load "" is now working after an inline load of a model for Jmol 12.0.RC25.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and htp://
chemapps.stolaf.edu/jmol/doc/examples-11/new.htm
And as a bonus now you can integrate model data directly into the LOAD
command. This makes all the options for LOAD now available for loading
inline models.
load data "model molfile"
data_global
_chemical_name Quartz
loop_
_publ_author_name
'Levien L'
'Prewitt C T'
'Weidner D J'
_journal_name_full "American Mineralogist"
_journal_volume 65
_journal_year 1980
_journal_page_first 920
_journal_page_last 930
_publ_section_title
;
Structure and elastic properties of quartz at pressure
P = 1 atm
;
_chemical_formula_sum 'Si O2'
_cell_length_a 4.916
_cell_length_b 4.916
_cell_length_c 5.4054
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_cell_volume 113.131
_symmetry_space_group_name_H-M 'P 32 2 1'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'y,x,2/3-z'
'-y,x-y,2/3+z'
'-x,-x+y,1/3-z'
'-x+y,-x,1/3+z'
'x-y,-y,-z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Si 0.46970 0.00000 0.00000
O 0.41350 0.26690 0.11910
loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
Si 0.00854 0.00716 0.00725 0.00358 -0.00001 -0.00002
O 0.01745 0.01322 0.01229 0.00973 -0.00291 -0.00408
end "model molfile" {3 3 3}
Bob
On Tue, Jul 13, 2010 at 12:20 AM, Robert Hanson <[email protected]> wrote:
> Point taken. Right -- what you were doing was a hack due to a bug that was
> there -- that some of the load defaults were not being processed with string
> data. The model data string is no longer stored, mostly because it could be
> very large. But it's a valid point.
>
> Bob
>
>
> On Mon, Jul 12, 2010 at 4:51 PM, Rickard Armiento <[email protected]
> > wrote:
>
>> Hi,
>>
>> Thank you all for your hard work with JMol.
>>
>> We recently upgraded from Jmol 11.7.16 to 12.0.RC23 and discovered that
>> some functionality of the 'load' command is missing. I have also
>> confirmed that the problem remains in the latest SVN version (labeled as
>> 12.0.RC25_dev.)
>>
>> The documentation states that 'load "" { 3 3 3 }' reloads the file and
>> copies the unit cell 3x3x3 times. However, in 11.7.16 one could do this
>> also with data that was entered via the data command. But in the new
>> versions this instead gives the error: "script ERROR: cannot find string
>> data".
>>
>> Steps to repeat the problem:
>> 1. Open jmol and enter script console.
>> 2. Use "data" command to enter a system. E.g.,
>> ==============
>> data "model example"
>> 2
>> testing
>> C 1 1 1
>> O 2 2 2
>> end "model example";
>> ==============
>> 3. Issue a load command:
>> load "" {3 3 3}
>>
>> Result on newer versions: "script ERROR: cannot find string data".
>> Result on e.g. 11.7.16: no error (but also no visible change in this
>> simple example since no supercell boundary is set).
>>
>> We have found a workaround. By issuing
>> set defaultLattice {3 3 3}
>> before one issues the data command gives the same effect as the 'load ""
>> {3 3 3}' did afterwards. Still, I think it would be nice to not break
>> this script syntax when people upgrade.
>>
>> Thanks,
>> Rickard
>>
>>
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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
>
--
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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