this command does not
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adjust the particle mass.
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Keyword *image* sets which image of the simulation box the atom is
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considered to be in. An image of 0 means it is inside the box as
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defined. A value of 2 means add 2 box lengths to get the true value.
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A value of -1 means subtract 1 box length to get the true value.
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LAMMPS updates these flags as atoms cross periodic boundaries during
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the simulation. The flags can be output with atom snapshots via the
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:doc:`dump <dump>` command. If a value of NULL is specified for any of
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nx,ny,nz, then the current image value for that dimension is
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unchanged. For non-periodic dimensions only a value of 0 can be
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specified. This keyword does not allow use of atom-style variables.
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This command can be useful after a system has been equilibrated and
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atoms have diffused one or more box lengths in various directions.
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This command can then reset the image values for atoms so that they
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are effectively inside the simulation box, e.g if a diffusion
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coefficient is about to be measured via the :doc:`compute msd <compute_msd>` command. Care should be taken not to reset the
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image flags of two atoms in a bond to the same value if the bond
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straddles a periodic boundary (rather they should be different by +/-
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1). This will not affect the dynamics of a simulation, but may mess
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up analysis of the trajectories if a LAMMPS diagnostic or your own
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analysis relies on the image flags to unwrap a molecule which
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straddles the periodic box.
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Keywords *bond*\ , *angle*\ , *dihedral*\ , and *improper*\ , set the bond
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type (angle type, etc) of all bonds (angles, etc) of selected atoms to
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the specified value from 1 to nbondtypes (nangletypes, etc). All
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atoms in a particular bond (angle, etc) must be selected atoms in
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order for the change to be made. The value of nbondtype (nangletypes,
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etc) was set by the *bond types* (\ *angle types*\ , etc) field in the
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header of the data file read by the :doc:`read_data <read_data>`
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command. These keywords do not allow use of an atom-style variable.
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Keywords *meso/e*\ , *meso/cv*\ , and *meso/rho* set the energy, heat
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capacity, and density of smmothed particle hydrodynamics (SPH)
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particles. See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to
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using SPH in LAMMPS.
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Keyword *smd/mass/density* sets the mass of all selected particles,
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but it is only applicable to the Smooth Mach Dynamics package
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USER-SMD. It assumes that the particle volume has already been
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correctly set and calculates particle mass from the provided mass
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density value.
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Keyword *smd/contact/radius* only applies to simulations with the
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Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius
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for computing short-range interactions, e.g. repulsive forces to
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prevent different individual physical bodies from penetrating each
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other. Note that the SPH smoothing kernel diameter used for computing
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long range, nonlocal interactions, is set using the *diameter*
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keyword.
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Keyword *dpd/theta* sets the internal temperature of a DPD particle as
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defined by the USER-DPD package. If the specified value is a number
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it must be >= 0.0. If the specified value is NULL, then the kinetic
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temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
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m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle's internal
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temperature is set to Tkin. If the specified value is an atom-style
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variable, then the variable is evaluated for each particle. If a
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value >= 0.0, the internal temperature is set to that value. If it is
|
|
< 0.0, the computation of Tkin is performed and the internal
|
|
temperature is set to that value.
|
|
|
|
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*\ .
|
|
|
|
Restrictions
|
|
""""""""""""
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|
|
|
|
|
You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if
|
|
the :doc:`atom_style <atom_style>` does not have that attribute.
|
|
|
|
This command requires inter-processor communication to coordinate the
|
|
setting of bond types (angle types, etc). This means that your system
|
|
must be ready to perform a simulation before using one of these
|
|
keywords (force fields set, atom mass set, etc). This is not
|
|
necessary for other keywords.
|
|
|
|
Using the *region* style with the bond (angle, etc) keywords can give
|
|
unpredictable results if there are bonds (angles, etc) that straddle
|
|
periodic boundaries. This is because the region may only extend up to
|
|
the boundary and partner atoms in the bond (angle, etc) may have
|
|
coordinates outside the simulation box if they are ghost atoms.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
|
|
:doc:`read_data <read_data>`
|
|
|
|
**Default:** none
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|