Re: [apbs-users] question about charge coordinates in a .dx files

[Baker, N. <Nat...@pn...>]

Interesting; thank you for looking into this!

Tucker, can you please see if/how this impacts any of our APBS validation test cases?

Thanks,

__________________________________________________ 
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me


-----Original Message-----
From: Francois Berenger [mailto:ber...@ri...] 
Sent: Monday, April 23, 2012 12:59 AM
To: apb...@li...
Subject: Re: [apbs-users] question about charge coordinates in a .dx files

I just observed this in OCaml: 1) accumulates floating point errors, as my intuition told me.

If 1) is used throughout apbs, then it should be fine.

However, if it is not, apbs electrostatic values at large grid coordinates (i,j,k) may not be the value that is at Cartesian position xmin + i*hx, ymin + j*hy, zmin + k*hz, but the value of a nearby position.

Regards,
F.

On 12/23/2011 03:48 AM, Baker, Nathan wrote:
> Hello --
>
> Both approaches should work equally well; #1 is how I usually implement this type of calculation.
>
> Thanks,
>
> __________________________________________________
> Nathan Baker
> Pacific Northwest National Laboratory
> Tel:  509-375-3997
> http://nabaker.me
>
>
> -----Original Message-----
> From: Francois Berenger [mailto:ber...@ri...]
> Sent: Wednesday, December 21, 2011 11:50 PM
> To: apb...@li...
> Subject: [apbs-users] question about charge coordinates in a .dx files
>
> Hello,
>
> I am a little worried about going to the Cartesian space from the i,j,k coordinates in a dx file. u(i,i,k) means charge at (i,j,k).
>
> I refer to the file format described here:
> http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/ope
> ndx-scalar-data
>
> should I do this:
>
> 1) x,y,z = xmin + i*hx, ymin + j*hy, zmin + k*hz
>
> or this:
>
> 2)
> xmax = nx * hx
> ymax = ny * hy
> zmax = nz * hz
> x,y,z = xmin + (xmax*i)/nx, ymin + (ymax*j)/ny, zmin + (zmax*k)/nz
>
> I am worried that 1) accumulates floating point errors.
>
> Is it OK with 2) or is it the same at the end.
>
> Thanks a lot,
> Francois.
>
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