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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7687 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-02-03 20:21:28 +00:00
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32
doc/Section_howto.txt
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@ -749,7 +749,7 @@ See the "dump"_dump.html command for more information on XTC files.
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
conditions of the box (periodic, non-,periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
@ -809,16 +809,26 @@ the x box length is 10 and the xy tilt factor must be between -5 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all
equivalent.
equivalent. If the box tilt exceeds this limit during a dynamics run
(e.g. via the "fix deform"_fix_deform.html command), then the box is
"flipped" to an equivalent shape with a tilt factor within the bounds,
so the run can continue. See the "fix deform"_fix_deform.html doc
page for further details.
The one exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
Triclinic crystal structures are often defined using three lattice
constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
{gamma}. Note that in this nomenclature, the a, b, and c lattice constants
are the scalar lengths of the edge vectors [a], [b], and [c] defined
above. The
relationship between these 6 quantities (a,b,c,alpha,beta,gamma) and
the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt
factors (xy,xz,yz) is as follows:
{gamma}. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors [a], [b], and [c]
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:c,image(Eqs/box.jpg)
@ -901,9 +911,9 @@ LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, "fix deform"_fix_deform.html can continuously strain
a box by an arbitrary amount. As discussed in the "fix
deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of periodic space. The strain rate can then continue to change
as before. In a long NEMD simulation these box re-shaping events may
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
In a NEMD simulation, the "remap" option of "fix