[Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell
Does anybody know if there is a relatively simple way to find all the crystallographic symmetry elements within a unit cell using Jmol? For example, if there is an inversion center at the origin, there may be several other inversion centers generated by the space group symmetry. I can "see" some of them by asking Jmol for the symmetry relationship(s) between two atoms or two molecules. But I'm interested in generating a list of all the inversion centers (or glide planes, etc.) within the cell. Thanks for any insights. Dean -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell
Dean,
Well, it's just the product of all the symmetry operators. Get the
collection of symmetry operators and multiply them until you get a complete
set. I'll have to think about whether you can get all those as variables
Yes, I think you can. You would have to normalize them to stay within the
unit cell.
strsymops = getproperty("auxiliaryinfo.models[1].symmetryOperations")
print strsymops.length
op = []
for (var i = 1; i < strsymops.length; i++) {
op[i] = symop(i)
print "" + strsymops[i] + "\n" + op[i]
}
op is then an array of the matrices, and you can multiply these at will.
The problem you might have is whether there is a simple way to limit this to
"within" the unit cell. For that, it's probably just as well to take a
random point and keep operating on it, returning its unit cell coordinates
each time. Anyway, since you can get the matrices for the space group
operations, you should be able to get all combinations of them.
Bob
On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston wrote:
> Does anybody know if there is a relatively simple way to find all the
> crystallographic symmetry elements within a unit cell using Jmol? For
> example, if there is an inversion center at the origin, there may be several
> other inversion centers generated by the space group symmetry. I can "see"
> some of them by asking Jmol for the symmetry relationship(s) between two
> atoms or two molecules. But I'm interested in generating a list of all the
> inversion centers (or glide planes, etc.) within the cell. Thanks for any
> insights.
>
> Dean
>
>
> --
> Benefiting from Server Virtualization: Beyond Initial Workload
> Consolidation -- Increasing the use of server virtualization is a top
> priority.Virtualization can reduce costs, simplify management, and improve
> application availability and disaster protection. Learn more about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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Consolidation -- Increasing the use of server virtualization is a top
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application availability and disaster protection. Learn more about boosting
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Re: [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell
OK - something along those lines was what I was thinking - thanks for the
code example.
Dean
On Thu, Apr 21, 2011 at 12:15 PM, Robert Hanson wrote:
> Dean,
>
> Well, it's just the product of all the symmetry operators. Get the
> collection of symmetry operators and multiply them until you get a complete
> set. I'll have to think about whether you can get all those as variables
> Yes, I think you can. You would have to normalize them to stay within the
> unit cell.
>
> strsymops = getproperty("auxiliaryinfo.models[1].symmetryOperations")
> print strsymops.length
> op = []
>
> for (var i = 1; i < strsymops.length; i++) {
>op[i] = symop(i)
>print "" + strsymops[i] + "\n" + op[i]
> }
>
> op is then an array of the matrices, and you can multiply these at will.
>
> The problem you might have is whether there is a simple way to limit this
> to "within" the unit cell. For that, it's probably just as well to take a
> random point and keep operating on it, returning its unit cell coordinates
> each time. Anyway, since you can get the matrices for the space group
> operations, you should be able to get all combinations of them.
>
> Bob
>
> On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston wrote:
>
>> Does anybody know if there is a relatively simple way to find all the
>> crystallographic symmetry elements within a unit cell using Jmol? For
>> example, if there is an inversion center at the origin, there may be several
>> other inversion centers generated by the space group symmetry. I can "see"
>> some of them by asking Jmol for the symmetry relationship(s) between two
>> atoms or two molecules. But I'm interested in generating a list of all the
>> inversion centers (or glide planes, etc.) within the cell. Thanks for any
>> insights.
>>
>> Dean
>>
>>
>> --
>> Benefiting from Server Virtualization: Beyond Initial Workload
>> Consolidation -- Increasing the use of server virtualization is a top
>> priority.Virtualization can reduce costs, simplify management, and improve
>> application availability and disaster protection. Learn more about
>> boosting
>> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
>
>
> --
> Benefiting from Server Virtualization: Beyond Initial Workload
> Consolidation -- Increasing the use of server virtualization is a top
> priority.Virtualization can reduce costs, simplify management, and improve
> application availability and disaster protection. Learn more about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___
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