Excellent, thanks Dan. That did the trick.
On 6/12/15, 1:19 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>Hi,
>
>For future reference, issues like this are better sent to the Amber
>developer's list,
>http://lists.ambermd.org/mailman/listinfo/amber-developers
>- I think most people are probably bored by the details of cpptraj code
>:-)
>
>On Fri, Jun 12, 2015 at 11:16 AM, Gard Nelson <Gard.Nelson.nantbio.com>
>wrote:
>
>> // Upper Triangle
>> for (AtomMask::const_iterator atom2 = mask1_.begin(); atom2 !=
>> mask1_.end(); ++atom2)
>> for (AtomMask::const_iterator atom1 = atom2; atom1 !=
>>mask1_.end();
>> ++atom1)
>> dst = sqrt(DIST2_NoImage(currentFrame.XYZ(*atom2),
>> currentFrame.XYZ(*atom1)));
>> *(mat++) += dst;
>>
>
>Your problem is that in the inner loop instead of a single statement you
>now have *two* statements you want to execute, which in C/C++ require the
>creation of a code block enclosed in curly braces ({}), e.g.
>
>for (AtomMask::const_iterator atom2 = mask1_.begin(); atom2 !=
>mask1_.end(); ++atom2)
> for (AtomMask::const_iterator atom1 = atom2; atom1 != mask1_.end();
>++atom1) {
> dst = sqrt(DIST2_NoImage(currentFrame.XYZ(*atom2),
>currentFrame.XYZ(*atom1)));
> *(mat++) += dst;
> }
>
>In your code, the 'dst =' statement is executed within the inner loop, but
>the *(mat++) statement is executed outside both loops. Therefore all the
>values you calculate except the last one are lost, and that final value is
>the only one added to the matrix.
>
>Hope this helps,
>
>-Dan
>
>
>> } else {
>> // Full matrix
>> for (AtomMask::const_iterator atom2 = mask2_.begin(); atom2 !=
>> mask2_.end(); ++atom2)
>> for (AtomMask::const_iterator atom1 = mask1_.begin(); atom1 !=
>> mask1_.end(); ++atom1)
>> dst = sqrt(DIST2_NoImage(currentFrame.XYZ(*atom2),
>> currentFrame.XYZ(*atom1)));
>> *(mat++) += dst;
>> }
>> }
>> The function I want to implement uses the distance in several places, so
>> making multiple calls to DIST2_NoImage slows things down dramatically.
>>All
>> I intended to do with the above code is assign the distance to a
>>variable
>> and then add that variable to the matrix. I could then use that variable
>> (dst) wherever it's needed.
>>
>> However, making this change results in the output matrix having a small
>> value in the (1,1) position and being uniformly 0 everywhere else,
>>which is
>> not the functionality I expected. I am stumped over why the change I
>>made
>> isn't transparent and would greatly appreciate any help in making the
>>code
>> work.
>> Thanks,
>> Gard
>>
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>
>
>
>--
>-------------------------
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 307
>Salt Lake City, UT 84112-5820
>http://home.chpc.utah.edu/~cheatham/
>(801) 587-9652
>(801) 585-6208 (Fax)
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Received on Fri Jun 12 2015 - 14:30:03 PDT
