2006-09-22 00:22:34 +08:00
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<HTML>
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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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<HR>
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<H3>create_atoms command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>create_atoms type style args keyword values ...
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</PRE>
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<UL><LI>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
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<LI>style = <I>box</I> or <I>region</I> or <I>single</I> or <I>random</I>
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<PRE> <I>box</I> args = none
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<I>region</I> args = region-ID
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region-ID = particles will only be created if contained in the region
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<I>single</I> args = x y z
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x,y,z = coordinates of a single particle (distance units)
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<I>random</I> args = N seed region-ID
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N = number of particles to create
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seed = random # seed (positive integer)
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region-ID = create atoms within this region, use NULL for entire simulation box
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>mol</I> or <I>basis</I> or <I>remap</I> or <I>var</I> or <I>set</I> or <I>units</I>
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<PRE> <I>mol</I> value = template-ID seed
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template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
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seed = random # seed (positive integer)
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<I>basis</I> values = M itype
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M = which basis atom
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itype = atom type (1-N) to assign to this basis atom
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<I>remap</I> value = <I>yes</I> or <I>no</I>
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<I>var</I> value = name = variable name to evaluate for test of atom creation
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<I>set</I> values = dim vname
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dim = <I>x</I> or <I>y</I> or <I>z</I>
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name = name of variable to set with x,y,z atom position
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<I>units</I> value = <I>lattice</I> or <I>box</I>
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<I>lattice</I> = the geometry is defined in lattice units
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<I>box</I> = the geometry is defined in simulation box units
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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>create_atoms 1 box
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create_atoms 3 region regsphere basis 2 3
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create_atoms 3 single 0 0 5
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create_atoms 1 box var v set x xpos set y ypos
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command creates atoms (or molecules) on a lattice, or a single
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atom (or molecule), or a random collection of atoms (or molecules), as
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an alternative to reading in their coordinates explicitly via a
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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command. A simulation box must already exist, which is typically
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created via the <A HREF = "create_box.html">create_box</A> command. Before using
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this command, a lattice must also be defined using the
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<A HREF = "lattice.html">lattice</A> command, unless you specify the <I>single</I> style
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with units = box or the <I>random</I> style. For the remainder of this doc
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page, a created atom or molecule is referred to as a "particle".
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</P>
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<P>If created particles are individual atoms, they are assigned the
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specified atom <I>type</I>, though this can be altered via the <I>basis</I>
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keyword as discussed below. If molecules are being created, the type
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of each atom in the created molecule is specified in the file read by
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the <A HREF = "molecule.html">molecule</A> command, and those values are added to
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the specified atom <I>type</I>. E.g. if <I>type</I> = 2, and the file specifies
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atom types 1,2,3, then each created molecule will have atom types
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3,4,5.
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</P>
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<P>For the <I>box</I> style, the create_atoms command fills the entire
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simulation box with particles on the lattice. If your simulation box
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is periodic, you should insure its size is a multiple of the lattice
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spacings, to avoid unwanted atom overlaps at the box boundaries. If
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your box is periodic and a multiple of the lattice spacing in a
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particular dimension, LAMMPS is careful to put exactly one particle at
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the boundary (on either side of the box), not zero or two.
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</P>
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<P>For the <I>region</I> style, a geometric volume is filled with particles on
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the lattice. This volume what is inside the simulation box and is
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also consistent with the region volume. See the <A HREF = "region.html">region</A>
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command for details. Note that a region can be specified so that its
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"volume" is either inside or outside a geometric boundary. Also note
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that if your region is the same size as a periodic simulation box (in
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some dimension), LAMMPS does not implement the same logic described
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above as for the <I>box</I> style, to insure exactly one particle at
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periodic boundaries. if this is what you desire, you should either
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use the <I>box</I> style, or tweak the region size to get precisely the
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particles you want.
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</P>
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<P>For the <I>single</I> style, a single particle is added to the system at
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the specified coordinates. This can be useful for debugging purposes
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or to create a tiny system with a handful of particles at specified
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positions.
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</P>
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<P>For the <I>random</I> style, N particles are added to the system at
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randomly generated coordinates, which can be useful for generating an
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amorphous system. The particles are created one by one using the
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speficied random number <I>seed</I>, resulting in the same set of particles
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coordinates, independent of how many processors are being used in the
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simulation. If the <I>region-ID</I> argument is specified as NULL, then
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the created particles will be anywhere in the simulation box. If a
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<I>region-ID</I> is specified, a geometric volume is filled which is both
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inside the simulation box and is also consistent with the region
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volume. See the <A HREF = "region.html">region</A> command for details. Note that
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a region can be specified so that its "volume" is either inside or
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outside a geometric boundary.
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</P>
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<P>IMPORTANT NOTE: Particles generated by the <I>random</I> style will
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typically be highly overlapped which will cause many interatomic
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potentials to compute large energies and forces. Thus you should
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either perform an <A HREF = "minimize.html">energy minimization</A> or run dynamics
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with <A HREF = "fix_nve_limit.html">fix nve/limit</A> to equilibrate such a system,
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before running normal dynamics.
