[AMBER-Developers] EVB test errors

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 1 Apr 2010 18:18:32 -0400

Hi All,

This is regarding the previously discussed EVB test cases that segfault:

cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF && ./Run.evb
cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF && ./Run.evb

I have made some modifications to the code that constitute a partial fix,
but I can't proceed further without input from EVB people.

These tests can both be protected from segfaults by making the loop at line
148 in pimd_force.f that references dmdlm dependent on the value of itimass
(which is what triggers the init of dmdlm), e.g.

pimd_force.f
148c148
< if( i_qi > 0 ) then
---
>    if( i_qi > 0 .and. itimass > 0) then
At this point the tests will run but the output energies don't match at all.
I was able to find a version of amber10 (from June 2008) that passed both of
these test cases.
I was able to recover the test results for the 2D-PMF test by modifying
evb_umb.f, setting the array fharm(:) to zero outside of loops it is
involved in (the way it was done previously) instead of inside (the way it
is currently done).
evb_umb.f
102c102
< !        fharm(:) = 0.0d0
---
>         fharm(:) = 0.0d0
106c106
<             fharm(:) = 0.0d0
---
> !            fharm(:) = 0.0d0
191c191
< !        fharm(:) = 0.0d0
---
>         fharm(:) = 0.0d0
195c195
<             fharm(:) = 0.0d0
---
> !            fharm(:) = 0.0d0
You can even see that the fharm(:) statements were only commented out and
not removed - does anyone familiar with the code know why it was changed?
According to comments in the code it seems to have been changed around Dec.
2008. Anyway, when I reverse these changes the 2D-PMF test results match
(aside from a few diffs that are output format-related). Of course, the test
case itself could be wrong, but I have no easy way of knowing that.
However, the corrF test still fails by a mile - as far as I can tell the
likely culprit is with the qi_corrf_les() subroutine in pimd_force.f - much
of it was changed around March 2009. These changes are far more extensive (>
100 lines at least) so I don't feel comfortable rolling them back.
Anyway, I am attaching a patch that makes the changes that I discussed. If
nothing else it prevents the ugly segfaults.
Someone more familiar with what EVB *should* be doing should definitely have
a close look at all of these changes.
-Dan
-- 
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854



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Received on Thu Apr 01 2010 - 15:30:02 PDT
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