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This commit is contained in:
sjplimp
parent
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commit
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@ -19,42 +19,44 @@
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<LI>deposit = style name of this fix command
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<LI>N = # of atoms to insert
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<LI>N = # of atoms or molecules to insert
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<LI>type = atom type to assign to inserted atoms
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<LI>type = atom type to assign to inserted atoms (for atom insertion)
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<LI>M = insert a single particle every M steps
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<LI>M = insert a single atom or molecule every M steps
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<LI>seed = random # seed (positive integer)
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<LI>one or more keyword/value pairs may be appended to args
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<LI>keyword = <I>region</I> or <I>id</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I>
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<LI>keyword = <I>region</I> or <I>mol</I> or <I>id</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I>
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<PRE> <I>region</I> value = region-ID
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region-ID = ID of region to use as insertion volume
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<I>mol</I> value = template-ID
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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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<I>id</I> value = <I>max</I> or <I>next</I>
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max = atom ID for new atom is max ID of all current atoms plus one
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next = atom ID for new atom increments by one for every deposition
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max = atom ID for new atom(s) is max ID of all current atoms plus one
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next = atom ID for new atom(s) increments by one for every deposition
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<I>global</I> values = lo hi
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lo,hi = put new particle a distance lo-hi above all other particles (distance units)
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lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
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<I>local</I> values = lo hi delta
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lo,hi = put new particle a distance lo-hi above any nearby particle beneath it (distance units)
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lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
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delta = lateral distance within which a neighbor is considered "nearby" (distance units)
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<I>near</I> value = R
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R = only insert particle if further than R from existing particles (distance units)
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R = only insert atom/molecule if further than R from existing particles (distance units)
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<I>attempt</I> value = Q
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Q = attempt a single insertion up to Q times
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<I>rate</I> value = V
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V = z velocity (y in 2d) at which insertion volume moves (velocity units)
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<I>vx</I> values = vxlo vxhi
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vxlo,vxhi = range of x velocities for inserted particle (velocity units)
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vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
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<I>vy</I> values = vylo vyhi
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vylo,vyhi = range of y velocities for inserted particle (velocity units)
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vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
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<I>vz</I> values = vzlo vzhi
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vzlo,vzhi = range of z velocities for inserted particle (velocity units)
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vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
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<I>target</I> values = tx ty tz
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tx,ty,tz = location of sputtering target (distance units)
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tx,ty,tz = location of target point (distance units)
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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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@ -64,28 +66,35 @@
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<P><B>Examples:</B>
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</P>
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<PRE>fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
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fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
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</PRE>
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<PRE>fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
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fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
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fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Insert a single particle into the simulation domain every M timesteps
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until N particles have been inserted. This is useful for simulating
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the deposition of particles onto a surface.
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<P>Insert a single atom or molecule into the simulation domain every M
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timesteps until N atoms or molecules have been inserted. This is
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useful for simulating deposition onto a surface. For the remainder of
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this doc page, a single inserted atom or molecule is referred to as a
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"particle".
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</P>
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<P>Inserted particles have the specified atom type and are assigned to
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two groups: the default group "all" and the group specified in the fix
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deposit command (which can also be "all").
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<P>If inserted particles are individual atoms, they are assigned the
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specified atom type. For molecules the specified type is ignored, and
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the type of each atom in the inserted molecule is specified in the
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file read by the <A HREF = "molecule.html">molecule</A> command.
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</P>
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<P>All atoms in the inserted particle are assigned to two groups: the
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default group "all" and the group specified in the fix deposit command
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(which can also be "all").
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</P>
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<P>If you are computing temperature values which include inserted
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particles, you will want to use the <A HREF = "compute_modify.html">compute_modify</A>
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dynamic option, which insures the current number of atoms is used as a
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normalizing factor each time temperature is computed.
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particles, you will want to use the
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<A HREF = "compute_modify.html">compute_modify</A> dynamic option, which insures the
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current number of atoms is used as a normalizing factor each time the
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temperature is computed.
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</P>
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<P>Care must be taken that inserted particles are not too near existing
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particles, using the options described below. When inserting
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particles above a surface in a non-periodic box (see the
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atoms, using the options described below. When inserting particles
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above a surface in a non-periodic box (see the
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<A HREF = "boundary.html">boundary</A> command), the possibility of a particle
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escaping the surface and flying upward should be considered, since the
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particle may be lost or the box size may grow infinitely large. A
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@ -93,17 +102,36 @@ particle may be lost or the box size may grow infinitely large. A
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prevent this behavior. Note that if a shrink-wrap boundary is used,
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it is OK to insert the new particle outside the box, however the box
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will immediately be expanded to include the new particle. When
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simulating a sputtering experiment it is probably more realistic
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to ignore those atoms using the <A HREF = "thermo_modify.html">thermo_modify</A>
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command with the <I>lost ignore</I> option and a fixed <A HREF = "boundary.html">boundary</A>.
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simulating a sputtering experiment it is probably more realistic to
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ignore those atoms using the <A HREF = "thermo_modify.html">thermo_modify</A>
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command with the <I>lost ignore</I> option and a fixed
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<A HREF = "boundary.html">boundary</A>.
