2010-01-09 06:54:29 +08:00
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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>fix wall/region command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID wall/region region-ID style epsilon sigma cutoff
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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>wall/region = style name of this fix command
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<LI>region-ID = region whose boundary will act as wall
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<LI>style = <I>lj93</I> or <I>lj126</I> or <I>colloid</I> or <I>harmonic</I>
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<LI>epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
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<LI>sigma = size factor for wall-particle interaction (distance units)
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<LI>cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix wall all wall/region mySphere lj93 1.0 1.0 2.5
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Treat the surface of the geometric region defined by the <I>region-ID</I>
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as a bounding wall which interacts with nearby particles according to
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the specified style. The distance between a particle and the surface
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is the distance to the nearest point on the surface and the force the
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wall exerts on the particle is along the direction between that point
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and the particle, which is the direction normal to the surface at that
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point.
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</P>
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<P>Regions are defined using the <A HREF = "region.html">region</A> command. Note that
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the region volume can be interior or exterior to the bounding surface,
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which will determine in which direction the surface interacts with
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particles, i.e. the direction of the surface normal. Regions can
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either be primitive shapes (block, sphere, cylinder, etc) or
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combinations of primitive shapes specified via the <I>union</I> or
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<I>intersect</I> region styles. These latter styles can be used to
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2010-01-12 04:54:59 +08:00
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construct particle containers with complex shapes. Regions can also
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change over time via keywords like <I>linear</I>, <I>wiggle</I>, and <I>rotate</I>,
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which when used with this fix, have the effect of moving the region
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surface in a prescribed manner.
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2010-01-09 06:54:29 +08:00
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</P>
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<P>IMPORTANT NOTE: As discussed on the <A HREF = "region.html">region</A> command doc
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page, regions in LAMMPS do not get wrapped across periodic boundaries.
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It is up to you to insure that periodic or non-periodic boundaries are
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specified appropriately via the <A HREF = "boundary.html">boundary</A> command when
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using a region as a wall that bounds particle motion.
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</P>
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<P>IMPORTANT NOTE: For primitive regions with sharp corners and/or edges
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(e.g. a block or cylinder), wall/particle forces are computed
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accurately for both interior and exterior regions. For <I>union</I> and
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<I>intersect</I> regions, additional sharp corners and edges may be present
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due to the intersection of the surfaces of 2 or more primitive
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volumes. These corners and edges can be of two types: concave or
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convex. Concave points/edges are like the corners of a cube as seen
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by particles in the interior of a cube. Wall/particle forces around
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these features are computed correctly. Convex points/edges are like
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the corners of a cube as seen by particles exterior to the cube,
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i.e. the points jut into the volume where particles are present.
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LAMMPS does NOT compute the location of these convex points directly,
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and hence wall/particle forces in the cutoff volume around these
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points suffer from inaccuracies. The basic problem is that the
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outward normal of the surface is not continuous at these points. This
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can cause particles to feel no force (they don't "see" the wall) when
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in one location, then move a distance epsilon, and suddenly feel a
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large force because they now "see" the wall. In the worst-case
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scenario, this can blow particles out of the simulation box. Thus, as
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a general rule you should not use the fix wall/region command with
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<I>union</I> or <I>interesect</I> regions that have convex points or edges.
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</P>
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<P>The energy of wall-particle interactions depends on the specified
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style.
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</P>
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<P>For style <I>lj93</I>, the energy E is given by the 9/3 potential:
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</P>
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<CENTER><IMG SRC = "Eqs/fix_wall_lj93.jpg">
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</CENTER>
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<P>For style <I>lj126</I>, the energy E is given by the 12/6 potential:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
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</CENTER>
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<P>For style <I>colloid</I>, the energy E is given by an integrated form of
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the <A HREF = "pair_colloid.html">pair_style colloid</A> potential:
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</P>
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<CENTER><IMG SRC = "Eqs/fix_wall_colloid.jpg">
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</CENTER>
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<P>For style <I>wall/harmonic</I>, the energy E is given by a harmonic spring
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potential:
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</P>
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<CENTER><IMG SRC = "Eqs/fix_wall_harmonic.jpg">
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</CENTER>
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<P>In all cases, <I>r</I> is the distance from the particle to the region
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surface, and Rc is the <I>cutoff</I> distance at which the particle and
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surface no longer interact. The energy of the wall potential is
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shifted so that the wall-particle interaction energy is 0.0 at the
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cutoff distance.
