We are trying to select some atoms and bonds that can represent the unit
cell crystal by our own way and build the periodic crystal based on these
atoms and bonds. Now we are able to have the "representative" unit cell and
trying to figure out how jmol builld its period cells and then would
develop an algorithm to build our periodic cell using jmol. Could you give
me some suggestions on this? Thanks.
On Thu, Jan 1, 2015 at 9:22 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Feel free to ask for advice -- "rebuilding a crystal" is not something
> that one would typically do; maybe I can help and suggest how to do that,
> probably without atom numbers.
>
> On Thu, Jan 1, 2015 at 8:12 PM, Jing Xie <sandie.b...@gmail.com> wrote:
>
>> Hi Robert,
>>
>> Thanks for the reply. I understand cif doesn't contain atomno
>> information. I got atomno from atomInfo and bondInfo and was trying to
>> rebuild the crystal. That's why I wonder how jmol index the atoms.
>>
>> Happy New Year.
>>
>> Jing
>>
>> On Thu, Jan 1, 2015 at 8:56 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>>
>>> Jing,
>>>
>>> ATOMNO is not particularly relevant for CIF files. For sure the atom
>>> numbers will be sequential based on the CIF file atom record order, and,
>>> after that, symmetry will be processed in order of appearance in the
>>> symmetry operator in the CIF file. But if there are atoms at special
>>> positions, then those of course will not be duplicated by redundant
>>> symmetry operators, and if the PACKED keyword is used, then there can be
>>> quite a bit of duplication that is removed along the way. Rather, I suggest
>>> using SYMOP=n where n is 1,2,3,... etc.
>>>
>>> Bob Hanson
>>>
>>> On Mon, Dec 29, 2014 at 1:32 PM, Jing Xie <sandie.b...@gmail.com> wrote:
>>>
>>>> Dear Angel,
>>>>
>>>> Thanks for the reply. I understand atomNo and atomIndex and would like
>>>> to know how jmol index the periodic crystal. For example, there would be 27
>>>> atoms if "load 1000041.cif {1,1,1}". It is easy to understand the indexing
>>>> of atomno 1 and atomno 2. I was wondering how jmol determine which atoms
>>>> should be atomno=3? Which atom goes to the next? Is there an algorithm
>>>> about this indexing rule and the rule regarding to periodic crystal?
>>>>
>>>> Jing
>>>>
>>>>
>>>
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>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming! The Go Parallel Website,
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> your
> hub for all things parallel software development, from weekly thought
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>
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sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net
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