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</P>
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<P>This command must use the <I>region</I> keyword to define an insertion
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volume. The specified region must have been previously defined with a
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<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
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<P>The fix deposit command must use the <I>region</I> keyword to define an
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insertion volume. The specified region must have been previously
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defined with a <A HREF = "region.html">region</A> command. It must be defined with
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side = <I>in</I>.
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</P>
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<P>Each timestep a particle is to be inserted, its coordinates are chosen
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as follows. A random position within the insertion volume is
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generated. If neither the <I>global</I> or <I>local</I> keyword is used, that
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<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
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specifies a previously defined <I>template-ID</I> used by the
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<A HREF = "molecule.html">molecule</A> command which reads a file that defines the
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molecule. The coordinates, atom types, charges, etc, as well as any
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bond/angle/etc information for the molecule must be specified in the
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molecule file. See the <A HREF = "molecule.html">molecule</A> command for details.
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The only required settings from this file are the coordinates and
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types of atoms in the molecule.
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</P>
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<P>Each timestep a particle is inserted, the coordinates for its atoms
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are chosen as follows. For insertion of individual atoms, the
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"position" referred to in the following description is the coordinate
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of the atom. For insertion of molecule, the "position<A HREF = "molecule.html"> is the
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geometric center of the molecule; see the (molecule</A> doc
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page for details. A random rotation of the molecule around its center
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point is performed, which determines the coordinates all the
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individual atoms.
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</P>
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<P>A random position within the region insertion volume is generated. If
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neither the <I>global</I> or <I>local</I> keyword is used, the random position
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is the trial position. If the <I>global</I> keyword is used, the random
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x,y values are used, but the z position of the new particle is set
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above the highest current atom in the simulation by a distance
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@ -112,14 +140,18 @@ the y position.) If the <I>local</I> keyword is used, the z position is
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set a distance between lo/hi above the highest current atom in the
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simulation that is "nearby" the chosen x,y position. In this context,
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"nearby" means the lateral distance (in x,y) between the new and old
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particles is less than the delta parameter.
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particles is less than the <I>delta</I> setting.
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</P>
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<P>Once a trial x,y,z location has been computed, the insertion is only
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performed if no current particle in the simulation is within a
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distance R of the new particle. If this test fails, a new random
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position within the insertion volume is chosen and another trial is
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made. Up to Q attempts are made. If an atom is not successfully
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deposited, LAMMPS prints a warning message.
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<P>Once a trial x,y,z position has been selected, the insertion is only
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performed if no current atom in the simulation is within a distance R
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of any atom in the new particle. Note that the default value for R is
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0.0, which will allow atoms to strongly overlap if you are inserting
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where other atoms are present. This distance test is performed
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independently for each atom in an inserted molecule, based on the
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randomly rotated configuration of the molecule. If this test fails, a
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new random position within the insertion volume is chosen and another
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trial is made. Up to Q attempts are made. If the particle is not
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successfully inserted, LAMMPS prints a warning message.
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</P>
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<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
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or y direction (2d). This enables particles to be inserted from a
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@ -130,22 +162,31 @@ options choose a z-coordinate for insertion independently.
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<P>The vx, vy, and vz components of velocity for the inserted particle
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are set using the values specified for the <I>vx</I>, <I>vy</I>, and <I>vz</I>
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keywords. Note that normally, new particles should be a assigned a
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negative vertical velocity so that they move towards the surface.
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negative vertical velocity so that they move towards the surface. For
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molecules, the same velocity is given to every particle (no rotation
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or bond vibration).
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</P>
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<P>In case the <I>target</I> option is used, the velocity vector of the
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inserted particle will be changed in a way so that it would pass
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through the specified coordinate. This allows convenient simulation
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of a sputtering process.
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<P>If the <I>target</I> option is used, the velocity vector of the inserted
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particle is changed so that it points from the insertion position
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towards the specified target point. The magnitude of the velocity is
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unchanged. This can be useful, for example, for simulating a
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sputtering process. E.g. the target point can be far away, so that
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all incident particles strike the surface as if they are in an
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incident beam of particles at a prescribed angle.
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</P>
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<P>The <I>id</I> keyword determines how an atom ID is assigned to newly
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deposited atoms. For the <I>max</I> setting, the IDs of all current atoms
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are checked and the new ID is the current maximum value plus one.
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This means that if atoms have left the system, the new ID may reflect
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this fact. For the <I>next</I> setting, the maximum ID of all atoms is
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stored at the time the fix is defined. Each time a deposited atom is
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added, this value is incremented by one and assigned to the new atom.
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Thus atom IDs for deposited atoms will be consecutive even if atoms
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leave the system over time.
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<P>The <I>id</I> keyword determines how atom IDs and molecule IDs are assigned
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to newly deposited particles. Molecule IDs are only assigned if
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molecules are being inserted. For the <I>max</I> setting, the atom and
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molecule IDs of all current atoms are checked. Atoms in the new
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particle are assigned IDs starting with the current maximum plus one.
