Hi,
Do we understand the different dates for when the
idecomp1 test started failing ?
Dave> > Date: Fri Feb 3 14:41:25 2012 +0100
Dave> > [I cherry-picked these into the olderDusseldorf branch: before, the tests
Dave> > pass; afterwards they failed. -- note: just "make sander" in that branch,
Scott> idecomp1 works in 9dde74cd71e6427297df86e36916277ba567d418
Scott> Date: Tue Feb 14 13:28:14 2012 -0500
scott
On Mon, Mar 05, 2012 at 06:11:20PM +0100, Holger Gohlke wrote:
> The changes we made in the ICOSA code removed bugs in the ICOSA calculation and decomposition.
>
> More specifically:
> - The first commit on Feb 3 14:41:25 2012 corrected a wrong initialization of fortran variables in the icosasurf.F90 subroutine icosa_init(). Without this change the variables angle, axis(1), axis(2), and axis(3) are not set to the default values if a second force() call is conducted, as it is done in line 651 of runmin.F90.
> - The second commit on Feb 3 14:41:52 2012 corrected a bug in the ICOSA decomposition analysis, which additionally caused example idecomp4 to fail. The problem can be seen in the decomp.out.save reference file provided currently for the example idecomp4. The total ESURF listed under FINAL RESULTS devided by surften (default = 0.005) is not equal to the surface area ESURF listed under TOTAL ENERGIES, which is calculated by summing up the decomposed SAS contributions. We corrected the calculation procedure in decomp.F90 subroutine decsasa_icosa(), so that now the two energies match.
>
> Nadine provided new decomp.out.save files for both cases which were pushed into origin/master. The idecomp1 and idecomp4 tests pass now.
>
> On 04.03.12, case wrote:
> > In addition to the changes in mm_pbsa_Examples, there have been
> > changes in the sander "decomposition" tests. In particular, the "idecomp1"
> > test uses GB (not PB), so problems there are (probably) unrelated to changes
> > in the PB code. These test cases look like they started to fail near the
> > beginning of Feb. Specifically, the following two commits appear to have
> > changed the idecomp1 test output:
> >
> > commit 8d206b3848de52d17549055b948848b1c1e558a9
> > Author: Holger Gohlke <gohlke.hhu.de>
> > Date: Fri Feb 3 14:41:25 2012 +0100
> >
> > Bugfix of initialization in icosa_init
> >
> > commit 6ac8353095b0adc12119a23193ffc7d29382d28d
> > Author: Holger Gohlke <gohlke.hhu.de>
> > Date: Fri Feb 3 14:41:52 2012 +0100
> >
> > Bugfix to ensure backward compatibility for ICOSA surface calculation to
> > Amb
> >
> > [I cherry-picked these into the olderDusseldorf branch: before, the tests
> > pass; afterwards they failed. -- note: just "make sander" in that branch,
> > then "mv sander ../../bin" in order to run the tests.] So, Holger and Nadine
> > should carefully revisit the above commits.
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Received on Mon Mar 05 2012 - 11:30:02 PST
