forked from lijiext/lammps
181 lines
7.9 KiB
HTML
181 lines
7.9 KiB
HTML
<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
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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 = atoms 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 atom (distance units)
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<I>random</I> args = N seed region-ID
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N = number of atoms 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>basis</I> or <I>units</I>
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<PRE> <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>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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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command creates atoms on a lattice, or a single atom, or a random
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collection of atoms, as an alternative to reading in their coordinates
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explicitly via a <A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A> command. A simulation box must
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already exist, which is typically created via the
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<A HREF = "create_box.html">create_box</A> command. Before using this command, a
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lattice must also be defined using the <A HREF = "lattice.html">lattice</A> command.
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The only exceptions are for the <I>single</I> style with units = box or the
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<I>random</I> style.
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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 atoms on the lattice. If your simulation box is
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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 atom at the
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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, the geometric volume is filled that is inside
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the simulation box and is also consistent with the region volume. See
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the <A HREF = "region.html">region</A> command for details. Note that a region can
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be specified so that its "volume" is either inside or outside a
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geometric boundary. Also note that if your region is the same size as
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a periodic simulation box (in some dimension), LAMMPS does not
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implement the same logic as with the <I>box</I> style, to insure exactly
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one atom at the boundary. if this is what you desire, you should
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either use the <I>box</I> style, or tweak the region size to get precisely
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the atoms you want.
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</P>
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<P>For the <I>single</I> style, a single atom is added to the system at the
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specified coordinates. This can be useful for debugging purposes or
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to create a tiny system with a handful of atoms at specified
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positions.
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</P>
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<P>For the <I>random</I> style, N atoms are added to the system at randomly
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generated coordinates, which can be useful for generating an amorphous
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system. The atoms are created one by one using the speficied random
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number <I>seed</I>, resulting in the same set of atom coordinates,
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independent of how many processors are being used in the simulation.
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If the <I>region-ID</I> argument is specified as NULL, then the created
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atoms will be anywhere in the simulation box. If a <I>region-ID</I> is
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specified, a geometric volume is filled that is inside the simulation
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box and is also consistent with the region volume. See the
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<A HREF = "region.html">region</A> command for details. Note that a region can be
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specified so that its "volume" is either inside or outside a geometric
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boundary.
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</P>
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<P>IMPORTANT NOTE: The atoms 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>The <I>basis</I> keyword specifies an atom type that will be assigned to
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specific basis atoms as they are created. See the
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<A HREF = "lattice.html">lattice</A> command for specifics on how basis atoms are
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defined for the unit cell of the lattice. By default, all created
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atoms are assigned the argument <I>type</I> as their atom type.
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</P>
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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 atom 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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<P>Note that this command adds atoms to those that already exist. By
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using the create_atoms command multiple times, multiple sets of atoms
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can be added to the simulation. For example, interleaving
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create_atoms with <A HREF = "lattice.html">lattice</A> commands specifying different
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orientations, grain boundaries can be created. By using the
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create_atoms command in conjunction with the
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<A HREF = "delete_atoms.html">delete_atoms</A> command, reasonably complex
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geometries can be created. The create_atoms command can also be used
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to add atoms to a system previously read in from a data or restart
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file. In all these cases, care should be taken to insure that new
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atoms do not overlap existing atoms inappropriately. The
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<A HREF = "delete_atoms.html">delete_atoms</A> command can be used to handle
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overlaps.
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</P>
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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.
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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 = 0.0
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<LI>diameter = 1.0
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<LI>volume = 1.0
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<LI>density = 1.0
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<LI>velocity = 0.0
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<LI>angular velocity = 0.0
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<LI>angular momentum = 0.0
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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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<P>The <I>granular</I> style sets the diameter and density to 1.0 and
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calculates a mass for the particle, which is PI/6 * diameter^3 =
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0.5236. The <I>peri</I> style sets the volume and density to 1.0 and
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calculates a mass for the particle, which is also 1.0.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>An <A HREF = "atom_style.html">atom_style</A> must be previously defined to use this
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command.
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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 = "lattice.html">lattice</A>, <A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
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<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default for the <I>basis</I> keyword, is all created atoms are assigned
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the argument <I>type</I> as their atom type. The default for the
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<I>units</I> keyword is lattice.
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</P>
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</HTML>
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