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If a molecule is inserted it is assigned an ID = current maximum plus
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one. This means that if particles leave the system, the new IDs may
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replace the lost ones. For the <I>next</I> setting, the maximum ID of any
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atom and molecule is stored at the time the fix is defined. Each time
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a new particle is added, this value is incremented to assign IDs to
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the new atom(s) or molecule. Thus atom and molecule IDs for deposited
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particles will be consecutive even if particles leave the system over
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time.
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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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for the other deposition parameters. A <I>box</I> value selects standard
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@ -159,9 +200,9 @@ units of distance or velocity.
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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>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
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files</A>. This includes information about how many atoms
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have been depositied, the random number generator seed, the next
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timestep for deposition, etc. See the
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files</A>. This includes information about how many
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particles have been depositied, the random number generator seed, the
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next timestep for deposition, etc. See the
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<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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@ -184,8 +225,9 @@ defined by the <A HREF = "region.html">region</A> command.
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are id = max, delta = 0.0, near = 0.0, attempt =
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10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, and units =
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lattice.
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<P>Insertions are performed for individual atoms, i.e. no <I>mol</I> setting
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is defined. Additional option defaults are id = max, delta = 0.0,
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near = 0.0, attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz =
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0.0 0.0, and units = lattice.
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</P>
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</HTML>
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@ -14,36 +14,38 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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deposit = style name of this fix command :l
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N = # of atoms to insert :l
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type = atom type to assign to inserted atoms :l
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M = insert a single particle every M steps :l
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N = # of atoms or molecules to insert :l
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type = atom type to assign to inserted atoms (for atom insertion) :l
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M = insert a single atom or molecule every M steps :l
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seed = random # seed (positive integer) :l
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one or more keyword/value pairs may be appended to args :l
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keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l
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keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l
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{region} value = region-ID
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region-ID = ID of region to use as insertion volume
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{mol} value = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
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{id} value = {max} or {next}
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max = atom ID for new atom is max ID of all current atoms plus one
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next = atom ID for new atom increments by one for every deposition
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max = atom ID for new atom(s) is max ID of all current atoms plus one
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next = atom ID for new atom(s) increments by one for every deposition
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{global} values = lo hi
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lo,hi = put new particle a distance lo-hi above all other particles (distance units)
|
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lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
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{local} values = lo hi delta
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lo,hi = put new particle a distance lo-hi above any nearby particle beneath it (distance units)
|
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lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
|
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delta = lateral distance within which a neighbor is considered "nearby" (distance units)
|
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{near} value = R
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R = only insert particle if further than R from existing particles (distance units)
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R = only insert atom/molecule if further than R from existing particles (distance units)
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{attempt} value = Q
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Q = attempt a single insertion up to Q times
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{rate} value = V
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V = z velocity (y in 2d) at which insertion volume moves (velocity units)
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{vx} values = vxlo vxhi
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vxlo,vxhi = range of x velocities for inserted particle (velocity units)
|
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vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
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{vy} values = vylo vyhi
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vylo,vyhi = range of y velocities for inserted particle (velocity units)
|
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vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
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{vz} values = vzlo vzhi
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vzlo,vzhi = range of z velocities for inserted particle (velocity units)
|
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vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
|
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{target} values = tx ty tz
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tx,ty,tz = location of sputtering target (distance units)
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tx,ty,tz = location of target point (distance units)
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{units} value = {lattice} or {box}
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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 :pre
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|
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@ -52,27 +54,35 @@ keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rat
|
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[Examples:]
|
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|
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fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
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fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8 :pre
|
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fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
|
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fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Insert a single particle into the simulation domain every M timesteps
|
||||
until N particles have been inserted. This is useful for simulating
|
||||
the deposition of particles onto a surface.
|
||||
Insert a single atom or molecule into the simulation domain every M
|
||||
timesteps until N atoms or molecules have been inserted. This is
|
||||
useful for simulating deposition onto a surface. For the remainder of
|
||||
this doc page, a single inserted atom or molecule is referred to as a
|
||||
"particle".
|
||||
|
||||
Inserted particles have the specified atom type and are assigned to
|
||||
two groups: the default group "all" and the group specified in the fix
|
||||
deposit command (which can also be "all").
|
||||
If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. For molecules the specified type is ignored, and
|
||||
the type of each atom in the inserted molecule is specified in the
|
||||
file read by the "molecule"_molecule.html command.
|
||||
|
||||
All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix deposit command
|
||||
(which can also be "all").
|
||||
|
||||
If you are computing temperature values which include inserted
|
||||
particles, you will want to use the "compute_modify"_compute_modify.html
|
||||
dynamic option, which insures the current number of atoms is used as a
|
||||
normalizing factor each time temperature is computed.
|
||||
particles, you will want to use the
|
||||
"compute_modify"_compute_modify.html dynamic option, which insures the
|
||||
current number of atoms is used as a normalizing factor each time the
|
||||
temperature is computed.
