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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9114 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-11-26 21:08:13 +00:00
parent 61b0e04dfb
commit a0e653f65c
2 changed files with 47 additions and 14 deletions
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28
doc/displace_atoms.html
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@ -17,7 +17,7 @@
</PRE>
<UL><LI>group-ID = ID of group of atoms to displace
<LI>style = <I>move</I> or <I>ramp</I> or <I>random</I>
<LI>style = <I>move</I> or <I>ramp</I> or <I>random</I> or <I>rotate</I>
<PRE> <I>move</I> args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
@ -29,6 +29,10 @@
<I>random</I> args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (positive integer)
<I>rotate</I> args = Px Py Pz Rx Ry Rz theta
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
theta = angle of rotation (degrees)
</PRE>
<LI>zero or more keyword/value pairs may be appended
@ -67,10 +71,18 @@ random displacement, uniformly sampled from a value between -dx and
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.
</P>
<P>Distance units for displacement are determined by the setting of <I>box</I>
or <I>lattice</I> for the <I>units</I> keyword. <I>Box</I> means distance units as
defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms for <I>real</I>
units. <I>Lattice</I> means distance units are in lattice spacings. The
<P>The <I>rotate</I> style rotates each atom in the group by the angle <I>theta</I>
around a rotation axis <I>R</I> = (Rx,Ry,Rz) that goes thru a point <I>P</I> =
(Px,Py,Pz). The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
right-hand's thumb points along <I>R</I>, then your fingers wrap around the
axis in the direction of positive theta.
</P>
<P>Distance units for displacements and the origin point of the <I>rotate</I>
style are determined by the setting of <I>box</I> or <I>lattice</I> for the
<I>units</I> keyword. <I>Box</I> means distance units as defined by the
<A HREF = "units.html">units</A> command - e.g. Angstroms for <I>real</I> units.
<I>Lattice</I> means distance units are in lattice spacings. The
<A HREF = "lattice.html">lattice</A> command must have been previously used to
define the lattice spacing.
</P>
@ -96,9 +108,13 @@ as the initial mapping attempted to be.
</P>
<P><B>Restrictions:</B> none
</P>
<P>You cannot rotate around any rotation vector except the z-axis for a
2d simulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "lattice.html">lattice</A>, <A HREF = "change_box.html">change_box</A>
<P><A HREF = "lattice.html">lattice</A>, <A HREF = "change_box.html">change_box</A>,
<A HREF = "fix_move.html">fix_move</A>
</P>
<P><B>Default:</B>
</P>

31
doc/displace_atoms.txt
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@ -13,7 +13,7 @@ displace_atoms command :h3
displace_atoms group-ID style args keyword value ... :pre
group-ID = ID of group of atoms to displace :ulb,l
style = {move} or {ramp} or {random} :l
style = {move} or {ramp} or {random} or {rotate} :l
{move} args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
{ramp} args = ddim dlo dhi dim clo chi
@ -23,7 +23,12 @@ style = {move} or {ramp} or {random} :l
clo,chi = lower and upper bound of domain to displace (distance units)
{random} args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (positive integer) :pre
seed = random # seed (positive integer)
{rotate} args = Px Py Pz Rx Ry Rz theta
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
theta = angle of rotation (degrees) :pre
zero or more keyword/value pairs may be appended :l
keyword = {units}
value = {box} or {lattice} :pre
@ -59,10 +64,18 @@ random displacement, uniformly sampled from a value between -dx and
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.
Distance units for displacement are determined by the setting of {box}
or {lattice} for the {units} keyword. {Box} means distance units as
defined by the "units"_units.html command - e.g. Angstroms for {real}
units. {Lattice} means distance units are in lattice spacings. The
The {rotate} style rotates each atom in the group by the angle {theta}
around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
(Px,Py,Pz). The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
right-hand's thumb points along {R}, then your fingers wrap around the
axis in the direction of positive theta.
Distance units for displacements and the origin point of the {rotate}
style are determined by the setting of {box} or {lattice} for the
{units} keyword. {Box} means distance units as defined by the
"units"_units.html command - e.g. Angstroms for {real} units.
{Lattice} means distance units are in lattice spacings. The
"lattice"_lattice.html command must have been previously used to
define the lattice spacing.
@ -88,9 +101,13 @@ as the initial mapping attempted to be.
[Restrictions:] none
You cannot rotate around any rotation vector except the z-axis for a
2d simulation.
[Related commands:]
"lattice"_lattice.html, "change_box"_change_box.html
"lattice"_lattice.html, "change_box"_change_box.html,
"fix_move"_fix_move.html
[Default:]