Re: [ESPResSo-users] Using two different Lennard-Jones potentials for same particles

[Henri Menke]

Hi Reza,

In your current interaction setup the second one will overwrite the first.  But
you can work around it by simply reversing the numbers in the second call.

system.non_bonded_inter[1, 2].lennard_jones.set_params(
    epsilon=ep1, sigma=1.0,
    cutoff=1.1225, shift="auto", offset=0.0, min=0.0)

system.non_bonded_inter[2, 1].lennard_jones.set_params(
    epsilon=ep2, sigma=1.0,
    cutoff=2.5, shift="auto", offset=0.0, min=1.1225)

The compiler error is not reproducible for me on Ubuntu 16.04 with libraries and
tools from the official repositories.  Do you happen to have a version of FFTW3
which you compiled yourself?  In that case it could be that you originally built
it without the -fPIC flag but after a system updated (or whatever) your linker
is now enforcing position independent executables to mitigate recent Intel
processor security bugs.
https://en.wikipedia.org/wiki/Position-independent_code

Currently the ESPResSo build system does not have a switch to disable algorithms
using FFTW3 because they are an integral part of ESPResSo's feature set.  You
could try removing the FFTW3 paths from the CMake configurations file by hand or
using the ccmake command line tool.

Kind regards,
Henri

On Tue, 2018-02-27 at 01:36 +0330, Mohammadreza Niknam Hamidabad wrote:
> Hello all,
> 
> I'm working on behavior of some proteins and I need to use two different LJ
> potentials for the same types. some thing like this:
> 
> system.non_bonded_inter[1, 2].lennard_jones.set_params(
>     epsilon=ep1, sigma=1.0,
>     cutoff=1.1225, shift="auto", offset=0.0, min=0.0)
> 
> system.non_bonded_inter[1, 2].lennard_jones.set_params(
>     epsilon=ep2, sigma=1.0,
>     cutoff=2.5, shift="auto", offset=0.0, min=1.1225)
> 
> Is it possible? Does the second potential overwrite the first one? If not,
> except tabulated interaction, you guys have any suggestion? 
> 
> Also I want to compile newer development version, but every time I encounter
> some errors about fftw3 and recompile with -fPIC.
> 
> Do you know how can I solve it? or how can I turn off and disable fftw3? (I
> don't need any algorithm for electrostatics or p3m)  
> I couldn't find options for make command in installation process to disable
> it:
> mkdir build
> cd build
> cmake ..
> make
> 
> Best regards, 
> Reza
> 
>