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</P>
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<P>Note that this command adds particles to those that already exist.
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This means it can be used to add particles to a system previously read
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in from a data or restart file. Or the create_atoms command can be
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used multiple times, to add multiple sets of particles to the
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simulation. For example, grain boundaries can be created, by
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interleaving create_atoms with <A HREF = "lattice.html">lattice</A> commands
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specifying different orientations. By using the create_atoms command
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in conjunction with the <A HREF = "delete_atoms.html">delete_atoms</A> command,
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reasonably complex geometries can be created, or a protein can be
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solvated with a surrounding box of water molecules.
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</P>
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<P>In all these cases, care should be taken to insure that new atoms do
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not overlap existing atoms inappropriately, especially if molecules
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are being added. The <A HREF = "delete_atoms.html">delete_atoms</A> command can be
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used to remove overlapping atoms or molecules.
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</P>
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<HR>
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<P>Individual atoms are inserted by this command, unless the <I>mol</I>
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keyword is used. It specifies a <I>template-ID</I> previously defined
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using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
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defines the molecule. The coordinates, atom types, charges, etc, as
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well as any bond/angle/etc and special neighbor information for the
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molecule can be specified in the molecule file. See the
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<A HREF = "molecule.html">molecule</A> command for details. The only settings
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required to be in this file are the coordinates and types of atoms in
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the molecule.
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</P>
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<P>Using a lattice to add molecules, e.g. via the <I>box</I> or <I>region</I> or
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<I>single</I> styles, is exactly the same as adding atoms on lattice
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points, except that entire molecules are added at each point, i.e. on
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the point defined by each basis atom in the unit cell as it tiles the
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simulation box or region. This is done by placing the geometric
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center of the molecule at the lattice point, and giving the molecule a
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random orientation about the point. The random <I>seed</I> specified with
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the <I>mol</I> keyword is used for this operation, and the random numbers
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generated by each processor are different. This means the coordinates
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of individual atoms (in the molecules) will be different when running
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on different numbers of processors, unlike when atoms are being
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created in parallel.
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</P>
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<P>Also note that because of the random rotations, it may be important to
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use a lattice with a large enough spacing that adjacent molecules will
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not overlap, regardless of their relative orientations.
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</P>
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<P>IMPORTANT NOTE: If the <A HREF = "create_box.html">create_box</A> command is used to
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create the simulation box, followed by the create_atoms command with
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its <I>mol</I> option for adding molecules, then you typically need to use
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the optional keywords allowed by the <A HREF = "create_box.html">create_box</A>
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command for extra bonds (angles,etc) or extra special neighbors. This
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is because by default, the <A HREF = "create_box.html">create_box</A> command sets
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up a non-molecular system which doesn't allow molecules to be added.
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</P>
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<HR>
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<P>This is the meaning of the other allowed keywords.
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</P>
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<P>The <I>basis</I> keyword is only used when atoms (not molecules) are being
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created. It specifies an atom type that will be assigned to specific
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basis atoms as they are created. See the <A HREF = "lattice.html">lattice</A>
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command for specifics on how basis atoms are defined for the unit cell
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of the lattice. By default, all created atoms are assigned the
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argument <I>type</I> as their atom type.
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</P>
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<P>The <I>remap</I> keyword only applies to the <I>single</I> style. If it is set
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to <I>yes</I>, then if the specified position is outside the simulation
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box, it will mapped back into the box, assuming the relevant
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dimensions are periodic. If it is set to <I>no</I>, no remapping is done
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and no particle is created if its position is outside the box.
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</P>
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2014-07-29 02:46:39 +08:00
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<P>The <I>var</I> and <I>set</I> keywords can be used to provide a criterion for
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accepting or rejecting the addition of an individual atom, based on
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its coordinates. The <I>vname</I> specified for the <I>var</I> keyword is the
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name of an <A HREF = "variable.html">equal-style variable</A> which should evaluate
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to a zero or non-zero value based on one or two or three variables
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which will store the x, y, or z coordinates of an atom (one variable
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per coordinate). These other variables must be <A HREF = "variable.html">equal-style
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variables</A> defined in the input script, but their
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formula can by anything. The <I>set</I> keyword is used to identify the
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names of these other variables, one variable for the x-coordinate of a
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created atom, one for y, and one for z.
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</P>
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<P>When an atom is created, its x, y, or z coordinates override the
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formula for any <I>set</I> variable that is defined. The <I>var</I> variable is
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then evaluated. If the returned value is 0.0, the atom is not
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created. If it is non-zero, the atom is created.
