var jmolwindow;
function openjmolwindow(url)
{
jmolwindow=window.open(url,'PTL3jmol','height=550,width=700');
if (window.focus) {jmolwindow.focus()}
}
var newWindow;
function makeNewJmolWindow(cif,solid,size,dummy) {
if (!newWindow || newWindow.closed) {
newWindow = window.open("","Jmolwindow","status,height=550,width=700");
if (!newWindow.opener) {
newWindow.opener = window;
}
// force small delay for IE to catch up
setTimeout(writeToJmolWindow(cif,solid,size,dummy), 50);
} else {
// window's already open; bring to front
newWindow.focus();
}
}
function writeToJmolWindow(cif,solid,size,dummy) {
// assemble content for new window
var newContent = '';
newContent += ' ';
newContent += ' ';
newContent += ' ';
newContent += ' Crystal Lattices of Element';
newContent += '';
newContent += '';
newContent += '
';
newContent += ' ';
// write HTML to new window document
newWindow.document.write(newContent);
// If I uncomment this line Jmol freezes and it is not interactive
// newWindow.document.close(); // close layout stream
}
function ptl3jmol(cif,solid,size,dummy){
jmolInitialize("../../../jmol");
jmolSetAppletColor("black");
if ( dummy != "pdb" ){
if ( solid == "molecular" ){
// this is the display for molecular solids (i.e. N, O) (range without normalizing the cell (444 666 0) will
// show the molecules inside the solute)
jmolApplet(size, "load "+cif+" {444 666 0} range 10; set displayCellParameters off; move 0 360 0 0 0 0 0 0 5 ");
}
if ( solid == "metal" ){
// this is the display for metals and monoatomic solids (Fe, Ar) i.e. without bonds
jmolApplet(size, "load "+cif+" {3 3 3}; wireframe off; set displayCellParameters off; move 0 360 0 0 0 0 0 0 5 ");
}
if ( solid == "covalent" ){
// this is the display for covalent solids (carbon, boron) i.e. with bonds
jmolApplet(size, "load "+cif+" {3 3 3}; set displayCellParameters off; move 0 360 0 0 0 0 0 0 5 ");
}
jmolBr();
jmolRadioGroup([
["display unitcell; center unitcell", "Display unit cell"],
["display *; centerAt AVERAGE ", "Display lattice","checked"],
]);
}
if ( dummy == "pdb" ){
jmolApplet(size, "load "+cif+"; move 0 360 0 0 0 0 0 0 5 ");
}
jmolBr();
// Display size
jmolRadioGroup([
["spacefill off; wireframe on", "wireframe"],
["spacefill 20%; wireframe 0.15", "ball & stick","checked"],
["spacefill 100%; wireframe off", "Van der Waals"],
]);
jmolBr();
// a button to reset (not sure if we need it)
jmolButton("reset", "Reset to original orientation");
jmolBr();
// a checkbox to spin it
jmolCheckbox("spin on", "spin off", "spin");
jmolBr();
if ( dummy != "pdb" ){
// displays a box to display the Cell parameters
jmolCheckbox("set displayCellParameters on", "set displayCellParameters off", "Display cell parameters");
jmolBr();
}
// show 3 random distances
jmolCheckbox("set measurements on ;set measurements angstroms; measure 1 2; measure 1 3; measure 1 4 ", "measurements delete", "Display distances in the cell");
// I need to display the closest distance between two atoms or the coordination sphere
jmolBr();
jmolBr();
jmolHtml("Double click on atoms to measure distances");
jmolBr();
}