Re: amber-developers: xray: new wrinkle on neb/pimd/les old creased face

From: Scott Brozell <>
Date: Fri, 19 Oct 2007 10:27:30 -0700


Below is the nebmodule.f cvs log.


TEMPORARY PATCH to get sander.MPI to compile.
See below for the compiler error.
This needs to be investigated by the NEB and PIMD developers in
conjunction with a thorough code inspection of LES/PIMD/NEB !!
This inspection should consider all sanders and the results
should be communicated to all developers !
See the amber-developers list messages that contain neb in the subject
for existing and potential issues.
Here is another question:
Why is there so much code duplication between modules pimd_force
and nebmodule ?

With configure -lam g95: mpif77 -c -O3 -fno-second-underscore -march=nocona -ffree-form -o force.o
In file _force.f:2041
         call mpi_reduce(nebrms,etmp,1,MPI_DOUBLE_PRECISION, &
Error: Symbol 'nebrms' at (1) is defined in multiple modules

On Fri, 19 Oct 2007, Scott Brozell wrote:

> On Fri, 19 Oct 2007, David A. Case wrote:
> > On Thu, Oct 18, 2007, Carlos Simmerling wrote:
> >
> > > I've also sent out requests for info on nebrms, several times, with no reply.
> > > I'm tempted to remove all of this code if nobody owns it or knows why
> > > it is there.
> >
> > It would clearly be very useful if we could get at least a temporary fix
> > in *today*, so that the code can compile. Unfortunately, I am tied up and
> > cannot volunteer.
> Based on Dave Mathews reply, a simple patch exists.
> I'll commit it, but we have to remember that this is only
> a temporary fix.
> Scott
> On Thu, 18 Oct 2007, David Mathews wrote:
> > I originally added nebrms to calcuate the RMS for energy
> > minimization during neb calculations. There are reduced degrees of freedom
> > because the atoms in the first and last image are frozen. This was a
> > report item that was helpful for debugging with small systems. For large
> > systems, it did not seem particularly important. That means that it can
> > now be removed unless somebody objects. I can probably help with that
> > cleanup next week. Hope this helps.
Received on Sun Oct 21 2007 - 06:07:51 PDT
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