|
||||
|
||||
Care must be taken that inserted particles are not too near existing
|
||||
particles, using the options described below. When inserting
|
||||
particles above a surface in a non-periodic box (see the
|
||||
atoms, using the options described below. When inserting particles
|
||||
above a surface in a non-periodic box (see the
|
||||
"boundary"_boundary.html command), the possibility of a particle
|
||||
escaping the surface and flying upward should be considered, since the
|
||||
particle may be lost or the box size may grow infinitely large. A
|
||||
|
|
@ -80,17 +90,36 @@ particle may be lost or the box size may grow infinitely large. A
|
|||
prevent this behavior. Note that if a shrink-wrap boundary is used,
|
||||
it is OK to insert the new particle outside the box, however the box
|
||||
will immediately be expanded to include the new particle. When
|
||||
simulating a sputtering experiment it is probably more realistic
|
||||
to ignore those atoms using the "thermo_modify"_thermo_modify.html
|
||||
command with the {lost ignore} option and a fixed "boundary"_boundary.html.
|
||||
simulating a sputtering experiment it is probably more realistic to
|
||||
ignore those atoms using the "thermo_modify"_thermo_modify.html
|
||||
command with the {lost ignore} option and a fixed
|
||||
"boundary"_boundary.html.
|
||||
|
||||
This command must use the {region} keyword to define an insertion
|
||||
volume. The specified region must have been previously defined with a
|
||||
"region"_region.html command. It must be defined with side = {in}.
|
||||
The fix deposit command must use the {region} keyword to define an
|
||||
insertion volume. The specified region must have been previously
|
||||
defined with a "region"_region.html command. It must be defined with
|
||||
side = {in}.
|
||||
|
||||
Each timestep a particle is to be inserted, its coordinates are chosen
|
||||
as follows. A random position within the insertion volume is
|
||||
generated. If neither the {global} or {local} keyword is used, that
|
||||
Individual atoms are inserted, unless the {mol} keyword is used. It
|
||||
specifies a previously defined {template-ID} used by the
|
||||
"molecule"_molecule.html command which reads a file that defines the
|
||||
molecule. The coordinates, atom types, charges, etc, as well as any
|
||||
bond/angle/etc information for the molecule must be specified in the
|
||||
molecule file. See the "molecule"_molecule.html command for details.
|
||||
The only required settings from this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
|
||||
Each timestep a particle is inserted, the coordinates for its atoms
|
||||
are chosen as follows. For insertion of individual atoms, the
|
||||
"position" referred to in the following description is the coordinate
|
||||
of the atom. For insertion of molecule, the "position" is the
|
||||
geometric center of the molecule; see the (molecule"_molecule.html doc
|
||||
page for details. A random rotation of the molecule around its center
|
||||
point is performed, which determines the coordinates all the
|
||||
individual atoms.
|
||||
|
||||
A random position within the region insertion volume is generated. If
|
||||
neither the {global} or {local} keyword is used, the random position
|
||||
is the trial position. If the {global} keyword is used, the random
|
||||
x,y values are used, but the z position of the new particle is set
|
||||
above the highest current atom in the simulation by a distance
|
||||
|
|
@ -99,14 +128,18 @@ the y position.) If the {local} keyword is used, the z position is
|
|||
set a distance between lo/hi above the highest current atom in the
|
||||
simulation that is "nearby" the chosen x,y position. In this context,
|
||||
"nearby" means the lateral distance (in x,y) between the new and old
|
||||
particles is less than the delta parameter.
|
||||
particles is less than the {delta} setting.
|
||||
|
||||
Once a trial x,y,z location has been computed, the insertion is only
|
||||
performed if no current particle in the simulation is within a
|
||||
distance R of the new particle. If this test fails, a new random
|
||||
position within the insertion volume is chosen and another trial is
|
||||
made. Up to Q attempts are made. If an atom is not successfully
|
||||
deposited, LAMMPS prints a warning message.
|
||||
Once a trial x,y,z position has been selected, the insertion is only
|
||||
performed if no current atom in the simulation is within a distance R
|
||||
of any atom in the new particle. Note that the default value for R is
|
||||
0.0, which will allow atoms to strongly overlap if you are inserting
|
||||
where other atoms are present. This distance test is performed
|
||||
independently for each atom in an inserted molecule, based on the
|
||||
randomly rotated configuration of the molecule. If this test fails, a
|
||||
new random position within the insertion volume is chosen and another
|
||||
trial is made. Up to Q attempts are made. If the particle is not
|
||||
successfully inserted, LAMMPS prints a warning message.
|
||||
|
||||
The {rate} option moves the insertion volume in the z direction (3d)
|
||||
or y direction (2d). This enables particles to be inserted from a
|
||||
|
|
@ -117,22 +150,31 @@ options choose a z-coordinate for insertion independently.
|
|||
The vx, vy, and vz components of velocity for the inserted particle
|
||||
are set using the values specified for the {vx}, {vy}, and {vz}
|
||||
keywords. Note that normally, new particles should be a assigned a
|
||||
negative vertical velocity so that they move towards the surface.
|
||||
negative vertical velocity so that they move towards the surface. For
|
||||
molecules, the same velocity is given to every particle (no rotation
|
||||
or bond vibration).
