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RE: [ESPResSo] Pressure calculation

From: Yelash, Dr. Leonid
Subject: RE: [ESPResSo] Pressure calculation
Date: Mon, 28 Jan 2008 20:14:32 +0100

Hi Christine and other Espresso-Users,

we also have similar problem in both the mpi and the fake versions:


add_bonded_virials: WARNING: Bond type 136622228 , atom 9 unhandled, Atom 2: 25
 line 45: 11147 Segmentation fault      $ESPRESSO


add_bonded_virials: WARNING: Bond type 137329180 , atom 23 unhandled, Atom 2: 25
add_bonded_virials: WARNING: Bond type 89 , atom 24 unhandled, Atom 2: 25
add_bonded_virials: WARNING: Bond type 137328856 , atom 26 unhandled, Atom 2: 25
p0_11474:  p4_error: interrupt SIGSEGV: 11


From: address@hidden address@hidden On Behalf Of Ben Reynwar address@hidden
Sent: Monday, January 28, 2008 5:29 PM
To: Christine Peter
Cc: address@hidden
Subject: Re: [ESPResSo] Pressure calculation

Hi Christine and all,
I'm the one that moved stuff into calc_bonded_force.  It was to avoid 
duplicating code for the pressure tensor and pressure calculations, but it's 
entirely possible I screwed something up.  Unfortunately if I did, I don't know 

On 1/28/08, Christine Peter <address@hidden<mailto:address@hidden>> wrote:
Hi all,

I have a problem with the pressure calculation in Espresso.
After Torstens email from last week about the bug in the pressure
calculation with tabulated bonded potentials I checked out the latest
release. This release gives idential results to my old runs if I do not
execute the analyze pressure command, so everything I observe seems to
be related to the pressure calculation:

As soon as I execute analyze pressure I get a segmentation fault with
the preceding error message:

add_bonded_virials: WARNING: Bond type 9277 , atom 8925 unhandled, Atom
2: 8926

It seems that at some point while looping through the atoms  and the
bonds in add_bonded_virials a pointer goes astray. But I could not
identify why at this atom and at this bond. My system has 1323 molecules
with 9 atoms each. Each molecule has 8 bonds, 7 angles and 6 dihedral
angles. Some of the bonds and angles are tabulated. The error occurs
sort of unmotivated it seems.

The debugger has just helped to identify that the error occurs in pressure.h
356      p2 = local_particles[p1->bl.e[i++]];

Could it be that it has sth to do with the change in pressure.h where
parts from add_bonded_virials have been taken out and are now executed
in calc_bonded_force (I do not know who mad that change) ?

BTW: The error is not caused by Torsten's change to calculate the
pressure for tabulated bonds, if I take that out I still get the
segmentation fault.

Has anybody observed anything similar?


Christine Peter
MPI for Polymer Research
Ackermannweg 10
55128 Mainz / Germany

Tel. +49-6131-379267
email: address@hidden<mailto:address@hidden>

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