[Evogrid-dev] EvoGrid - 3D viz. (webGL)

[Miroslav Karpis]

Now I understand - thanks.

-miro
On Sep 16, 2010, at 3:50 PM, Peter Newman wrote:

> Ah, in this case the box is not solid. There are no edge effects, there is no wall. The box wraps around, so that atoms traveling out one side come back in the other.
> 
> Peter N
> 
> On 16/09/2010 10:44 PM, Miroslav Karpis wrote:
>> 
>> Thank you Peter. A, B, C clear. With D I'm having little bit problem: - for me a box is 'solid' tank in a shape of a box, where the simulation occurs - nothing comes out, nothing comes in. But maybe I will understand it when I will draw the box and visualize the bonds.
>> 
>> -miro
>> 
>> On Thu, Sep 16, 2010 at 1:04 AM, Peter Newman <peter.newman at digitalspace.com> wrote:
>> A) The values specified in that file are defaults used but do not necessarily stay the same (although for what we are doing, they do). There is a parameters file that goes with the history, which that generators/molecules/main.cpp generates. This specifies the radius of the atom.
>> 
>> B) The box size can change in order to maintain constant pressure. And yes, the radius and the box size are in the same units. Atoms are SMALL! I ended up multiplying their radius by 10 when visualizing, but this meant near neighbors would obscure each other.
>> 
>> C) Each of the paired numbers specifies a bond. Each molecule may have one or more bonds. Each of these bonds will be specified as a pair. The number is the index of the atom.
>> 
>> D) The simulator will not actually duplicate the atoms, but it will duplicate the forces of the atoms, as if they had been duplicated. So, a molecule that is right up against the +X side of the box (or even extending past it, if it's a large molecule/chain), will affect the behavior of the atoms at the -X side of the box (except the box is 0,0,0 to box-size, not -box-size to +box-size). 
>> 
>> Does that help?
>> 
>> Peter N
>> 
>> 
>> On 15/09/2010 10:18 PM, Miroslav Karpis wrote:
>>> 
>>> Please can you help me with some questions, I'm facing? 
>>> 
>>> a) atom radius
>>> - not 100% sure if I understand. I can see default values for atom radius in (generators/molecules/main.cpp). For example for Sulphur = 0.180 (pm - picometers). So based on that definition table I should set-up radius for                       each atom-type, correct?
>>> 
>>> b) box
>>> - to be 100% sure we are talking about a 'box' where the simulation is happening, correct? So basically if I have [100.0, 100.0, 100.0] I can set up a box with all 6 sides of length 100, right? If atoms are in (pm) also the dimension of the box size is in (pm - picometers)?
>>> - what I don't understand is that in the file we get for example sometimes values  "box" = [99.9992, 99.9992, 99.9992] - why, the size changed?
>>> 
>>> c) atom bonds
>>> - for example if I have "nBonds":3, "bonds":[[113, 239], [361, 816], [405, 645]] would mean that:
>>> - 113th and 239th atom bond 1 molecule
>>> - 361st and 816th atom bond 2 molecule
>>> - 405th and 645th atom bond 3 molecule
>>> - the number is actually a sequential number of atom within the json file, correct?
>>> 
>>> d) [Suggestion from Peter]: Occasionally, to maintain a molecule, the simulator will move some of the atoms outside the box, and these should be also poking INTO the box from the other side.
>>> - Does that mean that when a molecule is created the simulator will duplicate the atoms? One copy will be the molecule and the 2nd copy will be outside the box? Peter, what do you mean with 'poking into the box from other side'?
>>> 
>>> Regards,
>>> -miro
>> 
>> 
>> 
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