|
||||
|
||||
In case the {target} option is used, the velocity vector of the
|
||||
inserted particle will be changed in a way so that it would pass
|
||||
through the specified coordinate. This allows convenient simulation
|
||||
of a sputtering process.
|
||||
If the {target} option is used, the velocity vector of the inserted
|
||||
particle is changed so that it points from the insertion position
|
||||
towards the specified target point. The magnitude of the velocity is
|
||||
unchanged. This can be useful, for example, for simulating a
|
||||
sputtering process. E.g. the target point can be far away, so that
|
||||
all incident particles strike the surface as if they are in an
|
||||
incident beam of particles at a prescribed angle.
|
||||
|
||||
The {id} keyword determines how an atom ID is assigned to newly
|
||||
deposited atoms. For the {max} setting, the IDs of all current atoms
|
||||
are checked and the new ID is the current maximum value plus one.
|
||||
This means that if atoms have left the system, the new ID may reflect
|
||||
this fact. For the {next} setting, the maximum ID of all atoms is
|
||||
stored at the time the fix is defined. Each time a deposited atom is
|
||||
added, this value is incremented by one and assigned to the new atom.
|
||||
Thus atom IDs for deposited atoms will be consecutive even if atoms
|
||||
leave the system over time.
|
||||
The {id} keyword determines how atom IDs and molecule IDs are assigned
|
||||
to newly deposited particles. Molecule IDs are only assigned if
|
||||
molecules are being inserted. For the {max} setting, the atom and
|
||||
molecule IDs of all current atoms are checked. Atoms in the new
|
||||
particle are assigned IDs starting with the current maximum plus one.
|
||||
If a molecule is inserted it is assigned an ID = current maximum plus
|
||||
one. This means that if particles leave the system, the new IDs may
|
||||
replace the lost ones. For the {next} setting, the maximum ID of any
|
||||
atom and molecule is stored at the time the fix is defined. Each time
|
||||
a new particle is added, this value is incremented to assign IDs to
|
||||
the new atom(s) or molecule. Thus atom and molecule IDs for deposited
|
||||
particles will be consecutive even if particles leave the system over
|
||||
time.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the other deposition parameters. A {box} value selects standard
|
||||
|
|
@ -146,9 +188,9 @@ units of distance or velocity.
|
|||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the state of the deposition to "binary restart
|
||||
files"_restart.html. This includes information about how many atoms
|
||||
have been depositied, the random number generator seed, the next
|
||||
timestep for deposition, etc. See the
|
||||
files"_restart.html. This includes information about how many
|
||||
particles have been depositied, the random number generator seed, the
|
||||
next timestep for deposition, etc. See the
|
||||
"read_restart"_read_restart.html command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
|
@ -171,6 +213,7 @@ defined by the "region"_region.html command.
|
|||
|
||||
[Default:]
|
||||
|
||||
The option defaults are id = max, delta = 0.0, near = 0.0, attempt =
|
||||
10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, and units =
|
||||
lattice.
|
||||
Insertions are performed for individual atoms, i.e. no {mol} setting
|
||||
is defined. Additional option defaults are id = max, delta = 0.0,
|
||||
near = 0.0, attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz =
|
||||
0.0 0.0, and units = lattice.
|
||||
|
|
|
|||
|
|
@ -0,0 +1,253 @@
|
|||
<HTML>
|
||||
<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>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>molecule command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>molecule ID file
|
||||
</PRE>
|
||||
<UL><LI>ID = user-assigned name or template ID for the molecule
|
||||
<LI>file = name of file containing molecule description
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>molecule 1 mymol
|
||||
molecule CO2 co2.txt
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a molecule that can be used as part of other LAMMPS commands,
|
||||
typically to define a collection of particles as a bonded molecule or
|
||||
a rigid body. Commands that use molecule definitions include (or will
|
||||
include) <A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>, and
|
||||
<A HREF = "fix_gcmc.html">fix gcmc</A>.
|
||||
</P>
|
||||
<P>The ID of a molecule can only contain alphanumeric characters and
|
||||
underscores.
|
||||
</P>
|
||||
<P>The format of the molecule description file is similar to
|
||||
the data file read by the <A HREF = "read_data.html">read_data</A> commands,
|
||||
and is as follows.
|
||||
</P>
|
||||
<P>A molecule file has a header and a body. The header appears first.
|
||||
The first line of the header is always skipped; it typically contains
|
||||
a description of the file. Then lines are read one at a time. Lines
|
||||
can have a trailing comment starting with '#' that is ignored. If the
|
||||
line is blank (only whitespace after comment is deleted), it is
|
||||
skipped. If the line contains a header keyword, the corresponding
|
||||
value(s) is read from the line. If it doesn't contain a header
|
||||
keyword, the line begins the body of the file.
|
||||
</P>
|
||||
<P>The body of the file contains zero or more sections. The first line
|
||||
of a section has only a keyword. The next line is skipped. The
|
||||
remaining lines of the section contain values. The number of lines
|
||||
depends on the section keyword as described below. Zero or more blank
|
||||
lines can be used between sections. Sections can appear in any order,
|
||||
with a few exceptions as noted below.
