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>fix indent command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2010-03-04 02:40:02 +08:00
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<PRE>fix ID group-ID indent K keyword values ...
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2006-09-22 00:22:34 +08:00
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>indent = style name of this fix command
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2010-03-04 02:40:02 +08:00
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<LI>K = force constant for indenter surface (force/distance^2 units)
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2006-09-22 00:22:34 +08:00
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2007-07-03 04:04:44 +08:00
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<LI>one or more keyword/value pairs may be appended
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2009-07-02 04:28:51 +08:00
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<LI>keyword = <I>sphere</I> or <I>cylinder</I> or <I>plane</I> or <I>vel</I> or <I>rstart</I> or <I>side</I> or <I>units</I>
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2006-09-22 00:22:34 +08:00
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<PRE> <I>sphere</I> args = x y z R
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2008-10-02 00:01:49 +08:00
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x,y,z = initial position of center of indenter (distance units)
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2006-09-22 00:22:34 +08:00
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R = sphere radius of indenter (distance units)
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any of x,y,z,R can be a variable (see below)
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2006-09-22 00:22:34 +08:00
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<I>cylinder</I> args = dim c1 c2 R
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2008-10-02 00:01:49 +08:00
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dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
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2006-09-22 00:22:34 +08:00
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c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
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R = cylinder radius of indenter (distance units)
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2010-03-04 02:40:02 +08:00
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any of c1,c2,R can be a variable (see below)
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2008-10-02 00:01:49 +08:00
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<I>plane</I> args = dim pos side
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dim = <I>x</I> or <I>y</I> or <I>z</I> = plane perpendicular to this dimension
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pos = position of plane in dimension x, y, or z (distance units)
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pos can be a variable (see below)
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2008-10-02 00:01:49 +08:00
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side = <I>lo</I> or <I>hi</I>
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2009-07-02 04:28:51 +08:00
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<I>side</I> value = <I>in</I> or <I>out</I>
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<I>in</I> = the indenter acts on particles inside the sphere or cylinder
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<I>out</I> = the indenter acts on particles outside the sphere or cylinder
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2006-09-22 00:22:34 +08:00
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<I>units</I> value = <I>lattice</I> or <I>box</I>
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lattice = the geometry is defined in lattice units
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box = 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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2010-03-04 02:40:02 +08:00
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<PRE>fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
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fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
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2006-09-22 00:22:34 +08:00
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fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Insert an indenter within a simulation box. The indenter repels all
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atoms that touch it, so it can be used to push into a material or as
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2009-07-02 04:28:51 +08:00
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an obstacle in a flow. Or it can be used as a constraining wall
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around a simulation; see the discussion of the <I>side</I> keyword below.
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2006-09-22 00:22:34 +08:00
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</P>
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2008-10-02 00:01:49 +08:00
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<P>The indenter can either be spherical or cylindrical or planar. You
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must set one of those 3 keywords.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>A spherical indenter exerts a force of magnitude
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</P>
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2010-03-04 02:40:02 +08:00
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<PRE>F(r) = - K (r - R)^2
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P>on each atom where <I>K</I> is the specified force constant, <I>r</I> is the
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2006-09-22 00:22:34 +08:00
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distance from the atom to the center of the indenter, and <I>R</I> is the
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radius of the indenter. The force is repulsive and F(r) = 0 for <I>r</I> >
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<I>R</I>.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>A cylindrical indenter exerts the same force, except that <I>r</I> is the
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distance from the atom to the center axis of the cylinder. The
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2010-03-04 02:40:02 +08:00
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cylinder extends infinitely along its axis.
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</P>
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<P>Spherical and cylindrical indenters account for periodic boundaries in
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two ways. First, the center point of a spherical indenter (x,y,z) or
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axis of a cylindrical indenter (c1,c2) is remapped back into the
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simulation box, if the box is periodic in a particular dimension.
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This occurs every timestep if the indenter geometry is specified with
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a variable (see below), e.g. it is moving over time. Second, the
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calculation of distance to the indenter center or axis accounts for
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periodic boundaries. Both of these mean that an indenter can
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effectively move through and straddle one or more periodic boundaries.
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2006-09-22 00:22:34 +08:00
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</P>
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2008-10-02 00:01:49 +08:00
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<P>A planar indenter is really an axis-aligned infinite-extent wall
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2008-11-13 23:34:21 +08:00
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exerting the same force on atoms in the system, where <I>R</I> is the
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position of the plane and <I>r-R</I> is the distance from the plane. If
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the <I>side</I> parameter of the plane is specified as <I>lo</I> then it will
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indent from the lo end of the simulation box, meaning that atoms with
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a coordinate less than the plane's current position will be pushed
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towards the hi end of the box and atoms with a coordinate higher than
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the plane's current position will feel no force. Vice versa if <I>side</I>
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is specified as <I>hi</I>.
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2008-10-02 00:01:49 +08:00
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</P>
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2010-03-04 02:40:02 +08:00
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<P>Any of the 4 quantities defining a spherical indenter's geometry can
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2010-05-07 23:11:21 +08:00
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be specified as an equal-style <A HREF = "variable.html">variable</A>, namely <I>x</I>,
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<I>y</I>, <I>z</I>, or <I>R</I>. Similarly, for a cylindrical indenter, any of <I>c1</I>,
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2010-03-04 02:40:02 +08:00
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<I>c2</I>, or <I>R</I>, can be a variable. For a planar indenter, <I>pos</I> can be
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a variable. If the value is a variable, it should be specified as
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2010-08-13 07:10:38 +08:00
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v_name, where name is the variable name. In this case, the variable
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will be evaluated each timestep, and its value used to define the
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indenter geometry.
