On Wed, Aug 4, 2010 at 4:35 PM, Thomas Manz <[email protected]> wrote:
> Hi,
>
> I'm using Jmol to display partial atomic charges for periodic and
> nonperiodic systems.
> This is being done using the following load command placed on the
> comment line of an xyz file:
>
> jmolscript: load "" {2 1 1} spacegroup "x,y,z" unitcell {5.871392
> 5.871392 5.871392 60 60 60}
>
> I have a few questions regarding the loading of unitcell parameters in
> Jmol.
>
> 1) Does Jmol currently support 1-D and 2-D periodicity, and if so how
> does one specify the unitcell parameters (lattice vectors) in this
> case?
>
>
It does, but I forgot to document it. Use -1 for the c length (slab) or -1
for the b and c lengths (polymer)
> 2) Is it possible to use fractional coordinates instead of cartesian
> coordinates to specify the atomic positions in the xyz file?
>
>
no, XYZ files are Cartesian. The simplest fractional coordinate file type is
SHELX:
TITL simple SLAB file
CELL 1.54180 8.619649 5.6778 -1 79.93961 103.2911 120.0852
O - 0.9062079820000 0.7382476400000 0.5127858400000 0
Na - 0.3257001410000 0.3251670870000 0.5101181680000 0
Mg - 0.6718684530000 0.3440356050000 0.0014820400000 0
Mg - 0.6740955230000 0.6757086980000 0.0182290920000 0
where for Jmol you can omit LATT, SFAC, and END, and the - here would be a
pointer into SFAC, but Jmol doesn't use it.
> 3) Is is possible to specify the lattice vectors as three cartesian
> vectors instead of using the {a b c alpha beta gamma} notation?
> For example, first lattice vector (-0.0038, 4.1517, 4.15170), second
> lattice vector (4.1517, -0.0038, 4.1516), third lattice vector
> (4.1517, 4.1517, -0.0038)
>
>
very interesting idea. This is something we could set up easily enough. Jmol
can do that, but there's no way to introduce that on the LOAD line.
> Sincere thanks,
>
> Tom
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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