> On Monday 22 August 2005 04:22 pm, Egon Willighagen wrote:
>> On Monday 22 August 2005 03:52 pm, Miguel wrote:
>> > > Ok, what approach shall we take?
>> > >
>> > > 2. have all new atoms as seperate internal objects
>> > > - easier to implement symmetry operations that could lead to
>> > > overlapping atoms
>> > > - memory is no problem for upto 10k atoms, so why worry
>> >
>> > In general, I think that having them separate is a better idea.
>>
>> Ok. I think I can manage adding new atoms...
First, a simple command for yourself (crystal? or whatever command name
you think is appropriate ... or you could even call it 'egon' for now) to
Token.java and Eval.java
Make the initial implementation of your command do nothing more than
System.out.println("Eval.crystal() was called");
When you get that done, check it in.
----
Start your own source file. You will need to be making many references to
Frame.java, so you should try to get familiar with it.
Add a method to Frame.java called getCrystal() ... that allocates an
instance of your Crystal class if necessary and saves it in a Frame member
variable.
Change your Eval method so that it calls frame.getCrystal() and then calls
some method in your Crystal class.
When you get that done, check it in.
----
Next step ... simply add one atom when your script command is called.
Place it someplace like 0,0,0. Make it some strange element and make the
size be large ... like 100% vdw. That way it will be easy to see.
Note that the Frame code was not really designed to accept new atoms after
finalizeBuild() is called. So it is possible that you will encounter
problems.
If you get to where you can add 1 atom when your command is called then
you should be very happy. Check in your code.
----
Next step:
- only duplicate the unit cell one time
- Shift the entire unit cell one fractional unit along one of the
fractional axes.
- do not worry about the bonds.
- do not worry about deletions.
When you get this working we will be very pleased.
>> but how would I remove them
>> again, to just have the original atoms again?
Do not worry about deletions at this time.
Currently, there is no concept of deleting atoms.
It is not clear to me that we would ever delete.
I have been thinking of building in a generic 'hide' mechanism ... and
perhaps we will just hide them.
> And how would I tell Jmol to draw more than one unit cell?
If the atoms are added to the frame then they will be drawn.
> I think I will need to add the lattice dimensions as fields somewhere...
> where could I best do that?
I do not know what you mean by 'lattice dimensions'
Q: Is it the case that these are the 'planes' that are multiples of the
fractional unit cell axes?
I think that all of your unitcell stuff should be in your Crystal.java
source file.
Miguel
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