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2010-03-04 02:40:02 +08:00
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</P>
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<P>Note that equal-style variables can specify formulas with various
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mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>
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command keywords for the simulation box parameters and timestep and
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elapsed time. Thus it is easy to specify indenter properties that
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change as a function of time or span consecutive runs in a continuous
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fashion. For the latter, see the <I>start</I> and <I>stop</I> keywords of the
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<A HREF = "run.html">run</A> command and the <I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style
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custom</A> for details.
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</P>
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<P>For example, if a spherical indenter's x-position is specfied as v_x,
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then this variable definition will keep it's center at a relative
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position in the simulation box, 1/4 of the way from the left edge to
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the right edge, even if the box size changes:
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</P>
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<PRE>variable x equal "xlo + 0.25*lx"
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</PRE>
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2010-10-29 08:17:32 +08:00
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<P>Similarly, either of these variable definitions will move the indenter
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from an initial position at 2.5 at a constant velocity of 5:
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2010-03-04 02:40:02 +08:00
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</P>
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2010-10-29 08:17:32 +08:00
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<PRE>variable x equal "2.5 + 5*elaplong*dt"
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variable x equal vdisplace(2.5,5)
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2010-03-04 02:40:02 +08:00
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</PRE>
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<P>If a spherical indenter's radius is specified as v_r, then these
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variable definitions will grow the size of the indenter at a specfied
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rate.
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2009-07-02 04:28:51 +08:00
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</P>
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2010-03-04 02:40:02 +08:00
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<PRE>variable r0 equal 0.0
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variable rate equal 1.0
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variable r equal "v_r0 + step*dt*v_rate"
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</PRE>
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2009-07-02 04:28:51 +08:00
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<P>If the <I>side</I> keyword is specified as <I>out</I>, which is the default,
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then particles outside the indenter are pushded away from its outer
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surface, as described above. This only applies to spherical or
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cylindrical indenters. If the <I>side</I> keyword is specified as <I>in</I>,
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the action of the indenter is reversed. Particles inside the indenter
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are pushed away from its inner surface. In other words, the indenter
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is now a containing wall that traps the particles inside it. If the
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radius shrinks over time, it will squeeze the particles.
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2006-09-22 00:22:34 +08:00
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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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2010-03-04 02:40:02 +08:00
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to define the indenter geometry. A <I>box</I> value selects standard
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distance units as defined by the <A HREF = "units.html">units</A> command,
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e.g. Angstroms for units = real or metal. A <I>lattice</I> value means the
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distance units are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
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command must have been previously used to define the lattice spacing.
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2010-03-04 02:46:27 +08:00
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The (x,y,z) coords of the indenter position are scaled by the x,y,z
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lattice spacings respectively. The radius of a spherical or
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cylindrical indenter is scaled by the x lattice spacing.
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</P>
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<P>Note that the units keyword only affects indenter geometry parameters
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2010-03-04 02:40:02 +08:00
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specified directly with numbers, not those specified as variables. In
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the latter case, you should use the <I>xlat</I>, <I>ylat</I>, <I>zlat</I> keywords of
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the <A HREF = "thermo_style.html">thermo_style</A> command if you want to include
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lattice spacings in a variable formula.
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</P>
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<P>The force constant <I>K</I> is not affected by the <I>units</I> keyword. It is
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always in force/distance^2 units where force and distance are defined
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by the <A HREF = "units.html">units</A> command. If you wish K to be scaled by the
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lattice spacing, you can define K with a variable whose formula
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contains <I>xlat</I>, <I>ylat</I>, <I>zlat</I> keywords of the
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<A HREF = "thermo_style.html">thermo_style</A> command, e.g.
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</P>
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<PRE>variable k equal 100.0/xlat/xlat
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fix 1 all indent $k sphere ...
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</PRE>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
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fix to add the energy of interaction between atoms and the indenter to
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the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
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output</A>. The energy of each particle interacting
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with the indenter is K/3 (r - R)^3.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>This fix computes a global scalar energy and a global 3-vector of
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forces (on the indenter), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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2008-01-03 03:25:15 +08:00
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commands</A>. The scalar and vector values
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2010-03-03 05:59:33 +08:00
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calculated by this fix are "extensive".
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2007-06-26 08:03:39 +08:00
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</P>
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<P>The forces due to this fix are imposed during an energy minimization,
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2010-03-04 02:40:02 +08:00
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invoked by the <A HREF = "minimize.html">minimize</A> command. Note that if you
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define the indenter geometry with a variable using a time-dependent
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formula, LAMMPS uses the iteration count in the minimizer as the
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timestep. But it is almost certainly a bad idea to have the indenter
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change its position or size during a minimization. LAMMPS does not
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check if you have done this.
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2007-06-26 08:03:39 +08:00
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</P>
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<P>IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
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included in the total potential energy of the system (the quantity
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2007-08-29 22:13:51 +08:00
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being minimized), you must enable the <A HREF = "fix_modify.html">fix_modify</A>
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2007-06-26 08:03:39 +08:00
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<I>energy</I> option for this fix.
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B>
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</P>
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2010-03-04 02:40:02 +08:00
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<P>The option defaults are side = out and units = lattice.
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2006-09-22 00:22:34 +08:00
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</P>
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</HTML>
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