Bugs item #831811, was opened at 2003-10-28 09:00
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You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=831811&group_id=23629
Category: File Input/Output
Group: v8
Status: Open
Resolution: None
Priority: 5
Submitted By: Richard P. Muller (rpmuller)
Assigned to: Nobody/Anonymous (nobody)
Summary: CML input of crystals misses some atom images
Initial Comment:
In v8, when inputting a <crystal> record from a CML
file, not all of the periodic images of atoms on the
unit cell boundaries are included. This problem only
occurs when using the unit cell lengths A, B, C and
angles alpha, beta, and gamma to specify the unit
cell, NOT when using a 3x3 floatArray to specify the
unit cell.
The difference can be seen by contrasting these two
structures.
This one has all of the proper periodic images:
<?xml version="1.0" ?>
<cml title="crystal example">
<molecule id="Si">
<string title="COMMENT"></string>
<crystal>
<floatArray convention="PMP" title="a" >5.100 0
0</floatArray>
<floatArray convention="PMP" title="b" >0 5.100
0</floatArray>
<floatArray convention="PMP" title="c" >0 0
5.100</floatArray>
</crystal>
<atomArray>
<atom id="Si1" elementType="Si" x3="0.0" y3="0.0"
z3="0.0"/>
<atom id="Si2" elementType="Si" x3="2.55"
y3="2.55" z3="0.0"/>
<atom id="Si3" elementType="Si" x3="2.55"
y3="0.0" z3="2.55"/>
<atom id="Si4" elementType="Si" x3="0.0"
y3="2.55" z3="2.55"/>
<atom id="Si5" elementType="Si" x3="1.275"
y3="1.275" z3="1.275"/>
<atom id="Si6" elementType="Si" x3="1.275"
y3="3.825" z3="3.825"/>
<atom id="Si7" elementType="Si" x3="3.825"
y3="1.275" z3="3.825"/>
<atom id="Si8" elementType="Si" x3="3.825"
y3="3.825" z3="1.275"/>
</atomArray>
</molecule>
</cml>
Whereas the one which uses the unit cell lengths A,
B, C and angles alpha, beta, gamma does not have the
proper images:
<?xml version="1.0" ?>
<cml title="crystal example">
<molecule id="Si">
<string title="COMMENT"></string>
<crystal>
<scalar title="a">5.1</scalar>
<scalar title="b">5.1</scalar>
<scalar title="c">5.1</scalar>
<scalar title="alpha">90</scalar>
<scalar title="beta">90</scalar>
<scalar title="gamma">90</scalar>
</crystal>
<atomArray>
<atom id="Si1" elementType="Si" x3="0.0" y3="0.0"
z3="0.0"/>
<atom id="Si2" elementType="Si" x3="2.55"
y3="2.55" z3="0.0"/>
<atom id="Si3" elementType="Si" x3="2.55"
y3="0.0" z3="2.55"/>
<atom id="Si4" elementType="Si" x3="0.0"
y3="2.55" z3="2.55"/>
<atom id="Si5" elementType="Si" x3="1.275"
y3="1.275" z3="1.275"/>
<atom id="Si6" elementType="Si" x3="1.275"
y3="3.825" z3="3.825"/>
<atom id="Si7" elementType="Si" x3="3.825"
y3="1.275" z3="3.825"/>
<atom id="Si8" elementType="Si" x3="3.825"
y3="3.825" z3="1.275"/>
</atomArray>
</molecule>
</cml>
It could be that there is some truncation error when
converting a,b,c,alpha,beta,gamma to the 3x3 matrix
that results in some of these images being lost.
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