see
https://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.6/
This release has a major fix for JavaScript that affects inorganic
structure CIF file reading or other formats where symmetry is applied and
the atoms are in very regular positions. It only relates to saving a PNGJ
or state in one mode (Java or HTML5) and then reading it in the other. See
below.
A few other goodies as well.
new feature: upgrade of application file...export...Gaussian Input File...
new feature: MOLDEN extensions [SpaceGroup] [Operators] [Cell]
new feature: pmesh files can contain triangle colors
bug fix: JavaScript drag-drop clears cache inappropriately when spt file is
dropped
bug fix: modulated magnetic moment scaling by VECTORS MAX x.x not saved in
state for modulations that are 0,0,0.
bug fix: magnetic CIF reader not automatically showing modulation
bug fix: load SUPERCELL {x y z} not working correctly in terms of packing
bug fix: load SUPERCELL not working correctly with modulation or magnetic
IMPORTANT NOTE: The problem described here only affects the reading of
states that
have been created for crystallographic files, and then only if the
state was created in Java and then displayed in JavaScript,
or vice-versa.
The problem is due to the fact that the Java implementation
of Jmol uses float values for atom coordinates, while JavaScript
is restricted to using only double values. The problem arises when
a comparison must be made between two decimal values. After symmetry
has been applied, it is possible for atom coordinates to be off in the
4th-7th decimal digit for floats and 14th-17th for doubles in the
range -256 to 256.
The problem is most acute for inorganic crystal systems where
symmetry has been applied and especially after the CONNECT NONE command
has been issued.
Aspects where a problem might arise include:
-- packing of unit cells, where atoms are discarded
-- iterating over atoms, where atom order is important
-- autobonding, where distances and order are critical
-- comparing Cartesian or fractional coordinate values
Solution to the problem is to automatically round all fractional
atom coordinates to a precision of 0.00001 and all Cartesian
atom coordinates to a precision of 0.0001. This forces both
double and float implementations to the same value and
results in no practical error, since these ranges are
well beyond the precision of atom coordinates in crystals.
Coincidence is assured for fractional coordinates up to
about 126 and for Cartesian coordinates up to about 838.
This rounding is not implemented for state or PNGJ file
with state version v where
v < 140206 || v >= 140300 && v < 140306
and in general only in the case where the file coordinates are
fractional. Thus, those files will be read exactly as in the
version they were created by. And they will have have the same
issues as well.
The result is also much cleaner-looking atom coordinates.
For example, in JavaScript:
print {*}.fxyz
{0.33333328149215147 0.999999891271352 1.0000000000000024}
{0.6666666148254848 0.999999891271352 1.0000000000000024}
{0.9999999844017011 1.000000000000001 0}
{0.9999999616049127 0.9999999316096356 0.6290004156275991}
{0.9999999709556066 0.9999999596617175 0.3709995843724032}
{0.9999999481588181 0.999999891271352 1.0000000000000024}
becomes:
{0.33333 1 1}
{0.66667 1 1}
{1 1 0}
{1 1 0.629}
{1 1 0.371}
{1 1 1}
new feature: set legacyJavaFloat
-- set by Jmol when a state is read that is before 14.2.6 or in the range
14.3.0 - 14.3.5;
-- prevents fractional and cartesian coordinate rounding.
-- cleared by ZAP or LOAD or loading of any later state script
--
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
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