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</P>
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<P>For the <I>lj93</I> and <I>lj126</I> styles, <I>epsilon</I> and <I>sigma</I> are the usual
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Lennard-Jones parameters, which determine the strength and size of the
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particle as it interacts with the wall. Epsilon has energy units.
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Note that this <I>epsilon</I> and <I>sigma</I> may be different than any
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<I>epsilon</I> or <I>sigma</I> values defined for a pair style that computes
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particle-particle interactions.
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</P>
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<P>The <I>lj93</I> interaction is derived by integrating over a 3d
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half-lattice of Lennard-Jones 12/6 particles. The <I>lj126</I> interaction
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is effectively a harder, more repulsive wall interaction.
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</P>
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<P>For the <I>colloid</I> style, <I>epsilon</I> is effectively a Hamaker constant
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with energy units for the colloid-wall interaction, <I>R</I> is the radius
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of the colloid particle, <I>D</I> is the distance from the surface of the
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colloid particle to the wall (r-R), and <I>sigma</I> is the size of a
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constituent LJ particle inside the colloid particle. Note that the
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cutoff distance Rc in this case is the distance from the colloid
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particle center to the wall.
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</P>
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<P>The <I>colloid</I> interaction is derived by integrating over constituent
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LJ particles of size <I>sigma</I> within the colloid particle and a 3d
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half-lattice of Lennard-Jones 12/6 particles of size <I>sigma</I> in the
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wall.
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</P>
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<P>For the <I>wall/harmonic</I> style, <I>epsilon</I> is effectively the spring
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constant K, and has units (energy/distance^2). The input parameter
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<I>sigma</I> is ignored. The minimum energy position of the harmonic
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spring is at the <I>cutoff</I>. This is a repulsive-only spring since the
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interaction is truncated at the <I>cutoff</I>
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</P>
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<P>IMPORTANT NOTE: For all of the styles, you must insure that r is
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always > 0 for all particles in the group, or LAMMPS will generate an
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error. This means you cannot start your simulation with particles on
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the region surface (r = 0) or with particles on the wrong side of the
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region surface (r < 0). For the <I>wall/lj93</I> and <I>wall/lj126</I> styles,
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the energy of the wall/particle interaction (and hence the force on
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the particle) blows up as r -> 0. The <I>wall/colloid</I> style is even
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more restrictive, since the energy blows up as D = r-R -> 0. This
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means the finite-size particles of radius R must be a distance larger
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than R from the region surface. The <I>harmonic</I> style is a softer
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potential and does not blow up as r -> 0, but you must use a large
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enough <I>epsilon</I> that particles always reamin on the correct side of
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the region surface (r > 0).
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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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 wall to the
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system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
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output</A>.
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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-length vector
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of forces, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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commands</A>. The scalar energy is the sum of
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energy interactions for all particles interacting with the wall
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represented by the region surface. The 3 vector quantities are the
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x,y,z components of the total force acting on the wall due to the
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2010-04-03 00:51:06 +08:00
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particles. The scalar and vector values calculated by this fix are
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"extensive".
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2010-01-09 06:54:29 +08:00
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command.
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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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invoked by the <A HREF = "minimize.html">minimize</A> command.
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</P>
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<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
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included in the total potential energy of the system (the quantity
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being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
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<I>energy</I> option for this fix.
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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>
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</P>
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<P><A HREF = "fix_wall.html">fix wall/lj93</A>,
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<A HREF = "fix_wall.html">fix wall/lj126</A>,
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<A HREF = "fix_wall.html">fix wall/colloid</A>,
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<A HREF = "fix_wall_gran.html">fix wall/gran</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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