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220 lines
10 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>set command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>set style ID keyword values ...
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</PRE>
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<UL><LI>style = <I>atom</I> or <I>group</I> or <I>region</I>
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<LI>ID = atom ID or group ID or region ID
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<LI>one or more keyword/value pairs may be appended
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<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>diameter</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
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<I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
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<PRE> <I>type</I> value = atom type
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<I>type/fraction</I> 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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<I>mol</I> value = molecule ID
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<I>x</I>,<I>y</I>,<I>z</I> value = atom coordinate (distance units)
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<I>charge</I> value = atomic charge (charge units)
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<I>dipole</I> values = x y z
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x,y,z = orientation of dipole moment vector
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<I>dipole/random</I> value = seed
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seed = random # seed (positive integer) for dipole moment orientations
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<I>quat</I> 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 in degrees
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<I>quat/random</I> value = seed
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seed = random # seed (positive integer) for quaternion orientations
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<I>diameter</I> value = particle diameter (distance units)
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<I>density</I> value = particle density (mass/distance^3 units)
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<I>volume</I> value = particle volume (distance^3 units)
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<I>image</I> 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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<I>bond</I> value = bond type for all bonds between selected atoms
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<I>angle</I> value = angle type for all angles between selected atoms
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<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
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<I>improper</I> value = improper type for all impropers between selected atoms
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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 atom 100 x 0.5 y 1.0
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set atom 1492 type 3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Set one or more properties of one or more atoms. Since atom
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properties are initially assigned by the <A HREF = "read_data.html">read_data</A>,
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<A HREF = "read_restart.html">read_restart</A> or <A HREF = "create_atoms.html">create_atoms</A>
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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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<A HREF = "create_atoms.html">create_atoms</A> 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 when they are
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output in <A HREF = "dump.html">dump</A> files. It can be useful for debugging
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purposes; i.e. positioning an atom at a precise location to compute
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subsequent forces or energy.
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</P>
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<P>The style <I>atom</I> selects a single atom. The style <I>group</I> selects the
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entire group of atoms. The style <I>region</I> selects all atoms in the
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geometric region. The associated ID for each of these styles is
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either the unique atom ID (typically a number from 1 to N = the number
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of atoms in the simulation), the group ID, or the region ID. See the
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<A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands for details of
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how to specify a group or region.
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</P>
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<HR>
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<P>Keyword <I>type</I> 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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<A HREF = "create_box.html">create_box</A> command or the <I>atom types</I> field in the
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header of the data file read by the <A HREF = "read_data.html">read_data</A>
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command.
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</P>
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<P>Keyword <I>type/fraction</I> 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.
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</P>
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<P>Keyword <I>mol</I> sets the molecule ID for all selected atoms. The <A HREF = "atom_style.html">atom
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style</A> being used must support the use of molecule
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IDs.
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</P>
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<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, and <I>charge</I> set the coordinates or charge of
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all selected atoms. For <I>charge</I>, the <A HREF = "atom_style.html">atom style</A>
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being used must support the use of atomic charge.
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</P>
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<P>Keyword <I>dipole</I> 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 for each atom is
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set by the <A HREF = "dipole.html">dipole</A> command.
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</P>
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<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
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moment vectors of the selected atoms. The magnitude of the dipole
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moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command. For
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2d systems, the z component of the orientation is set to 0.0. Random
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numbers are used in such a way that the orientation of a particular
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atom is the same, regardless of how many processors are being used.
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</P>
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<P>Keyword <I>quat</I> uses the specified values to create a quaternion
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(4-vector) that represents the orientation of the selected atoms.
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Note that the <A HREF = "shape.html">shape</A> command is used to specify the aspect
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ratios of an ellipsoidal particle, which is oriented by default with
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its x-axis along the simulation box's x-axis, and similarly for y and
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z. If this body is rotated (via the right-hand rule) by an angle
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theta around a unit rotation vector (a,b,c), then the quaternion that
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represents its new orientation is given by (cos(theta/2),
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a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
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values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the
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quaternion in case (a,b,c) was not specified as a unit vector. For 2d
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systems, the a,b,c values are ignored, since a rotation vector of
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(0,0,1) is the only valid choice.
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</P>
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<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
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the selected atoms. Random numbers are used in such a way that the
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orientation of a particular atom is the same, regardless of how many
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processors are being used. For 2d systems, only orientations in the
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xy plane are generated.
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</P>
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<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
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being used must support the use of dipoles or quaternions.
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</P>
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<P>Keyword <I>diameter</I> sets the size of all selected particles. If the
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particles have a per-atom mass and density, then it also sets their
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mass.
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</P>
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<P>Keyword <I>density</I> sets the density of all selected particles. If the
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particles have a per-atom mass and diameter, then it also sets their
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mass. If the particles have a per-atom mass and volume (as defined by
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PeriDynamics), then it also sets their mass.
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</P>
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<P>Keyword <I>volume</I> sets the volume of all selected particles, as defined
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by PeriDynamics.
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</P>
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<P>Keyword <I>image</I> sets which image of the simulation box the atom is
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considered to be in. It is only applied to periodic dimensions. An
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image of 0 means it is inside the box as defined. A value of 2 means
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add 2 box lengths to get the true value. A value of -1 means subtract
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1 box length to get the true value. LAMMPS updates these flags as
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atoms cross periodic boundaries during the simulation. The flags can
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be output with atom snapshots via the <A HREF = "dump.html">dump</A> command. If a
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value of NULL is specified for any of nx,ny,nz, then the current image
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value for that dimension is unchanged.
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</P>
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<P>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 <A HREF = "compute_msd.html">compute
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msd</A> 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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</P>
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<P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
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style</A> being used must support the use of those
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parameters. For example, granular particles store a diameter and
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density. Peridynamic particles store a volume and density.
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</P>
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<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, 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 <I>bond types</I> (<I>angle types</I>, etc) field in the
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header of the data file read by the <A HREF = "read_data.html">read_data</A>
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command.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I> or <I>volume</I>) if
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the <A HREF = "atom_style.html">atom_style</A> does not have that attribute.
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</P>
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<P>This command requires inter-processor communication to coordinate the
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setting of bond types (angle types, etc). This means that your system
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must be ready to perform a simulation before using one of these
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keywords (force fields set, atom mass set, etc). This is not
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necessary for other keywords.
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</P>
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<P>Using the <I>region</I> style with the bond (angle, etc) keywords can give
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unpredictable results if there are bonds (angles, etc) that straddle
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periodic boundaries. This is because the region may only extend up to
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the boundary and partner atoms in the bond (angle, etc) may have
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coordinates outside the simulation box if they are ghost atoms.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>,
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<A HREF = "read_data.html">read_data</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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