Hi all,
I try to change atom coordinates dynamically in Jmol 14.3.12_2015.03.01
(and other recent versions) but I got stuck with a strange assignement
problem/bug.
I am using three global arrays (xc,yc,zc) as intermediate coordinate
storage while calculating the changes.
When I try to assign the new coordinates, only the first assignment
works correctly. All others assign the coordinates of the first node
instead of the correct one.
Below is shown a minimal version (using only 'xc' and a simplified
change function) to ilustrate the problem.
The coordinate update function looks like this:
#-----------------------------
function updateCoordinates(atomSet) {
for (var i=1; i<=atomSet.size; i++) {
print "UPDATE: i=" + i + " oldXCord=" + atomSet[i].x + " x=" +
xc[i];
print atomSet[i];
atomSet[i].x = xc[i];
print "UPDATE2: i=" + i + " newXCoord=" + atomSet[i].x;
}
show xc;
show atomSet;
}
#------------------------------
The following function copies the current X coordinates to the 'xc' array:
#-----------------------------
function initialize(atomSet) {
xc = [];
for (var i=atomSet.size; i>=1; i--) {
xc[i] = atomSet[i].x;
print "INIT: i=" + i + " xCoord=" + atomSet[i].x + " x=" + xc[i]
}
}
#------------------------------
And this function changes the X coordinates by adding '1.0':
#-----------------------------
function changeCoordinates(atomSet) {
for (var i=atomSet.size; i>=1; i--) {
print "CHANGE: i=" + i + " oldX=" + xc[i];
xc[i] += 1.0;
print "CHANGE2: i=" + i + " newX=" + xc[i];
}
}
#------------------------------
Example run:
#------------------------------
load =1deh;
set1 = {atomno<5};
initialize(set1);
changeCoordinates(set1);
updateCoordinates(set1);
#------------------------------
The debug output of the example run is shown below. It demonstrates that
the 'xc' array as such seems to be intact but during replacing the X
coordinate it seems to be handled incorrectly:
----- DEBUG OUTPUT ------------------
INIT: i=4 xCoord=14.566 x=14.566
INIT: i=3 xCoord=15.426 x=15.426
INIT: i=2 xCoord=16.318 x=16.318
INIT: i=1 xCoord=15.489 x=15.489
CHANGE: i=4 oldX=14.566
CHANGE2: i=4 newX=15.566
CHANGE: i=3 oldX=15.426
CHANGE2: i=3 newX=16.425999
CHANGE: i=2 oldX=16.318
CHANGE2: i=2 newX=17.318
CHANGE: i=1 oldX=15.489
CHANGE2: i=1 newX=16.489
UPDATE: i=1 oldXCord=15.489 x=16.489
UPDATE2: i=1 newXCoord=16.489
UPDATE: i=2 oldXCord=16.318 x=17.318
UPDATE2: i=2 newXCoord=16.489
UPDATE: i=3 oldXCord=15.426 x=16.425999
UPDATE2: i=3 newXCoord=16.489
UPDATE: i=4 oldXCord=14.566 x=15.566
UPDATE2: i=4 newXCoord=16.489
xc = [ 16.489,17.318,16.425999,15.566 ]
atomSet = ({0:3})
-------------------------------------
The example does work as expected in Jmol version 14.0.5:
-----------------------------------------------
INIT: i=4 xCoord=14.566 x=14.566
INIT: i=3 xCoord=15.426 x=15.426
INIT: i=2 xCoord=16.318 x=16.318
INIT: i=1 xCoord=15.489 x=15.489
CHANGE: i=4 oldX=14.566
CHANGE2: i=4 newX=15.566
CHANGE: i=3 oldX=15.426
CHANGE2: i=3 newX=16.426000000000002
CHANGE: i=2 oldX=16.318
CHANGE2: i=2 newX=17.318
CHANGE: i=1 oldX=15.489
CHANGE2: i=1 newX=16.489
UPDATE: i=1 oldXCord=15.489 x=16.489
({0})
UPDATE2: i=1 newXCoord=16.489
UPDATE: i=2 oldXCord=16.318 x=17.318
({1})
UPDATE2: i=2 newXCoord=17.318
UPDATE: i=3 oldXCord=15.426 x=16.426000000000002
({2})
UPDATE2: i=3 newXCoord=16.426000000000002
UPDATE: i=4 oldXCord=14.566 x=15.566
({3})
UPDATE2: i=4 newXCoord=15.566
xc = [16.489,17.318,16.426000000000002,15.566]
atomset = ({0:3})
---------------------------
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail: [email protected]
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Head of Administration: Dr. Daniele Barthel
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