|
||||
</P>
|
||||
<P>These are the recognized header keywords. Header lines can come in
|
||||
any order. The value(s) are read from the beginning of the line.
|
||||
Thus the keyword <I>atoms</I> should be in a line like "10 atoms"; the
|
||||
keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
|
||||
keyword <I>xy xz yz</I> should be in a line like "0.0 5.0 6.0 xy xz yz".
|
||||
All these settings have a default value of 0, except the lo/hi box
|
||||
size defaults are -0.5 and 0.5. A line need only appear if the value
|
||||
is different than the default.
|
||||
</P>
|
||||
<UL><LI><I>atoms</I> = # of atoms in molecule
|
||||
<LI><I>bonds</I> = # of bonds in molecule
|
||||
<LI><I>angles</I> = # of angles in molecule
|
||||
<LI><I>dihedrals</I> = # of dihedrals in molecule
|
||||
<LI><I>impropers</I> = # of impropers in molecule
|
||||
</UL>
|
||||
<P>These are the allowed section keywords for the body of the file.
|
||||
</P>
|
||||
<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
|
||||
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
|
||||
<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
|
||||
</UL>
|
||||
<P>IMPORTANT NOTE: Whether a section is required depends on how the
|
||||
molecule definition is used by other LAMMPS commands. For example, to
|
||||
add a molecule via the <A HREF = "fix_deposit.html">fix deposit</A> command, the
|
||||
Coords and Types sections are required. To add a rigid body via the
|
||||
<A HREF = "fix_pout.html">fix pour</A> command, the Bonds (Angles, etc) sections are
|
||||
not required, since the molecule will be treated as a rigid body.
|
||||
Some sections are optional. For example, the <A HREF = "fix_pour.html">fix pour</A>
|
||||
command can add finite-size granular particles. If the Diameters
|
||||
section is not specified, added particles will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use read-in
|
||||
molecules for more details.
|
||||
</P>
|
||||
<P>Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
||||
rules (if any) for whether it can appear in the data file. In each
|
||||
case the ID is ignored; it is simply included for readability as a
|
||||
number from 1 to Nlines for the section, indicating which atom (or
|
||||
bond, etc) the entry applies to. The lines must be listed in order
|
||||
from 1 to Nlines.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Coords</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID x y z
|
||||
<LI>x,y,z = coordinate of atom
|
||||
</UL>
|
||||
<HR>
|
||||
|
||||
<P><I>Types</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID type
|
||||
<LI>type = atom type of atom
|
||||
</UL>
|
||||
<HR>
|
||||
|
||||
<P><I>Charges</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID q
|
||||
<LI>q = charge on atom
|
||||
</UL>
|
||||
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
|
||||
support charge. If not listed, the default charge on each atom in the
|
||||
molecule is 0.0.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Diameters</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID diam
|
||||
<LI>diam = diameter of atom
|
||||
</UL>
|
||||
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
|
||||
support finite-size spherical particles, e.g. atom_style sphere. If
|
||||
not listed, the default diameter of each atom in the molecule is 1.0.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Masses</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID mass
|
||||
<LI>mass = mass of atom
|
||||
</UL>
|
||||
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
|
||||
support per-atom mass, as opposed to per-type mass. See the
|
||||
<A HREF = "mass.html">mass</A> command for details. If not listed, the default mass
|
||||
for each atom is derived from its volume (see Diameters section) and a
|
||||
default density of 1.0, in <A HREF = "units.html">units</A> of mass/volume.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Bonds</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per bond
|
||||
<LI>line syntax: ID type atom1 atom2
|
||||
<LI>type = bond type (1-Nbondtype)
|
||||
<LI>atom1,atom2 = IDs of atoms in bond
|
||||
</UL>
|
||||
<P>The IDs for the two atoms in each bond should be values
|
||||
from 1 to Natoms, where Natoms = # of atoms in the molecule.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Angles</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per angle
|
||||
<LI>line syntax: ID type atom1 atom2 atom3
|
||||
<LI>type = angle type (1-Nangletype)
|
||||
<LI>atom1,atom2,atom3 = IDs of atoms in angle
|
||||
</UL>
|
||||
<P>The IDs for the three atoms in each angle should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
|
||||
ordered linearly within the angle. Thus the central atom (around
|
||||
which the angle is computed) is the atom2 in the list.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Dihedrals</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per dihedral
|
||||
<LI>line syntax: ID type atom1 atom2 atom3 atom4
|
||||
<LI>type = dihedral type (1-Ndihedraltype)
|
||||
<LI>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
|
||||
</UL>
|
||||
<P>The IDs for the four atoms in each dihedral should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
|
||||
ordered linearly within the dihedral.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Impropers</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per improper
|
||||
<LI>line syntax: ID type atom1 atom2 atom3 atom4
|
||||
<LI>type = improper type (1-Nimpropertype)
|
||||
<LI>atom1,atom2,atom3,atom4 = IDs of atoms in improper
|
||||
</UL>
|
||||
<P>The IDs for the four atoms in each improper should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The ordering of
|
||||
the 4 atoms determines the definition of the improper angle used in
|
||||
the formula for the defined <A HREF = "improper_style.html">improper style</A>. See
|
||||
the doc pages for individual styles for details.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Special Bond Counts</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID N1 N2 N3
|
||||
<LI>N1 = # of 1-2 bonds
|
||||
<LI>N2 = # of 1-3 bonds
|
||||
<LI>N3 = # of 1-4 bonds
|
||||
</UL>
|
||||
<P>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
|
||||
this atom within the topology of the molecule. See the
|
||||
<A HREF = "special_bonds.html">special_bonds</A> doc page for more discussion of
|
||||
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
|
||||
section must also appear. If this section is not specied, the
|
||||
atoms in the molecule will have no special bonds.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Special Bonds</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per atom
|
||||
<LI>line syntax: ID a b c d ...
