[gmx-developers] tabulated potential energy=nan for r=0 nm and charged atoms

[chris.neale at utoronto.ca]

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.

export GMX_NB_GENERIC=1
export GMX_NO_SOLV_OPT=1

module purge
module load intel/intel-v11.1.072
module load cmake/2.8.0
export CCDIR=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/
export FFTW_LOCATION=/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2/exec
export CXX=icpc
export CC=icc
cmake ../source/ \
       -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
       -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
       -DCMAKE_INSTALL_PREFIX=$(pwd) \
       -DGMX_X11=OFF \
       -DCMAKE_CXX_COMPILER=${CCDIR}/icpc \
       -DCMAKE_C_COMPILER=${CCDIR}/icc \
       -DGMX_PREFER_STATIC_LIBS=ON \
       -DGMX_MPI=OFF
make
make install

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 (  
http://permalink.gmane.org/gmane.science.biology.gromacs.devel/2213 )  
where they noted "Found environment variable GMX_NB_GENERIC. Disabling  
all interaction-specific nonbonded kernels" but I don;t see anything  
like this.

Thank you,
Chris.

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.
>
> Berk
>
> 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,
>> Chris.
>>
>> Quoting Berk Hess <hess at cbr.su.se>:
>>
>>> Hi,
>>>
>>> In the innerloop r is calculated as rsquared*invsqrt(rsquared).
>>>
>>> Berk
>>>
>>> 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 (    
>>>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials  
>>>>  )  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:
>>>> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061140.html
>>>>
>>>> Thank you very much,
>>>> Chris.
>>>>
>>>
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>>
>>
>>
>
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