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</P>
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<P>As an example, these commands can be used in a 2d simulation, to
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create a sinusoidal surface. Note that the surface is "rough" due to
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individual lattice points being "above" or "below" the mathematical
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expression for the sinusoidal curve. If a finer lattice were used,
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the sinusoid would appear to be "smoother". Also note the use of the
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"xlat" and "ylat" <A HREF = "thermo_style.html">thermo_style</A> keywords which
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converts lattice spacings to distance. Click on the image for a
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larger version.
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</P>
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<PRE>variable x equal 100
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variable y equal 25
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lattice hex 0.8442
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region box block 0 $x 0 $y -0.5 0.5
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create_box 1 box
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</PRE>
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<PRE>variable xx equal 0.0
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variable yy equal 0.0
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variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
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create_atoms 1 box var v set x xx set y yy
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</PRE>
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<CENTER><A HREF = "JPG/sinusoid.jpg"><IMG SRC = "JPG/sinusoid_small.jpg"></A>
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</CENTER>
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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to specify the coordinates of the one particle created by the <I>single</I>
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style. A <I>box</I> value selects standard distance units as defined by
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the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
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metal. A <I>lattice</I> value means the distance units are in lattice
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spacings.
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</P>
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<HR>
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2007-06-20 20:56:17 +08:00
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<P>Atom IDs are assigned to created atoms in the following way. The
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collection of created atoms are assigned consecutive IDs that start
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immediately following the largest atom ID existing before the
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create_atoms command was invoked. When a simulation is performed on
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different numbers of processors, there is no guarantee a particular
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created atom will be assigned the same ID. If molecules are being
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created, molecule IDs are assigned to created molecules in a similar
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fashion.
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</P>
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<P>Aside from their ID, atom type, and xyz position, other properties of
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created atoms are set to default values, depending on which quantities
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are defined by the chosen <A HREF = "atom_style.html">atom style</A>. See the <A HREF = "atom_style.html">atom
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style</A> command for more details. See the
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<A HREF = "set.html">set</A> and <A HREF = "velocity.html">velocity</A> commands for info on how
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to change these values.
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</P>
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<UL><LI>charge = 0.0
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<LI>dipole moment magnitude = 0.0
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<LI>diameter = 1.0
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<LI>shape = 0.0 0.0 0.0
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<LI>density = 1.0
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2011-04-14 05:39:34 +08:00
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<LI>volume = 1.0
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<LI>velocity = 0.0 0.0 0.0
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<LI>angular velocity = 0.0 0.0 0.0
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<LI>angular momentum = 0.0 0.0 0.0
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2009-01-20 01:17:01 +08:00
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<LI>quaternion = (1,0,0,0)
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<LI>bonds, angles, dihedrals, impropers = none
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</UL>
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2014-01-09 04:38:18 +08:00
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|
<P>If molecules are being created, these defaults can be overridden by
|
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|
values specified in the file read by the <A HREF = "molecule.html">molecule</A>
|
|
|
|
command. E.g. the file typically defines bonds (angles,etc) between
|
|
|
|
atoms in the molecule, and can optionally define charges on each atom.
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|
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|
</P>
|
2011-04-16 07:14:41 +08:00
|
|
|
<P>Note that the <I>sphere</I> atom style sets the default particle diameter
|
|
|
|
to 1.0 as well as the density. This means the mass for the particle
|
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|
is not 1.0, but is PI/6 * diameter^3 = 0.5236.
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|
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|
</P>
|
|
|
|
<P>Note that the <I>ellipsoid</I> atom style sets the default particle shape
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|
|
to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
|
|
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|
particle, not an ellipsoid, and has a mass of 1.0.
|
|
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|
</P>
|
|
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|
<P>Note that the <I>peri</I> style sets the default volume and density to 1.0
|
|
|
|
and thus also set the mass for the particle to 1.0.
|
|
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|
</P>
|
|
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|
<P>The <A HREF = "set.html">set</A> command can be used to override many of these
|
|
|
|
default settings.
|
2009-01-20 01:17:01 +08:00
|
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|
</P>
|
2014-05-07 05:37:03 +08:00
|
|
|
<HR>
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Restrictions:</B>
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|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>An <A HREF = "atom_style.html">atom_style</A> must be previously defined to use this
|
|
|
|
command.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
</P>
|
2006-11-14 06:18:34 +08:00
|
|
|
<P><A HREF = "lattice.html">lattice</A>, <A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
|
2006-09-22 00:22:34 +08:00
|
|
|
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>
|
|
|
|
</P>
|
2010-05-22 01:30:18 +08:00
|
|
|
<P><B>Default:</B>
|
|
|
|
</P>
|
2012-02-29 01:46:36 +08:00
|
|
|
<P>The default for the <I>basis</I> keyword is that all created atoms are
|
2014-01-09 04:38:18 +08:00
|
|
|
assigned the argument <I>type</I> as their atom type (when single atoms are
|
|
|
|
being created). The other defaults are <I>remap</I> = no and <I>units</I> =
|
|
|
|
lattice.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
</HTML>
|