|
||||
<LI>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds
|
||||
</UL>
|
||||
<P>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
|
||||
1-4 neighbors of this atom. The IDs should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The first N1
|
||||
values should be the 1-2 neighbors, the next N2 should be the 1-3
|
||||
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
|
||||
appear more than once. See the <A HREF = "special_bonds.html">special_bonds</A> doc
|
||||
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
|
||||
appears, the Special Bond Counts section must also appear. If this
|
||||
section is not specied, the atoms in the molecule will have no special
|
||||
bonds.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>,
|
||||
<A HREF = "fix_gcmc.html">fix_gcmc</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,248 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
molecule command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
molecule ID file :pre
|
||||
|
||||
ID = user-assigned name or template ID for the molecule
|
||||
file = name of file containing molecule description :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
molecule 1 mymol
|
||||
molecule CO2 co2.txt :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a molecule that can be used as part of other LAMMPS commands,
|
||||
typically to define a collection of particles as a bonded molecule or
|
||||
a rigid body. Commands that use molecule definitions include (or will
|
||||
include) "fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html, and
|
||||
"fix gcmc"_fix_gcmc.html.
|
||||
|
||||
The ID of a molecule can only contain alphanumeric characters and
|
||||
underscores.
|
||||
|
||||
The format of the molecule description file is similar to
|
||||
the data file read by the "read_data"_read_data.html commands,
|
||||
and is as follows.
|
||||
|
||||
A molecule file has a header and a body. The header appears first.
|
||||
The first line of the header is always skipped; it typically contains
|
||||
a description of the file. Then lines are read one at a time. Lines
|
||||
can have a trailing comment starting with '#' that is ignored. If the
|
||||
line is blank (only whitespace after comment is deleted), it is
|
||||
skipped. If the line contains a header keyword, the corresponding
|
||||
value(s) is read from the line. If it doesn't contain a header
|
||||
keyword, the line begins the body of the file.
|
||||
|
||||
The body of the file contains zero or more sections. The first line
|
||||
of a section has only a keyword. The next line is skipped. The
|
||||
remaining lines of the section contain values. The number of lines
|
||||
depends on the section keyword as described below. Zero or more blank
|
||||
lines can be used between sections. Sections can appear in any order,
|
||||
with a few exceptions as noted below.
|
||||
|
||||
These are the recognized header keywords. Header lines can come in
|
||||
any order. The value(s) are read from the beginning of the line.
|
||||
Thus the keyword {atoms} should be in a line like "10 atoms"; the
|
||||
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
|
||||
keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz".
|
||||
All these settings have a default value of 0, except the lo/hi box
|
||||
size defaults are -0.5 and 0.5. A line need only appear if the value
|
||||
is different than the default.
|
||||
|
||||
{atoms} = # of atoms in molecule
|
||||
{bonds} = # of bonds in molecule
|
||||
{angles} = # of angles in molecule
|
||||
{dihedrals} = # of dihedrals in molecule
|
||||
{impropers} = # of impropers in molecule :ul
|
||||
|
||||
These are the allowed section keywords for the body of the file.
|
||||
|
||||
{Coords, Types, Charges, Diameters, Masses} = atom-property sections
|
||||
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
|
||||
{Special Bond Counts, Special Bonds} = special neighbor info :ul
|
||||
|
||||
IMPORTANT NOTE: Whether a section is required depends on how the
|
||||
molecule definition is used by other LAMMPS commands. For example, to
|
||||
add a molecule via the "fix deposit"_fix_deposit.html command, the
|
||||
Coords and Types sections are required. To add a rigid body via the
|
||||
"fix pour"_fix_pout.html command, the Bonds (Angles, etc) sections are
|
||||
not required, since the molecule will be treated as a rigid body.
|
||||
Some sections are optional. For example, the "fix pour"_fix_pour.html
|
||||
command can add finite-size granular particles. If the Diameters
|
||||
section is not specified, added particles will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use read-in
|
||||
molecules for more details.
