[gmx-developers] tabulated potential energy=nan for r=0 nm and charged atoms
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Tue May 10 02:22:52 CEST 2011
Thank you Berk. I can not seem to get the generic kernel to activate.
To test, I modified gromacs 4.5.4 src/gmxlib/nonbonded/nb_generic.c to
include exit(0) at line 87 (early inside gmx_nb_generic_kernel) and
then compiled as follows and the run still proceeds through the full
nsteps=10 set in my .mdp file.
module load intel/intel-v11.1.072
module load cmake/2.8.0
cmake ../source/ \
Perhaps it is a specific problem with cmake? I see old posts where
people report seeing a notification of using the generic kernel in the
.log file (
where they noted "Found environment variable GMX_NB_GENERIC. Disabling
all interaction-specific nonbonded kernels" but I don;t see anything
Quoting Berk Hess <hess at cbr.su.se>:
> That depends on the kernel you are using.
> If you are using tabulated Coulomb only, no LJ, this is kernel number 300.
> In which directory you have to look depends on your architecture.
> It might be sse assembly kernels.
> In that case you might want to use the generic kernel instead.
> On 05/09/2011 05:30 PM, chris.neale at utoronto.ca wrote:
>> Could you please point me to the file and line number so that I can
>> change this to a simple sqrt? If it impacts the timing too much,
>> then I may just leave r=r^2 and remake my table to provide values
>> based on r^2.
>> Thank you very much for your assistance,
>> Quoting Berk Hess <hess at cbr.su.se>:
>>> In the innerloop r is calculated as rsquared*invsqrt(rsquared).
>>> On 05/09/2011 04:54 PM, chris.neale at utoronto.ca wrote:
>>>> Dear Developers:
>>>> I find that even when tabulated potentials specify f(x)=0 and
>>>> -f'(x)=0 for x=0, I still get a coulomb(SR) energy=nan when two
>>>> charges occupy the exact same spot.
>>>> Both the manual 4.5.4 page 151 equation 6.23 and the
>>>> gromacs_nb.pdf tabulated potentials tutorial (
>>>> ) indicate that setting f(x)=0 and -f'(x)=0 for x=0 should lead
>>>> to an energy of zero in this case.
>>>> Is this a bug or a case of WYSIWYG? Can anybody offer any hints
>>>> on where I might start searching through the source code with
>>>> printf statements to see where the nan develops? I'm guessing
>>>> there is some if(r>0) in the code that doesn't technically need
>>>> to be there.
>>>> More information and a test system is available in my users-list
>>>> post for which I received no responses:
>>>> Thank you very much,
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