|
||||
|
||||
Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
||||
rules (if any) for whether it can appear in the data file. In each
|
||||
case the ID is ignored; it is simply included for readability as a
|
||||
number from 1 to Nlines for the section, indicating which atom (or
|
||||
bond, etc) the entry applies to. The lines must be listed in order
|
||||
from 1 to Nlines.
|
||||
|
||||
:line
|
||||
|
||||
{Coords} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID x y z
|
||||
x,y,z = coordinate of atom :ul
|
||||
|
||||
:line
|
||||
|
||||
{Types} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID type
|
||||
type = atom type of atom :ul
|
||||
|
||||
:line
|
||||
|
||||
{Charges} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID q
|
||||
q = charge on atom :ul
|
||||
|
||||
This section is only allowed for "atom styles"_atom_style.html that
|
||||
support charge. If not listed, the default charge on each atom in the
|
||||
molecule is 0.0.
|
||||
|
||||
:line
|
||||
|
||||
{Diameters} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID diam
|
||||
diam = diameter of atom :ul
|
||||
|
||||
This section is only allowed for "atom styles"_atom_style.html that
|
||||
support finite-size spherical particles, e.g. atom_style sphere. If
|
||||
not listed, the default diameter of each atom in the molecule is 1.0.
|
||||
|
||||
:line
|
||||
|
||||
{Masses} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID mass
|
||||
mass = mass of atom :ul
|
||||
|
||||
This section is only allowed for "atom styles"_atom_style.html that
|
||||
support per-atom mass, as opposed to per-type mass. See the
|
||||
"mass"_mass.html command for details. If not listed, the default mass
|
||||
for each atom is derived from its volume (see Diameters section) and a
|
||||
default density of 1.0, in "units"_units.html of mass/volume.
|
||||
|
||||
:line
|
||||
|
||||
{Bonds} section:
|
||||
|
||||
one line per bond
|
||||
line syntax: ID type atom1 atom2
|
||||
type = bond type (1-Nbondtype)
|
||||
atom1,atom2 = IDs of atoms in bond :ul
|
||||
|
||||
The IDs for the two atoms in each bond should be values
|
||||
from 1 to Natoms, where Natoms = # of atoms in the molecule.
|
||||
|
||||
:line
|
||||
|
||||
{Angles} section:
|
||||
|
||||
one line per angle
|
||||
line syntax: ID type atom1 atom2 atom3
|
||||
type = angle type (1-Nangletype)
|
||||
atom1,atom2,atom3 = IDs of atoms in angle :ul
|
||||
|
||||
The IDs for the three atoms in each angle should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
|
||||
ordered linearly within the angle. Thus the central atom (around
|
||||
which the angle is computed) is the atom2 in the list.
|
||||
|
||||
:line
|
||||
|
||||
{Dihedrals} section:
|
||||
|
||||
one line per dihedral
|
||||
line syntax: ID type atom1 atom2 atom3 atom4
|
||||
type = dihedral type (1-Ndihedraltype)
|
||||
atom1,atom2,atom3,atom4 = IDs of atoms in dihedral :ul
|
||||
|
||||
The IDs for the four atoms in each dihedral should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
|
||||
ordered linearly within the dihedral.
|
||||
|
||||
:line
|
||||
|
||||
{Impropers} section:
|
||||
|
||||
one line per improper
|
||||
line syntax: ID type atom1 atom2 atom3 atom4
|
||||
type = improper type (1-Nimpropertype)
|
||||
atom1,atom2,atom3,atom4 = IDs of atoms in improper :ul
|
||||
|
||||
The IDs for the four atoms in each improper should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The ordering of
|
||||
the 4 atoms determines the definition of the improper angle used in
|
||||
the formula for the defined "improper style"_improper_style.html. See
|
||||
the doc pages for individual styles for details.
|
||||
|
||||
:line
|
||||
|
||||
{Special Bond Counts} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID N1 N2 N3
|
||||
N1 = # of 1-2 bonds
|
||||
N2 = # of 1-3 bonds
|
||||
N3 = # of 1-4 bonds :ul
|
||||
|
||||
N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
|
||||
this atom within the topology of the molecule. See the
|
||||
"special_bonds"_special_bonds.html doc page for more discussion of
|
||||
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
|
||||
section must also appear. If this section is not specied, the
|
||||
atoms in the molecule will have no special bonds.
|
||||
|
||||
:line
|
||||
|
||||
{Special Bonds} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID a b c d ...
|
||||
a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds :ul
|
||||
|
||||
A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
|
||||
1-4 neighbors of this atom. The IDs should be values from 1 to
|
||||
Natoms, where Natoms = # of atoms in the molecule. The first N1
|
||||
values should be the 1-2 neighbors, the next N2 should be the 1-3
|
||||
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
|
||||
appear more than once. See the "special_bonds"_special_bonds.html doc
|
||||
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
|
||||
appears, the Special Bond Counts section must also appear. If this
|
||||
section is not specied, the atoms in the molecule will have no special
|
||||
bonds.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
|
||||
"fix_gcmc"_fix_gcmc.html
|
||||
|
||||
[Default:] none
|
||||
Loading…
Reference in New Issue